Leigh Carmody Peter Robinson An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. Medical Action Ontology 2024-02-05 definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note editor note has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu IAO:0000700 uberon has_ontology_root_term true has_ontology_root_term has ontology root term has ontology root term preferred_root term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive abbreviation http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator creator http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description description http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title title http://purl.org/dc/terms/contributor uberon dc-contributor true dc-contributor contributor http://purl.org/dc/terms/date uberon dcterms-date true dcterms-date date http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has_synonym_type http://www.w3.org/2000/01/rdf-schema#seeAlso uberon seeAlso true seeAlso see also is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 quality uberon has_part has_part has part has part has_part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 uberon preceded_by preceded_by preceded by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in https://wiki.geneontology.org/Occurs_in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process BSPO:0000096 uberon anterior_to anterior_to anterior to BSPO:0000097 uberon distal_to distal_to distal to BSPO:0000098 uberon dorsal_to dorsal_to dorsal to BSPO:0000099 uberon posterior_to posterior_to posterior to BSPO:0000100 uberon proximal_to proximal_to proximal to BSPO:0000102 uberon ventral_to ventral_to ventral to BSPO:0000107 uberon deep_to deep_to deep to BSPO:0000108 uberon superficial_to superficial_to superficial to BSPO:0000120 uberon in_left_side_of in_left_side_of in left side of BSPO:0000121 uberon in_right_side_of in_right_side_of in right side of BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in posterior side of BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in anterior side of BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in proximal side of BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in lateral side of BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost part of BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately deep to BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost part of BSPO:0001113 uberon preaxialmost_part_of preaxialmost_part_of preaxialmost part of BSPO:0001115 uberon postaxialmost_part_of postaxialmost_part_of postaxialmost part of BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects midsagittal plane of BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in dorsal side of has_not_completed http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. Damion Dooley FoodOn For example, 'bean soup' has a defining ingredient of some 'bean'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. has defining ingredient A relation attaching between a food material and another food material that has been added to it at some point in its history. Damion Dooley FoodOn has ingredient Refraining from performing, acting, or behaving some behavior. 2020-01-28T19:01:13Z avoided behavior Uses of chemicals which affect the course of conditions, diseases, syndromes or pathology to benefit the health of an individual. 2021-02-24T19:27:35Z MeSH:D045506 drug uses pharmocological uses therapeutic uses Action of refraining from recommending, performing, or participating in some medical actions. 2019-06-12T14:23:27Z avoided medical action Refraining from consumption of some types of food. 2019-07-12T14:23:27Z avoided food inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in RO:0000052 inheres_in inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 uberon participates_in participates_in participates in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 uberon has_quality has_quality has quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of RO:0001015 uberon location_of location_of location of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 uberon located_in located_in located in located in https://wiki.geneontology.org/Located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of surface of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has 2D boundary http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 uberon innervated_by innervated_by innervated_by innervated_by X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. 2017-05-24T09:49:21Z has component process 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous with David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of RO:0002087 uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002103 uberon synapsed_by synapsed_by synapsed by synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps true Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous with FMA:85972 d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. ancestral_stucture_of evolutionarily_descended_from derived by descent from inverse of derived by descent from has derived by descendant two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' RO:0002158 uberon homologous_to homologous_to VBO calls this homologous_to shares ancestor with lactation SubClassOf 'only in taxon' some 'Mammalia' x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria RO:0002160 uberon only_in_taxon only_in_taxon only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attached to part of true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 uberon supplies supplies supplies supplies Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 uberon drains drains drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 uberon has_component has_component has component has component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops from inverse of develops from RO:0002203 uberon develops_into develops_into develops into develops into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. FBbt RO:0002207 has developmental precursor uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly develops from inverse of directly develops from developmental precursor of directly develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 uberon capable_of capable_of capable of capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO RO:0002220 uberon adjacent_to adjacent_to adjacent to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by RO:0002221 uberon surrounds surrounds surrounds surrounds Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops from part of x develops_in y if x is located in y whilst x is developing EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in develops in develops in inverse of ends with Chris Mungall RO:0002229 uberon ends ends ends ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y starts with process that occurs in has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y ends with process that occurs in has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces has output https://wiki.geneontology.org/Has_output In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. RO:0002252 uberon connecting_branch_of connecting_branch_of connecting branch of inverse of connecting branch of has connecting branch Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from developmentally contributes to t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by developmentally induced by developmentally induced by Inverse of developmentally induced by developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally replaces Inverse of developmentally preceded by developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue part of developmental precursor of p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of RO:0002314 inheres_in_part_of inheres_in_part_of characteristic of part of inheres in part of true A relationship that holds via some environmental process Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in https://wiki.geneontology.org/Involved_in inverse of enables enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by A relationship that holds via some process of localization Do not use this relation directly. It is a grouping relation. related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. has target end location 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) results in transport to from or in An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input RO:0002352 uberon input_of input_of input of input of inverse of has output RO:0002353 uberon output_of output_of output of output of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attached to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin has muscle origin has muscle origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion has muscle insertion has muscle insertion We need to import uberon muscle into RO to use as a stricter domain constraint false x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat has fused element RO:0002374 uberon has_fused_element has_fused_element A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. derived from ancestral fusion of derived from ancestral fusion of A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon tributary_of tributary_of tributary of tributary of http://en.wikipedia.org/wiki/Tributary A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y RO:0002380 uberon branching_part_of branching_part_of branching part of branching part of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y has potential to directly develop into inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. has part that occurs in true is kinase activity See notes for inverse relation receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. sends output to Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). RO:0002488 uberon existence_starts_during existence_starts_during existence starts during x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). RO:0002489 uberon existence_starts_with existence_starts_with existence starts with x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) RO:0002491 exists during uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. https://orcid.org/0000-0002-6601-2165 x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships RO:0002494 uberon transformation_of transformation_of transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t RO:0002495 uberon immediate_transformation_of immediate_transformation_of immediate transformation of x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. RO:0002503 towards towards towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Wikipedia:Antagonist_(muscle) RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist inverse of branching part of RO:0002569 uberon has_branching_part has_branching_part has branching part x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 uberon conduit_for conduit_for conduit for x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity RO:0002572 uberon luminal_space_of luminal_space_of luminal space of A relation that holds between an attribute or a qualifier and another attribute. This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. RO:0002180 qualifier qualifier placeholder relation to indicate normality/abnormality. has modifier inverse of has skeleton RO:0002576 uberon skeleton_of skeleton_of skeleton of p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates https://wiki.geneontology.org/Directly_positively_regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. RO:0003000 uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. RO:0003001 uberon produced_by produced_by produced by produced by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect https://wiki.geneontology.org/Acts_upstream_of,_positive_effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect muffin 'has substance added' some 'baking soda' "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. has substance added The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z indirectly regulates q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. different in magnitude relative to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased in magnitude relative to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. https://orcid.org/0000-0002-6601-2165 has relative magnitude s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has cross section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. https://orcid.org/0000-0002-6601-2165 q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. https://orcid.org/0000-0002-6601-2165 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. has high plasma membrane amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. PMID:19243617 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. has low plasma membrane amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. PMID:19243617 A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into extends_fibers_into X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y https://orcid.org/0000-0002-7073-9172 Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s. add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon sexually_homologous_to sexually_homologous_to c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of uberon transitively_anteriorly_connected_to transitively anteriorly connected to http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon transitively_distally_connected_to transitively distally connected to http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon transitively_proximally_connected_to transitively proximally connected to http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon trunk_part_of trunk_part_of entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. -1 0.000548579903 0.0 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC The conjugate base of gamma-amino-beta-hydroxybutyric acid arising from deprotonation of the carboxy group. -1 C4H8NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 YQGDEPYYFWUPGO-UHFFFAOYSA-M 118.11126 118.05097 NCC(O)CC([O-])=O CAS:352-21-6 KEGG:C03678 4-Amino-3-hydroxybutanoate chebi_ontology CHEBI:11955 4-amino-3-hydroxybutanoate CAS:352-21-6 KEGG COMPOUND KEGG:C03678 ChEBI 4-Amino-3-hydroxybutanoate KEGG_COMPOUND Any member of a group of fat-soluble retinoids produced via metabolism of provitamin A carotenoids that exhibit biological activity against vitamin A deficiency. Vitamin A is involved in immune function, vision, reproduction, and cellular communication. MetaCyc:Vitamin-A Wikipedia:Vitamin_A chebi_ontology vitamin A vitamer vitamin A vitamers vitamin-A vitamins A CHEBI:12777 vitamin A vitamin A vitamer ChEBI vitamin A vitamers ChEBI vitamin-A ChEBI vitamins A ChEBI A pyridinium ion obtained by protonation of the ring nitrogen of pyridoxal. +1 C8H10NO3 InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3/p+1 RADKZDMFGJYCBB-UHFFFAOYSA-O 168.170 168.06552 C1(O)=C(C)[NH+]=CC(CO)=C1C([H])=O 4-formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium chebi_ontology pyridoxal cation CHEBI:131530 pyridoxal(1+) 4-formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium IUPAC pyridoxal cation ChEBI Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 27-carbon (cholestane) skeleton. chebi_ontology C27-steroids CHEBI:131619 C27-steroid C27-steroids ChEBI A steroid compound with a structure based on a 24-carbon (cholane) skeleton. chebi_ontology C24-steroids CHEBI:131620 C24-steroid C24-steroids ChEBI Any steroid (or derivative) based on a cholane skeleton. chebi_ontology cholane derivatives CHEBI:131657 cholane derivative cholane derivatives ChEBI A DNA polymerase inhibitor that interferes with the action of a DNA-directed DNA polymerase (EC 2.7.7.7). Wikipedia:DNA_polymerase chebi_ontology DNA duplicase inhibitor DNA duplicase inhibitors DNA nucleotidyltransferase (DNA-directed) inhibitor DNA nucleotidyltransferase (DNA-directed) inhibitors DNA nucleotidyltransferase inhibitor DNA nucleotidyltransferase inhibitors DNA polymerase I inhibitor DNA polymerase I inhibitors DNA polymerase II inhibitor DNA polymerase II inhibitors DNA polymerase III inhibitor DNA polymerase III inhibitors DNA polymerase alpha inhibitor DNA polymerase alpha inhibitors DNA polymerase beta inhibitor DNA polymerase beta inhibitors DNA polymerase gamma inhibitor DNA polymerase gamma inhibitors DNA polymerase inhibitor DNA polymerase inhibitors DNA replicase inhibitor DNA replicase inhibitors DNA-dependent DNA polymerase inhibitor DNA-dependent DNA polymerase inhibitors DNA-directed DNA polymerase (EC 2.7.7.7) inhibitor DNA-directed DNA polymerase (EC 2.7.7.7) inhibitors EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitors EC 2.7.7.7 inhibitor EC 2.7.7.7 inhibitors Klenow fragment inhibitor Klenow fragment inhibitors Taq DNA polymerase inhibitor Taq DNA polymerase inhibitors Taq Pol I inhibitor Taq Pol I inhibitors Tca DNA polymerase inhibitor Tca DNA polymerase inhibitors deoxynucleate polymerase inhibitor deoxynucleate polymerase inhibitors deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitor deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitors deoxyribonucleate nucleotidyltransferase inhibitor deoxyribonucleate nucleotidyltransferase inhibitors deoxyribonucleic acid duplicase inhibitor deoxyribonucleic acid duplicase inhibitors deoxyribonucleic acid polymerase inhibitor deoxyribonucleic acid polymerase inhibitors deoxyribonucleic duplicase inhibitor deoxyribonucleic duplicase inhibitors deoxyribonucleic polymerase I inhibitor deoxyribonucleic polymerase I inhibitors deoxyribonucleic polymerase inhibitor deoxyribonucleic polymerase inhibitors duplicase inhibitor duplicase inhibitors sequenase inhibitor sequenase inhibitors CHEBI:131699 EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor DNA duplicase inhibitor ChEBI DNA duplicase inhibitors ChEBI DNA nucleotidyltransferase (DNA-directed) inhibitor ChEBI DNA nucleotidyltransferase (DNA-directed) inhibitors ChEBI DNA nucleotidyltransferase inhibitor ChEBI DNA nucleotidyltransferase inhibitors ChEBI DNA polymerase I inhibitor ChEBI DNA polymerase I inhibitors ChEBI DNA polymerase II inhibitor ChEBI DNA polymerase II inhibitors ChEBI DNA polymerase III inhibitor ChEBI DNA polymerase III inhibitors ChEBI DNA polymerase alpha inhibitor ChEBI DNA polymerase alpha inhibitors ChEBI DNA polymerase beta inhibitor ChEBI DNA polymerase beta inhibitors ChEBI DNA polymerase gamma inhibitor ChEBI DNA polymerase gamma inhibitors ChEBI DNA polymerase inhibitor ChEBI DNA polymerase inhibitors ChEBI DNA replicase inhibitor ChEBI DNA replicase inhibitors ChEBI DNA-dependent DNA polymerase inhibitor ChEBI DNA-dependent DNA polymerase inhibitors ChEBI DNA-directed DNA polymerase (EC 2.7.7.7) inhibitor ChEBI DNA-directed DNA polymerase (EC 2.7.7.7) inhibitors ChEBI EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitors ChEBI EC 2.7.7.7 inhibitor ChEBI EC 2.7.7.7 inhibitors ChEBI Klenow fragment inhibitor ChEBI Klenow fragment inhibitors ChEBI Taq DNA polymerase inhibitor ChEBI Taq DNA polymerase inhibitors ChEBI Taq Pol I inhibitor ChEBI Taq Pol I inhibitors ChEBI Tca DNA polymerase inhibitor ChEBI Tca DNA polymerase inhibitors ChEBI deoxynucleate polymerase inhibitor ChEBI deoxynucleate polymerase inhibitors ChEBI deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitor ChEBI deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) inhibitors ChEBI deoxyribonucleate nucleotidyltransferase inhibitor ChEBI deoxyribonucleate nucleotidyltransferase inhibitors ChEBI deoxyribonucleic acid duplicase inhibitor ChEBI deoxyribonucleic acid duplicase inhibitors ChEBI deoxyribonucleic acid polymerase inhibitor ChEBI deoxyribonucleic acid polymerase inhibitors ChEBI deoxyribonucleic duplicase inhibitor ChEBI deoxyribonucleic duplicase inhibitors ChEBI deoxyribonucleic polymerase I inhibitor ChEBI deoxyribonucleic polymerase I inhibitors ChEBI deoxyribonucleic polymerase inhibitor ChEBI deoxyribonucleic polymerase inhibitors ChEBI duplicase inhibitor ChEBI duplicase inhibitors ChEBI sequenase inhibitor ChEBI sequenase inhibitors ChEBI Any steroid acid anion based on a cholanic acid skeleton. PMID:1527482 chebi_ontology cholanic acid anions cholanoic acid anion cholanoic acid anions CHEBI:131878 cholanic acid anion PMID:1527482 SUBMITTER cholanic acid anions ChEBI cholanoic acid anion SUBMITTER cholanoic acid anions ChEBI A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives. 0 C6O2R4 104.063 103.98983 O=C1C(*)=C(*)C(=O)C(*)=C1* chebi_ontology a quinone p-benzoquinones para-benzoquinones CHEBI:132124 1,4-benzoquinones a quinone UniProt p-benzoquinones ChEBI para-benzoquinones ChEBI Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group. chebi_ontology hydroxyquinones CHEBI:132130 hydroxyquinone hydroxyquinones ChEBI A naphthoquinone in which the oxo groups of the quinone moiety are at positions 1 and 4 of the parent naphthalene ring. chebi_ontology CHEBI:132142 1,4-naphthoquinones A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3. -1 (C14H20NO11)n.H2O chebi_ontology hyaluronan hyaluronate polyanion CHEBI:132153 hyaluronate hyaluronan UniProt hyaluronate polyanion ChEBI Any polyunsaturated fatty acid containing 22 carbons and 6 double bonds. 0 C22H32O2 328.496 328.24023 C(=O)(O)* chebi_ontology FA 22:6 FA(22:6) free fatty acid 22:6 CHEBI:132544 fatty acid 22:6 FA 22:6 ChEBI FA(22:6) ChEBI free fatty acid 22:6 ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of oxalic acid. chebi_ontology ethanedioic acid anion ethanedioic acid anions oxalate anion oxalate anions oxalates oxalic acid anion oxalic acid anions CHEBI:132952 oxalate ethanedioic acid anion ChEBI ethanedioic acid anions ChEBI oxalate anion ChEBI oxalate anions ChEBI oxalates ChEBI oxalic acid anion ChEBI oxalic acid anions ChEBI Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI An N-oxide where there are three organic groups bonded to the nitrogen atom. 0 NOR3 30.006 29.99799 *[N+](*)([O-])* Patent:EP0545208 Patent:EP0757983 Patent:EP0866058 Patent:EP1068179 Patent:US4206204 Patent:WO9950236 chebi_ontology tertiary amine oxides CHEBI:134363 tertiary amine oxide tertiary amine oxides ChEBI 0 C8H20NO6P InChI=1S/C8H20NO6P/c1-9(2,3)4-5-14-16(12,13)15-7-8(11)6-10/h8,10-11H,4-7H2,1-3H3 SUHOQUVVVLNYQR-UHFFFAOYSA-N 257.222 257.10282 P(OCC(CO)O)(OCC[N+](C)(C)C)(=O)[O-] CAS:563-24-6 Drug_Central:3906 chebi_ontology glycerol phosphorylcholine glycerophosphocholine glycerophosphoric acid choline ester glycerophosphorylcholine glycerylphosphocholine CHEBI:135063 glycerylphosphorylcholine CAS:563-24-6 DrugCentral Drug_Central:3906 DrugCentral glycerol phosphorylcholine DrugCentral glycerophosphocholine DrugCentral glycerophosphoric acid choline ester DrugCentral glycerophosphorylcholine DrugCentral glycerylphosphocholine DrugCentral A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent. PMID:26449612 chebi_ontology pro-agents proagent proagents CHEBI:136859 pro-agent PMID:26449612 Europe PMC pro-agents ChEBI proagent ChEBI proagents ChEBI Any steroid that has beta-configuration at position 5. chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI A cardiovascular drug that tends to raise reduced blood pressure. Wikipedia:Antihypotensive_agent chebi_ontology antihypotensive agents pressor pressors vasopressor agent vasopressor agents CHEBI:137431 antihypotensive agent antihypotensive agents ChEBI pressor ChEBI pressors ChEBI vasopressor agent ChEBI vasopressor agents ChEBI An organic cation obtained by protonation of the amino group of any tertiary amino compound. +1 HNR3 15.015 15.01090 [NH+](*)(*)* chebi_ontology a tertiary amine tertiary amine(1+) tertiary ammonium ions CHEBI:137982 tertiary ammonium ion a tertiary amine UniProt tertiary amine(1+) ChEBI tertiary ammonium ions ChEBI A quaternary ammonium ion obtained by methylation of any tertiary amine +1 CH3NR3 29.041 29.02655 [N+](C)(*)(*)* chebi_ontology a methylated tertiary amine CHEBI:137983 methylated tertiary amine a methylated tertiary amine UniProt Any compound that can disrupt the functions of the endocrine (hormone) system PMID:27929035 PMID:28356401 PMID:28526231 Wikipedia:Endocrine_disruptor chebi_ontology endocrine disrupting chemical endocrine disrupting chemicals endocrine disrupting compound endocrine disrupting compounds endocrine disruptors endocrine-disrupting chemical endocrine-disrupting chemicals hormonally active agent hormonally active agents CHEBI:138015 endocrine disruptor PMID:27929035 Europe PMC PMID:28356401 Europe PMC PMID:28526231 Europe PMC endocrine disrupting chemical ChEBI endocrine disrupting chemicals ChEBI endocrine disrupting compound ChEBI endocrine disrupting compounds ChEBI endocrine disruptors ChEBI endocrine-disrupting chemical ChEBI endocrine-disrupting chemicals ChEBI hormonally active agent ChEBI hormonally active agents ChEBI A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids CHEBI:138103 inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration. chebi_ontology CHEBI:138366 bile acids Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI Any carotenoid derivative with an beta-end group 0 C19H27R 255.418 255.21128 C1(=C(CCCC1(C)C)C)/C=C/C(=C/C=C/C(=C/*)/C)/C MetaCyc:Carotenoid-beta-end-group chebi_ontology a carotenoid beta-end derivative CHEBI:139120 carotenoid beta-end derivative MetaCyc:Carotenoid-beta-end-group SUBMITTER a carotenoid beta-end derivative UniProt -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. PMID:15326516 PMID:19908854 PMID:20382022 PMID:23295224 chebi_ontology alpha-hydroxy ketones alpha-hydroxy-ketone alpha-hydroxy-ketones alpha-hydroxyketone alpha-hydroxyketones CHEBI:139588 alpha-hydroxy ketone PMID:15326516 Europe PMC PMID:19908854 Europe PMC PMID:20382022 Europe PMC PMID:23295224 Europe PMC alpha-hydroxy ketones ChEBI alpha-hydroxy-ketone ChEBI alpha-hydroxy-ketones ChEBI alpha-hydroxyketone ChEBI alpha-hydroxyketones ChEBI A carboxylic acid anion obtained by deprotonation of any retinoid carboxy group. chebi_ontology retinoate retinoates retinoid anions retinoid carboxylate anion retinoid carboxylate anions retinoid carboxylic acid anion retinoid carboxylic acid anions CHEBI:139589 retinoid anion retinoate ChEBI retinoates ChEBI retinoid anions ChEBI retinoid carboxylate anion ChEBI retinoid carboxylate anions ChEBI retinoid carboxylic acid anion ChEBI retinoid carboxylic acid anions ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. 0 C2HO2R3 57.028 56.99765 C(C(=O)*)(O)(*)* chebi_ontology tertiary alpha-hydroxy ketones tertiary alpha-hydroxy-ketone tertiary alpha-hydroxy-ketones tertiary alpha-hydroxyketone tertiary alpha-hydroxyketones CHEBI:139592 tertiary alpha-hydroxy ketone tertiary alpha-hydroxy ketones ChEBI tertiary alpha-hydroxy-ketone ChEBI tertiary alpha-hydroxy-ketones ChEBI tertiary alpha-hydroxyketone ChEBI tertiary alpha-hydroxyketones ChEBI Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 0 C62H88CoN13O14PR 1329.350 1328.56433 [Co-3]1234(N5C6=C(C7=[N+]4C(=CC8=[N+]3C(=C(C9=[N+]2[C@@]([C@]5([C@@H]([C@@]6(C)CCC(=O)NC[C@H](OP(O[C@@H]%10[C@H](O[C@H](N%11C=[N+]1C%12=CC(=C(C=C%12%11)C)C)[C@@H]%10O)CO)(=O)[O-])C)CC(=O)N)[H])([C@]([C@@H]9CCC(N)=O)(CC(=O)N)C)C)C)[C@](C)([C@@H]8CCC(=O)N)CC(N)=O)C([C@@H]7CCC(=O)N)(C)C)C)* MetaCyc:CPD-20938 chebi_ontology an R-cob(III)alamin CHEBI:140785 R-cob(III)alamin MetaCyc:CPD-20938 SUBMITTER an R-cob(III)alamin UniProt An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22. 0 C7H6N2O 134.136 134.04801 C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)* chebi_ontology CHEBI:142163 24G7 epitope An organic anion arising from deprotonation of the hydroxy group of an enol. -1 C2OR3 40.021 39.99491 [O-]C(=C(*)*)* chebi_ontology enolate anion enolate anions enolates CHEBI:142839 enolate enolate anion ChEBI enolate anions ChEBI enolates ChEBI An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN 0 C21H17N2O7R5 409.370 409.10358 C12=C(C=C(C(=C1C(C=3[C@]([C@@H]([C@]4([C@@H](C([O-])=C(C([C@@]4(O)C3O)=O)C(N)=O)[NH+](C)C)[H])*)(C2(*)*)[H])=O)O)*)* chebi_ontology a tetracycline CHEBI:144644 a tetracycline zwitterion a tetracycline UniProt A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. PMID:12137720 PMID:19251032 PMID:25848166 PMID:5941964 PMID:6069707 Wikipedia:Insulin chebi_ontology CHEBI:145810 insulin PMID:12137720 Europe PMC PMID:19251032 Europe PMC PMID:25848166 Europe PMC PMID:5941964 Europe PMC PMID:6069707 Europe PMC A cardiovascular drug that prevents atherosclerosis (a disease in which the inside of an artery narrows due to the build up of plaque). Compare with antiatherogenic agent. antiatherosclerotic agent chebi_ontology anti-atherosclerotic agent anti-atherosclerotic agents anti-atherosclerotic drug anti-atherosclerotic drugs antiatherosclerotic agents antiatherosclerotic drug antiatherosclerotic drugs CHEBI:145947 antiatherosclerotic agent antiatherosclerotic agent ChEBI anti-atherosclerotic agent ChEBI anti-atherosclerotic agents ChEBI anti-atherosclerotic drug ChEBI anti-atherosclerotic drugs ChEBI antiatherosclerotic agents ChEBI antiatherosclerotic drug ChEBI antiatherosclerotic drugs ChEBI Any EC 3.4.17.* (metallocarboxypeptidase) inhibitor that inhibits the action of angiotensin-converting enzyme 2 (EC 3.4.17.23). Wikipedia:Angiotensin-converting_enzyme_2 EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor chebi_ontology ACE-2 inhibitor ACE-2 inhibitors ACE2 inhibitor ACE2 inhibitors EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitors EC 3.4.17.23 inhibitor EC 3.4.17.23 inhibitors angiotensin converting enzyme 2 inhibitor angiotensin converting enzyme 2 inhibitors angiotensin converting enzyme-2 inhibitor angiotensin converting enzyme-2 inhibitors angiotensin-converting enzyme 2 inhibitor angiotensin-converting enzyme 2 inhibitors hACE2 inhibitor hACE2 inhibitors CHEBI:147289 EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor ChEBI ACE-2 inhibitor ChEBI ACE-2 inhibitors ChEBI ACE2 inhibitor ChEBI ACE2 inhibitors ChEBI EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitors ChEBI EC 3.4.17.23 inhibitor ChEBI EC 3.4.17.23 inhibitors ChEBI angiotensin converting enzyme 2 inhibitor ChEBI angiotensin converting enzyme 2 inhibitors ChEBI angiotensin converting enzyme-2 inhibitor ChEBI angiotensin converting enzyme-2 inhibitors ChEBI angiotensin-converting enzyme 2 inhibitor ChEBI angiotensin-converting enzyme 2 inhibitors ChEBI hACE2 inhibitor ChEBI hACE2 inhibitors ChEBI Any EC 3.4.* (hydrolases acting on peptide bond) inhibitor that inhibits the action of a metallocarboxypeptidase (EC 3.4.17.*). EC 3.4.17* (metallocarboxypeptidase) inhibitor chebi_ontology EC 3.4.17* (metallocarboxypeptidase) inhibitors EC 3.4.17.* inhibitor EC 3.4.17.* inhibitors metallocarboxypeptidase inhibitor metallocarboxypeptidase inhibitors CHEBI:147290 EC 3.4.17* (metallocarboxypeptidase) inhibitor EC 3.4.17* (metallocarboxypeptidase) inhibitor ChEBI EC 3.4.17* (metallocarboxypeptidase) inhibitors ChEBI EC 3.4.17.* inhibitor ChEBI EC 3.4.17.* inhibitors ChEBI metallocarboxypeptidase inhibitor ChEBI metallocarboxypeptidase inhibitors ChEBI Any agent that induces nausea and vomiting. chebi_ontology emetics CHEBI:149552 emetic emetics ChEBI A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function. +1 C5H14NO InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1 OEYIOHPDSNJKLS-UHFFFAOYSA-N 104.17080 104.10699 C[N+](C)(C)CCO CHEBI:13985 CHEBI:23212 CHEBI:3665 CHEBI:41524 Beilstein:1736748 CAS:62-49-7 DrugBank:DB00122 Drug_Central:3097 ECMDB:ECMDB00097 Gmelin:324597 HMDB:HMDB0000097 KEGG:C00114 KEGG:D07690 KNApSAcK:C00007298 MetaCyc:CHOLINE PDBeChem:CHT PMID:10930630 PMID:12826235 PMID:12946691 PMID:14972364 PMID:16210714 PMID:17087106 PMID:17283071 PMID:17344490 PMID:18204095 PMID:18230680 PMID:18786517 PMID:18786520 PMID:19246089 PMID:20038853 PMID:20446114 PMID:22770225 PMID:22961562 PMID:23095202 PMID:23616508 PMID:23637565 PMID:23733158 PMID:6420466 PMID:7590654 PMID:9517478 Reaxys:1736748 Wikipedia:Choline YMDB:YMDB00227 2-hydroxy-N,N,N-trimethylethanaminium Choline choline chebi_ontology Bilineurine CHOLINE ION N,N,N-trimethylethanol-ammonium N-trimethylethanolamine trimethylethanolamine CHEBI:15354 choline Beilstein:1736748 Beilstein CAS:62-49-7 ChemIDplus CAS:62-49-7 KEGG COMPOUND Drug_Central:3097 DrugCentral Gmelin:324597 Gmelin PMID:10930630 Europe PMC PMID:12826235 Europe PMC PMID:12946691 Europe PMC PMID:14972364 Europe PMC PMID:16210714 Europe PMC PMID:17087106 Europe PMC PMID:17283071 Europe PMC PMID:17344490 Europe PMC PMID:18204095 Europe PMC PMID:18230680 Europe PMC PMID:18786517 Europe PMC PMID:18786520 Europe PMC PMID:19246089 Europe PMC PMID:20038853 Europe PMC PMID:20446114 Europe PMC PMID:22770225 Europe PMC PMID:22961562 Europe PMC PMID:23095202 Europe PMC PMID:23616508 Europe PMC PMID:23637565 Europe PMC PMID:23733158 Europe PMC PMID:6420466 Europe PMC PMID:7590654 Europe PMC PMID:9517478 Europe PMC Reaxys:1736748 Reaxys 2-hydroxy-N,N,N-trimethylethanaminium IUPAC Choline KEGG_COMPOUND choline UniProt Bilineurine KEGG_COMPOUND CHOLINE ION PDBeChem N,N,N-trimethylethanol-ammonium ChEBI N-trimethylethanolamine ChEBI trimethylethanolamine ChEBI A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 NC(CS)C(O)=O CHEBI:14061 CHEBI:23508 CHEBI:4050 Beilstein:1721406 CAS:3374-22-9 Gmelin:2933 KEGG:C00736 KNApSAcK:C00001351 KNApSAcK:C00007323 PMID:17439666 PMID:25181601 Reaxys:1721406 Wikipedia:Cysteine Cysteine cysteine chebi_ontology 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C Cys Cystein Hcys Zystein cisteina CHEBI:15356 cysteine Beilstein:1721406 Beilstein CAS:3374-22-9 ChemIDplus CAS:3374-22-9 KEGG COMPOUND CAS:3374-22-9 NIST Chemistry WebBook Gmelin:2933 Gmelin PMID:17439666 Europe PMC PMID:25181601 Europe PMC Reaxys:1721406 Reaxys Cysteine KEGG_COMPOUND cysteine ChEBI cysteine IUPAC 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI Cys ChEBI Cystein ChEBI Hcys IUPAC Zystein ChEBI cisteina ChEBI A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, arising from deprotonation of the carboxy group. -1 C3H3O3 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 LCTONWCANYUPML-UHFFFAOYSA-M 87.05412 87.00877 CC(=O)C([O-])=O CHEBI:14987 CHEBI:26462 Beilstein:3587721 CAS:57-60-3 Gmelin:2502 KEGG:C00022 PMID:17190852 PMID:21603897 PMID:21823181 PMID:21854850 PMID:22006570 PMID:22016370 PMID:22215378 PMID:22311625 PMID:22451307 PMID:22458763 Reaxys:3587721 UM-BBD_compID:c0159 2-oxopropanoate pyruvate chebi_ontology 2-oxopropanoate 2-oxopropanoic acid, ion(1-) CHEBI:15361 pyruvate Beilstein:3587721 Beilstein CAS:57-60-3 ChemIDplus Gmelin:2502 Gmelin PMID:17190852 Europe PMC PMID:21603897 Europe PMC PMID:21823181 Europe PMC PMID:21854850 Europe PMC PMID:22006570 Europe PMC PMID:22016370 Europe PMC PMID:22215378 Europe PMC PMID:22311625 Europe PMC PMID:22451307 Europe PMC PMID:22458763 Europe PMC Reaxys:3587721 Reaxys UM-BBD_compID:c0159 UM-BBD 2-oxopropanoate IUPAC pyruvate UniProt 2-oxopropanoate ChEBI 2-oxopropanoic acid, ion(1-) ChemIDplus A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC AcOH ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI A sulfonium compound that is the S-adenosyl derivative of L-methionine. It is an intermediate in the metabolic pathway of methionine. +1 C15H23N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-O 399.44500 399.14452 C[S+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 CHEBI:10786 CHEBI:10833 CHEBI:12742 CHEBI:12757 CHEBI:12760 CHEBI:22036 CHEBI:45607 CHEBI:527887 CHEBI:8946 Beilstein:3576439 CAS:29908-03-0 COMe:MOL000172 DrugBank:DB00118 HMDB:HMDB0001185 KEGG:C00019 KNApSAcK:C00007347 MetaCyc:S-ADENOSYLMETHIONINE PMID:11017945 PMID:17439666 Reaxys:3919754 Wikipedia:S-Adenosyl_methionine S-Adenosyl-L-methionine S-adenosyl-L-methionine [(3S)-3-amino-3-carboxypropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium chebi_ontology (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt Acylcarnitine AdoMet S-(5'-deoxyadenosin-5'-yl)-L-methionine S-Adenosylmethionine S-adenosylmethionine SAM SAMe [1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium CHEBI:15414 S-adenosyl-L-methionine Beilstein:3576439 Beilstein CAS:29908-03-0 ChemIDplus CAS:29908-03-0 KEGG COMPOUND PMID:11017945 Europe PMC PMID:17439666 Europe PMC Reaxys:3919754 Reaxys S-Adenosyl-L-methionine KEGG_COMPOUND S-adenosyl-L-methionine ChEBI [(3S)-3-amino-3-carboxypropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium IUPAC (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt ChemIDplus Acylcarnitine KEGG_COMPOUND AdoMet JCBN S-(5'-deoxyadenosin-5'-yl)-L-methionine JCBN S-Adenosylmethionine KEGG_COMPOUND S-adenosylmethionine ChEBI SAM JCBN SAMe ChemIDplus [1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium IUPAC The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06664 75.03203 NCC(O)=O CHEBI:10792 CHEBI:14344 CHEBI:24368 CHEBI:42964 CHEBI:5460 Beilstein:635782 CAS:56-40-6 DrugBank:DB00145 Drug_Central:1319 ECMDB:ECMDB00123 Gmelin:1808 HMDB:HMDB0000123 KEGG:C00037 KEGG:D00011 KNApSAcK:C00001361 MetaCyc:GLY PDBeChem:GLY PMID:10930630 PMID:11019925 PMID:11174716 PMID:11542461 PMID:11806864 PMID:12631515 PMID:12754315 PMID:12770151 PMID:12921899 PMID:15331688 PMID:15388434 PMID:15710237 PMID:16105183 PMID:16151895 PMID:16214212 PMID:16417482 PMID:16444815 PMID:16664855 PMID:16901953 PMID:16918424 PMID:16986325 PMID:16998855 PMID:17154252 PMID:17383967 PMID:17582620 PMID:17970719 PMID:18079355 PMID:18396796 PMID:18440992 PMID:18593588 PMID:18816054 PMID:18840508 PMID:19028609 PMID:19120667 PMID:19449910 PMID:19526731 PMID:19544666 PMID:19738917 PMID:19916621 PMID:19924257 PMID:21751272 PMID:22044190 PMID:22079563 PMID:22234938 PMID:22264337 PMID:22293292 PMID:22401276 PMID:22434786 Reaxys:635782 Wikipedia:Glycine YMDB:YMDB00016 GLYCINE Glycine aminoacetic acid glycine chebi_ontology Aminoacetic acid Aminoessigsaeure G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly Leimzucker aminoethanoic acid CHEBI:15428 glycine Beilstein:635782 Beilstein CAS:56-40-6 ChemIDplus CAS:56-40-6 KEGG COMPOUND CAS:56-40-6 NIST Chemistry WebBook Drug_Central:1319 DrugCentral Gmelin:1808 Gmelin PMID:10930630 Europe PMC PMID:11019925 Europe PMC PMID:11174716 Europe PMC PMID:11542461 Europe PMC PMID:11806864 Europe PMC PMID:12631515 Europe PMC PMID:12754315 Europe PMC PMID:12770151 Europe PMC PMID:12921899 Europe PMC PMID:15331688 Europe PMC PMID:15388434 Europe PMC PMID:15710237 Europe PMC PMID:16105183 Europe PMC PMID:16151895 Europe PMC PMID:16214212 Europe PMC PMID:16417482 Europe PMC PMID:16444815 Europe PMC PMID:16664855 Europe PMC PMID:16901953 Europe PMC PMID:16918424 Europe PMC PMID:16986325 Europe PMC PMID:16998855 Europe PMC PMID:17154252 Europe PMC PMID:17383967 Europe PMC PMID:17582620 Europe PMC PMID:17970719 Europe PMC PMID:18079355 Europe PMC PMID:18396796 Europe PMC PMID:18440992 Europe PMC PMID:18593588 Europe PMC PMID:18816054 Europe PMC PMID:18840508 Europe PMC PMID:19028609 Europe PMC PMID:19120667 Europe PMC PMID:19449910 Europe PMC PMID:19526731 Europe PMC PMID:19544666 Europe PMC PMID:19738917 Europe PMC PMID:19916621 Europe PMC PMID:19924257 Europe PMC PMID:21751272 Europe PMC PMID:22044190 Europe PMC PMID:22079563 Europe PMC PMID:22234938 Europe PMC PMID:22264337 Europe PMC PMID:22293292 Europe PMC PMID:22401276 Europe PMC PMID:22434786 Europe PMC Reaxys:635782 Reaxys GLYCINE PDBeChem Glycine KEGG_COMPOUND aminoacetic acid IUPAC glycine IUPAC Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC Leimzucker ChemIDplus aminoethanoic acid ChEBI aminoethanoic acid JCBN A triterpene consisting of 2,6,10,15,19,23-hexamethyltetracosane having six double bonds at the 2-, 6-, 10-, 14-, 18- and 22-positions with (all-E)-configuration. 0 C30H50 InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+ YYGNTYWPHWGJRM-AAJYLUCBSA-N 410.730 410.39125 CC(C)=CCC\C(C)=C\CC\C(C)=C\CC\C=C(/C)CC\C=C(/C)CCC=C(C)C CHEBI:10795 CHEBI:10843 CHEBI:15104 CHEBI:26746 CHEBI:9245 Beilstein:1728920 CAS:111-02-4 HMDB:HMDB0000256 KEGG:C00751 KNApSAcK:C00003755 LIPID_MAPS_instance:LMPR0106010002 MetaCyc:SQUALENE PDBeChem:SQL PMID:16341241 PMID:23625688 PMID:24362891 PMID:25286851 PMID:25286853 PMID:25987292 Wikipedia:Squalene (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene Squalene squalene chebi_ontology (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene Spinacene Supraene CHEBI:15440 squalene Beilstein:1728920 Beilstein CAS:111-02-4 ChemIDplus CAS:111-02-4 KEGG COMPOUND CAS:111-02-4 NIST Chemistry WebBook LIPID_MAPS_instance:LMPR0106010002 LIPID MAPS PMID:16341241 Europe PMC PMID:23625688 Europe PMC PMID:24362891 Europe PMC PMID:25286851 Europe PMC PMID:25286853 Europe PMC PMID:25987292 Europe PMC (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene IUPAC Squalene KEGG_COMPOUND squalene UniProt (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene NIST_Chemistry_WebBook Spinacene KEGG_COMPOUND Supraene KEGG_COMPOUND +1 C15H23N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8-,10-,11-,14-,27?/m1/s1 MEFKEPWMEQBLKI-XCPQSEKJSA-O 399.450 399.14452 [S+](C[C@H]1O[C@@H](N2C3=NC=NC(N)=C3N=C2)[C@H](O)[C@@H]1O)(CC[C@@H](N)C(O)=O)C chebi_ontology CHEBI:156255 S-adenosyl-D-methionine Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. 0 C2H4O2(CH2O)n CHEBI:13755 CHEBI:22305 CHEBI:2561 KEGG:C01370 Wikipedia:Aldose Aldose chebi_ontology aldoses an aldose CHEBI:15693 aldose Aldose KEGG_COMPOUND aldoses ChEBI an aldose UniProt Any alpha-amino acid having L-configuration at the alpha-carbon. 0 C2H4NO2R 74.05870 74.02420 N[C@@H]([*])C(O)=O CHEBI:13072 CHEBI:13243 CHEBI:13797 CHEBI:21224 CHEBI:6175 KEGG:C00151 L-alpha-amino acid L-alpha-amino acids chebi_ontology L-2-Amino acid L-Amino acid L-alpha-amino acids CHEBI:15705 L-alpha-amino acid L-alpha-amino acid IUPAC L-alpha-amino acids IUPAC L-2-Amino acid KEGG_COMPOUND L-Amino acid KEGG_COMPOUND L-alpha-amino acids ChEBI A tertiary amine oxide resulting from the oxidation of the amino group of trimethylamine. 0 C3H9NO InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3 UYPYRKYUKCHHIB-UHFFFAOYSA-N 75.110 75.06841 C[N+](C)([O-])C CHEBI:15262 CHEBI:15263 CHEBI:27126 CHEBI:9733 Beilstein:1734787 CAS:1184-78-7 Gmelin:1839 HMDB:HMDB0000925 KEGG:C01104 MetaCyc:TRIMENTHLAMINE-N-O PDBeChem:TMO PMID:12683801 PMID:1453985 PMID:17697669 PMID:19425246 PMID:22770225 PMID:3170512 PMID:3674879 Reaxys:1734787 Wikipedia:Trimethylamine_oxide N,N-dimethylmethanamine oxide Trimethylamine N-oxide trimethylamine N-oxide chebi_ontology (CH3)3NO Me3N(+)O(-) Me3N(O) N(CH3)3O TMAO Trimethylaminoxid trimethylamine oxide trimethyloxamine CHEBI:15724 trimethylamine N-oxide Beilstein:1734787 Beilstein CAS:1184-78-7 ChemIDplus CAS:1184-78-7 KEGG COMPOUND CAS:1184-78-7 NIST Chemistry WebBook Gmelin:1839 Gmelin PMID:12683801 Europe PMC PMID:1453985 Europe PMC PMID:17697669 Europe PMC PMID:19425246 Europe PMC PMID:22770225 Europe PMC PMID:3170512 Europe PMC PMID:3674879 Europe PMC Reaxys:1734787 Reaxys N,N-dimethylmethanamine oxide IUPAC Trimethylamine N-oxide KEGG_COMPOUND trimethylamine N-oxide UniProt (CH3)3NO IUPAC Me3N(+)O(-) ChEBI Me3N(O) ChEBI N(CH3)3O ChEBI TMAO NIST_Chemistry_WebBook Trimethylaminoxid ChEBI trimethylamine oxide NIST_Chemistry_WebBook trimethyloxamine ChemIDplus A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. 0 CH3OR 31.034 31.01839 *C(O)([H])[H] CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 KEGG:C00226 Primary alcohol chebi_ontology 1-Alcohol a primary alcohol primary alcohols CHEBI:15734 primary alcohol Primary alcohol KEGG_COMPOUND 1-Alcohol KEGG_COMPOUND a primary alcohol UniProt primary alcohols ChEBI A monocarboxylic acid anion that is the conjugate base of formic acid. Induces severe metabolic acidosis and ocular injury in human subjects. -1 CHO2 InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)/p-1 BDAGIHXWWSANSR-UHFFFAOYSA-M 45.01744 44.99820 [H]C([O-])=O CHEBI:14276 CHEBI:24081 Beilstein:1901205 CAS:71-47-6 Gmelin:1006 HMDB:HMDB0000142 KEGG:C00058 MetaCyc:FORMATE PMID:17190852 PMID:3946945 Reaxys:1901205 UM-BBD_compID:c0106 Wikipedia:Formate formate chebi_ontology HCO2 anion aminate formiate formic acid, ion(1-) formylate hydrogen carboxylate methanoate CHEBI:15740 formate Beilstein:1901205 Beilstein CAS:71-47-6 ChemIDplus CAS:71-47-6 NIST Chemistry WebBook Gmelin:1006 Gmelin PMID:17190852 Europe PMC PMID:3946945 Europe PMC Reaxys:1901205 Reaxys UM-BBD_compID:c0106 UM-BBD formate IUPAC formate UniProt HCO2 anion NIST_Chemistry_WebBook aminate ChEBI formiate ChEBI formic acid, ion(1-) ChemIDplus formylate ChEBI hydrogen carboxylate ChEBI methanoate ChEBI A straight-chain, sixteen-carbon, saturated long-chain fatty acid. 0 C16H32O2 InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18) IPCSVZSSVZVIGE-UHFFFAOYSA-N 256.42410 256.24023 CCCCCCCCCCCCCCCC(O)=O CHEBI:14730 CHEBI:233028 CHEBI:24540 CHEBI:24541 CHEBI:24542 CHEBI:24550 CHEBI:29889 CHEBI:35978 CHEBI:44952 Beilstein:607489 CAS:57-10-3 DrugBank:DB03796 Gmelin:190200 HMDB:HMDB0000220 KEGG:C00249 KEGG:D05341 KNApSAcK:C00001233 KNApSAcK:C00030479 LIPID_MAPS_instance:LMFA01010001 MetaCyc:PALMITATE PDBeChem:PLM PMID:12492626 PMID:15357969 PMID:1589452 PMID:16509590 PMID:16884313 PMID:17439666 PMID:17502136 PMID:20001317 PMID:22735334 PMID:25584012 PMID:28600633 PPDB:1336 Reaxys:607489 Wikipedia:Palmitic_acid hexadecanoic acid chebi_ontology 1-Pentadecanecarboxylic acid 1-hexyldecanoic acid 16:00 C16 C16 fatty acid C16:0 CH3-[CH2]14-COOH FA 16:0 Hexadecanoate Hexadecylic acid Hexaectylic acid PALMITIC ACID Palmitate Palmitic acid Palmitinic acid Palmitinsaeure Pentadecanecarboxylic acid cetylic acid hexadecoic acid n-hexadecanoic acid n-hexadecoic acid palmitic acid CHEBI:15756 hexadecanoic acid Beilstein:607489 Beilstein CAS:57-10-3 ChemIDplus CAS:57-10-3 KEGG COMPOUND CAS:57-10-3 NIST Chemistry WebBook Gmelin:190200 Gmelin LIPID_MAPS_instance:LMFA01010001 LIPID MAPS PMID:12492626 Europe PMC PMID:15357969 ChEMBL PMID:1589452 Europe PMC PMID:16509590 ChEMBL PMID:16884313 ChEMBL PMID:17439666 Europe PMC PMID:17502136 ChEMBL PMID:20001317 Europe PMC PMID:22735334 Europe PMC PMID:25584012 Europe PMC PMID:28600633 Europe PMC Reaxys:607489 Reaxys hexadecanoic acid IUPAC 1-Pentadecanecarboxylic acid ChemIDplus 1-hexyldecanoic acid HMDB 16:00 ChEBI C16 ChEBI C16 fatty acid HMDB C16:0 LIPID_MAPS CH3-[CH2]14-COOH IUPAC FA 16:0 ChEBI Hexadecanoate KEGG_COMPOUND Hexadecylic acid HMDB Hexadecylic acid KEGG_COMPOUND Hexaectylic acid HMDB PALMITIC ACID PDBeChem Palmitate KEGG_COMPOUND Palmitic acid KEGG_COMPOUND Palmitinic acid HMDB Palmitinsaeure ChEBI Pentadecanecarboxylic acid ChemIDplus cetylic acid KEGG_COMPOUND hexadecoic acid ChEBI n-hexadecanoic acid NIST_Chemistry_WebBook n-hexadecoic acid NIST_Chemistry_WebBook palmitic acid ChEBI Any N-acyl-amino acid in which the amino acid moiety has D configuration. 0 C3H3NO3R2 101.06080 101.01129 OC(=O)[C@@H]([*])NC([*])=O CHEBI:12474 CHEBI:21631 CHEBI:7224 chebi_ontology CHEBI:15778 N-acyl-D-amino acid A peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n CHEBI:14860 CHEBI:8314 KEGG:C00403 Polypeptide polypeptides chebi_ontology Polypeptid polipeptido CHEBI:15841 polypeptide Polypeptide KEGG_COMPOUND polypeptides IUPAC Polypeptid ChEBI polipeptido ChEBI +1 C62H90CoN13O15P InChI=1S/C62H90N13O14P.Co.H2O/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;1H2/q;+3;/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 YOZNUFWCRFCGIH-WZHZPDAFSA-L 1347.36310 1346.57434 [H][O+]([H])[Co-3]1234N5C6=C(C)C7=[N+]1C(=CC1=[N+]2C(=C(C)C2=[N+]3[C@@](C)([C@@]5([H])[C@H](CC(N)=O)[C@@]6(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@@H]3[C@@H](CO)O[C@@H]([C@@H]3O)n3c[n+]4c4cc(C)c(C)cc34)[C@@](C)(CC(N)=O)[C@@H]2CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]1CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O CHEBI:13851 CHEBI:22589 CHEBI:2794 CAS:13422-52-1 HMDB:HMDB0003458 KEGG:C00992 MetaCyc:AQUACOBIIIALAMIN Aquacob(III)alamin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-aquacobamide aquacob(III)alamin chebi_ontology Aquacobalamin H2OCbl aquacobalamin vitamin B-12a CHEBI:15852 aquacob(III)alamin CAS:13422-52-1 ChemIDplus CAS:13422-52-1 KEGG COMPOUND Aquacob(III)alamin KEGG_COMPOUND Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-aquacobamide IUPAC aquacob(III)alamin UniProt Aquacobalamin KEGG_COMPOUND H2OCbl ChEBI aquacobalamin CBN vitamin B-12a CBN Any 3-hydroxy steroid whose skeleton is closely related to cholestan-3-ol (additional carbon atoms may be present in the side chain). 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCC(C4)O)C CHEBI:13688 CHEBI:15114 CHEBI:26771 CHEBI:9266 KEGG:C00370 LIPID_MAPS_class:LMST01 MetaCyc:Sterols Wikipedia:Sterol Sterol sterols chebi_ontology 3-hydroxysteroids a sterol CHEBI:15889 sterol LIPID_MAPS_class:LMST01 LIPID MAPS Sterol KEGG_COMPOUND sterols IUPAC 3-hydroxysteroids ChEBI a sterol UniProt A fatty acid with a chain length ranging from C13 to C22. 0 CHO2R 45.017 44.99765 OC([*])=O CHEBI:13655 CHEBI:14529 CHEBI:25075 CHEBI:6528 KEGG:C00638 Long-chain fatty acid chebi_ontology Higher fatty acid LCFA LCFAs long-chain fatty acids CHEBI:15904 long-chain fatty acid Long-chain fatty acid KEGG_COMPOUND Higher fatty acid KEGG_COMPOUND LCFA ChEBI LCFAs ChEBI long-chain fatty acids ChEBI A pyridinemonocarboxylic acid that is pyridine in which the hydrogen at position 3 is replaced by a carboxy group. 0 C6H5NO2 InChI=1S/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9) PVNIIMVLHYAWGP-UHFFFAOYSA-N 123.10944 123.03203 OC(=O)c1cccnc1 CHEBI:25538 CHEBI:44319 CHEBI:7559 AGR:IND607088605 Beilstein:109591 CAS:59-67-6 Chemspider:913 DrugBank:DB00627 Drug_Central:2835 FooDB:FDB001014 Gmelin:3340 HMDB:HMDB0001488 KEGG:C00253 KEGG:D00049 KNApSAcK:C00000208 LINCS:LSM-4676 MetaCyc:NIACINE PDBeChem:NIO PMID:10540864 PMID:113218 PMID:12563315 PMID:12789870 PMID:135660 PMID:14550884 PMID:15037193 PMID:15183629 PMID:15205990 PMID:15311728 PMID:15627518 PMID:15651982 PMID:16018787 PMID:16172771 PMID:16322787 PMID:16400392 PMID:16449845 PMID:16767301 PMID:16877271 PMID:16945375 PMID:18037924 PMID:182198 PMID:186078 PMID:18993152 PMID:18996527 PMID:19369827 PMID:19592242 PMID:19678716 PMID:19779335 PMID:20979384 PMID:21632263 PMID:22116693 PMID:22155410 PMID:22229411 PMID:22366213 PMID:22458880 PMID:22770225 PMID:24029555 PMID:24568240 PMID:24675661 PMID:24848081 PMID:24975217 PMID:25040591 PMID:25241762 PMID:25429652 PMID:32954525 PMID:33273654 PMID:33932650 PMID:34066686 PMID:34085526 PMID:34117670 PMID:4033386 PMID:4259917 PMID:582105 PMID:699281 PMID:7217784 PMID:7581845 PMID:8306147 PMID:8423912 PMID:8679452 PMID:9107536 Reaxys:109591 Wikipedia:Niacin NICOTINIC ACID Nicotinic acid nicotinic acid pyridine-3-carboxylic acid chebi_ontology 3-Pyridylcarboxylic acid 3-carboxylpyridine 3-carboxypyridine 3-pyridinecarboxylic acid Niacin Niacor Niaspan Nicotinsaure Nikotinsaeure P.P. factor PP factor acide nicotinique acido nicotinico acidum nicotinicum anti-pellagra vitamin beta-pyridinecarboxylic acid m-pyridinecarboxylic acid nicotinic acid pellagra preventive factor pyridine-beta-carboxylic acid pyridine-carboxylique-3 vitamin B3 CHEBI:15940 nicotinic acid AGR:IND607088605 Europe PMC Beilstein:109591 Beilstein CAS:59-67-6 ChemIDplus CAS:59-67-6 KEGG COMPOUND CAS:59-67-6 NIST Chemistry WebBook Drug_Central:2835 DrugCentral Gmelin:3340 Gmelin PMID:10540864 Europe PMC PMID:113218 Europe PMC PMID:12563315 Europe PMC PMID:12789870 Europe PMC PMID:135660 Europe PMC PMID:14550884 Europe PMC PMID:15037193 Europe PMC PMID:15183629 Europe PMC PMID:15205990 Europe PMC PMID:15311728 Europe PMC PMID:15627518 Europe PMC PMID:15651982 Europe PMC PMID:16018787 Europe PMC PMID:16172771 Europe PMC PMID:16322787 Europe PMC PMID:16400392 Europe PMC PMID:16449845 Europe PMC PMID:16767301 Europe PMC PMID:16877271 Europe PMC PMID:16945375 Europe PMC PMID:18037924 Europe PMC PMID:182198 Europe PMC PMID:186078 Europe PMC PMID:18993152 Europe PMC PMID:18996527 Europe PMC PMID:19369827 Europe PMC PMID:19592242 Europe PMC PMID:19678716 Europe PMC PMID:19779335 Europe PMC PMID:20979384 Europe PMC PMID:21632263 Europe PMC PMID:22116693 Europe PMC PMID:22155410 Europe PMC PMID:22229411 Europe PMC PMID:22366213 Europe PMC PMID:22458880 Europe PMC PMID:22770225 Europe PMC PMID:24029555 Europe PMC PMID:24568240 Europe PMC PMID:24675661 Europe PMC PMID:24848081 Europe PMC PMID:24975217 Europe PMC PMID:25040591 Europe PMC PMID:25241762 Europe PMC PMID:25429652 Europe PMC PMID:32954525 Europe PMC PMID:33273654 Europe PMC PMID:33932650 Europe PMC PMID:34066686 Europe PMC PMID:34085526 Europe PMC PMID:34117670 Europe PMC PMID:4033386 Europe PMC PMID:4259917 Europe PMC PMID:582105 Europe PMC PMID:699281 Europe PMC PMID:7217784 Europe PMC PMID:7581845 Europe PMC PMID:8306147 Europe PMC PMID:8423912 Europe PMC PMID:8679452 Europe PMC PMID:9107536 Europe PMC Reaxys:109591 Reaxys NICOTINIC ACID PDBeChem Nicotinic acid KEGG_COMPOUND nicotinic acid IUPAC pyridine-3-carboxylic acid IUPAC 3-Pyridylcarboxylic acid HMDB 3-carboxylpyridine ChemIDplus 3-carboxypyridine NIST_Chemistry_WebBook 3-pyridinecarboxylic acid KEGG_COMPOUND Niacin KEGG_COMPOUND Niacor KEGG_DRUG Niaspan KEGG_DRUG Nicotinsaure ChemIDplus Nikotinsaeure ChEBI P.P. factor NIST_Chemistry_WebBook PP factor NIST_Chemistry_WebBook acide nicotinique WHO_MedNet acido nicotinico WHO_MedNet acidum nicotinicum WHO_MedNet anti-pellagra vitamin NIST_Chemistry_WebBook beta-pyridinecarboxylic acid ChEBI m-pyridinecarboxylic acid NIST_Chemistry_WebBook nicotinic acid WHO_MedNet pellagra preventive factor NIST_Chemistry_WebBook pyridine-beta-carboxylic acid NIST_Chemistry_WebBook pyridine-carboxylique-3 ChemIDplus vitamin B3 ChEBI An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. 0 C10H16N2O3S InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 244.31172 244.08816 [H][C@]12CS[C@@H](CCCCC(O)=O)[C@@]1([H])NC(=O)N2 CHEBI:13905 CHEBI:22882 CHEBI:22884 CHEBI:3108 CHEBI:41236 Beilstein:86838 CAS:58-85-5 COMe:MOL000144 Chemspider:149962 DrugBank:DB00121 Drug_Central:373 FooDB:FDB014510 Gmelin:1918703 HMDB:HMDB0000030 KEGG:C00120 KEGG:D00029 KNApSAcK:C00000756 LINCS:LSM-3994 MetaCyc:BIOTIN PDBeChem:BTN PMCID:PMC8089577 PMID:10064317 PMID:10215065 PMID:10577274 PMID:11435506 PMID:11481419 PMID:11800048 PMID:12055344 PMID:12070309 PMID:12603856 PMID:12803839 PMID:15012185 PMID:15202718 PMID:15272000 PMID:15690449 PMID:15863846 PMID:15899401 PMID:15992684 PMID:16011464 PMID:16195795 PMID:16419467 PMID:16676358 PMID:16677798 PMID:16704206 PMID:16769720 PMID:17297119 PMID:1814646 PMID:18202531 PMID:18452485 PMID:18509457 PMID:19212411 PMID:19319844 PMID:19727438 PMID:19928962 PMID:20967359 PMID:20974274 PMID:2100006 PMID:21248194 PMID:21356565 PMID:21373679 PMID:21596550 PMID:21871906 PMID:25515858 PMID:33346513 PMID:33461365 PMID:34077272 PMID:8333586 PMID:8750932 PMID:9022537 PMID:9038855 PMID:9094878 PMID:9164991 PMID:9176832 PMID:9371938 PMID:9416479 Reaxys:86838 Wikipedia:Biotin 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid BIOTIN chebi_ontology (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid Coenzyme R D-(+)-biotin D-Biotin Vitamin H biotin biotina biotine biotinum cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid vitamin B7 CHEBI:15956 biotin Beilstein:86838 Beilstein CAS:58-85-5 ChemIDplus CAS:58-85-5 KEGG COMPOUND CAS:58-85-5 NIST Chemistry WebBook Drug_Central:373 DrugCentral Gmelin:1918703 Gmelin PMCID:PMC8089577 Europe PMC PMID:10064317 Europe PMC PMID:10215065 Europe PMC PMID:10577274 Europe PMC PMID:11435506 Europe PMC PMID:11481419 Europe PMC PMID:11800048 Europe PMC PMID:12055344 Europe PMC PMID:12070309 Europe PMC PMID:12603856 Europe PMC PMID:12803839 Europe PMC PMID:15012185 Europe PMC PMID:15202718 Europe PMC PMID:15272000 Europe PMC PMID:15690449 Europe PMC PMID:15863846 Europe PMC PMID:15899401 Europe PMC PMID:15992684 Europe PMC PMID:16011464 Europe PMC PMID:16195795 Europe PMC PMID:16419467 Europe PMC PMID:16676358 Europe PMC PMID:16677798 Europe PMC PMID:16704206 Europe PMC PMID:16769720 Europe PMC PMID:17297119 Europe PMC PMID:1814646 Europe PMC PMID:18202531 Europe PMC PMID:18452485 Europe PMC PMID:18509457 Europe PMC PMID:19212411 Europe PMC PMID:19319844 Europe PMC PMID:19727438 Europe PMC PMID:19928962 Europe PMC PMID:20967359 Europe PMC PMID:20974274 Europe PMC PMID:2100006 Europe PMC PMID:21248194 Europe PMC PMID:21356565 Europe PMC PMID:21373679 Europe PMC PMID:21596550 Europe PMC PMID:21871906 Europe PMC PMID:25515858 Europe PMC PMID:33346513 Europe PMC PMID:33461365 Europe PMC PMID:34077272 Europe PMC PMID:8333586 Europe PMC PMID:8750932 Europe PMC PMID:9022537 Europe PMC PMID:9038855 Europe PMC PMID:9094878 Europe PMC PMID:9164991 Europe PMC PMID:9176832 Europe PMC PMID:9371938 Europe PMC PMID:9416479 Europe PMC Reaxys:86838 Reaxys 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid IUPAC BIOTIN PDBeChem (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid HMDB (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid HMDB 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid HMDB Coenzyme R KEGG_COMPOUND D-(+)-biotin NIST_Chemistry_WebBook D-Biotin KEGG_COMPOUND Vitamin H KEGG_COMPOUND biotin WHO_MedNet biotina WHO_MedNet biotine WHO_MedNet biotinum WHO_MedNet cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid HMDB cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid HMDB cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid HMDB vitamin B7 NIST_Chemistry_WebBook An optically active form of glutamic acid having D-configuration. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-N 147.12930 147.05316 N[C@H](CCC(O)=O)C(O)=O CHEBI:21023 CHEBI:4183 Beilstein:1723800 CAS:6893-26-1 DrugBank:DB02517 Gmelin:201189 HMDB:HMDB0003339 KEGG:C00217 KNApSAcK:C00019577 MetaCyc:D-GLT PDBeChem:DGL Reaxys:1723800 (2R)-2-aminopentanedioic acid D-Glutamic acid D-glutamic acid chebi_ontology (R)-2-aminopentanedioic acid D-2-Aminoglutaric acid D-Glutaminic acid D-Glutaminsaeure DGL glutamic acid D-form CHEBI:15966 D-glutamic acid Beilstein:1723800 Beilstein CAS:6893-26-1 ChemIDplus CAS:6893-26-1 KEGG COMPOUND CAS:6893-26-1 NIST Chemistry WebBook Gmelin:201189 Gmelin Reaxys:1723800 Reaxys (2R)-2-aminopentanedioic acid IUPAC D-Glutamic acid KEGG_COMPOUND D-glutamic acid IUPAC (R)-2-aminopentanedioic acid ChEBI D-2-Aminoglutaric acid KEGG_COMPOUND D-Glutaminic acid KEGG_COMPOUND D-Glutaminsaeure ChEBI DGL PDBeChem glutamic acid D-form ChemIDplus An optically active form of glutamic acid having L-configuration. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-N 147.12930 147.05316 N[C@@H](CCC(O)=O)C(O)=O CHEBI:21304 CHEBI:42825 CHEBI:6224 BPDB:2297 Beilstein:1723801 CAS:56-86-0 DrugBank:DB00142 Drug_Central:1310 Gmelin:3502 HMDB:HMDB0000148 KEGG:C00025 KEGG:D00007 KNApSAcK:C00001358 LINCS:LSM-36375 MetaCyc:GLT PDBeChem:GLU_LFOH PMID:15739367 PMID:15930465 PMID:16719819 PMID:16892196 PMID:19581495 PMID:22219301 PMID:22735334 Reaxys:1723801 Wikipedia:L-Glutamic_Acid (2S)-2-aminopentanedioic acid L-Glutamic acid L-glutamic acid chebi_ontology (S)-2-aminopentanedioic acid (S)-glutamic acid E GLUTAMIC ACID Glu Glutamate L-Glu L-Glutaminic acid L-Glutaminsaeure acide glutamique acido glutamico acidum glutamicum glutamic acid CHEBI:16015 L-glutamic acid Beilstein:1723801 Beilstein CAS:56-86-0 ChemIDplus CAS:56-86-0 KEGG COMPOUND CAS:56-86-0 NIST Chemistry WebBook Drug_Central:1310 DrugCentral Gmelin:3502 Gmelin PMID:15739367 Europe PMC PMID:15930465 Europe PMC PMID:16719819 Europe PMC PMID:16892196 Europe PMC PMID:19581495 Europe PMC PMID:22219301 Europe PMC PMID:22735334 Europe PMC Reaxys:1723801 Reaxys (2S)-2-aminopentanedioic acid IUPAC L-Glutamic acid KEGG_COMPOUND L-glutamic acid IUPAC (S)-2-aminopentanedioic acid ChEBI (S)-glutamic acid NIST_Chemistry_WebBook E ChEBI GLUTAMIC ACID PDBeChem Glu ChEBI Glutamate KEGG_COMPOUND L-Glu ChEBI L-Glutaminic acid KEGG_COMPOUND L-Glutaminsaeure ChEBI acide glutamique ChEBI acido glutamico ChEBI acidum glutamicum ChEBI glutamic acid ChEBI A monoatomic monoanion resulting from the addition of an electron to any halogen atom. -1 X 0.0 0.0 [*-] CHEBI:14384 CHEBI:5605 KEGG:C00462 halide ions chebi_ontology HX Halide a halide anion halide anions halide(1-) halides halogen anion CHEBI:16042 halide anion halide ions IUPAC HX KEGG_COMPOUND Halide KEGG_COMPOUND a halide anion UniProt halide anions ChEBI halide(1-) ChEBI halides ChEBI halogen anion ChEBI A gamma-amino acid comprising 4-aminobutyric acid having a 2-hydroxy substituent. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8) YQGDEPYYFWUPGO-UHFFFAOYSA-N 119.11920 119.05824 NCC(O)CC(O)=O CHEBI:1780 CHEBI:20311 Beilstein:1721708 Beilstein:1752568 CAS:352-21-6 Drug_Central:1263 KEGG:C03678 KEGG:D00174 4-amino-3-hydroxybutanoic acid gamma-Amino-beta-hydroxybutyric acid chebi_ontology 3-hydroxy-GABA 4-Amino-3-hydroxybutanoic acid 4-amino-3-hydroxybutyric acid GABOB CHEBI:16080 gamma-amino-beta-hydroxybutyric acid Beilstein:1721708 Beilstein Beilstein:1752568 Beilstein CAS:352-21-6 ChemIDplus CAS:352-21-6 KEGG COMPOUND Drug_Central:1263 DrugCentral 4-amino-3-hydroxybutanoic acid IUPAC gamma-Amino-beta-hydroxybutyric acid KEGG_COMPOUND 3-hydroxy-GABA ChemIDplus 4-Amino-3-hydroxybutanoic acid KEGG_COMPOUND 4-amino-3-hydroxybutyric acid ChemIDplus GABOB KEGG_COMPOUND A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. 0 C27H46O InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 HVYWMOMLDIMFJA-DPAQBDIFSA-N 386.655 386.35487 C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC=C2C[C@H](C1)O)[H])(CC[C@@]4([C@H](C)CCCC(C)C)[H])[H])C)[H])C CHEBI:13982 CHEBI:23204 CHEBI:3659 CHEBI:41564 Beilstein:2060565 CAS:57-88-5 DrugBank:DB04540 Gmelin:550297 HMDB:HMDB0000067 KEGG:C00187 KEGG:D00040 KNApSAcK:C00003648 LIPID_MAPS_instance:LMST01010001 MetaCyc:CHOLESTEROL PDBeChem:CLR PMID:10901445 PMID:11412894 PMID:16341241 PMID:24287311 PMID:25308664 PMID:25451949 PMID:25522988 PMID:25658343 PMID:25977713 PMID:4696527 PMID:8838010 Reaxys:2060565 Wikipedia:Cholesterol CHOLESTEROL Cholesterol cholest-5-en-3beta-ol cholesterol chebi_ontology (3beta,14beta,17alpha)-cholest-5-en-3-ol Cholest-5-en-3beta-ol Cholesterin CHEBI:16113 cholesterol Beilstein:2060565 Beilstein CAS:57-88-5 ChemIDplus CAS:57-88-5 KEGG COMPOUND CAS:57-88-5 NIST Chemistry WebBook Gmelin:550297 Gmelin LIPID_MAPS_instance:LMST01010001 LIPID MAPS PMID:10901445 Europe PMC PMID:11412894 Europe PMC PMID:16341241 Europe PMC PMID:24287311 Europe PMC PMID:25308664 Europe PMC PMID:25451949 Europe PMC PMID:25522988 Europe PMC PMID:25658343 Europe PMC PMID:25977713 Europe PMC PMID:4696527 Europe PMC PMID:8838010 Europe PMC Reaxys:2060565 Reaxys CHOLESTEROL PDBeChem Cholesterol KEGG_COMPOUND cholest-5-en-3beta-ol IUPAC cholesterol UniProt (3beta,14beta,17alpha)-cholest-5-en-3-ol IUPAC Cholest-5-en-3beta-ol KEGG_COMPOUND Cholesterin NIST_Chemistry_WebBook An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn CHEBI:16134 ammonia Beilstein:3587154 Beilstein CAS:7664-41-7 ChemIDplus CAS:7664-41-7 KEGG COMPOUND CAS:7664-41-7 NIST Chemistry WebBook Drug_Central:4625 DrugCentral Gmelin:79 Gmelin PMID:110589 Europe PMC PMID:11139349 Europe PMC PMID:11540049 Europe PMC PMID:11746427 Europe PMC PMID:11783653 Europe PMC PMID:13753780 Europe PMC PMID:14663195 Europe PMC PMID:15092448 Europe PMC PMID:15094021 Europe PMC PMID:15554424 Europe PMC PMID:15969015 Europe PMC PMID:16008360 Europe PMC PMID:16050680 Europe PMC PMID:16348008 Europe PMC PMID:16349403 Europe PMC PMID:16614889 Europe PMC PMID:16664306 Europe PMC PMID:16842901 Europe PMC PMID:17025297 Europe PMC PMID:17439666 Europe PMC PMID:17569513 Europe PMC PMID:17737668 Europe PMC PMID:18670398 Europe PMC PMID:22002069 Europe PMC PMID:22081570 Europe PMC PMID:22088435 Europe PMC PMID:22100291 Europe PMC PMID:22130175 Europe PMC PMID:22150211 Europe PMC PMID:22240068 Europe PMC PMID:22290316 Europe PMC PMID:22342082 Europe PMC PMID:22385337 Europe PMC PMID:22443779 Europe PMC PMID:22560242 Europe PMC Reaxys:3587154 Reaxys AMMONIA PDBeChem Ammonia KEGG_COMPOUND ammonia IUPAC azane IUPAC Ammoniak ChemIDplus NH3 IUPAC NH3 KEGG_COMPOUND NH3 UniProt R-717 ChEBI [NH3] MolBase ammoniac ChEBI amoniaco ChEBI spirit of hartshorn ChemIDplus A mucopolysaccharide composed of repeating beta-D-glucopyranuronosyl-(1->3)-beta-D-N-acetylgalactosaminyl units. (C14H21NO11)nH2O CHEBI:13989 CHEBI:13992 CHEBI:23221 CHEBI:3673 KEGG:C00401 KEGG:G11334 chebi_ontology Chondroitin Chondroitin-D-glucuronate CHEBI:16137 chondroitin D-glucuronate Chondroitin KEGG_COMPOUND Chondroitin-D-glucuronate KEGG_COMPOUND A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid. -2 O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 QAOWNCQODCNURD-UHFFFAOYSA-L 96.06360 95.95283 [O-]S([O-])(=O)=O CHEBI:15135 CHEBI:45687 CHEBI:9335 Beilstein:3648446 CAS:14808-79-8 Gmelin:2120 HMDB:HMDB0001448 KEGG:C00059 KEGG:D05963 MetaCyc:SULFATE PDBeChem:SO4 PMID:11200094 PMID:11452993 PMID:11581495 PMID:11798107 PMID:12166931 PMID:12668033 PMID:14597181 PMID:15093386 PMID:15984785 PMID:16186560 PMID:16345535 PMID:16347366 PMID:16348007 PMID:16483812 PMID:16534979 PMID:16656509 PMID:16742508 PMID:16742518 PMID:17120760 PMID:17420092 PMID:17439666 PMID:17709180 PMID:18398178 PMID:18815700 PMID:18846414 PMID:19047345 PMID:19244483 PMID:19544990 PMID:19628332 PMID:19812358 PMID:30398859 Reaxys:3648446 Wikipedia:Sulfate Sulfate sulfate tetraoxidosulfate(2-) tetraoxosulfate(2-) tetraoxosulfate(VI) chebi_ontology SO4(2-) SULFATE ION Sulfate anion(2-) Sulfate dianion Sulfate(2-) Sulfuric acid ion(2-) [SO4](2-) sulphate sulphate ion CHEBI:16189 sulfate Beilstein:3648446 Beilstein CAS:14808-79-8 ChemIDplus CAS:14808-79-8 NIST Chemistry WebBook Gmelin:2120 Gmelin PMID:11200094 Europe PMC PMID:11452993 Europe PMC PMID:11581495 Europe PMC PMID:11798107 Europe PMC PMID:12166931 Europe PMC PMID:12668033 Europe PMC PMID:14597181 Europe PMC PMID:15093386 Europe PMC PMID:15984785 Europe PMC PMID:16186560 Europe PMC PMID:16345535 Europe PMC PMID:16347366 Europe PMC PMID:16348007 Europe PMC PMID:16483812 Europe PMC PMID:16534979 Europe PMC PMID:16656509 Europe PMC PMID:16742508 Europe PMC PMID:16742518 Europe PMC PMID:17120760 Europe PMC PMID:17420092 Europe PMC PMID:17439666 Europe PMC PMID:17709180 Europe PMC PMID:18398178 Europe PMC PMID:18815700 Europe PMC PMID:18846414 Europe PMC PMID:19047345 Europe PMC PMID:19244483 Europe PMC PMID:19544990 Europe PMC PMID:19628332 Europe PMC PMID:19812358 Europe PMC PMID:30398859 Europe PMC Reaxys:3648446 Reaxys Sulfate KEGG_COMPOUND sulfate IUPAC sulfate UniProt tetraoxidosulfate(2-) IUPAC tetraoxosulfate(2-) IUPAC tetraoxosulfate(VI) IUPAC SO4(2-) IUPAC SULFATE ION PDBeChem Sulfate anion(2-) HMDB Sulfate dianion HMDB Sulfate(2-) HMDB Sulfuric acid ion(2-) HMDB [SO4](2-) IUPAC sulphate ChEBI sulphate ion ChEBI A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O). 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(N)=O CHEBI:15292 CHEBI:27218 CHEBI:46379 CHEBI:9888 Beilstein:635724 CAS:57-13-6 DrugBank:DB03904 Drug_Central:4264 ECMDB:ECMDB04172 Gmelin:1378 HMDB:HMDB0000294 KEGG:C00086 KEGG:D00023 KNApSAcK:C00007314 MetaCyc:UREA PDBeChem:URE PMID:18037357 PMID:22770225 PPDB:1728 Reaxys:635724 UM-BBD_compID:c0165 Wikipedia:Urea YMDB:YMDB00003 UREA Urea urea chebi_ontology 1728 Carbamide E927b H2NC(O)NH2 Harnstoff Karbamid carbamide carbonyldiamide ur uree CHEBI:16199 urea Beilstein:635724 Beilstein CAS:57-13-6 ChemIDplus CAS:57-13-6 KEGG COMPOUND CAS:57-13-6 NIST Chemistry WebBook Drug_Central:4264 DrugCentral Gmelin:1378 Gmelin PMID:18037357 Europe PMC PMID:22770225 Europe PMC Reaxys:635724 Reaxys UM-BBD_compID:c0165 UM-BBD UREA PDBeChem Urea KEGG_COMPOUND urea IUPAC urea UniProt 1728 PPDB Carbamide KEGG_COMPOUND E927b ChEBI H2NC(O)NH2 ChEBI Harnstoff NIST_Chemistry_WebBook Karbamid ChEBI carbamide ChEBI carbonyldiamide NIST_Chemistry_WebBook ur IUPAC uree ChEBI A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. CHEBI:14816 CHEBI:26063 CHEBI:8150 KEGG:C00865 Phospholipid chebi_ontology a phospholipid derivative phospholipids CHEBI:16247 phospholipid Phospholipid KEGG_COMPOUND a phospholipid derivative UniProt phospholipids ChEBI A branched-chain saturated fatty acid consisting of hexadecanoic acid carrying methyl substituents at positions 3, 7, 11 and 15. 0 C20H40O2 InChI=1S/C20H40O2/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)15-20(21)22/h16-19H,6-15H2,1-5H3,(H,21,22) RLCKHJSFHOZMDR-UHFFFAOYSA-N 312.53040 312.30283 CC(C)CCCC(C)CCCC(C)CCCC(C)CC(O)=O CHEBI:26111 CHEBI:8189 Beilstein:1789963 CAS:14721-66-5 KEGG:C01607 LIPID_MAPS_instance:LMFA01020251 PMID:12187408 PMID:17956237 PMID:9819701 Reaxys:1789963 3,7,11,15-tetramethylhexadecanoic acid Phytanic acid chebi_ontology 3,7,11,15-Tetramethyl-hexadecansaeure 3,7,11,15-tetramethyl hexadecanoic acid 3,7,11,15-tetramethyl-hexadecanoic acid CHEBI:16285 phytanic acid Beilstein:1789963 Beilstein CAS:14721-66-5 ChemIDplus CAS:14721-66-5 KEGG COMPOUND LIPID_MAPS_instance:LMFA01020251 LIPID MAPS PMID:12187408 Europe PMC PMID:17956237 Europe PMC PMID:9819701 Europe PMC Reaxys:1789963 Reaxys 3,7,11,15-tetramethylhexadecanoic acid IUPAC Phytanic acid KEGG_COMPOUND 3,7,11,15-Tetramethyl-hexadecansaeure ChEBI 3,7,11,15-tetramethyl hexadecanoic acid ChEBI 3,7,11,15-tetramethyl-hexadecanoic acid LIPID_MAPS A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells. 0 (C14H21NO12)n CHEBI:14412 CHEBI:24622 CHEBI:24623 CHEBI:5772 Beilstein:8538277 CAS:9004-61-9 HMDB:HMDB0010366 KEGG:C00518 KEGG:D08043 KEGG:G10505 PMID:11122186 PMID:18056362 PMID:18290544 Reaxys:8187837 Wikipedia:Hyaluronan Hyaluronic acid chebi_ontology Hyaluronsaeure [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n acide hyaluronique acido hialuronico hyaluronan CHEBI:16336 hyaluronic acid Beilstein:8538277 Beilstein CAS:9004-61-9 ChemIDplus CAS:9004-61-9 KEGG COMPOUND PMID:11122186 Europe PMC PMID:18056362 Europe PMC PMID:18290544 Europe PMC Reaxys:8187837 Reaxys Hyaluronic acid KEGG_COMPOUND Hyaluronsaeure ChEBI [beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n ChEBI [beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n KEGG_COMPOUND acide hyaluronique ChEBI acido hialuronico ChEBI hyaluronan ChEBI A bile acid that is 5beta-cholan-24-oic acid bearing three alpha-hydroxy substituents at position 3, 7 and 12. 0 C24H40O5 InChI=1S/C24H40O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-20,22,25-27H,4-12H2,1-3H3,(H,28,29)/t13-,14+,15-,16-,17+,18+,19-,20+,22+,23+,24-/m1/s1 BHQCQFFYRZLCQQ-OELDTZBJSA-N 408.57140 408.28757 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])C[C@H](O)[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC(O)=O CHEBI:1694 CHEBI:20223 CHEBI:23210 CHEBI:41494 Beilstein:2822009 CAS:81-25-4 DrugBank:DB02659 Drug_Central:3096 HMDB:HMDB0000619 KEGG:C00695 LINCS:LSM-5541 LIPID_MAPS_instance:LMST04010001 MetaCyc:CHOLATE PDBeChem:CHD PMID:22770225 Reaxys:2822009 Wikipedia:Cholic_Acid 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oic acid CHOLIC ACID Cholic acid chebi_ontology (3alpha,5beta,7alpha,12alpha)-3,7,12-trihydroxycholan-24-oic acid 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanate 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid 3alpha,7alpha,12alpha-trihydroxy-5beta-cholanic acid Cholsaeure CHEBI:16359 cholic acid Beilstein:2822009 ChemIDplus CAS:81-25-4 ChemIDplus CAS:81-25-4 KEGG COMPOUND CAS:81-25-4 NIST Chemistry WebBook Drug_Central:3096 DrugCentral LIPID_MAPS_instance:LMST04010001 LIPID MAPS PMID:22770225 Europe PMC Reaxys:2822009 Reaxys 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oic acid IUPAC CHOLIC ACID PDBeChem Cholic acid KEGG_COMPOUND (3alpha,5beta,7alpha,12alpha)-3,7,12-trihydroxycholan-24-oic acid NIST_Chemistry_WebBook 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanate KEGG_COMPOUND 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid KEGG_COMPOUND 3alpha,7alpha,12alpha-trihydroxy-5beta-cholanic acid NIST_Chemistry_WebBook Cholsaeure ChEBI An optically active form of cysteine having D-configuration. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-N 121.15922 121.01975 N[C@H](CS)C(O)=O CHEBI:12919 CHEBI:20921 CHEBI:4111 CHEBI:41887 Beilstein:1721407 CAS:921-01-7 DrugBank:DB03201 ECMDB:ECMDB03417 Gmelin:363236 HMDB:HMDB0003417 KEGG:C00793 KNApSAcK:C00007323 PDBeChem:DCY PMID:13761469 PMID:23340406 PMID:24800864 Reaxys:1721407 YMDB:YMDB00913 D-CYSTEINE D-Cysteine D-cysteine chebi_ontology (2S)-2-amino-3-mercaptopropanoic acid (2S)-2-amino-3-sulfanylpropanoic acid (S)-2-amino-3-mercaptopropanoic acid D-Amino-3-mercaptopropionic acid D-Cystein D-Zystein DCY CHEBI:16375 D-cysteine Beilstein:1721407 Beilstein CAS:921-01-7 ChemIDplus CAS:921-01-7 KEGG COMPOUND Gmelin:363236 Gmelin PMID:13761469 Europe PMC PMID:23340406 Europe PMC PMID:24800864 Europe PMC Reaxys:1721407 Reaxys D-CYSTEINE PDBeChem D-Cysteine KEGG_COMPOUND D-cysteine IUPAC (2S)-2-amino-3-mercaptopropanoic acid JCBN (2S)-2-amino-3-sulfanylpropanoic acid IUPAC (S)-2-amino-3-mercaptopropanoic acid ChEBI D-Amino-3-mercaptopropionic acid KEGG_COMPOUND D-Cystein ChEBI D-Zystein ChEBI DCY PDBeChem Any benzoquinone derived from 2,3-dimethoxy-5-methylbenzoquinone; one of a group of naturally occurring homologues. The redox-active quinoid moiety usually carries a polyprenoid side chain at position 6, the number of isoprenoid units in which is species-specific. Ubiquinones are involved in the control of mitochondrial electron transport, and are also potent anti-oxidants. 0 C9H10O4(C5H8)n CHEBI:15279 CHEBI:27186 CHEBI:9852 CAS:1339-63-5 KEGG:C00399 PMID:15788391 PMID:7599208 Ubiquinones chebi_ontology CoQ Coenzym Q Coenzyme Q Koenzym Q Q Ubichinon Ubiquinone a ubiquinone coenzyme Q coenzymes Q mitochondrial ubiquinone mitochondrial ubiquinones mitoquinones CHEBI:16389 ubiquinones CAS:1339-63-5 ChemIDplus CAS:1339-63-5 KEGG COMPOUND PMID:15788391 Europe PMC PMID:7599208 Europe PMC Ubiquinones ChemIDplus CoQ KEGG_COMPOUND Coenzym Q ChEBI Coenzyme Q KEGG_COMPOUND Koenzym Q ChEBI Q KEGG_COMPOUND Ubichinon ChEBI Ubiquinone KEGG_COMPOUND a ubiquinone UniProt coenzyme Q ChEBI coenzymes Q ChEBI mitochondrial ubiquinone ChEBI mitochondrial ubiquinones ChEBI mitoquinones ChEBI A monocarboxylic acid anion that is the conjugate base of pantothenic acid, obtained by deprotonation of the carboxy group. -1 C9H16NO5 InChI=1S/C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13)/p-1 GHOKWGTUZJEAQD-UHFFFAOYSA-M 218.22700 218.10340 CC(C)(CO)C(O)C(=O)NCCC([O-])=O CHEBI:14739 CHEBI:25846 PMID:21463532 3-(2,4-dihydroxy-3,3-dimethylbutanamido)propanoate pantothenate chebi_ontology N-(2,4-dihydroxy-3,3-dimethylbutanoyl)-beta-alaninate CHEBI:16454 pantothenate PMID:21463532 Europe PMC 3-(2,4-dihydroxy-3,3-dimethylbutanamido)propanoate IUPAC pantothenate UniProt N-(2,4-dihydroxy-3,3-dimethylbutanoyl)-beta-alaninate ChEBI The R-enantiomer of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-N 105.09262 105.04259 N[C@H](CO)C(O)=O CHEBI:13019 CHEBI:143888 CHEBI:21090 CHEBI:42262 CHEBI:4245 Beilstein:1721403 CAS:312-84-5 DrugBank:DB03929 ECMDB:ECMDB03406 Gmelin:1041392 HMDB:HMDB0003406 KEGG:C00740 MetaCyc:D-SERINE PDBeChem:DSN PMID:11864625 PMID:12850593 PMID:19212759 PMID:19217074 PMID:21295046 PMID:21914633 PMID:21956571 PMID:22117694 PMID:22128843 PMID:22266400 PMID:22280157 PMID:22362148 PMID:22369458 PMID:22445805 PMID:22465696 PMID:22486999 Reaxys:1721403 YMDB:YMDB00284 D-SERINE D-Serine D-serine chebi_ontology (2R)-2-amino-3-hydroxypropanoic acid (R)-2-Amino-3-hydroxy-propionic acid (R)-2-amino-3-hydroxypropanoic acid D-Serin DSN CHEBI:16523 D-serine Beilstein:1721403 Beilstein CAS:312-84-5 ChemIDplus CAS:312-84-5 KEGG COMPOUND CAS:312-84-5 NIST Chemistry WebBook Gmelin:1041392 Gmelin PMID:11864625 Europe PMC PMID:12850593 Europe PMC PMID:19212759 Europe PMC PMID:19217074 Europe PMC PMID:21295046 Europe PMC PMID:21914633 Europe PMC PMID:21956571 Europe PMC PMID:22117694 Europe PMC PMID:22128843 Europe PMC PMID:22266400 Europe PMC PMID:22280157 Europe PMC PMID:22362148 Europe PMC PMID:22369458 Europe PMC PMID:22445805 Europe PMC PMID:22465696 Europe PMC PMID:22486999 Europe PMC Reaxys:1721403 Reaxys D-SERINE PDBeChem D-Serine KEGG_COMPOUND D-serine IUPAC (2R)-2-amino-3-hydroxypropanoic acid IUPAC (R)-2-Amino-3-hydroxy-propionic acid ChEMBL (R)-2-amino-3-hydroxypropanoic acid ChEBI D-Serin ChEBI DSN PDBeChem A naturally occurring polypeptide synthesized at the ribosome. CHEBI:8526 KEGG:C00017 chebi_ontology Protein a protein polypeptide chain protein polypeptide chains CHEBI:16541 protein polypeptide chain Protein KEGG_COMPOUND a protein UniProt polypeptide chain ChEBI protein polypeptide chains ChEBI The L-enantiomer of methionine. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-N 149.21238 149.05105 CSCC[C@H](N)C(O)=O CHEBI:13141 CHEBI:21360 CHEBI:43990 CHEBI:6271 CAS:63-68-3 DrugBank:DB00134 Drug_Central:3347 ECMDB:ECMDB00696 Gmelin:26935 HMDB:HMDB0000696 KEGG:C00073 KEGG:D00019 KNApSAcK:C00001379 MetaCyc:MET PDBeChem:MET_LFOH PMID:16575097 PMID:21683740 PMID:21946918 PMID:22200379 PMID:22370952 PMID:22448874 PMID:22517898 PMID:24126240 PMID:24939187 PMID:5764336 Reaxys:1722294 YMDB:YMDB00318 L-Methionine L-methionine chebi_ontology (2S)-2-amino-4-(methylsulfanyl)butanoic acid (S)-2-amino-4-(methylthio)butanoic acid (S)-2-amino-4-(methylthio)butyric acid (S)-methionine L-(-)-methionine L-Methionin L-alpha-amino-gamma-methylmercaptobutyric acid M METHIONINE Met Methionine CHEBI:16643 L-methionine CAS:63-68-3 ChemIDplus CAS:63-68-3 KEGG COMPOUND CAS:63-68-3 NIST Chemistry WebBook Drug_Central:3347 DrugCentral Gmelin:26935 Gmelin PMID:16575097 Europe PMC PMID:21683740 Europe PMC PMID:21946918 Europe PMC PMID:22200379 Europe PMC PMID:22370952 Europe PMC PMID:22448874 Europe PMC PMID:22517898 Europe PMC PMID:24126240 Europe PMC PMID:24939187 Europe PMC PMID:5764336 Europe PMC Reaxys:1722294 Reaxys L-Methionine KEGG_COMPOUND L-methionine IUPAC (2S)-2-amino-4-(methylsulfanyl)butanoic acid IUPAC (S)-2-amino-4-(methylthio)butanoic acid ChemIDplus (S)-2-amino-4-(methylthio)butyric acid ChemIDplus (S)-methionine ChEBI L-(-)-methionine NIST_Chemistry_WebBook L-Methionin ChEBI L-alpha-amino-gamma-methylmercaptobutyric acid NIST_Chemistry_WebBook M ChEBI METHIONINE PDBeChem Met ChEBI Methionine KEGG_COMPOUND Methionine KEGG_DRUG Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. CHEBI:15131 CHEBI:23008 CHEBI:9318 Wikipedia:Carbohydrate carbohydrate carbohydrates chebi_ontology Kohlenhydrat Kohlenhydrate a carbohydrate carbohidrato carbohidratos glucide glucides glucido glucidos hydrates de carbone saccharide saccharides saccharidum CHEBI:16646 carbohydrate carbohydrate IUPAC carbohydrates IUPAC Kohlenhydrat ChEBI Kohlenhydrate ChEBI a carbohydrate UniProt carbohidrato IUPAC carbohidratos IUPAC glucide ChEBI glucides ChEBI glucido ChEBI glucidos ChEBI hydrates de carbone ChEBI saccharide IUPAC saccharides IUPAC saccharidum ChEBI Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. 0 (C2H2NOR)nC2H3NOR CHEBI:14753 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptide peptides chebi_ontology Peptid peptido peptidos CHEBI:16670 peptide Peptide KEGG_COMPOUND peptides IUPAC Peptid ChEBI peptido ChEBI peptidos ChEBI A chelator that is any compound containing a ligand (typically organic) which is able to form a bond to a central copper atom at two or more points. PMID:24934357 PMID:29710396 copper chelator chebi_ontology copper chelate copper chelating agent copper chelating agents copper chelators CHEBI:166831 copper chelator PMID:24934357 Europe PMC PMID:29710396 Europe PMC copper chelator ChEBI copper chelate ChEBI copper chelating agent ChEBI copper chelating agents ChEBI copper chelators ChEBI A methylated tertiary amine that is trimethylammonium in which the hydrogen attached to the nitrogen is replaced by a hydroxy group. +1 C3H10NO InChI=1S/C3H10NO/c1-4(2,3)5/h5H,1-3H3/q+1 LGHYUXIXXNHKSE-UHFFFAOYSA-N 76.118 76.07569 C[N+](C)(C)O hydroxy(trimethyl)ammonium chebi_ontology (CH3)3NOH hydroxy(trimethyl)azanium hydroxytrimethylazanium CHEBI:166856 hydroxytrimethylaminium hydroxy(trimethyl)ammonium IUPAC (CH3)3NOH ChEBI hydroxy(trimethyl)azanium IUPAC hydroxytrimethylazanium IUPAC A ribonucleoside composed of a molecule of uracil attached to a ribofuranose moiety via a beta-N(1)-glycosidic bond. 0 C9H12N2O6 InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1 DRTQHJPVMGBUCF-XVFCMESISA-N 244.20146 244.06954 OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1ccc(=O)[nH]c1=O CHEBI:15296 CHEBI:27227 CHEBI:46386 CHEBI:46391 CHEBI:46460 CHEBI:9893 Beilstein:754904 CAS:58-96-8 DrugBank:DB02745 ECMDB:ECMDB00296 Gmelin:397474 HMDB:HMDB0000296 KEGG:C00299 KNApSAcK:C00019674 MetaCyc:URIDINE PDBeChem:URI PMID:12084455 PMID:15621516 PMID:16839635 PMID:17190852 PMID:22392515 PMID:22770225 Reaxys:754904 Wikipedia:Uridine YMDB:YMDB00127 URIDINE Uridine uridine chebi_ontology 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione 1-beta-D-ribofuranosyluracil Urd Uridin beta-Uridine u CHEBI:16704 uridine Beilstein:754904 Beilstein CAS:58-96-8 ChemIDplus CAS:58-96-8 KEGG COMPOUND Gmelin:397474 Gmelin PMID:12084455 Europe PMC PMID:15621516 Europe PMC PMID:16839635 Europe PMC PMID:17190852 Europe PMC PMID:22392515 Europe PMC PMID:22770225 Europe PMC Reaxys:754904 Reaxys URIDINE PDBeChem Uridine KEGG_COMPOUND uridine IUPAC uridine UniProt 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione ChEBI 1-beta-D-ribofuranosyluracil HMDB Urd CBN Uridin ChemIDplus beta-Uridine HMDB u ChEBI A penicillanic acid compound having a (6R)-amino substituent. The active nucleus common to all penicillins, it may be substituted at the 6-amino position to form the semisynthetic penicillins, resulting in a variety of antibacterial and pharmacologic characteristics. 0 C8H12N2O3S InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1 NGHVIOIJCVXTGV-ALEPSDHESA-N 216.260 216.05686 C([C@H]1C(S[C@@]2([C@@H](C(N12)=O)N)[H])(C)C)(O)=O CHEBI:20705 CHEBI:2172 Beilstein:15080 Beilstein:959078 CAS:551-16-6 Gmelin:1876702 KEGG:C02954 PDBeChem:X1E PMID:12569987 PMID:1384868 PMID:14687482 PMID:1701026 PMID:20970923 PMID:21614893 PMID:24293403 PMID:24389703 PMID:24631718 PMID:25057428 PMID:26852849 PMID:26986755 PMID:6166603 Patent:US2941995 Reaxys:15080 Wikipedia:6-APA 6-Aminopenicillanic acid 6-amino-2,2-dimethylpenam-3alpha-carboxylic acid chebi_ontology (+)-6-aminopenicillanic acid (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid 6-APA 6-Aminopenicillamine acid 6-Aminopenicillanate 6-Apa 6-Aps 6beta-aminopenicillanic acid Aminopenicillanic acid Penicin Penin Phenacyl 6-aminopenicillinate CHEBI:16705 6-aminopenicillanic acid Beilstein:15080 Beilstein Beilstein:959078 Beilstein CAS:551-16-6 ChemIDplus CAS:551-16-6 KEGG COMPOUND Gmelin:1876702 Gmelin PMID:12569987 Europe PMC PMID:1384868 Europe PMC PMID:14687482 Europe PMC PMID:1701026 Europe PMC PMID:20970923 Europe PMC PMID:21614893 Europe PMC PMID:24293403 Europe PMC PMID:24389703 Europe PMC PMID:24631718 Europe PMC PMID:25057428 Europe PMC PMID:26852849 Europe PMC PMID:26986755 Europe PMC PMID:6166603 Europe PMC Reaxys:15080 Reaxys 6-Aminopenicillanic acid KEGG_COMPOUND 6-amino-2,2-dimethylpenam-3alpha-carboxylic acid IUPAC (+)-6-aminopenicillanic acid ChEBI (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid IUPAC 6-APA ChEBI 6-Aminopenicillamine acid ChemIDplus 6-Aminopenicillanate KEGG_COMPOUND 6-Apa ChemIDplus 6-Aps ChemIDplus 6beta-aminopenicillanic acid ChEBI Aminopenicillanic acid ChemIDplus Penicin ChemIDplus Penin ChemIDplus Phenacyl 6-aminopenicillinate ChemIDplus A hydroxymethylpyridine with hydroxymethyl groups at positions 4 and 5, a hydroxy group at position 3 and a methyl group at position 2. The 4-methanol form of vitamin B6, it is converted intoto pyridoxal phosphate which is a coenzyme for synthesis of amino acids, neurotransmitters, sphingolipids and aminolevulinic acid. 0 C8H11NO3 InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3 LXNHXLLTXMVWPM-UHFFFAOYSA-N 169.180 169.07389 CC1=C(O)C(CO)=C(CO)C=N1 CHEBI:14981 CHEBI:26429 CHEBI:8671 AGR:IND607198670 Beilstein:139854 CAS:65-23-6 Chemspider:1025 DrugBank:DB00165 Drug_Central:2836 FooDB:FDB000574 Gmelin:563676 HMDB:HMDB0000239 KEGG:C00314 KEGG:D08454 KNApSAcK:C00001551 LINCS:LSM-5324 MetaCyc:PYRIDOXINE PDBeChem:UEG PMID:10687314 PMID:10894227 PMID:11562405 PMID:12640345 PMID:12768081 PMID:13046427 PMID:15132238 PMID:15369738 PMID:15756083 PMID:16236150 PMID:16277693 PMID:16690736 PMID:17044573 PMID:22932811 PMID:24035968 PMID:24601602 PMID:2580028 PMID:27113583 PMID:2885064 PMID:31093449 PMID:32105687 PMID:33549283 PMID:33665688 PMID:3710434 PMID:559690 PMID:6624427 PMID:6801073 PMID:9625217 Reaxys:139854 Wikipedia:Pyridoxine 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol pyridoxine chebi_ontology 2-Methyl-3-hydroxy-4,5-dihydroxymethyl-pyridin 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine 2-methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridine 2-methyl-3-hydroxy-4,5-dihydroxymethylpyridine 2-methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridine 2-methyl-4,5-dimethylol-pyridin-3-ol 3-hydroxy-2-picoline-4,5-dimethanol 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine 3-hydroxy-4,5-dimethylol-alpha-picoline 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol 5-hydroxy-6-methyl-3,4-pyridinedimethanol Pyridoxol piridossina pyridoxina pyridoxine pyridoxinum pyridoxolum vitamin B6 CHEBI:16709 pyridoxine AGR:IND607198670 Europe PMC Beilstein:139854 Beilstein CAS:65-23-6 ChemIDplus CAS:65-23-6 KEGG COMPOUND CAS:65-23-6 NIST Chemistry WebBook Drug_Central:2836 DrugCentral Gmelin:563676 Gmelin PMID:10687314 Europe PMC PMID:10894227 Europe PMC PMID:11562405 Europe PMC PMID:12640345 Europe PMC PMID:12768081 Europe PMC PMID:13046427 Europe PMC PMID:15132238 Europe PMC PMID:15369738 Europe PMC PMID:15756083 Europe PMC PMID:16236150 Europe PMC PMID:16277693 Europe PMC PMID:16690736 Europe PMC PMID:17044573 Europe PMC PMID:22932811 Europe PMC PMID:24035968 Europe PMC PMID:24601602 Europe PMC PMID:2580028 Europe PMC PMID:27113583 Europe PMC PMID:2885064 Europe PMC PMID:31093449 Europe PMC PMID:32105687 Europe PMC PMID:33549283 Europe PMC PMID:33665688 Europe PMC PMID:3710434 Europe PMC PMID:559690 Europe PMC PMID:6624427 Europe PMC PMID:6801073 Europe PMC PMID:9625217 Europe PMC Reaxys:139854 Reaxys 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol IUPAC pyridoxine UniProt 2-Methyl-3-hydroxy-4,5-dihydroxymethyl-pyridin ChemIDplus 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine ChemIDplus 2-methyl-3-hydroxy-4,5-di(hydroxymethyl)pyridine ChemIDplus 2-methyl-3-hydroxy-4,5-dihydroxymethylpyridine NIST_Chemistry_WebBook 2-methyl-4,5-bis(hydroxymethyl)-3-hydroxypyridine ChemIDplus 2-methyl-4,5-dimethylol-pyridin-3-ol ChEBI 3-hydroxy-2-picoline-4,5-dimethanol ChemIDplus 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine ChEBI 3-hydroxy-4,5-dimethylol-alpha-picoline NIST_Chemistry_WebBook 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol ChEBI 5-hydroxy-6-methyl-3,4-pyridinedimethanol NIST_Chemistry_WebBook Pyridoxol KEGG_COMPOUND piridossina HMDB pyridoxina WHO_MedNet pyridoxine WHO_MedNet pyridoxinum WHO_MedNet pyridoxolum HMDB vitamin B6 NIST_Chemistry_WebBook A six-carbon aromatic annulene in which each carbon atom donates one of its two 2p electrons into a delocalised pi system. A toxic, flammable liquid byproduct of coal distillation, it is used as an industrial solvent. Benzene is a carcinogen that also damages bone marrow and the central nervous system. 0 C6H6 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N 78.11184 78.04695 c1ccccc1 CHEBI:13876 CHEBI:22703 CHEBI:3025 CHEBI:41187 Beilstein:969212 CAS:71-43-2 Gmelin:1671 HMDB:HMDB0001505 KEGG:C01407 PDBeChem:BNZ PMID:11684179 PMID:11993966 PMID:12857942 PMID:14677922 PMID:15468289 PMID:15935818 PMID:16161967 PMID:17373369 PMID:18072742 PMID:18407866 PMID:18409691 PMID:18836923 PMID:19228219 PMID:21325737 PMID:23088855 PMID:23222815 PMID:23534829 PMID:6353911 PMID:8124204 Reaxys:969212 UM-BBD_compID:c0142 Wikipedia:Benzene BENZENE Benzene benzene chebi_ontology Benzen Benzine Benzol Bicarburet of hydrogen Coal naphtha Mineral naphtha Phene Pyrobenzol Pyrobenzole [6]annulene benzole cyclohexatriene phenyl hydride CHEBI:16716 benzene Beilstein:969212 Beilstein CAS:71-43-2 ChemIDplus CAS:71-43-2 KEGG COMPOUND CAS:71-43-2 NIST Chemistry WebBook Gmelin:1671 Gmelin PMID:11684179 Europe PMC PMID:11993966 Europe PMC PMID:12857942 Europe PMC PMID:14677922 Europe PMC PMID:15468289 Europe PMC PMID:15935818 Europe PMC PMID:16161967 Europe PMC PMID:17373369 Europe PMC PMID:18072742 Europe PMC PMID:18407866 Europe PMC PMID:18409691 Europe PMC PMID:18836923 Europe PMC PMID:19228219 Europe PMC PMID:21325737 Europe PMC PMID:23088855 Europe PMC PMID:23222815 Europe PMC PMID:23534829 Europe PMC PMID:6353911 Europe PMC PMID:8124204 Europe PMC Reaxys:969212 Reaxys UM-BBD_compID:c0142 UM-BBD BENZENE PDBeChem Benzene KEGG_COMPOUND benzene ChEBI benzene IUPAC benzene UniProt Benzen IUPAC Benzine UM-BBD Benzol ChemIDplus Bicarburet of hydrogen ChemIDplus Coal naphtha ChemIDplus Mineral naphtha ChemIDplus Phene ChemIDplus Pyrobenzol ChemIDplus Pyrobenzole ChemIDplus [6]annulene NIST_Chemistry_WebBook benzole NIST_Chemistry_WebBook cyclohexatriene UM-BBD phenyl hydride UM-BBD A mineral that is an inorganic nutrient which must be ingested and absorbed in adequate amounts to satisfy a wide range of essential metabolic and/or structural functions in the human body. Wikipedia:Mineral_(nutrient) mineral nutrient chebi_ontology mineral nutrients nutrient mineral nutrient minerals CHEBI:167164 mineral nutrient mineral nutrient ChEBI mineral nutrients ChEBI nutrient mineral ChEBI nutrient minerals ChEBI 0 C2H4NO2R 74.05870 74.02420 N[C@H]([*])C(O)=O CHEBI:12909 CHEBI:13625 CHEBI:20906 CHEBI:4097 KEGG:C00405 D-alpha-amino acid D-alpha-amino acids chebi_ontology D-Amino acid D-alpha-amino acids CHEBI:16733 D-alpha-amino acid D-alpha-amino acid ChEBI D-alpha-amino acids IUPAC D-Amino acid KEGG_COMPOUND D-alpha-amino acids ChEBI A dihydroxy-5beta-cholanic acid that is (5beta)-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 7 respectively. 0 C24H40O4 InChI=1S/C24H40O4/c1-14(4-7-21(27)28)17-5-6-18-22-19(9-11-24(17,18)3)23(2)10-8-16(25)12-15(23)13-20(22)26/h14-20,22,25-26H,4-13H2,1-3H3,(H,27,28)/t14-,15+,16-,17-,18+,19+,20-,22+,23+,24-/m1/s1 RUDATBOHQWOJDD-BSWAIDMHSA-N 392.57200 392.29266 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC(O)=O CHEBI:23094 CHEBI:3588 CHEBI:3593 Beilstein:3219887 CAS:474-25-9 DrugBank:DB06777 Drug_Central:4361 HMDB:HMDB0000518 KEGG:C02528 KEGG:D00163 LINCS:LSM-5353 LIPID_MAPS_instance:LMST04010032 PDBeChem:JN3 PMID:11530998 PMID:16037564 PMID:24448653 PMID:24464484 Reaxys:3219887 Wikipedia:Chenodiol 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid Chenodeoxycholic acid chebi_ontology 3alpha,7alpha-Dihydroxy-5beta-cholanic acid 7alpha-hydroxylithocholic acid CDCA Chenix Chenodiol anthropodeoxycholic acid anthropodesoxycholic acid chenic acid gallodesoxycholic acid CHEBI:16755 chenodeoxycholic acid Beilstein:3219887 Beilstein CAS:474-25-9 ChemIDplus CAS:474-25-9 KEGG COMPOUND Drug_Central:4361 DrugCentral LIPID_MAPS_instance:LMST04010032 LIPID MAPS PMID:11530998 Europe PMC PMID:16037564 Europe PMC PMID:24448653 Europe PMC PMID:24464484 Europe PMC Reaxys:3219887 Reaxys 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid IUPAC Chenodeoxycholic acid KEGG_COMPOUND 3alpha,7alpha-Dihydroxy-5beta-cholanic acid KEGG_COMPOUND 7alpha-hydroxylithocholic acid ChemIDplus CDCA IUPHAR Chenix ChemIDplus Chenodiol KEGG_COMPOUND anthropodeoxycholic acid ChemIDplus anthropodesoxycholic acid ChemIDplus chenic acid ChemIDplus gallodesoxycholic acid ChemIDplus Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. chebi_ontology glycans CHEBI:167559 glycan glycans ChEBI A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8) FFEARJCKVFRZRR-UHFFFAOYSA-N 149.21238 149.05105 CSCCC(N)C(O)=O CHEBI:14590 CHEBI:25229 CHEBI:6829 Beilstein:636185 CAS:59-51-8 Gmelin:3117 KEGG:C01733 KEGG:D04983 PMID:16702333 PMID:22264337 PMID:2543976 Reaxys:636185 UM-BBD_compID:c0094 Wikipedia:Methionine Methionine methionine chebi_ontology 2-Amino-4-(methylthio)butyric acid 2-amino-4-(methylsulfanyl)butanoic acid 2-amino-4-(methylthio)butanoic acid DL-Methionine Hmet M Met Methionin Racemethionine alpha-amino-gamma-methylmercaptobutyric acid metionina CHEBI:16811 methionine Beilstein:636185 Beilstein CAS:59-51-8 ChemIDplus CAS:59-51-8 KEGG COMPOUND CAS:59-51-8 NIST Chemistry WebBook Gmelin:3117 Gmelin PMID:16702333 Europe PMC PMID:22264337 Europe PMC PMID:2543976 Europe PMC Reaxys:636185 Reaxys UM-BBD_compID:c0094 UM-BBD Methionine KEGG_COMPOUND methionine ChEBI methionine IUPAC 2-Amino-4-(methylthio)butyric acid KEGG_COMPOUND 2-amino-4-(methylsulfanyl)butanoic acid IUPAC 2-amino-4-(methylthio)butanoic acid JCBN DL-Methionine KEGG_DRUG Hmet IUPAC M ChEBI Met ChEBI Methionin ChEBI Racemethionine KEGG_DRUG alpha-amino-gamma-methylmercaptobutyric acid NIST_Chemistry_WebBook metionina ChEBI An optically active form of methionine having D-configuration. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-N 149.21238 149.05105 CSCC[C@@H](N)C(O)=O CHEBI:13005 CHEBI:21065 CHEBI:4215 CHEBI:44071 Beilstein:1722293 CAS:348-67-4 DrugBank:DB02893 ECMDB:ECMDB21203 Gmelin:26934 KEGG:C00855 MetaCyc:CPD-218 PDBeChem:MED PMID:15375647 PMID:20431016 PMID:20872028 PMID:21480759 PMID:21750343 PMID:21924333 PMID:22192214 PMID:22304623 PMID:318639 Reaxys:1722293 YMDB:YMDB00816 D-METHIONINE D-Methionine D-methionine chebi_ontology (2R)-2-amino-4-(methylsulfanyl)butanoic acid (R)-2-amino-4-(methylthio)butanoic acid (R)-methionine D-2-Amino-4-(methylthio)butyric acid D-Methionin MED CHEBI:16867 D-methionine Beilstein:1722293 Beilstein CAS:348-67-4 ChemIDplus CAS:348-67-4 KEGG COMPOUND CAS:348-67-4 NIST Chemistry WebBook Gmelin:26934 Gmelin PMID:15375647 Europe PMC PMID:20431016 Europe PMC PMID:20872028 Europe PMC PMID:21480759 Europe PMC PMID:21750343 Europe PMC PMID:21924333 Europe PMC PMID:22192214 Europe PMC PMID:22304623 Europe PMC PMID:318639 Europe PMC Reaxys:1722293 Reaxys D-METHIONINE PDBeChem D-Methionine KEGG_COMPOUND D-methionine IUPAC (2R)-2-amino-4-(methylsulfanyl)butanoic acid IUPAC (R)-2-amino-4-(methylthio)butanoic acid JCBN (R)-methionine ChemIDplus D-2-Amino-4-(methylthio)butyric acid KEGG_COMPOUND D-Methionin ChEBI MED PDBeChem A glycine derivative having methyl and amidino groups attached to the nitrogen. 0 C4H9N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) CVSVTCORWBXHQV-UHFFFAOYSA-N 131.13328 131.06948 CN(CC(O)=O)C(N)=N CHEBI:14028 CHEBI:23404 CHEBI:3909 CHEBI:41678 Beilstein:907175 CAS:57-00-1 Chemspider:566 DrugBank:DB00148 Drug_Central:4661 Gmelin:240513 HMDB:HMDB0000064 KEGG:C00300 MetaCyc:CREATINE PDBeChem:CRN PMID:11356982 PMID:11483809 PMID:11867929 PMID:12085493 PMID:12184144 PMID:12878267 PMID:16445883 PMID:17190852 PMID:17253521 PMID:17416441 PMID:18555535 PMID:19082141 PMID:19651674 PMID:19741514 PMID:19968328 PMID:21556832 PMID:21660517 PMID:21698493 PMID:22038587 PMID:22101931 PMID:22196490 PMID:22252611 PMID:22347384 PMID:22386973 PMID:22422801 PMID:22429992 PMID:22465051 PMID:22521466 PMID:7752905 Reaxys:907175 Wikipedia:Creatine Creatine N-[amino(imino)methyl]-N-methylglycine chebi_ontology ((amino(imino)methyl)(methyl)amino)acetic acid (N-methylcarbamimidamido)acetic acid (alpha-methylguanido)acetic acid Creatin Kreatin Methylglycocyamine N-(aminoiminomethyl)-N-methylglycine N-Methyl-N-guanylglycine N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE N-amidinosarcosine N-carbamimidoyl-N-methylglycine N-methyl-N-guanylglycine alpha-Methylguanidino acetic acid CHEBI:16919 creatine Beilstein:907175 Beilstein CAS:57-00-1 ChemIDplus CAS:57-00-1 KEGG COMPOUND CAS:57-00-1 NIST Chemistry WebBook Drug_Central:4661 DrugCentral Gmelin:240513 Gmelin PMID:11356982 Europe PMC PMID:11483809 Europe PMC PMID:11867929 Europe PMC PMID:12085493 Europe PMC PMID:12184144 Europe PMC PMID:12878267 Europe PMC PMID:16445883 Europe PMC PMID:17190852 Europe PMC PMID:17253521 Europe PMC PMID:17416441 Europe PMC PMID:18555535 Europe PMC PMID:19082141 Europe PMC PMID:19651674 Europe PMC PMID:19741514 Europe PMC PMID:19968328 Europe PMC PMID:21556832 Europe PMC PMID:21660517 Europe PMC PMID:21698493 Europe PMC PMID:22038587 Europe PMC PMID:22101931 Europe PMC PMID:22196490 Europe PMC PMID:22252611 Europe PMC PMID:22347384 Europe PMC PMID:22386973 Europe PMC PMID:22422801 Europe PMC PMID:22429992 Europe PMC PMID:22465051 Europe PMC PMID:22521466 Europe PMC PMID:7752905 Europe PMC Reaxys:907175 Reaxys Creatine KEGG_COMPOUND N-[amino(imino)methyl]-N-methylglycine IUPAC ((amino(imino)methyl)(methyl)amino)acetic acid HMDB (N-methylcarbamimidamido)acetic acid ChEBI (alpha-methylguanido)acetic acid HMDB (alpha-methylguanido)acetic acid NIST_Chemistry_WebBook Creatin ChemIDplus Kreatin ChemIDplus Methylglycocyamine KEGG_COMPOUND N-(aminoiminomethyl)-N-methylglycine NIST_Chemistry_WebBook N-Methyl-N-guanylglycine HMDB N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE PDBeChem N-amidinosarcosine ChemIDplus N-carbamimidoyl-N-methylglycine PDBeChem N-methyl-N-guanylglycine ChemIDplus alpha-Methylguanidino acetic acid KEGG_COMPOUND A naturally-occurring beta-amino acid comprising propionic acid with the amino group in the 3-position. 0 C3H7NO2 InChI=1S/C3H7NO2/c4-2-1-3(5)6/h1-2,4H2,(H,5,6) UCMIRNVEIXFBKS-UHFFFAOYSA-N 89.09322 89.04768 NCCC(O)=O CHEBI:10343 CHEBI:12389 CHEBI:22821 CHEBI:41050 Beilstein:906793 CAS:107-95-9 DrugBank:DB03107 Gmelin:49614 HMDB:HMDB0000056 KEGG:C00099 KEGG:D07561 KNApSAcK:C00001333 MetaCyc:B-ALANINE PDBeChem:BAL PMID:11139233 PMID:11850512 PMID:12107759 PMID:12887142 PMID:14363188 PMID:16934791 PMID:18528519 PMID:18613640 PMID:19239140 PMID:19955842 PMID:20199122 PMID:20386120 PMID:20479615 PMID:20994958 PMID:22735334 Reaxys:906793 Wikipedia:Beta-Alanine 3-aminopropanoic acid BETA-ALANINE beta-Alanine beta-alanine chebi_ontology 3-Aminopropionic acid 3-aminopropanoic acid H-beta-Ala-OH bAla beta-aminopropionic acid omega-aminopropionic acid CHEBI:16958 beta-alanine Beilstein:906793 Beilstein CAS:107-95-9 ChemIDplus CAS:107-95-9 KEGG COMPOUND CAS:107-95-9 NIST Chemistry WebBook Gmelin:49614 Gmelin PMID:11139233 Europe PMC PMID:11850512 Europe PMC PMID:12107759 Europe PMC PMID:12887142 Europe PMC PMID:14363188 Europe PMC PMID:16934791 Europe PMC PMID:18528519 Europe PMC PMID:18613640 Europe PMC PMID:19239140 Europe PMC PMID:19955842 Europe PMC PMID:20199122 Europe PMC PMID:20386120 Europe PMC PMID:20479615 Europe PMC PMID:20994958 Europe PMC PMID:22735334 Europe PMC Reaxys:906793 Reaxys 3-aminopropanoic acid IUPAC BETA-ALANINE PDBeChem beta-Alanine KEGG_COMPOUND beta-alanine IUPAC 3-Aminopropionic acid KEGG_COMPOUND 3-aminopropanoic acid ChEBI H-beta-Ala-OH ChEBI bAla ChEBI beta-aminopropionic acid NIST_Chemistry_WebBook omega-aminopropionic acid ChEBI A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. 0 C33H36N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-N 584.673 584.26348 CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(N2)\C=C2/NC(=O)C(C=C)=C2C)N1 CHEBI:13898 CHEBI:22870 CHEBI:3099 Beilstein:74376 CAS:635-65-4 Gmelin:411033 HMDB:HMDB0000054 KEGG:C00486 KNApSAcK:C00029828 MetaCyc:BILIRUBIN PDBeChem:BLR PMID:12799017 PMID:18442622 PMID:23763371 PMID:23768684 PMID:30224965 PMID:8605219 PMID:9587403 Reaxys:74376 Wikipedia:Bilirubin 3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid bilirubin chebi_ontology 1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid 2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid 8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione Bilirubin bilirubin(Z,Z) bilirubin-IXalpha CHEBI:16990 bilirubin IXalpha Beilstein:74376 Beilstein CAS:635-65-4 ChemIDplus CAS:635-65-4 KEGG COMPOUND Gmelin:411033 Gmelin PMID:12799017 Europe PMC PMID:18442622 Europe PMC PMID:23763371 Europe PMC PMID:23768684 Europe PMC PMID:30224965 Europe PMC PMID:8605219 Europe PMC PMID:9587403 Europe PMC Reaxys:74376 Reaxys 3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid IUPAC bilirubin IUPAC 1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid ChemIDplus 2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid ChemIDplus 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid IUPAC 8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione JCBN Bilirubin KEGG_COMPOUND bilirubin(Z,Z) ChEBI bilirubin-IXalpha ChEBI An alpha,omega-dicarboxylic acid that is ethane substituted by carboxyl groups at positions 1 and 2. 0 C2H2O4 InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6) MUBZPKHOEPUJKR-UHFFFAOYSA-N 90.03490 89.99531 OC(=O)C(O)=O CHEBI:25730 CHEBI:44583 CHEBI:7811 Beilstein:385686 CAS:144-62-7 DrugBank:DB03902 Gmelin:2208 HMDB:HMDB0002329 KEGG:C00209 KNApSAcK:C00001198 LIPID_MAPS_instance:LMFA01170031 MetaCyc:OXALATE PDBeChem:OXD PMID:15587083 PMID:22735334 Reaxys:385686 Wikipedia:Oxalic_acid OXALIC ACID Oxalic acid oxalic acid chebi_ontology Ethandisaeure Ethanedioic acid H2ox HOOCCOOH Oxalsaeure ethane-1,2-dioic acid CHEBI:16995 oxalic acid Beilstein:385686 Beilstein CAS:144-62-7 ChemIDplus CAS:144-62-7 KEGG COMPOUND CAS:144-62-7 NIST Chemistry WebBook Gmelin:2208 Gmelin LIPID_MAPS_instance:LMFA01170031 LIPID MAPS PMID:15587083 Europe PMC PMID:22735334 Europe PMC Reaxys:385686 Reaxys OXALIC ACID PDBeChem Oxalic acid KEGG_COMPOUND oxalic acid IUPAC Ethandisaeure ChEBI Ethanedioic acid KEGG_COMPOUND H2ox IUPAC HOOCCOOH NIST_Chemistry_WebBook Oxalsaeure ChEBI ethane-1,2-dioic acid NIST_Chemistry_WebBook D-Ribitol in which the hydroxy group at position 5 is substituted by a 7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl moiety. It is a nutritional factor found in milk, eggs, malted barley, liver, kidney, heart, and leafy vegetables, but the richest natural source is yeast. The free form occurs only in the retina of the eye, in whey, and in urine; its principal forms in tissues and cells are as flavin mononucleotide and flavin-adenine dinucleotide. 0 C17H20N4O6 InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1 AUNGANRZJHBGPY-SCRDCRAPSA-N 376.369 376.13828 CC1=C(C)C=C2N(C[C@H](O)[C@H](O)[C@H](O)CO)C3=NC(=O)NC(=O)C3=NC2=C1 CHEBI:15044 CHEBI:27299 CHEBI:45214 CHEBI:529204 CHEBI:8843 Beilstein:97831 CAS:83-88-5 Chemspider:431981 DrugBank:DB00140 Drug_Central:2834 FooDB:FDB012160 HMDB:HMDB0000244 KEGG:C00255 KEGG:D00050 KNApSAcK:C00001552 LINCS:LSM-4084 MetaCyc:RIBOFLAVIN PDBeChem:RBF PMID:10566553 PMID:11399071 PMID:11606856 PMID:12083520 PMID:12354259 PMID:12927541 PMID:14963913 PMID:16273338 PMID:16460756 PMID:16658098 PMID:182198 PMID:18832377 PMID:19169240 PMID:19212411 PMID:19854891 PMID:22770225 PMID:2369885 PMID:23818044 PMID:24643482 PMID:24816110 PMID:25108762 PMID:25468971 PMID:25887755 PMID:2631092 PMID:29937405 PMID:3142982 PMID:33154451 PMID:33304888 PMID:33886098 PMID:33892358 PMID:34156642 PMID:3592624 PMID:3878498 PMID:4019261 PMID:6475825 PMID:6546833 PMID:6650303 PMID:7101408 PMID:7883462 PMID:8487103 PMID:8604671 PMID:8678471 PMID:8976642 PMID:9184778 PMID:9808225 PMID:9874201 Patent:US2807611 Patent:US2876169 Reaxys:97831 Wikipedia:Riboflavin 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol chebi_ontology 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol 5-deoxy-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol 6,7-dimethyl-9-D-ribitylisoalloxazine 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)benzo[g]pteridine-2,4(3H,10H)-dione 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)isoalloxazine 7,8-dimethyl-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]benzo[g]pteridine-2,4(3H,10H)-dione 7,8-dimethyl-10-ribitylisoalloxazine Aqua-Flave Beflavin Beflavine Bisulase Dermadram E101 Fiboflavin Flavaxin Flavin Bb Flaxain Hyflavin Vitamin B2 lactoflavin riboflavin riboflavin (vit B2) riboflavina riboflavine riboflavinum vitamin B2 vitamin G vitasan B2 CHEBI:17015 riboflavin Beilstein:97831 Beilstein CAS:83-88-5 ChemIDplus CAS:83-88-5 KEGG COMPOUND CAS:83-88-5 NIST Chemistry WebBook Drug_Central:2834 DrugCentral PMID:10566553 Europe PMC PMID:11399071 Europe PMC PMID:11606856 Europe PMC PMID:12083520 Europe PMC PMID:12354259 Europe PMC PMID:12927541 Europe PMC PMID:14963913 Europe PMC PMID:16273338 Europe PMC PMID:16460756 Europe PMC PMID:16658098 Europe PMC PMID:182198 Europe PMC PMID:18832377 Europe PMC PMID:19169240 Europe PMC PMID:19212411 Europe PMC PMID:19854891 Europe PMC PMID:22770225 Europe PMC PMID:2369885 Europe PMC PMID:23818044 Europe PMC PMID:24643482 Europe PMC PMID:24816110 Europe PMC PMID:25108762 Europe PMC PMID:25468971 Europe PMC PMID:25887755 Europe PMC PMID:2631092 Europe PMC PMID:29937405 Europe PMC PMID:3142982 Europe PMC PMID:33154451 Europe PMC PMID:33304888 Europe PMC PMID:33886098 Europe PMC PMID:33892358 Europe PMC PMID:34156642 Europe PMC PMID:3592624 Europe PMC PMID:3878498 Europe PMC PMID:4019261 Europe PMC PMID:6475825 Europe PMC PMID:6546833 Europe PMC PMID:6650303 Europe PMC PMID:7101408 Europe PMC PMID:7883462 Europe PMC PMID:8487103 Europe PMC PMID:8604671 Europe PMC PMID:8678471 Europe PMC PMID:8976642 Europe PMC PMID:9184778 Europe PMC PMID:9808225 Europe PMC PMID:9874201 Europe PMC Reaxys:97831 Reaxys 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol IUPAC 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol NIST_Chemistry_WebBook 5-deoxy-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol ChEBI 6,7-dimethyl-9-D-ribitylisoalloxazine ChemIDplus 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)benzo[g]pteridine-2,4(3H,10H)-dione ChEBI 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)isoalloxazine ChemIDplus 7,8-dimethyl-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]benzo[g]pteridine-2,4(3H,10H)-dione IUPAC 7,8-dimethyl-10-ribitylisoalloxazine KEGG_COMPOUND Aqua-Flave ChemIDplus Beflavin ChemIDplus Beflavine ChemIDplus Bisulase KEGG_DRUG Dermadram ChemIDplus E101 ChEBI Fiboflavin ChemIDplus Flavaxin ChemIDplus Flavin Bb ChemIDplus Flaxain ChemIDplus Hyflavin ChemIDplus Vitamin B2 KEGG_COMPOUND lactoflavin KEGG_COMPOUND riboflavin WHO_MedNet riboflavin (vit B2) DrugCentral riboflavina WHO_MedNet riboflavine WHO_MedNet riboflavinum WHO_MedNet vitamin B2 ChEBI vitamin G DrugBank vitasan B2 ChemIDplus -1 F InChI=1S/FH/h1H/p-1 KRHYYFGTRYWZRS-UHFFFAOYSA-M 18.99840 18.99895 [F-] CHEBI:14271 CHEBI:49593 CHEBI:5113 CAS:16984-48-8 Gmelin:14905 KEGG:C00742 PDBeChem:F Fluoride fluoride fluoride(1-) chebi_ontology F(-) F- FLUORIDE ION Fluoride ion Fluorine anion CHEBI:17051 fluoride CAS:16984-48-8 ChemIDplus CAS:16984-48-8 NIST Chemistry WebBook Gmelin:14905 Gmelin Fluoride KEGG_COMPOUND fluoride IUPAC fluoride UniProt fluoride(1-) IUPAC F(-) IUPAC F- KEGG_COMPOUND FLUORIDE ION PDBeChem Fluoride ion KEGG_COMPOUND Fluorine anion NIST_Chemistry_WebBook 0 CH4NR 30.04920 30.03437 NC[*] CHEBI:13431 CHEBI:8749 KEGG:C00375 chebi_ontology RCH2NH2 primary aliphatic amines CHEBI:17062 primary aliphatic amine RCH2NH2 ChEBI RCH2NH2 KEGG_COMPOUND primary aliphatic amines ChEBI A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). 0 COR2 28.010 27.99491 [*]C([*])=O CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 KEGG:C01450 Wikipedia:Ketone Ketone ketones chebi_ontology Keton R-CO-R' a ketone cetone ketones CHEBI:17087 ketone Ketone KEGG_COMPOUND ketones IUPAC Keton ChEBI R-CO-R' KEGG_COMPOUND a ketone UniProt cetone ChEBI ketones ChEBI A compound in which a carbohydrate component is covalently bound to a protein component. CHEBI:14349 CHEBI:5481 CHEBI:5493 KEGG:C00326 Glycoprotein glycoproteins chebi_ontology Glykoprotein Glykoproteine a glycoprotein glicoproteina glicoproteinas glycoproteine glycoproteines CHEBI:17089 glycoprotein Glycoprotein KEGG_COMPOUND glycoproteins IUPAC Glykoprotein ChEBI Glykoproteine ChEBI a glycoprotein UniProt glicoproteina ChEBI glicoproteinas ChEBI glycoproteine ChEBI glycoproteines ChEBI The L-enantiomer of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-N 105.09262 105.04259 N[C@@H](CO)C(O)=O CHEBI:13167 CHEBI:21387 CHEBI:45440 CHEBI:45451 CHEBI:45590 CHEBI:45597 CHEBI:45677 CHEBI:6301 Beilstein:1721404 CAS:56-45-1 DrugBank:DB00133 Drug_Central:4127 ECMDB:ECMDB00187 Gmelin:2570 HMDB:HMDB0000187 KEGG:C00065 KEGG:D00016 KNApSAcK:C00001393 MetaCyc:SER PDBeChem:SER PMID:1650428 PMID:17439666 PMID:19062365 PMID:21956576 PMID:22265470 PMID:22393170 PMID:22547037 PMID:22566084 PMID:22566694 Reaxys:1721404 Wikipedia:L-serine YMDB:YMDB00112 L-Serine L-serine chebi_ontology (2S)-2-amino-3-hydroxypropanoic acid (S)-(-)-serine (S)-2-amino-3-hydroxypropanoic acid (S)-alpha-Amino-beta-hydroxypropionic acid (S)-serine L-(-)-serine L-2-Amino-3-hydroxypropionic acid L-3-Hydroxy-2-aminopropionic acid L-3-Hydroxy-alanine L-Ser L-Serin S SERINE Ser Serine beta-Hydroxy-L-alanine beta-Hydroxyalanine CHEBI:17115 L-serine Beilstein:1721404 Beilstein CAS:56-45-1 ChemIDplus CAS:56-45-1 KEGG COMPOUND CAS:56-45-1 NIST Chemistry WebBook Drug_Central:4127 DrugCentral Gmelin:2570 Gmelin PMID:1650428 Europe PMC PMID:17439666 Europe PMC PMID:19062365 Europe PMC PMID:21956576 Europe PMC PMID:22265470 Europe PMC PMID:22393170 Europe PMC PMID:22547037 Europe PMC PMID:22566084 Europe PMC PMID:22566694 Europe PMC Reaxys:1721404 Reaxys L-Serine KEGG_COMPOUND L-serine IUPAC (2S)-2-amino-3-hydroxypropanoic acid IUPAC (S)-(-)-serine NIST_Chemistry_WebBook (S)-2-amino-3-hydroxypropanoic acid NIST_Chemistry_WebBook (S)-alpha-Amino-beta-hydroxypropionic acid HMDB (S)-serine ChemIDplus L-(-)-serine NIST_Chemistry_WebBook L-2-Amino-3-hydroxypropionic acid KEGG_COMPOUND L-3-Hydroxy-2-aminopropionic acid HMDB L-3-Hydroxy-alanine KEGG_COMPOUND L-Ser DrugBank L-Serin ChEBI S ChEBI SERINE PDBeChem Ser ChEBI Serine KEGG_COMPOUND beta-Hydroxy-L-alanine HMDB beta-Hydroxyalanine HMDB A short-chain fatty acid anion that is the conjugate base of hexanoic acid (also known as caproic acid). -1 C6H11O2 InChI=1S/C6H12O2/c1-2-3-4-5-6(7)8/h2-5H2,1H3,(H,7,8)/p-1 FUZZWVXGSFPDMH-UHFFFAOYSA-M 115.15034 115.07645 CCCCCC([O-])=O CHEBI:14398 CHEBI:24569 Beilstein:3601453 CAS:151-33-7 ECMDB:ECMDB21229 Gmelin:326340 KEGG:C01585 MetaCyc:HEXANOATE hexanoate chebi_ontology 1-hexanoate 1-pentacarboxylate 1-pentanecarboxylate CH3-[CH2]4-COO(-) butylacetate caproate capronate hexoate hexylate n-caproate n-hexanoate n-hexoate n-hexylate nPnCO2 anion pentanecarboxylate pentylformate CHEBI:17120 hexanoate Beilstein:3601453 Beilstein CAS:151-33-7 Beilstein Gmelin:326340 Gmelin hexanoate IUPAC hexanoate UniProt 1-hexanoate ChEBI 1-pentacarboxylate ChEBI 1-pentanecarboxylate ChEBI CH3-[CH2]4-COO(-) IUPAC butylacetate ChEBI caproate ChEBI capronate ChEBI hexoate ChEBI hexylate ChEBI n-caproate ChEBI n-hexanoate ChEBI n-hexoate ChEBI n-hexylate ChEBI nPnCO2 anion NIST_Chemistry_WebBook pentanecarboxylate ChEBI pentylformate ChEBI An amino-acid betaine that is butanoate substituted with a hydroxy group at position C-3 and a trimethylammonium group at C-4. 0 C7H15NO3 InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3 PHIQHXFUZVPYII-UHFFFAOYSA-N 161.19894 161.10519 C[N+](C)(C)CC(O)CC([O-])=O CHEBI:11817 CHEBI:13947 CHEBI:20047 CHEBI:23038 Beilstein:1866665 CAS:461-06-3 DrugBank:DB02648 KEGG:C00487 MetaCyc:DL-CARNITINE PMID:22770225 PMID:23868375 Patent:US4255449 Patent:US4315944 Reaxys:1866665 Wikipedia:Carnitine 3-hydroxy-4-(trimethylammonio)butanoate carnitine chebi_ontology D,L-carnitine CHEBI:17126 carnitine Beilstein:1866665 Beilstein CAS:461-06-3 ChemIDplus PMID:22770225 Europe PMC PMID:23868375 Europe PMC Reaxys:1866665 Reaxys 3-hydroxy-4-(trimethylammonio)butanoate IUPAC carnitine UniProt D,L-carnitine MetaCyc -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1 LSNNMFCWUKXFEE-UHFFFAOYSA-M 81.07214 80.96519 OS([O-])=O CHEBI:13367 CHEBI:5598 CAS:15181-46-1 Gmelin:1455 KEGG:C11481 PDBeChem:SO3 hydrogen(trioxidosulfate)(1-) hydrogensulfite(1-) hydrogentrioxosulfate(1-) hydrogentrioxosulfate(IV) hydroxidodioxidosulfate(1-) monohydrogentrioxosulfate chebi_ontology Bisulfite HSO3(-) HSO3- Hydrogen sulfite [SO2(OH)](-) bisulfite bisulphite hydrogen sulfite(1-) hydrosulfite anion CHEBI:17137 hydrogensulfite CAS:15181-46-1 ChemIDplus CAS:15181-46-1 KEGG COMPOUND Gmelin:1455 Gmelin hydrogen(trioxidosulfate)(1-) IUPAC hydrogensulfite(1-) IUPAC hydrogentrioxosulfate(1-) IUPAC hydrogentrioxosulfate(IV) IUPAC hydroxidodioxidosulfate(1-) IUPAC monohydrogentrioxosulfate IUPAC Bisulfite KEGG_COMPOUND HSO3(-) IUPAC HSO3- KEGG_COMPOUND Hydrogen sulfite KEGG_COMPOUND [SO2(OH)](-) IUPAC bisulfite ChemIDplus bisulphite ChemIDplus hydrogen sulfite(1-) ChemIDplus hydrosulfite anion ChemIDplus Any 3beta-hydroxy-steroid that contains a double bond between positions 5 and 6. 0 C19H29OR 273.434 273.22184 C12C(C3C(C(CC3)*)(C)CC1)CC=C4C2(CC[C@@H](C4)O)C CHEBI:13608 CHEBI:136845 CHEBI:20245 KEGG:C03836 MetaCyc:3b-hydroxy-D5-steroids chebi_ontology 3beta-hydroxy Delta(5)-steroids 3beta-hydroxy-Delta(5)-steroids a 3beta-hydroxy-Delta(5)-steroid CHEBI:1722 3beta-hydroxy-Delta(5)-steroid 3beta-hydroxy Delta(5)-steroids ChEBI 3beta-hydroxy-Delta(5)-steroids ChEBI a 3beta-hydroxy-Delta(5)-steroid UniProt An aldohexose used as a source of energy and metabolic intermediate. 0 C6H12O6 180.15588 180.06339 CHEBI:14313 CHEBI:24277 CHEBI:33929 CHEBI:5418 CAS:50-99-7 KEGG:C00293 Wikipedia:Glucose Glucose gluco-hexose glucose chebi_ontology DL-glucose Glc Glukose CHEBI:17234 glucose CAS:50-99-7 KEGG COMPOUND Glucose KEGG_COMPOUND gluco-hexose IUPAC glucose IUPAC DL-glucose ChEBI Glc JCBN Glukose ChEBI The conjugate base of propionic acid; a key precursor in lipid biosynthesis. -1 C3H5O2 InChI=1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5)/p-1 XBDQKXXYIPTUBI-UHFFFAOYSA-M 73.07060 73.02950 CCC([O-])=O CHEBI:14903 CHEBI:26290 Beilstein:3587503 CAS:72-03-7 Gmelin:1820 KEGG:C00163 PMID:17951291 PMID:18375549 PMID:2647392 UM-BBD_compID:c0277 propanoate propionate chebi_ontology CH3-CH2-COO(-) EtCO2 anion carboxylatoethane ethanecarboxylate ethylformate metacetonate methylacetate propanate propanoate propanoic acid, ion(1-) pseudoacetate CHEBI:17272 propionate Beilstein:3587503 Beilstein CAS:72-03-7 ChemIDplus CAS:72-03-7 NIST Chemistry WebBook Gmelin:1820 Gmelin PMID:17951291 Europe PMC PMID:18375549 Europe PMC PMID:2647392 Europe PMC UM-BBD_compID:c0277 UM-BBD propanoate IUPAC propionate IUPAC CH3-CH2-COO(-) IUPAC EtCO2 anion NIST_Chemistry_WebBook carboxylatoethane ChEBI ethanecarboxylate ChEBI ethylformate ChEBI metacetonate ChEBI methylacetate ChEBI propanate ChEBI propanoate UniProt propanoic acid, ion(1-) ChemIDplus pseudoacetate ChEBI A phosphoamino acid consisting of creatine having a phospho group attached at the primary nitrogen of the guanidino group. 0 C4H10N3O5P InChI=1S/C4H10N3O5P/c1-7(2-3(8)9)4(5)6-13(10,11)12/h2H2,1H3,(H,8,9)(H4,5,6,10,11,12) DRBBFCLWYRJSJZ-UHFFFAOYSA-N 211.11318 211.03581 CN(CC(O)=O)C(=N)NP(O)(O)=O CHEBI:12526 CHEBI:14813 CHEBI:26053 CHEBI:8145 Beilstein:1797096 CAS:67-07-2 Drug_Central:3464 HMDB:HMDB0001511 KEGG:C02305 MetaCyc:CREATINE-P PMID:1160340 PMID:11867929 PMID:13772879 PMID:13881337 PMID:14421251 PMID:5879486 Reaxys:1797096 Wikipedia:Phosphocreatine N-Phosphocreatine N-[imino(phosphonoamino)methyl]-N-methylglycine N-phosphocreatine chebi_ontology Creatine phosphate Creatine phosphic acid N(omega)-phosphonocreatine N-(N-phosphonoamido)sarcosine N-(Phosphonoamidino)sarcosine N-Phosphorylcreatine Phosphocreatine phosphorylcreatine {[imino(phosphonoamino)methyl](methyl)amino}acetic acid CHEBI:17287 N-phosphocreatine Beilstein:1797096 Beilstein CAS:67-07-2 ChemIDplus CAS:67-07-2 KEGG COMPOUND Drug_Central:3464 DrugCentral PMID:1160340 Europe PMC PMID:11867929 Europe PMC PMID:13772879 Europe PMC PMID:13881337 Europe PMC PMID:14421251 Europe PMC PMID:5879486 Europe PMC Reaxys:1797096 Reaxys N-Phosphocreatine KEGG_COMPOUND N-[imino(phosphonoamino)methyl]-N-methylglycine IUPAC N-phosphocreatine ChEBI Creatine phosphate KEGG_COMPOUND Creatine phosphic acid HMDB N(omega)-phosphonocreatine CBN N-(N-phosphonoamido)sarcosine CBN N-(Phosphonoamidino)sarcosine HMDB N-Phosphorylcreatine HMDB Phosphocreatine KEGG_COMPOUND phosphorylcreatine HMDB {[imino(phosphonoamino)methyl](methyl)amino}acetic acid ChEBI Any substance that inhibits the process of ferroptosis (a type of programmed cell death dependent on iron and characterized by the accumulation of lipid peroxides) in organisms. PMID:32015325 PMID:32256352 PMID:32413317 PMID:33495651 Wikipedia:Ferroptosis chebi_ontology ferroptosis inhibitors CHEBI:173084 ferroptosis inhibitor PMID:32015325 SUBMITTER PMID:32256352 Europe PMC PMID:32413317 Europe PMC PMID:33495651 Europe PMC ferroptosis inhibitors ChEBI Any substance that induces or promotes ferroptosis (a type of programmed cell death dependent on iron and characterized by the accumulation of lipid peroxides) in organisms. PMID:31899616 PMID:32015325 PMID:33167414 PMID:34012798 Wikipedia:Ferroptosis chebi_ontology ferroptosis inducers CHEBI:173085 ferroptosis inducer PMID:31899616 Europe PMC PMID:32015325 SUBMITTER PMID:33167414 Europe PMC PMID:34012798 Europe PMC ferroptosis inducers ChEBI A pyridinecarbaldehyde that is pyridine-4-carbaldehyde bearing methyl, hydroxy and hydroxymethyl substituents at positions 2, 3 and 5 respectively. The 4-carboxyaldehyde form of vitamin B6, it is converted into pyridoxal phosphate, a coenzyme for the synthesis of amino acids, neurotransmitters, sphingolipids and aminolevulinic acid. 0 C8H9NO3 InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3 RADKZDMFGJYCBB-UHFFFAOYSA-N 167.16200 167.05824 [H]C(=O)c1c(CO)cnc(C)c1O CHEBI:14976 CHEBI:26423 CHEBI:45112 CHEBI:8667 Beilstein:383768 CAS:66-72-8 Chemspider:1021 DrugBank:DB00147 Drug_Central:4134 Gmelin:218674 HMDB:HMDB0001545 KEGG:C00250 KNApSAcK:C00007509 MetaCyc:PYRIDOXAL PDBeChem:PXL PMID:12001008 PMID:150790 PMID:1621875 PMID:16495081 PMID:16710308 PMID:17765195 PMID:20381632 PMID:22770225 PMID:23801094 PMID:24365359 PMID:31915818 PMID:3663392 PMID:4051187 PMID:433818 PMID:6853710 PMID:7159754 PMID:7440576 PMID:8116826 Reaxys:383768 Wikipedia:Pyridoxal 3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde Pyridoxal pyridoxal chebi_ontology 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE pyridoxaldehyde CHEBI:17310 pyridoxal Beilstein:383768 Beilstein CAS:66-72-8 ChemIDplus CAS:66-72-8 KEGG COMPOUND Drug_Central:4134 DrugCentral Gmelin:218674 Gmelin PMID:12001008 Europe PMC PMID:150790 Europe PMC PMID:1621875 Europe PMC PMID:16495081 Europe PMC PMID:16710308 Europe PMC PMID:17765195 Europe PMC PMID:20381632 Europe PMC PMID:22770225 Europe PMC PMID:23801094 Europe PMC PMID:24365359 Europe PMC PMID:31915818 Europe PMC PMID:3663392 Europe PMC PMID:4051187 Europe PMC PMID:433818 Europe PMC PMID:6853710 Europe PMC PMID:7159754 Europe PMC PMID:7440576 Europe PMC PMID:8116826 Europe PMC Reaxys:383768 Reaxys 3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde IUPAC Pyridoxal KEGG_COMPOUND pyridoxal UniProt 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE PDBeChem pyridoxaldehyde ChemIDplus Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6. 0 C9H11N2O4SR 243.26000 243.04395 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C(O)=O CHEBI:14742 CHEBI:25869 CHEBI:7961 KEGG:C00395 PMID:11851248 PMID:12833570 PMID:1502708 PMID:16033609 PMID:7061385 PMID:7798534 Wikipedia:Penicillin Penicillin penicillins chebi_ontology penicillins CHEBI:17334 penicillin PMID:11851248 Europe PMC PMID:12833570 Europe PMC PMID:1502708 Europe PMC PMID:16033609 Europe PMC PMID:7061385 Europe PMC PMID:7798534 Europe PMC Penicillin KEGG_COMPOUND penicillins IUPAC penicillins ChEBI A sulfur oxoanion that is the conjugate base of hydrogen sulfite (H2SO3). -2 O3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-2 LSNNMFCWUKXFEE-UHFFFAOYSA-L 80.06420 79.95791 [O-]S([O-])=O CHEBI:15139 CHEBI:45548 CAS:14265-45-3 Gmelin:1449 PDBeChem:SO3 sulfite trioxidosulfate(2-) trioxosulfate(2-) trioxosulfate(IV) chebi_ontology SO3 SO3(2-) SULFITE ION [SO3](2-) sulphite CHEBI:17359 sulfite CAS:14265-45-3 ChemIDplus Gmelin:1449 Gmelin sulfite IUPAC sulfite UniProt trioxidosulfate(2-) IUPAC trioxosulfate(2-) IUPAC trioxosulfate(IV) IUPAC SO3 ChEBI SO3(2-) IUPAC SULFITE ION PDBeChem [SO3](2-) IUPAC sulphite ChEBI A straight-chain saturated fatty acid containing five carbon atoms. 0 C5H10O2 InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7) NQPDZGIKBAWPEJ-UHFFFAOYSA-N 102.13170 102.06808 CCCCC(O)=O CHEBI:113448 CHEBI:27263 CHEBI:27264 CHEBI:43606 CHEBI:44803 CHEBI:7980 Beilstein:969454 CAS:109-52-4 DrugBank:DB02406 Gmelin:26714 HMDB:HMDB0000892 KEGG:C00803 KNApSAcK:C00001208 LIPID_MAPS_instance:LMFA01010005 PDBeChem:LEA PMID:20507156 PPDB:3130 Reaxys:969454 Wikipedia:Valeric_acid Valeric acid pentanoic acid chebi_ontology 1-butanecarboxylic acid CH3-[CH2]3-COOH PENTANOIC ACID Pentanoate Pentanoic acid Valerate Valerianic acid Valeriansaeure n-BuCOOH n-Pentanoate n-Valeric acid n-pentanoic acid n-valeric acid pentoic acid propylacetic acid valeric acid, normal CHEBI:17418 valeric acid Beilstein:969454 Beilstein CAS:109-52-4 ChemIDplus CAS:109-52-4 KEGG COMPOUND CAS:109-52-4 NIST Chemistry WebBook Gmelin:26714 Gmelin LIPID_MAPS_instance:LMFA01010005 LIPID MAPS PMID:20507156 Europe PMC Reaxys:969454 Reaxys Valeric acid KEGG_COMPOUND pentanoic acid IUPAC 1-butanecarboxylic acid ChemIDplus 1-butanecarboxylic acid NIST_Chemistry_WebBook CH3-[CH2]3-COOH IUPAC PENTANOIC ACID PDBeChem Pentanoate KEGG_COMPOUND Pentanoic acid KEGG_COMPOUND Valerate KEGG_COMPOUND Valerianic acid KEGG_COMPOUND Valeriansaeure ChEBI n-BuCOOH ChEBI n-Pentanoate KEGG_COMPOUND n-Valeric acid KEGG_COMPOUND n-pentanoic acid ChemIDplus n-valeric acid ChemIDplus pentoic acid ChEBI propylacetic acid ChemIDplus valeric acid, normal ChemIDplus A complex cob(III)alamin in which cobalt is positioned in the centre of a planar corrin tetrapyrrole ring and bound axially to a 5,6-dimethylbenzimidazole moiety and a cyano group. It is one of several forms of the vitamin known as vitamin B12. 0 C63H88CoN14O14P InChI=1S/C62H90N13O14P.CN.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-2;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;/q;;+2/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 RMRCNWBMXRMIRW-WZHZPDAFSA-L 1355.36520 1354.56740 [H][C@@]1(C)CNC(=O)CC[C@]2(C)[C@@H](CC(N)=O)[C@@]3([H])N4C2=C(C)C2=[N+]5C(=CC6=[N+]7C(=C(C)C8=[N+]([C@]3(C)[C@@](C)(CC(N)=O)[C@@H]8CCC(N)=O)[Co-3]457(C#N)[n+]3cn([C@H]4O[C@H](CO)[C@@H](OP([O-])(=O)O1)[C@H]4O)c1cc(C)c(C)cc31)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O)C(C)(C)[C@@H]2CCC(N)=O CHEBI:14041 CHEBI:23435 CHEBI:3979 CHEBI:48820 CHEBI:60496 CAS:68-19-9 DrugBank:DB00115 Gmelin:249901 Gmelin:457955 KEGG:C02823 KEGG:D00166 KNApSAcK:C00001534 PDBeChem:CNC PMID:29286160 Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-cyanocobamide Cyanocob(III)alamin cyanocob(III)alamin chebi_ontology CN-Cbl CO-CYANOCOBALAMIN Dicopac Vitamin B12 complex cyanocobalamin vitamin B-12 CHEBI:17439 cyanocob(III)alamin CAS:68-19-9 ChemIDplus CAS:68-19-9 KEGG COMPOUND Gmelin:249901 Gmelin Gmelin:457955 Gmelin PMID:29286160 Europe PMC Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-cyanocobamide IUPAC Cyanocob(III)alamin KEGG_COMPOUND cyanocob(III)alamin IUPAC cyanocob(III)alamin UniProt CN-Cbl CBN CO-CYANOCOBALAMIN PDBeChem Dicopac KEGG_COMPOUND Vitamin B12 complex KEGG_COMPOUND cyanocobalamin KEGG_DRUG vitamin B-12 CBN A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group. 0 CHOR 29.01800 29.00274 [H]C([*])=O CHEBI:13432 CHEBI:13753 CHEBI:13805 CHEBI:13806 CHEBI:22291 CHEBI:2554 CHEBI:8750 KEGG:C00071 Aldehyde aldehyde aldehydes chebi_ontology Aldehyd RC(=O)H RCHO aldehido aldehidos aldehydes aldehydum an aldehyde CHEBI:17478 aldehyde Aldehyde KEGG_COMPOUND aldehyde ChEBI aldehyde IUPAC aldehydes IUPAC Aldehyd ChEBI RC(=O)H IUPAC RCHO KEGG_COMPOUND aldehido ChEBI aldehidos ChEBI aldehydes ChEBI aldehydum ChEBI an aldehyde UniProt A carbohydrate that is an acyclic polyol having the general formula HOCH2[CH(OH)]nCH2OH (formally derivable from an aldose by reduction of the carbonyl group). 0 (CH2O)nC2H6O2 CHEBI:13754 CHEBI:22298 CHEBI:2556 KEGG:C00717 Wikipedia:Glycerin Alditol alditol chebi_ontology Glycitol Sugar alcohol alditols CHEBI:17522 alditol Alditol KEGG_COMPOUND alditol UniProt Glycitol KEGG_COMPOUND Sugar alcohol KEGG_COMPOUND alditols ChEBI The carbon oxoanion resulting from the removal of a proton from carbonic acid. -1 CHO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 BVKZGUZCCUSVTD-UHFFFAOYSA-M 61.01684 60.99312 OC([O-])=O CHEBI:13363 CHEBI:22863 CHEBI:40961 CHEBI:5589 Beilstein:3903504 CAS:71-52-3 Gmelin:49249 HMDB:HMDB0000595 KEGG:C00288 MetaCyc:HCO3 PDBeChem:BCT PMID:17215880 PMID:17505962 PMID:18439416 PMID:28732801 PMID:29150416 PMID:29460248 PMID:29466234 PMID:4208463 Wikipedia:Bicarbonate Hydrogencarbonate hydrogen(trioxidocarbonate)(1-) hydrogencarbonate hydrogencarbonate(1-) hydrogentrioxocarbonate(1-) hydrogentrioxocarbonate(IV) hydroxidodioxidocarbonate(1-) chebi_ontology Acid carbonate BICARBONATE ION Bicarbonate HCO3(-) HCO3- [CO2(OH)](-) hydrogen carbonate CHEBI:17544 hydrogencarbonate Beilstein:3903504 Beilstein CAS:71-52-3 ChemIDplus Gmelin:49249 Gmelin PMID:17215880 Europe PMC PMID:17505962 Europe PMC PMID:18439416 Europe PMC PMID:28732801 Europe PMC PMID:29150416 Europe PMC PMID:29460248 Europe PMC PMID:29466234 Europe PMC PMID:4208463 Europe PMC Hydrogencarbonate KEGG_COMPOUND hydrogen(trioxidocarbonate)(1-) IUPAC hydrogencarbonate IUPAC hydrogencarbonate UniProt hydrogencarbonate(1-) IUPAC hydrogentrioxocarbonate(1-) IUPAC hydrogentrioxocarbonate(IV) IUPAC hydroxidodioxidocarbonate(1-) IUPAC Acid carbonate KEGG_COMPOUND BICARBONATE ION PDBeChem Bicarbonate KEGG_COMPOUND HCO3(-) IUPAC HCO3- KEGG_COMPOUND [CO2(OH)](-) IUPAC hydrogen carbonate PDBeChem An optically active form of cysteine having L-configuration. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-N 121.15800 121.01975 N[C@@H](CS)C(O)=O CHEBI:13095 CHEBI:21261 CHEBI:41227 CHEBI:41700 CHEBI:41768 CHEBI:41781 CHEBI:41811 CHEBI:6207 Beilstein:1721408 CAS:52-90-4 DrugBank:DB00151 Drug_Central:769 ECMDB:ECMDB00574 Gmelin:49991 HMDB:HMDB0000574 KEGG:C00097 KEGG:D00026 KNApSAcK:C00001351 MetaCyc:CYS PDBeChem:CYS PMID:11732994 PMID:13761469 PMID:22735334 Reaxys:1721408 Wikipedia:Cysteine YMDB:YMDB00046 L-Cysteine L-cysteine chebi_ontology (2R)-2-amino-3-mercaptopropanoic acid (2R)-2-amino-3-sulfanylpropanoic acid (R)-2-amino-3-mercaptopropanoic acid C CYSTEINE Cys E 920 E-920 E920 FREE CYSTEINE L-2-Amino-3-mercaptopropionic acid L-Cystein L-Zystein CHEBI:17561 L-cysteine Beilstein:1721408 Beilstein CAS:52-90-4 ChemIDplus CAS:52-90-4 KEGG COMPOUND CAS:52-90-4 NIST Chemistry WebBook Drug_Central:769 DrugCentral Gmelin:49991 Gmelin PMID:11732994 Europe PMC PMID:13761469 Europe PMC PMID:22735334 Europe PMC Reaxys:1721408 Reaxys L-Cysteine KEGG_COMPOUND L-cysteine IUPAC (2R)-2-amino-3-mercaptopropanoic acid JCBN (2R)-2-amino-3-sulfanylpropanoic acid IUPAC (R)-2-amino-3-mercaptopropanoic acid NIST_Chemistry_WebBook C ChEBI CYSTEINE PDBeChem Cys ChEBI E 920 ChEBI E-920 ChEBI E920 ChEBI FREE CYSTEINE PDBeChem L-2-Amino-3-mercaptopropionic acid KEGG_COMPOUND L-Cystein ChEBI L-Zystein ChEBI A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription. 0 C4H4N2O2 InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) ISAKRJDGNUQOIC-UHFFFAOYSA-N 112.08684 112.02728 O=c1cc[nH]c(=O)[nH]1 CHEBI:15288 CHEBI:27210 CHEBI:46375 CHEBI:9882 Beilstein:606623 CAS:66-22-8 DrugBank:DB03419 Gmelin:2896 HMDB:HMDB0000300 KEGG:C00106 KEGG:D00027 KNApSAcK:C00001513 MetaCyc:URACIL PDBeChem:URA PMID:11279060 PMID:12855717 PMID:15274295 PMID:16834123 PMID:17439666 PMID:18533995 PMID:18815805 PMID:19175333 PMID:22020693 PMID:22074393 PMID:22120518 PMID:22171528 PMID:22237209 PMID:22299724 PMID:22356544 PMID:22447672 PMID:22483865 PMID:22567906 PMID:22685418 PMID:3654008 Reaxys:606623 Wikipedia:Uracil URACIL Uracil pyrimidine-2,4(1H,3H)-dione uracil chebi_ontology 2,4(1H,3H)-pyrimidinedione 2,4-Dioxopyrimidine 2,4-Pyrimidinedione U Ura Urazil CHEBI:17568 uracil Beilstein:606623 Beilstein CAS:66-22-8 ChemIDplus CAS:66-22-8 KEGG COMPOUND CAS:66-22-8 NIST Chemistry WebBook Gmelin:2896 Gmelin PMID:11279060 Europe PMC PMID:12855717 Europe PMC PMID:15274295 Europe PMC PMID:16834123 Europe PMC PMID:17439666 Europe PMC PMID:18533995 Europe PMC PMID:18815805 Europe PMC PMID:19175333 Europe PMC PMID:22020693 Europe PMC PMID:22074393 Europe PMC PMID:22120518 Europe PMC PMID:22171528 Europe PMC PMID:22237209 Europe PMC PMID:22299724 Europe PMC PMID:22356544 Europe PMC PMID:22447672 Europe PMC PMID:22483865 Europe PMC PMID:22567906 Europe PMC PMID:22685418 Europe PMC PMID:3654008 Europe PMC Reaxys:606623 Reaxys URACIL PDBeChem Uracil KEGG_COMPOUND pyrimidine-2,4(1H,3H)-dione IUPAC uracil UniProt 2,4(1H,3H)-pyrimidinedione NIST_Chemistry_WebBook 2,4-Dioxopyrimidine HMDB 2,4-Pyrimidinedione HMDB U ChEBI Ura CBN Urazil ChEBI The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent. 0 C7H8 InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3 YXFVVABEGXRONW-UHFFFAOYSA-N 92.13842 92.06260 Cc1ccccc1 CHEBI:15248 CHEBI:27022 CHEBI:44023 CHEBI:9624 Beilstein:635760 CAS:108-88-3 DrugBank:DB01900 Gmelin:2456 KEGG:C01455 PDBeChem:MBN PMID:11182169 PMID:11314682 PMID:11846266 PMID:11991009 PMID:12062755 PMID:12213539 PMID:12237258 PMID:12784113 PMID:12876426 PMID:14512097 PMID:14559343 PMID:14605898 PMID:15015825 PMID:15019953 PMID:15119846 PMID:15193425 PMID:15542760 PMID:15567510 PMID:15695158 PMID:15796064 PMID:16316648 PMID:16348226 PMID:16601996 PMID:17145141 PMID:17175136 PMID:17497535 PMID:17725881 PMID:18397809 PMID:18832024 PMID:19261054 PMID:19384711 PMID:19429395 PMID:19635754 PMID:19765629 PMID:19825861 PMID:19928203 PMID:19969016 PMID:20347282 PMID:20837561 PMID:21430649 PMID:21655021 PMID:21731073 PMID:21802510 PMID:21840036 Reaxys:635760 UM-BBD_compID:c0114 Wikipedia:Toluene TOLUENE Toluene toluene chebi_ontology Toluen Toluol methylbenzene phenylmethane CHEBI:17578 toluene Beilstein:635760 Beilstein CAS:108-88-3 ChemIDplus CAS:108-88-3 KEGG COMPOUND CAS:108-88-3 NIST Chemistry WebBook Gmelin:2456 Gmelin PMID:11182169 Europe PMC PMID:11314682 Europe PMC PMID:11846266 Europe PMC PMID:11991009 Europe PMC PMID:12062755 Europe PMC PMID:12213539 Europe PMC PMID:12237258 Europe PMC PMID:12784113 Europe PMC PMID:12876426 Europe PMC PMID:14512097 Europe PMC PMID:14559343 Europe PMC PMID:14605898 Europe PMC PMID:15015825 Europe PMC PMID:15019953 Europe PMC PMID:15119846 Europe PMC PMID:15193425 Europe PMC PMID:15542760 Europe PMC PMID:15567510 Europe PMC PMID:15695158 Europe PMC PMID:15796064 Europe PMC PMID:16316648 Europe PMC PMID:16348226 Europe PMC PMID:16601996 Europe PMC PMID:17145141 Europe PMC PMID:17175136 Europe PMC PMID:17497535 Europe PMC PMID:17725881 Europe PMC PMID:18397809 Europe PMC PMID:18832024 Europe PMC PMID:19261054 Europe PMC PMID:19384711 Europe PMC PMID:19429395 Europe PMC PMID:19635754 Europe PMC PMID:19765629 Europe PMC PMID:19825861 Europe PMC PMID:19928203 Europe PMC PMID:19969016 Europe PMC PMID:20347282 Europe PMC PMID:20837561 Europe PMC PMID:21430649 Europe PMC PMID:21655021 Europe PMC PMID:21731073 Europe PMC PMID:21802510 Europe PMC PMID:21840036 Europe PMC Reaxys:635760 Reaxys UM-BBD_compID:c0114 UM-BBD TOLUENE PDBeChem Toluene KEGG_COMPOUND toluene ChEBI toluene IUPAC toluene UniProt Toluen NIST_Chemistry_WebBook Toluol NIST_Chemistry_WebBook methylbenzene PDBeChem phenylmethane ChemIDplus A cyclic carotene obtained by dimerisation of all-trans-retinol. A strongly-coloured red-orange pigment abundant in plants and fruit and the most active and important provitamin A carotenoid. 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-22,25-28H,15-16,23-24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+ OENHQHLEOONYIE-JLTXGRSLSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\C1=C(C)CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C CHEBI:10355 CHEBI:12392 CHEBI:22834 CHEBI:40987 Beilstein:1917416 CAS:7235-40-7 COMe:MOL000093 Drug_Central:345 HMDB:HMDB0000561 KEGG:C02094 KEGG:D03101 KNApSAcK:C00000919 LIPID_MAPS_instance:LMPR01070000 LIPID_MAPS_instance:LMPR01070001 MetaCyc:CPD1F-129 PDBeChem:BCR PMID:11171227 PMID:11182771 PMID:11332447 PMID:11359610 PMID:11382814 PMID:11567548 PMID:11677037 PMID:11714348 PMID:11962062 PMID:12081834 PMID:12891827 PMID:14658721 PMID:14764912 PMID:14976384 PMID:14997360 PMID:15113067 PMID:15333155 PMID:15695449 PMID:15789045 PMID:15909543 PMID:15949680 PMID:15949683 PMID:16036331 PMID:16087476 PMID:16338959 PMID:16563447 PMID:17004738 PMID:17625873 PMID:17708644 PMID:17851775 PMID:18429004 PMID:18766464 PMID:18767554 PMID:18794175 PMID:19480350 PMID:19574250 PMID:19669835 PMID:19703237 PMID:19852884 PMID:19888275 PMID:19896667 PMID:19937581 PMID:20074992 PMID:20515074 PMID:22079732 PMID:22309480 PMID:22428124 PMID:22489215 PMID:22534340 PMID:22575730 Reaxys:1917416 Wikipedia:Beta_Carotene BETA-CAROTENE beta,beta-carotene beta-Carotene chebi_ontology 1,1'-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaene-1,18-diyl]bis(2,6,6-trimethylcyclohexene) all-trans-beta-carotene beta-Karotin CHEBI:17579 beta-carotene Beilstein:1917416 Beilstein CAS:7235-40-7 ChemIDplus CAS:7235-40-7 KEGG COMPOUND CAS:7235-40-7 NIST Chemistry WebBook Drug_Central:345 DrugCentral LIPID_MAPS_instance:LMPR01070000 LIPID MAPS LIPID_MAPS_instance:LMPR01070001 LIPID MAPS PMID:11171227 Europe PMC PMID:11182771 Europe PMC PMID:11332447 Europe PMC PMID:11359610 Europe PMC PMID:11382814 Europe PMC PMID:11567548 Europe PMC PMID:11677037 Europe PMC PMID:11714348 Europe PMC PMID:11962062 Europe PMC PMID:12081834 Europe PMC PMID:12891827 Europe PMC PMID:14658721 Europe PMC PMID:14764912 Europe PMC PMID:14976384 Europe PMC PMID:14997360 Europe PMC PMID:15113067 Europe PMC PMID:15333155 Europe PMC PMID:15695449 Europe PMC PMID:15789045 Europe PMC PMID:15909543 Europe PMC PMID:15949680 Europe PMC PMID:15949683 Europe PMC PMID:16036331 Europe PMC PMID:16087476 Europe PMC PMID:16338959 Europe PMC PMID:16563447 Europe PMC PMID:17004738 Europe PMC PMID:17625873 Europe PMC PMID:17708644 Europe PMC PMID:17851775 Europe PMC PMID:18429004 Europe PMC PMID:18766464 Europe PMC PMID:18767554 Europe PMC PMID:18794175 Europe PMC PMID:19480350 Europe PMC PMID:19574250 Europe PMC PMID:19669835 Europe PMC PMID:19703237 Europe PMC PMID:19852884 Europe PMC PMID:19888275 Europe PMC PMID:19896667 Europe PMC PMID:19937581 Europe PMC PMID:20074992 Europe PMC PMID:20515074 Europe PMC PMID:22079732 Europe PMC PMID:22309480 Europe PMC PMID:22428124 Europe PMC PMID:22489215 Europe PMC PMID:22534340 Europe PMC PMID:22575730 Europe PMC Reaxys:1917416 Reaxys BETA-CAROTENE PDBeChem beta,beta-carotene IUPAC beta-Carotene KEGG_COMPOUND 1,1'-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaene-1,18-diyl]bis(2,6,6-trimethylcyclohexene) ChEBI all-trans-beta-carotene NIST_Chemistry_WebBook all-trans-beta-carotene UniProt beta-Karotin ChEBI Any compound that supports healthy aging, slows the biological aging process, or extends lifespan. PMID:23372317 PMID:28580190 PMID:30885572 PMID:33144142 PMID:33973253 PMID:34606237 Wikipedia:Geroprotector chebi_ontology anti-aging agent anti-aging agents anti-aging drug anti-aging drugs geroprotective agent geroprotective agents geroprotectors CHEBI:176497 geroprotector PMID:23372317 Europe PMC PMID:28580190 Europe PMC PMID:30885572 Europe PMC PMID:33144142 Europe PMC PMID:33973253 Europe PMC PMID:34606237 Europe PMC anti-aging agent ChEBI anti-aging agents ChEBI anti-aging drug ChEBI anti-aging drugs ChEBI geroprotective agent ChEBI geroprotective agents ChEBI geroprotectors ChEBI Any member of a group of vitamers that belong to the chemical structural class called butenolides that exhibit biological activity against vitamin C deficiency in animals. The vitamers include L-ascorbic acid and its salt, ionized and oxidized forms. CHEBI:21241 PMCID:PMC8088531 PMID:21885436 PMID:33916257 PMID:34064549 Wikipedia:Vitamin_C Vitamin C chebi_ontology vitamin C vitamer vitamin C vitamers vitamina C vitamine C vitaminum C CHEBI:176783 vitamin C PMCID:PMC8088531 Europe PMC PMID:21885436 Europe PMC PMID:33916257 Europe PMC PMID:34064549 Europe PMC Vitamin C ChEBI vitamin C vitamer ChEBI vitamin C vitamers ChEBI vitamina C ChEBI vitamine C ChEBI vitaminum C ChEBI Any member of a group of vitamers that belong to the chemical structural class called flavins that exhibit biological activity against vitamin B2 deficiency. Symptoms associated with vitamin B2 deficiency include glossitis, seborrhea, angular stomaitis, cheilosis and photophobia. The vitamers include riboflavin and its phosphate derivatives (and includes their salt, ionised and hydrate forms). vitamin B2 chebi_ontology vitamin B-2 vitamins B2 vitamins B2 vitamer vitamins B2 vitamers CHEBI:176838 vitamin B2 vitamin B2 ChEBI vitamin B-2 ChEBI vitamins B2 ChEBI vitamins B2 vitamer ChEBI vitamins B2 vitamers ChEBI Any member of a group of vitamers that belong to the chemical structural class called pyridines that exhibit biological activity against vitamin B3 deficiency. Vitamin B3 deficiency causes a condition known as pellagra whose symptoms include depression, dermatitis and diarrhea. The vitamers include nicotinic acid and nicotinamide (and their ionized and salt forms). vitamin B3 chebi_ontology vitamin B-3 vitamin B3 vitamer vitamin B3 vitamers vitamins B3 CHEBI:176839 vitamin B3 vitamin B3 ChEBI vitamin B-3 ChEBI vitamin B3 vitamer ChEBI vitamin B3 vitamers ChEBI vitamins B3 ChEBI Any member of a group of vitamers that belong to the chemical structural class called pantothenic acids that exhibit biological activity against vitamin B5 deficiency. Deficiency of vitamin B5 is rare due to its widespread distribution in whole grain cereals, legumes and meat. Symptoms associated with vitamin B5 deficiency are difficult to asses since they are subtle and resemble those of other B vitamin deficiencies. The vitamers include (R)-pantothenic acid and its ionized and salt forms. vitamin B5 chebi_ontology vitamin B-5 vitamin B5 vitamer vitamin B5 vitamers vitamins B5 CHEBI:176840 vitamin B5 vitamin B5 ChEBI vitamin B-5 ChEBI vitamin B5 vitamer ChEBI vitamin B5 vitamers ChEBI vitamins B5 ChEBI Any member of a group of vitamers that belong to the chemical structural class called biotins that exhibit biological activity against vitamin B7 deficiency. Vitamin B7 deficiency is very rare in individuals who take a normal balanced diet. Foods rich in biotin are egg yolk, liver, cereals, vegetables (spinach, mushrooms) and rice. Symptoms associated with vitamin B7 deficiency include thinning hair, scaly skin rashes around eyes, nose and mouth, and brittle nails. The vitamers include biotin and its ionized and salt forms. vitamin B7 chebi_ontology vitamin B-7 vitamin B7 vitamer vitamin B7 vitamers vitamins B7 CHEBI:176841 vitamin B7 vitamin B7 ChEBI vitamin B-7 ChEBI vitamin B7 vitamer ChEBI vitamin B7 vitamers ChEBI vitamins B7 ChEBI Any B-vitamin that exhibits biological activity against vitamin B9 deficiency. Vitamin B9 refers to the many forms of folic acid and its derivatives, including tetrahydrofolic acid (the active form), methyltetrahydrofolate (the primary form found in blood), methenyltetrahydrofolate, folinic acid amongst others. They are present in abundance in green leafy vegetables, citrus fruits, and animal products. Lack of vitamin B9 leads to anemia, a condition in which the body cannot produce sufficient number of red blood cells. Symptoms of vitamin B9 deficiency include fatigue, muscle weakness, and pale skin. vitamin B9 chebi_ontology folate vitamer folate vitamers vitamin B-9 vitamin B9 vitamer vitamin B9 vitamers vitamins B9 CHEBI:176842 vitamin B9 vitamin B9 ChEBI folate vitamer ChEBI folate vitamers ChEBI vitamin B-9 ChEBI vitamin B9 vitamer ChEBI vitamin B9 vitamers ChEBI vitamins B9 ChEBI Any member of a group of cobalamin vitamers that exhibit biological activity against vitamin B12 deficiency. Vitamin B12 deficiency is associated with low red blood cell count and anemia. The vitamers are found in foods such as cereals, meat, fish, and poultry. The vitamers include adenosylcobalamin, hydroxocobalamin, cyanocobalamin, aquacobalamin, nitritocobalamin and methylcobabalamin (also includes their ionized, salt and phosphate derivatives). vitamin B12 chebi_ontology vitamin B-12 vitamin B12 vitamer vitamin B12 vitamers vitamins B12 CHEBI:176843 vitamin B12 vitamin B12 ChEBI vitamin B-12 ChEBI vitamin B12 vitamer ChEBI vitamin B12 vitamers ChEBI vitamins B12 ChEBI chebi_ontology vitamin B-6 phosphate anion vitamin B-6 phosphate anions vitamin B6 phosphate anions CHEBI:176894 vitamin B6 phosphate anion vitamin B-6 phosphate anion ChEBI vitamin B-6 phosphate anions ChEBI vitamin B6 phosphate anions ChEBI A glycosylglucose disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form. 0 C12H22O11 InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10-,11?,12+/m1/s1 GUBGYTABKSRVRQ-QKKXKWKRSA-N 342.297 342.11621 OC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](O)C(O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@H]1O CHEBI:10296 CHEBI:10380 CHEBI:14497 CHEBI:22460 CHEBI:22760 CHEBI:25005 CHEBI:27755 CHEBI:613009 Beilstein:1292745 CAS:63-42-3 GlyGen:G74621DY GlyTouCan:G74621DY Gmelin:882872 KEGG:C00243 KEGG:D00046 KEGG:G10504 KNApSAcK:C00001136 PMID:1292745 PMID:17329833 PMID:18300214 PMID:19053747 PMID:19846069 PMID:19913595 PMID:20094999 PMID:20503067 PMID:20699559 PMID:20873837 PMID:20961532 PMID:21403918 PMID:2432147 PMID:2456994 PMID:28690131 PMID:28807538 PMID:6194884 PMID:7574700 Reaxys:1292745 beta-D-galactopyranosyl-(1->4)-D-glucopyranose lactose chebi_ontology (+)-lactose (Gal)1 (Glc)1 1-beta-D-Galactopyranosyl-4-D-glucopyranose 4-(beta-D-galactosido)-D-glucose 4-O-beta-D-galactopyranosyl-D-glucose D-lactose Galbeta1-4Glc Lac Laktobiose Laktose Milchzucker Milk sugar WURCS=2.0/2,2,1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1 beta-D-Gal-(1->4)-D-Glc beta-D-Galp-(1->4)-D-Glcp beta-Gal1,4-Glc lactobiose milk sugar CHEBI:17716 lactose Beilstein:1292745 Beilstein CAS:63-42-3 ChemIDplus CAS:63-42-3 KEGG COMPOUND CAS:63-42-3 NIST Chemistry WebBook Gmelin:882872 Gmelin PMID:1292745 Europe PMC PMID:17329833 Europe PMC PMID:18300214 Europe PMC PMID:19053747 ChEMBL PMID:19846069 Europe PMC PMID:19913595 Europe PMC PMID:20094999 Europe PMC PMID:20503067 Europe PMC PMID:20699559 Europe PMC PMID:20873837 Europe PMC PMID:20961532 Europe PMC PMID:21403918 Europe PMC PMID:2432147 Europe PMC PMID:2456994 Europe PMC PMID:28690131 Europe PMC PMID:28807538 Europe PMC PMID:6194884 Europe PMC PMID:7574700 Europe PMC Reaxys:1292745 Reaxys beta-D-galactopyranosyl-(1->4)-D-glucopyranose IUPAC lactose UniProt (+)-lactose NIST_Chemistry_WebBook (Gal)1 (Glc)1 KEGG_GLYCAN 1-beta-D-Galactopyranosyl-4-D-glucopyranose KEGG_COMPOUND 4-(beta-D-galactosido)-D-glucose NIST_Chemistry_WebBook 4-O-beta-D-galactopyranosyl-D-glucose IUPAC D-lactose ChemIDplus Galbeta1-4Glc ChEBI Lac JCBN Laktobiose ChEBI Laktose ChEBI Milchzucker ChEBI Milk sugar KEGG_COMPOUND WURCS=2.0/2,2,1/[a2122h-1x_1-5][a2112h-1b_1-5]/1-2/a4-b1 GlyTouCan beta-D-Gal-(1->4)-D-Glc KEGG_COMPOUND beta-D-Galp-(1->4)-D-Glcp IUPAC beta-Gal1,4-Glc ChEBI lactobiose NIST_Chemistry_WebBook milk sugar NIST_Chemistry_WebBook A triol with a structure of propane substituted at positions 1, 2 and 3 by hydroxy groups. 0 C3H8O3 InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2 PEDCQBHIVMGVHV-UHFFFAOYSA-N 92.09382 92.04734 OCC(O)CO CHEBI:131422 CHEBI:14334 CHEBI:24351 CHEBI:42998 CHEBI:5448 Beilstein:635685 CAS:56-81-5 Chemspider:733 DrugBank:DB04077 Drug_Central:1316 ECMDB:ECMDB00131 FooDB:FDB000756 Gmelin:26279 HMDB:HMDB0000131 KEGG:C00116 KEGG:D00028 KNApSAcK:C00001163 LINCS:LSM-37180 MetaCyc:GLYCEROL PDB:2AJS PDB:2D03 PDBeChem:GOL PMID:11302662 PMID:11958517 PMID:11994365 PMID:12672239 PMID:12687625 PMID:12689633 PMID:12713573 PMID:14559393 PMID:14563847 PMID:15026783 PMID:15342117 PMID:15786693 PMID:15983192 PMID:16244855 PMID:16258193 PMID:16319039 PMID:16349488 PMID:16475911 PMID:16651733 PMID:16664750 PMID:16901854 PMID:17336832 PMID:17439666 PMID:17979222 PMID:19184438 PMID:19231894 PMID:19460032 PMID:19548674 PMID:19795216 PMID:19956799 PMID:22705534 PMID:23562176 PMID:23747440 PMID:24643482 PMID:24835191 PMID:25108762 PMID:558160 PMID:6299616 PMID:7031247 PMID:7392035 PPDB:1317 Reaxys:635685 UM-BBD_compID:c0066 Wikipedia:Glycerol YMDB:YMDB00283 GLYCEROL Glycerol glycerol propane-1,2,3-triol chebi_ontology 1,2,3-Propanetriol 1,2,3-Trihydroxypropane Glycerin Glyceritol Glyzerin Gro Oelsuess Propanetriol Trihydroxypropane glycerine glycerol glycerolum glycyl alcohol CHEBI:17754 glycerol Beilstein:635685 Beilstein CAS:56-81-5 ChemIDplus CAS:56-81-5 KEGG COMPOUND CAS:56-81-5 NIST Chemistry WebBook Drug_Central:1316 DrugCentral Gmelin:26279 Gmelin PMID:11302662 Europe PMC PMID:11958517 Europe PMC PMID:11994365 Europe PMC PMID:12672239 ChEMBL PMID:12687625 Europe PMC PMID:12689633 Europe PMC PMID:12713573 Europe PMC PMID:14559393 Europe PMC PMID:14563847 Europe PMC PMID:15026783 Europe PMC PMID:15342117 Europe PMC PMID:15786693 Europe PMC PMID:15983192 Europe PMC PMID:16244855 Europe PMC PMID:16258193 Europe PMC PMID:16319039 Europe PMC PMID:16349488 Europe PMC PMID:16475911 Europe PMC PMID:16651733 Europe PMC PMID:16664750 Europe PMC PMID:16901854 Europe PMC PMID:17336832 Europe PMC PMID:17439666 Europe PMC PMID:17979222 Europe PMC PMID:19184438 Europe PMC PMID:19231894 Europe PMC PMID:19460032 Europe PMC PMID:19548674 Europe PMC PMID:19795216 Europe PMC PMID:19956799 Europe PMC PMID:22705534 Europe PMC PMID:23562176 Europe PMC PMID:23747440 Europe PMC PMID:24643482 Europe PMC PMID:24835191 Europe PMC PMID:25108762 Europe PMC PMID:558160 Europe PMC PMID:6299616 Europe PMC PMID:7031247 ChEMBL PMID:7392035 ChEMBL Reaxys:635685 Reaxys UM-BBD_compID:c0066 UM-BBD GLYCEROL PDBeChem Glycerol KEGG_COMPOUND glycerol ChEBI glycerol UniProt propane-1,2,3-triol IUPAC 1,2,3-Propanetriol KEGG_COMPOUND 1,2,3-Trihydroxypropane KEGG_COMPOUND Glycerin KEGG_COMPOUND Glyceritol HMDB Glyzerin ChEBI Gro JCBN Oelsuess ChEBI Propanetriol HMDB Trihydroxypropane HMDB glycerine ChEBI glycerol ChemIDplus glycerolum ChemIDplus glycyl alcohol NIST_Chemistry_WebBook A compound showing blue fluorescence, formed by a photolysis of riboflavin in acid or neutral solution. 0 C12H10N4O2 InChI=1S/C12H10N4O2/c1-5-3-7-8(4-6(5)2)14-10-9(13-7)11(17)16-12(18)15-10/h3-4H,1-2H3,(H2,14,15,16,17,18) ZJTJUVIJVLLGSP-UHFFFAOYSA-N 242.23356 242.08038 Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C CHEBI:14534 CHEBI:25080 CHEBI:43772 CHEBI:6561 Beilstein:226631 CAS:1086-80-2 DrugBank:DB04345 KEGG:C01727 KNApSAcK:C00030694 MetaCyc:CPD-605 PDBeChem:LUM PMID:15819908 PMID:21126007 PMID:22953948 PMID:24001807 PMID:24451190 PMID:24643482 Reaxys:226631 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione LUMICHROME Lumichrome lumichrome chebi_ontology 7,8-Dimethylalloxazine CHEBI:17781 lumichrome Beilstein:226631 Beilstein CAS:1086-80-2 ChemIDplus CAS:1086-80-2 KEGG COMPOUND CAS:1086-80-2 NIST Chemistry WebBook PMID:15819908 Europe PMC PMID:21126007 Europe PMC PMID:22953948 Europe PMC PMID:24001807 Europe PMC PMID:24451190 Europe PMC PMID:24643482 Europe PMC Reaxys:226631 Reaxys 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione IUPAC LUMICHROME PDBeChem Lumichrome KEGG_COMPOUND lumichrome UniProt 7,8-Dimethylalloxazine KEGG_COMPOUND The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. 0 CH4O InChI=1S/CH4O/c1-2/h2H,1H3 OKKJLVBELUTLKV-UHFFFAOYSA-N 32.04186 32.02621 CO CHEBI:14588 CHEBI:25227 CHEBI:44080 CHEBI:44553 CHEBI:6816 Beilstein:1098229 CAS:67-56-1 Gmelin:449 HMDB:HMDB0001875 KEGG:C00132 KEGG:D02309 MetaCyc:METOH PDBeChem:MOH PMID:11141607 PMID:11430978 PMID:11489599 PMID:11680737 PMID:11684179 PMID:14012711 PMID:14678513 PMID:14760634 PMID:15172721 PMID:15906011 PMID:16705261 PMID:17451998 PMID:17733096 PMID:19064074 PMID:19850112 PMID:20314698 Reaxys:1098229 UM-BBD_compID:c0132 Wikipedia:Methanol METHANOL Methanol methanol chebi_ontology CH3OH MeOH Methyl alcohol Methylalkohol carbinol spirit of wood wood alcohol wood naphtha wood spirit CHEBI:17790 methanol Beilstein:1098229 Beilstein CAS:67-56-1 ChemIDplus CAS:67-56-1 KEGG COMPOUND CAS:67-56-1 NIST Chemistry WebBook Gmelin:449 Gmelin PMID:11141607 Europe PMC PMID:11430978 Europe PMC PMID:11489599 Europe PMC PMID:11680737 Europe PMC PMID:11684179 Europe PMC PMID:14012711 Europe PMC PMID:14678513 Europe PMC PMID:14760634 Europe PMC PMID:15172721 Europe PMC PMID:15906011 Europe PMC PMID:16705261 Europe PMC PMID:17451998 Europe PMC PMID:17733096 Europe PMC PMID:19064074 Europe PMC PMID:19850112 Europe PMC PMID:20314698 Europe PMC Reaxys:1098229 Reaxys UM-BBD_compID:c0132 UM-BBD METHANOL PDBeChem Methanol KEGG_COMPOUND methanol IUPAC methanol UniProt CH3OH ChEBI MeOH ChEBI Methyl alcohol KEGG_COMPOUND Methylalkohol NIST_Chemistry_WebBook carbinol ChemIDplus spirit of wood HMDB wood alcohol ChemIDplus wood naphtha ChemIDplus wood spirit NIST_Chemistry_WebBook An alpha-amino acid that is alanine substituted at position 3 by a hydroxy group. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7) MTCFGRXMJLQNBG-UHFFFAOYSA-N 105.09262 105.04259 NC(CO)C(O)=O CHEBI:15081 CHEBI:26648 CHEBI:9116 Beilstein:1721402 CAS:302-84-1 Gmelin:26429 KEGG:C00716 KNApSAcK:C00001393 Reaxys:1721402 Wikipedia:Serine Serine serine chebi_ontology 2-Amino-3-hydroxypropionic acid 2-amino-3-hydroxypropanoic acid 3-Hydroxyalanine Serin CHEBI:17822 serine Beilstein:1721402 Beilstein CAS:302-84-1 ChemIDplus CAS:302-84-1 KEGG COMPOUND CAS:302-84-1 NIST Chemistry WebBook Gmelin:26429 Gmelin Reaxys:1721402 Reaxys Serine KEGG_COMPOUND serine IUPAC 2-Amino-3-hydroxypropionic acid KEGG_COMPOUND 2-amino-3-hydroxypropanoic acid IUPAC 3-Hydroxyalanine KEGG_COMPOUND Serin ChEBI Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. 0 C6H5O6R3 173.10030 173.00861 [*]C(=O)OCC(COC([*])=O)OC([*])=O CHEBI:15255 CHEBI:27085 CHEBI:9664 KEGG:C00422 LIPID_MAPS_class:LMGL0301 PMID:2474544 Triglyceride triglycerides chebi_ontology Triacylglycerol Triglycerid Triglyzerid a triacylglycerol triacylglycerols triglycerides CHEBI:17855 triglyceride LIPID_MAPS_class:LMGL0301 LIPID MAPS PMID:2474544 Europe PMC Triglyceride KEGG_COMPOUND triglycerides IUPAC Triacylglycerol KEGG_COMPOUND Triglycerid ChEBI Triglyzerid ChEBI a triacylglycerol UniProt triacylglycerols LIPID_MAPS triglycerides ChEBI A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. CHEBI:14202 CHEBI:4697 KEGG:C01351 Donor chebi_ontology Donator donneur CHEBI:17891 donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group. -1 C4H7O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)/p-1 FERIUCNNQQJTOY-UHFFFAOYSA-M 87.09718 87.04515 CCCC([O-])=O CHEBI:13924 CHEBI:22946 Beilstein:3601060 CAS:461-55-2 Gmelin:324289 KEGG:C00246 MetaCyc:BUTYRIC_ACID PMID:17190852 PMID:7496326 Reaxys:3601060 UM-BBD_compID:c0035 butanoate butyrate chebi_ontology 1-butanoate 1-butyrate 1-propanecarboxylate CH3-[CH2]2-COO(-) butanate butanoate butanoic acid, ion(1-) n-butanoate n-butyrate propanecarboxylate propylformate CHEBI:17968 butyrate Beilstein:3601060 Beilstein CAS:461-55-2 ChemIDplus Gmelin:324289 Gmelin PMID:17190852 Europe PMC PMID:7496326 Europe PMC Reaxys:3601060 Reaxys UM-BBD_compID:c0035 UM-BBD butanoate IUPAC butyrate IUPAC 1-butanoate ChEBI 1-butyrate ChEBI 1-propanecarboxylate ChEBI CH3-[CH2]2-COO(-) IUPAC butanate ChEBI butanoate ChEBI butanoate UniProt butanoic acid, ion(1-) ChemIDplus n-butanoate ChEBI n-butyrate ChemIDplus propanecarboxylate ChEBI propylformate ChEBI A glycosyl glycoside formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. 0 C12H22O11 InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 CZMRCDWAGMRECN-UGDNZRGBSA-N 342.29650 342.11621 OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O CHEBI:15128 CHEBI:26812 CHEBI:45795 CHEBI:9314 Beilstein:90825 CAS:57-50-1 DrugBank:DB02772 Drug_Central:4610 Gmelin:97695 HMDB:HMDB0000258 KEGG:C00089 KEGG:D00025 KEGG:D06533 KEGG:G00370 KNApSAcK:C00001151 MetaCyc:SUCROSE PDBeChem:SUC PMID:11021636 PMID:11093712 PMID:11111003 PMID:12065720 PMID:12706980 PMID:13508893 PMID:15291457 PMID:15660210 PMID:15792978 PMID:15845855 PMID:16228482 PMID:16304615 PMID:16313996 PMID:16525719 PMID:16660545 PMID:16663947 PMID:16665852 PMID:17233733 PMID:17439666 PMID:17597061 PMID:18625236 PMID:19199566 PMID:19726178 PMID:21703290 PMID:21972845 PMID:22085755 PMID:22311778 PMID:22404833 PMID:22751876 Reaxys:1435311 Reaxys:90825 Wikipedia:Sucrose SUCROSE Sucrose beta-D-fructofuranosyl alpha-D-glucopyranoside sucrose chebi_ontology 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside Cane sugar Saccharose Sacharose White sugar beta-D-Fruf-(2<->1)-alpha-D-Glcp sacarosa table sugar CHEBI:17992 sucrose Beilstein:90825 Beilstein CAS:57-50-1 ChemIDplus CAS:57-50-1 KEGG COMPOUND CAS:57-50-1 NIST Chemistry WebBook Drug_Central:4610 DrugCentral Gmelin:97695 Gmelin PMID:11021636 Europe PMC PMID:11093712 Europe PMC PMID:11111003 Europe PMC PMID:12065720 Europe PMC PMID:12706980 Europe PMC PMID:13508893 Europe PMC PMID:15291457 Europe PMC PMID:15660210 Europe PMC PMID:15792978 Europe PMC PMID:15845855 Europe PMC PMID:16228482 Europe PMC PMID:16304615 Europe PMC PMID:16313996 Europe PMC PMID:16525719 Europe PMC PMID:16660545 Europe PMC PMID:16663947 Europe PMC PMID:16665852 Europe PMC PMID:17233733 Europe PMC PMID:17439666 Europe PMC PMID:17597061 Europe PMC PMID:18625236 Europe PMC PMID:19199566 Europe PMC PMID:19726178 Europe PMC PMID:21703290 Europe PMC PMID:21972845 Europe PMC PMID:22085755 Europe PMC PMID:22311778 Europe PMC PMID:22404833 Europe PMC PMID:22751876 Europe PMC Reaxys:1435311 Reaxys Reaxys:90825 Reaxys SUCROSE PDBeChem Sucrose KEGG_COMPOUND beta-D-fructofuranosyl alpha-D-glucopyranoside IUPAC sucrose UniProt 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside KEGG_COMPOUND Cane sugar KEGG_COMPOUND Saccharose KEGG_COMPOUND Sacharose ChEBI White sugar HMDB beta-D-Fruf-(2<->1)-alpha-D-Glcp JCBN sacarosa ChEBI table sugar ChemIDplus 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid Lipid KEGG_COMPOUND lipids IUPAC Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. CHEBI:14361 CHEBI:24398 CHEBI:5495 KEGG:C02545 Wikipedia:Glycosaminoglycan Glycosaminoglycan glycosaminoglycan chebi_ontology Glykosaminoglykan glicosaminoglicano glycosaminoglycane glycosaminoglycans CHEBI:18085 glycosaminoglycan Glycosaminoglycan KEGG_COMPOUND glycosaminoglycan IUPAC Glykosaminoglykan ChEBI glicosaminoglicano IUPAC glycosaminoglycane IUPAC glycosaminoglycans ChEBI Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose). CHEBI:14399 CHEBI:24590 CHEBI:5709 GlyGen:G70994MS GlyTouCan:G70994MS KEGG:C00738 Hexose chebi_ontology WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ hexoses CHEBI:18133 hexose Hexose KEGG_COMPOUND WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ GlyTouCan hexoses ChEBI A tertiary amine that is ammonia in which each hydrogen atom is substituted by an methyl group. 0 C3H9N InChI=1S/C3H9N/c1-4(2)3/h1-3H3 GETQZCLCWQTVFV-UHFFFAOYSA-N 59.11030 59.07350 CN(C)C CHEBI:15261 CHEBI:27125 CHEBI:27127 CHEBI:9732 Beilstein:956566 CAS:75-50-3 Gmelin:1309 HMDB:HMDB0000906 KEGG:C00565 KNApSAcK:C00001433 MetaCyc:TRIMETHYLAMINE PDBeChem:KEN PMID:14047118 PMID:15304308 PMID:15752091 PMID:17190852 PMID:1801314 PMID:24591617 PMID:2501587 PMID:5161463 Reaxys:956566 Wikipedia:Trimethylamine N,N-dimethylmethanamine Trimethylamine chebi_ontology (CH3)3N N(CH3)3 N,N,N-trimethylamine N,N-Dimethylmethanamine NMe3 TMA Trimethylamin tridimethylaminomethane CHEBI:18139 trimethylamine Beilstein:956566 Beilstein CAS:75-50-3 ChemIDplus CAS:75-50-3 KEGG COMPOUND CAS:75-50-3 NIST Chemistry WebBook Gmelin:1309 Gmelin PMID:14047118 Europe PMC PMID:15304308 Europe PMC PMID:15752091 Europe PMC PMID:17190852 Europe PMC PMID:1801314 Europe PMC PMID:24591617 Europe PMC PMID:2501587 Europe PMC PMID:5161463 Europe PMC Reaxys:956566 Reaxys N,N-dimethylmethanamine IUPAC Trimethylamine KEGG_COMPOUND (CH3)3N KEGG_COMPOUND N(CH3)3 ChEBI N,N,N-trimethylamine ChEBI N,N-Dimethylmethanamine KEGG_COMPOUND NMe3 ChEBI TMA NIST_Chemistry_WebBook Trimethylamin ChEBI tridimethylaminomethane ChEBI 0 HX 1.008 1.00783 *[H] CHEBI:13368 CHEBI:37140 CHEBI:5599 hydrogen halide hydrogen halides chebi_ontology hydrogen halides CHEBI:18140 hydrogen halide hydrogen halide IUPAC hydrogen halides IUPAC hydrogen halides ChEBI A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. CHEBI:14864 CHEBI:26205 CHEBI:8322 KEGG:C00420 Polysaccharide polysaccharides chebi_ontology Glycan Glycane Glykan Glykane glycans polisacarido polisacaridos CHEBI:18154 polysaccharide Polysaccharide KEGG_COMPOUND polysaccharides IUPAC Glycan KEGG_COMPOUND Glycane ChEBI Glykan ChEBI Glykane ChEBI glycans IUPAC polisacarido ChEBI polisacaridos IUPAC An alpha-amino acid that is phenylalanine bearing a hydroxy substituent at position 4 on the phenyl ring. 0 C9H11NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13) OUYCCCASQSFEME-UHFFFAOYSA-N 181.18858 181.07389 NC(Cc1ccc(O)cc1)C(O)=O CHEBI:15277 CHEBI:27176 CHEBI:9800 Beilstein:515881 CAS:55520-40-6 CAS:556-03-6 Gmelin:27744 KEGG:C01536 KNApSAcK:C00001397 PMID:17190852 Reaxys:515881 Tyrosine tyrosine chebi_ontology 2-Amino-3-(p-hydroxyphenyl)propionic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 3-(p-Hydroxyphenyl)alanine Tyr Tyrosin Y tirosina CHEBI:18186 tyrosine Beilstein:515881 Beilstein CAS:55520-40-6 ChemIDplus CAS:556-03-6 KEGG COMPOUND Gmelin:27744 Gmelin PMID:17190852 Europe PMC Reaxys:515881 Reaxys Tyrosine KEGG_COMPOUND tyrosine IUPAC 2-Amino-3-(p-hydroxyphenyl)propionic acid KEGG_COMPOUND 2-amino-3-(4-hydroxyphenyl)propanoic acid IUPAC 3-(p-Hydroxyphenyl)alanine KEGG_COMPOUND Tyr ChEBI Tyrosin ChEBI Y ChEBI tirosina ChEBI The parent compound of the citrulline class consisting of ornithine having a carbamoyl group at the N(5)-position. 0 C6H13N3O3 InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12) RHGKLRLOHDJJDR-UHFFFAOYSA-N 175.18584 175.09569 NC(CCCNC(N)=O)C(O)=O CHEBI:14002 CHEBI:3730 Beilstein:1725417 Beilstein:2328251 CAS:627-77-0 PMID:11094453 PMID:11113071 PMID:11696417 PMID:1378088 PMID:16082501 PMID:16708633 PMID:17005970 PMID:17513438 PMID:17558653 PMID:17693747 PMID:18437289 PMID:18440672 PMID:18989563 PMID:19144577 PMID:21129371 PMID:21482070 Reaxys:1725417 Wikipedia:Citrulline 2-amino-5-(carbamoylamino)pentanoic acid Citrulline N(5)-carbamoylornithine citrulline chebi_ontology 2-Amino-5-uredovaleric acid Cit Citrullin DL-2-amino-5-ureidovaleric acid N(5)-(aminocarbonyl)-DL-ornithine N(5)-(aminocarbonyl)ornithine N(5)-carbamoyl-DL-ornithine citrulina dl-citrulline CHEBI:18211 citrulline Beilstein:1725417 Beilstein Beilstein:2328251 Beilstein CAS:627-77-0 ChemIDplus CAS:627-77-0 NIST Chemistry WebBook PMID:11094453 Europe PMC PMID:11113071 Europe PMC PMID:11696417 Europe PMC PMID:1378088 Europe PMC PMID:16082501 Europe PMC PMID:16708633 Europe PMC PMID:17005970 Europe PMC PMID:17513438 Europe PMC PMID:17558653 Europe PMC PMID:17693747 Europe PMC PMID:18437289 Europe PMC PMID:18440672 Europe PMC PMID:18989563 Europe PMC PMID:19144577 Europe PMC PMID:21129371 Europe PMC PMID:21482070 Europe PMC Reaxys:1725417 Reaxys 2-amino-5-(carbamoylamino)pentanoic acid IUPAC Citrulline KEGG_COMPOUND N(5)-carbamoylornithine IUPAC citrulline IUPAC 2-Amino-5-uredovaleric acid KEGG_COMPOUND Cit IUPAC Citrullin ChEBI DL-2-amino-5-ureidovaleric acid ChemIDplus N(5)-(aminocarbonyl)-DL-ornithine NIST_Chemistry_WebBook N(5)-(aminocarbonyl)ornithine ChEBI N(5)-carbamoyl-DL-ornithine NIST_Chemistry_WebBook citrulina ChEBI dl-citrulline NIST_Chemistry_WebBook An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10) WHUUTDBJXJRKMK-UHFFFAOYSA-N 147.12930 147.05316 NC(CCC(O)=O)C(O)=O CHEBI:24314 CHEBI:5431 Beilstein:1723799 CAS:617-65-2 Gmelin:101971 KEGG:C00302 KEGG:D04341 KNApSAcK:C00001358 KNApSAcK:C00019577 PMID:15739367 PMID:17190852 PMID:24616376 PMID:24984001 Reaxys:1723799 Wikipedia:Glutamic_acid 2-aminopentanedioic acid Glutamic acid glutamic acid chebi_ontology 2-Aminoglutaric acid DL-Glutamic acid DL-Glutaminic acid E Glu Glutamate Glutaminic acid Glutaminsaeure CHEBI:18237 glutamic acid Beilstein:1723799 Beilstein CAS:617-65-2 ChemIDplus CAS:617-65-2 KEGG COMPOUND CAS:617-65-2 NIST Chemistry WebBook Gmelin:101971 Gmelin PMID:15739367 Europe PMC PMID:17190852 Europe PMC PMID:24616376 Europe PMC PMID:24984001 Europe PMC Reaxys:1723799 Reaxys 2-aminopentanedioic acid IUPAC Glutamic acid KEGG_COMPOUND glutamic acid IUPAC 2-Aminoglutaric acid KEGG_COMPOUND DL-Glutamic acid KEGG_DRUG DL-Glutaminic acid KEGG_COMPOUND E ChEBI Glu ChEBI Glutamate KEGG_COMPOUND Glutaminic acid KEGG_COMPOUND Glutaminsaeure ChEBI An iron group element atom that has atomic number 26. 0 Fe InChI=1S/Fe XEEYBQQBJWHFJM-UHFFFAOYSA-N 55.84500 55.93494 [Fe] CHEBI:13322 CHEBI:24872 CHEBI:5974 CAS:7439-89-6 DrugBank:DB01592 HMDB:HMDB0015531 KEGG:C00023 Reaxys:4122945 WebElements:Fe iron chebi_ontology 26Fe Eisen Fe Iron fer ferrum hierro iron CHEBI:18248 iron atom CAS:7439-89-6 ChemIDplus CAS:7439-89-6 KEGG COMPOUND CAS:7439-89-6 NIST Chemistry WebBook Reaxys:4122945 Reaxys iron IUPAC 26Fe IUPAC Eisen ChEBI Fe IUPAC Fe UniProt Iron KEGG_COMPOUND fer ChEBI ferrum IUPAC hierro ChEBI iron ChEBI Any nucleoside where the sugar component is D-ribose. 0 C5H9O4R 133.123 133.05008 OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O CHEBI:13014 CHEBI:13015 CHEBI:13685 CHEBI:21085 CHEBI:26560 CHEBI:4240 CHEBI:8844 KEGG:C00911 Ribonucleoside chebi_ontology a ribonucleoside ribonucleosides CHEBI:18254 ribonucleoside Ribonucleoside KEGG_COMPOUND a ribonucleoside UniProt ribonucleosides ChEBI An alpha-amino acid that is pentanoic acid bearing two amino substituents at positions 2 and 5. 0 C5H12N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9) AHLPHDHHMVZTML-UHFFFAOYSA-N 132.16106 132.08988 NCCCC(N)C(O)=O CHEBI:7784 Beilstein:1722296 CAS:616-07-9 Gmelin:847696 KEGG:C01602 KNApSAcK:C00001384 PMID:15449570 PMID:17190852 PMID:22264337 Reaxys:1722296 2,5-diaminopentanoic acid Ornithine ornithine chebi_ontology 2,5-Diaminopentanoic acid 2,5-Diaminovaleric acid DL-Ornithine Orn CHEBI:18257 ornithine Beilstein:1722296 Beilstein CAS:616-07-9 ChemIDplus Gmelin:847696 Gmelin PMID:15449570 Europe PMC PMID:17190852 Europe PMC PMID:22264337 Europe PMC Reaxys:1722296 Reaxys 2,5-diaminopentanoic acid IUPAC Ornithine KEGG_COMPOUND ornithine IUPAC 2,5-Diaminopentanoic acid KEGG_COMPOUND 2,5-Diaminovaleric acid KEGG_COMPOUND DL-Ornithine ChemIDplus Orn IUPAC That part of DNA or RNA that may be involved in pairing. CHEBI:13873 CHEBI:25598 CHEBI:2995 KEGG:C00701 Wikipedia:Nucleobase chebi_ontology Base nucleobases CHEBI:18282 nucleobase Base KEGG_COMPOUND nucleobases ChEBI An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms. 0 CH3R 15.035 15.02348 C[*] CHEBI:13435 CHEBI:22317 CHEBI:2576 KEGG:C01371 Alkane alkane alkanes chebi_ontology Alkan RH alcane alcanes alcano alcanos an alkane CHEBI:18310 alkane Alkane KEGG_COMPOUND alkane IUPAC alkanes IUPAC Alkan ChEBI RH KEGG_COMPOUND alcane IUPAC alcanes IUPAC alcano IUPAC alcanos IUPAC an alkane UniProt A phosphate ion that is the conjugate base of hydrogenphosphate. -3 O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 NBIIXXVUZAFLBC-UHFFFAOYSA-K 94.97136 94.95507 [O-]P([O-])([O-])=O CHEBI:14791 CHEBI:45024 CHEBI:7793 Beilstein:3903772 CAS:14265-44-2 Gmelin:1997 KEGG:C00009 PDBeChem:PO4 Reaxys:3903772 phosphate tetraoxidophosphate(3-) tetraoxophosphate(3-) tetraoxophosphate(V) chebi_ontology Orthophosphate PHOSPHATE ION PO4(3-) Phosphate [PO4](3-) CHEBI:18367 phosphate(3-) Beilstein:3903772 Beilstein CAS:14265-44-2 ChemIDplus CAS:14265-44-2 KEGG COMPOUND Gmelin:1997 Gmelin PDBeChem:PO4 ChEBI Reaxys:3903772 Reaxys phosphate IUPAC tetraoxidophosphate(3-) IUPAC tetraoxophosphate(3-) IUPAC tetraoxophosphate(V) IUPAC Orthophosphate KEGG_COMPOUND PHOSPHATE ION PDBeChem PO4(3-) IUPAC Phosphate KEGG_COMPOUND [PO4](3-) IUPAC The monophosphate ester obtained by condensation of phosphoric acid with the primary hydroxy group of pyridoxal. 0 C8H10NO6P InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14) NGVDGCNFYWLIFO-UHFFFAOYSA-N 247.14190 247.02457 [H]C(=O)c1c(COP(O)(O)=O)cnc(C)c1O CHEBI:14977 CHEBI:234571 CHEBI:26424 CHEBI:358848 CHEBI:45145 CHEBI:8668 Beilstein:234749 CAS:54-47-7 COMe:MOL000108 DrugBank:DB00114 Drug_Central:3506 Gmelin:465416 HMDB:HMDB0001491 KEGG:C00018 KNApSAcK:C00007503 PDBeChem:PLP PMID:14651974 PMID:16277678 PMID:18491919 PMID:6339724 PMID:7284379 PMID:9866693 Reaxys:234749 Wikipedia:Pyridoxal_phosphate (4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate Pyridoxal 5'-phosphate chebi_ontology 3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinecarboxaldehyde 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate PLP PYRIDOXAL-5'-PHOSPHATE Phosphoric acid mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester Pyridoxal 5-phosphate Pyridoxal phosphate codecarboxylase pyridoxal 5'-(dihydrogen phosphate) pyridoxal 5-monophosphoric acid ester CHEBI:18405 pyridoxal 5'-phosphate Beilstein:234749 Beilstein CAS:54-47-7 ChemIDplus CAS:54-47-7 KEGG COMPOUND Drug_Central:3506 DrugCentral Gmelin:465416 Gmelin PMID:14651974 Europe PMC PMID:16277678 Europe PMC PMID:18491919 Europe PMC PMID:6339724 ChEMBL PMID:7284379 Europe PMC PMID:9866693 Europe PMC Reaxys:234749 Reaxys (4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate IUPAC Pyridoxal 5'-phosphate KEGG_COMPOUND 3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinecarboxaldehyde ChEBI 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate ChEBI PLP KEGG_COMPOUND PYRIDOXAL-5'-PHOSPHATE PDBeChem Phosphoric acid mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester ChEMBL Pyridoxal 5-phosphate KEGG_COMPOUND Pyridoxal phosphate KEGG_COMPOUND codecarboxylase ChEBI pyridoxal 5'-(dihydrogen phosphate) ChEBI pyridoxal 5-monophosphoric acid ester ChEBI A calcium salt that lacks C-H bonds PMID:28457049 chebi_ontology CHEBI:190295 inorganic calcium salt PMID:28457049 SUBMITTER 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18+,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-OBUPQJQESA-N 330.59028 330.32865 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC Beilstein:2048472 5beta-cholane chebi_ontology CHEBI:20664 5beta-cholane Beilstein:2048472 Beilstein 5beta-cholane IUPAC An N-acetyl-amino acid having D-configuration. CHEBI:7109 KEGG:C03135 chebi_ontology N-Acetyl-D-amino-acid N-acetyl-D-amino acids CHEBI:21501 N-acetyl-D-amino acid N-Acetyl-D-amino-acid KEGG_COMPOUND N-acetyl-D-amino acids ChEBI An L-amino acid having an N-acetyl substituent. chebi_ontology CHEBI:21545 N-acetyl-L-amino acid An N-acyl-amino acid that has acetyl as the acyl group. CHEBI:7105 KEGG:C02847 chebi_ontology N-Acetyl amino acid N-acetyl-amino acids CHEBI:21575 N-acetyl-amino acid N-Acetyl amino acid KEGG_COMPOUND N-acetyl-amino acids ChEBI Any N-acylamino acid having L-configuration. chebi_ontology CHEBI:21644 N-acyl-L-amino acid A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. glycosylamine chebi_ontology N-glycoside N-glycosides N-glycosyl compounds glycosylamines CHEBI:21731 N-glycosyl compound glycosylamine IUPAC N-glycoside ChEBI N-glycosides ChEBI N-glycosyl compounds ChEBI glycosylamines IUPAC Compounds with the general formula RNHC(=O)CH3. chebi_ontology CHEBI:22160 acetamides Any amino acid derivative that is the N-acetyl or O-acetyl derivative of an amino acid. chebi_ontology acetyl-amino acids CHEBI:22195 acetyl-amino acid acetyl-amino acids ChEBI chebi_ontology CHEBI:22198 acetylcysteine An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids. acyl group alkanoyl chebi_ontology acyl groups alkanoyl group groupe acyle CHEBI:22221 acyl group acyl group IUPAC alkanoyl IUPAC acyl groups ChEBI alkanoyl group ChEBI groupe acyle IUPAC alkaline earth metals chebi_ontology Erdalkalimetall Erdalkalimetalle alkaline earth metal alkaline-earth metal alkaline-earth metals metal alcalino-terreux metal alcalinoterreo metales alcalinoterreos metaux alcalino-terreux CHEBI:22313 alkaline earth metal atom alkaline earth metals IUPAC Erdalkalimetall ChEBI Erdalkalimetalle ChEBI alkaline earth metal ChEBI alkaline-earth metal ChEBI alkaline-earth metals ChEBI metal alcalino-terreux ChEBI metal alcalinoterreo ChEBI metales alcalinoterreos ChEBI metaux alcalino-terreux ChEBI alkali metals chebi_ontology Alkalimetall Alkalimetalle alkali metal metal alcalin metal alcalino metales alcalinos metaux alcalins CHEBI:22314 alkali metal atom alkali metals IUPAC Alkalimetall ChEBI Alkalimetalle ChEBI alkali metal ChEBI metal alcalin ChEBI metal alcalino ChEBI metales alcalinos ChEBI metaux alcalins ChEBI Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. Wikipedia:Alkaloid Alkaloid alkaloids chebi_ontology Alkaloide alcaloide alcaloides CHEBI:22315 alkaloid Alkaloid ChEBI alkaloids IUPAC Alkaloide ChEBI alcaloide ChEBI alcaloides ChEBI A univalent group -CnH2n+1 derived from an alkane by removal of a hydrogen atom from any carbon atom. alkyl group alkyl groups chebi_ontology groupe alkyle grupo alquilo grupos alquilo CHEBI:22323 alkyl group alkyl group IUPAC alkyl groups IUPAC groupe alkyle IUPAC grupo alquilo IUPAC grupos alquilo IUPAC Any amine formally derived from ammonia by replacing one, two or three hydrogen atoms by alkyl groups. chebi_ontology CHEBI:22331 alkylamines Highly reactive chemical that introduces alkyl radicals into biologically active molecules and thereby prevents their proper functioning. It could be used as an antineoplastic agent, but it might be very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. It could also be used as a component of poison gases. chebi_ontology CHEBI:22333 alkylating agent chebi_ontology aminobenzoates CHEBI:22494 aminobenzoate aminobenzoates ChEBI 0 C7H7NO2 137.136 137.04768 aminobenzoic acid chebi_ontology Aminobenzoesaeure CHEBI:22495 aminobenzoic acid aminobenzoic acid IUPAC Aminobenzoesaeure ChEBI chebi_ontology aminoglycans CHEBI:22506 aminoglycan aminoglycans ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions CHEBI:22563 anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. chebi_ontology antioxidants antioxydant antoxidant CHEBI:22586 antioxidant antioxidants ChEBI antioxydant ChEBI antoxidant ChEBI A substance that destroys or inhibits replication of viruses. chebi_ontology anti-viral agent anti-viral agents antiviral antiviral agents antivirals CHEBI:22587 antiviral agent anti-viral agent ChEBI anti-viral agents ChEBI antiviral ChEBI antiviral agents ChEBI antivirals ChEBI A ketoaldonate that is the conjugate base of ascorbic acid. chebi_ontology CHEBI:22651 ascorbate chebi_ontology CHEBI:22652 ascorbic acid An L-alpha-amino acid which is L-aspartic acid or any of the essential amino acids biosynthesised from it (asparagine, lysine, methionine, threonine and isoleucine). A closed class. PMID:4386082 PMID:4394351 PMID:4721772 PMID:5016260 PMID:5074276 chebi_ontology aspartate family amino acids aspartic acid family amino acid aspartic acid family amino acids oxaloacetate family amino acid oxaloacetate family amino acids oxaloacetate/aspartate family amino acid oxaloacetate/aspartate family amino acids CHEBI:22658 aspartate family amino acid PMID:4386082 Europe PMC PMID:4394351 Europe PMC PMID:4721772 Europe PMC PMID:5016260 Europe PMC PMID:5074276 Europe PMC aspartate family amino acids ChEBI aspartic acid family amino acid ChEBI aspartic acid family amino acids ChEBI oxaloacetate family amino acid ChEBI oxaloacetate family amino acids ChEBI oxaloacetate/aspartate family amino acid ChEBI oxaloacetate/aspartate family amino acids ChEBI A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). KEGG:C00701 Base base chebi_ontology Base1 Base2 Basen Nucleobase bases CHEBI:22695 base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. chebi_ontology CHEBI:22712 benzenes A monocarboxylic acid anion obtained by deprotonation of the carboxy group of any benzoic acid. chebi_ontology benzoate anion CHEBI:22718 benzoates benzoate anion ChEBI Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. chebi_ontology CHEBI:22723 benzoic acids Wikipedia:Benzopyran chebi_ontology benzopyrans CHEBI:22727 benzopyran benzopyrans ChEBI Any quinone resulting from the formal oxidation of catechol, hydroquinone, or their C-substituted derivatives. chebi_ontology CHEBI:22729 benzoquinones 0 C7H7 91.13048 91.05478 C1=C(C=CC=C1)C* benzyl chebi_ontology Bn C6H5-CH2- phenylalanine side-chain phenylmethyl CHEBI:22744 benzyl group benzyl IUPAC Bn ChEBI C6H5-CH2- IUPAC phenylalanine side-chain ChEBI phenylmethyl IUPAC chebi_ontology CHEBI:22823 beta-alanine derivative Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries methyl substituents and bears no hydrogen atoms. chebi_ontology amino acid betaines amino-acid betaines betaines CHEBI:22860 amino-acid betaine amino acid betaines ChEBI amino-acid betaines ChEBI betaines ChEBI A sodium salt of the conjugate of any bile acid with either glycine or taurine. KEGG:C01558 chebi_ontology Bile acid bile salts CHEBI:22868 bile salt Bile acid KEGG_COMPOUND bile salts ChEBI Any amino acid in which the parent hydrocarbon chain has one or more alkyl substituents chebi_ontology branched chain amino acids CHEBI:22918 branched-chain amino acid branched chain amino acids ChEBI 0 Ca InChI=1S/Ca OYPRJOBELJOOCE-UHFFFAOYSA-N 40.07800 39.96259 [Ca] CAS:7440-70-2 DrugBank:DB01373 KEGG:C00076 WebElements:Ca calcium chebi_ontology 20Ca Ca Calcium Kalzium calcio calcium CHEBI:22984 calcium atom CAS:7440-70-2 ChemIDplus calcium IUPAC 20Ca IUPAC Ca IUPAC Ca UniProt Calcium KEGG_COMPOUND Kalzium ChEBI calcio ChEBI calcium ChEBI calcium molecular entity chebi_ontology calcium compounds calcium molecular entities CHEBI:22985 calcium molecular entity calcium molecular entity ChEBI calcium compounds ChEBI calcium molecular entities ChEBI The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O PMID:24168430 carbamoyl chebi_ontology -C(O)NH2 -CONH2 aminocarbonyl carbamyl carbamyl group carboxamide CHEBI:23004 carbamoyl group PMID:24168430 Europe PMC carbamoyl IUPAC -C(O)NH2 ChEBI -CONH2 IUPAC aminocarbonyl IUPAC carbamyl ChEBI carbamyl group ChEBI carboxamide IUPAC Organooxygen compounds that are salts or esters of carbonic acid, H2CO3. chebi_ontology CHEBI:23016 carbonates 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC Hydrocarbon carotenoids. carotene carotenes chebi_ontology carotenes CHEBI:23042 carotene carotene ChEBI carotenes IUPAC carotenes ChEBI One of a class of tetraterpenoids (C40), formally derived from the acyclic parent, psi,psi-carotene by hydrogenation, dehydrogenation, cyclization, oxidation, or combination of these processes. This class includes carotenes, xanthophylls and certain compounds that arise from rearrangement of the skeleton of psi,psi-carotene or by loss of part of this structure. Retinoids are excluded. CAS:36-88-4 carotenoid chebi_ontology carotenes and carotenoids carotenoids CHEBI:23044 carotenoid CAS:36-88-4 ChemIDplus carotenoid IUPAC carotenes and carotenoids ChemIDplus carotenoids ChEBI chebi_ontology carotenols hydroxycarotenoids CHEBI:23045 carotenol carotenols ChEBI hydroxycarotenoids ChEBI A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. 0 C7H5NO3SR2 183.18500 182.99901 [H][C@]12SCC([*])=C(N1C(=O)[C@H]2[*])C(O)=O CHEBI:3538 KEGG:C00875 PMID:10069359 PMID:11936371 PMID:12833570 PMID:24269048 PMID:3320614 PMID:6762896 PMID:8426246 Wikipedia:Cephalosporin Cephalosporin chebi_ontology cephalosphorin cephalosphorins cephalosporins CHEBI:23066 cephalosporin PMID:10069359 Europe PMC PMID:11936371 Europe PMC PMID:12833570 Europe PMC PMID:24269048 Europe PMC PMID:3320614 Europe PMC PMID:6762896 Europe PMC PMID:8426246 Europe PMC Cephalosporin KEGG_COMPOUND cephalosphorin ChEBI cephalosphorins ChEBI cephalosporins ChEBI CHEBI:3666 chebi_ontology choline esters CHEBI:23213 choline ester choline esters ChEBI A quaternary ammonium ion based on the choline ion and its substituted derivatives thereof. chebi_ontology CHEBI:23217 cholines Any member of the class of chromanes that is chromane substituted by one or more hydroxy groups. chebi_ontology CHEBI:23229 chromanol chebi_ontology CHEBI:23230 chromanes chebi_ontology CHEBI:23324 citrullines chebi_ontology CHEBI:23333 cob(III)alamins chebi_ontology CHEBI:23334 cobalamins chebi_ontology CHEBI:23341 cobamides A low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons. coenzyme chebi_ontology coenzymes CHEBI:23354 coenzyme coenzyme IUPAC coenzymes ChEBI An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). Wikipedia:Cofactor_(biochemistry) cofactor cofactors chebi_ontology CHEBI:23357 cofactor cofactor IUPAC cofactors IUPAC Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI chebi_ontology CHEBI:23390 cobalt-corrinoid hexaamide CHEBI:3990 cyclic amide chebi_ontology cyclic amides CHEBI:23443 cyclic amide cyclic amide ChEBI cyclic amides ChEBI chebi_ontology Cyclopeptid Zyklopeptid cyclic peptides peptide cyclique peptido ciclico CHEBI:23449 cyclic peptide Cyclopeptid ChEBI Zyklopeptid ChEBI cyclic peptides ChEBI peptide cyclique IUPAC peptido ciclico IUPAC An amino acid derivative resulting from reaction of cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of cysteine by a heteroatom. The definition normally excludes peptides containing cysteine residues. CHEBI:25309 cysteine derivative chebi_ontology cysteine derivatives CHEBI:23509 cysteine derivative cysteine derivative ChEBI cysteine derivatives ChEBI A hydroxy-5beta-cholanic acid carrying two hydroxy groups at unspecified positions. 0 C24H40O4 392.573 392.29266 chebi_ontology dihydroxy-5beta-cholanic acids CHEBI:23775 dihydroxy-5beta-cholanic acid dihydroxy-5beta-cholanic acids ChEBI Any terpenoid derived from a diterpene. The term includes compounds in which the C20 skeleton of the parent diterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups). LIPID_MAPS_class:LMPR0104 diterpenoids chebi_ontology C20 isoprenoids diterpenoides CHEBI:23849 diterpenoid LIPID_MAPS_class:LMPR0104 LIPID MAPS diterpenoids IUPAC C20 isoprenoids LIPID_MAPS diterpenoides ChEBI Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. chebi_ontology drugs medicine CHEBI:23888 drug drugs ChEBI medicine ChEBI chebi_ontology monoatomic anions CHEBI:23905 monoatomic anion monoatomic anions ChEBI chebi_ontology monoatomic cations CHEBI:23906 monoatomic cation monoatomic cations ChEBI A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. enzyme inhibitor chebi_ontology enzyme inhibitors inhibidor enzimatico inhibidores enzimaticos inhibiteur enzymatique inhibiteurs enzymatiques CHEBI:23924 enzyme inhibitor enzyme inhibitor IUPAC enzyme inhibitors ChEBI inhibidor enzimatico ChEBI inhibidores enzimaticos ChEBI inhibiteur enzymatique ChEBI inhibiteurs enzymatiques ChEBI Any vitamin that dissolves in fats and are stored in body tissues. Unlike the water-soluble vitamins, they are stored in the body for long periods of time and generally pose a greater risk for toxicity when consumed in excess. PMID:31838543 PMID:32057251 PMID:33549284 PMID:34045883 chebi_ontology fat-soluble vitamin fat-soluble vitamins fettloesliche Vitamine CHEBI:24020 fat-soluble vitamin (role) PMID:31838543 Europe PMC PMID:32057251 Europe PMC PMID:33549284 Europe PMC PMID:34045883 Europe PMC fat-soluble vitamin ChEBI fat-soluble vitamins ChEBI fettloesliche Vitamine ChEBI Compounds containing at least one furan ring. chebi_ontology oxacyclopenta-2,4-dienes CHEBI:24129 furans oxacyclopenta-2,4-dienes ChEBI Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. chebi_ontology glucocorticoids CHEBI:24261 glucocorticoid glucocorticoids ChEBI An amino acid derivative resulting from reaction of glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing glutamic acid residues. chebi_ontology CHEBI:24315 glutamic acid derivative An L-alpha-amino acid which is L-glutamic acid or any of the essential amino acids biosynthesised from it (glutamine, proline and arginine). A closed class. PMID:20716061 chebi_ontology glutamine family amino acids CHEBI:24318 glutamine family amino acid PMID:20716061 Europe PMC glutamine family amino acids ChEBI An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of glutamate--ammonia ligase (EC 6.3.1.2). Wikipedia:Glutamine_synthetase chebi_ontology EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors EC 6.3.1.2 inhibitor EC 6.3.1.2 inhibitors L-glutamate:ammonia ligase (ADP-forming) inhibitor L-glutamate:ammonia ligase (ADP-forming) inhibitors L-glutamine synthetase inhibitor L-glutamine synthetase inhibitors glutamate--ammonia ligase (EC 6.3.1.2) inhibitor glutamate--ammonia ligase (EC 6.3.1.2) inhibitors glutamate--ammonia ligase inhibitor glutamate--ammonia ligase inhibitors glutamine synthetase inhibitor glutamine synthetase inhibitors glutamylhydroxamic synthetase inhibitor glutamylhydroxamic synthetase inhibitors CHEBI:24319 EC 6.3.1.2 (glutamate--ammonia ligase) inhibitor EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors ChEBI EC 6.3.1.2 inhibitor ChEBI EC 6.3.1.2 inhibitors ChEBI L-glutamate:ammonia ligase (ADP-forming) inhibitor ChEBI L-glutamate:ammonia ligase (ADP-forming) inhibitors ChEBI L-glutamine synthetase inhibitor ChEBI L-glutamine synthetase inhibitors ChEBI glutamate--ammonia ligase (EC 6.3.1.2) inhibitor ChEBI glutamate--ammonia ligase (EC 6.3.1.2) inhibitors ChEBI glutamate--ammonia ligase inhibitor ChEBI glutamate--ammonia ligase inhibitors ChEBI glutamine synthetase inhibitor ChEBI glutamine synthetase inhibitors ChEBI glutamylhydroxamic synthetase inhibitor ChEBI glutamylhydroxamic synthetase inhibitors ChEBI A proteinogenic amino acid derivative resulting from reaction of glycine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. chebi_ontology CHEBI:24373 glycine derivative chebi_ontology glycosylglucoses CHEBI:24405 glycosylglucose glycosylglucoses ChEBI Any disaccharide in which the two monosaccharide components are connected by a glycosidic linkage between their anomeric centres. glycosyl glycoside chebi_ontology glycosyl glycosides CHEBI:24407 glycosyl glycoside glycosyl glycoside ChEBI glycosyl glycosides ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group chebi_ontology Gruppe Rest groupe grupo grupos CHEBI:24433 group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas. chebi_ontology CHEBI:24436 guanidines chebi_ontology CHEBI:24531 heterocyclic antibiotic A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound organic heterocycle ChEBI organic heterocyclic compounds ChEBI A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond. heterodetic cyclic peptide chebi_ontology heterodetic cyclic peptides peptide cyclique heterodetique peptido ciclico heterodetico CHEBI:24533 heterodetic cyclic peptide heterodetic cyclic peptide IUPAC heterodetic cyclic peptides ChEBI peptide cyclique heterodetique IUPAC peptido ciclico heterodetico IUPAC Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. chebi_ontology endocrine hormones CHEBI:24621 hormone endocrine ChEBI hormones ChEBI A compound consisting of carbon and hydrogen only. hydrocarbon hydrocarbons chebi_ontology Kohlenwasserstoff Kohlenwasserstoffe hidrocarburo hidrocarburos hydrocarbure CHEBI:24632 hydrocarbon hydrocarbon IUPAC hydrocarbons IUPAC Kohlenwasserstoff ChEBI Kohlenwasserstoffe ChEBI hidrocarburo IUPAC hidrocarburos IUPAC hydrocarbure IUPAC Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides Any member of the class of 5beta-cholanic acids carrying at least one hydroxy group at unspecified position. chebi_ontology hydroxy-5beta-cholanic acids CHEBI:24663 hydroxy-5beta-cholanic acid hydroxy-5beta-cholanic acids ChEBI Any carboxylic acid with at least one hydroxy group. chebi_ontology hydroxy carboxylic acids hydroxycarboxylic acid hydroxycarboxylic acids CHEBI:24669 hydroxy carboxylic acid hydroxy carboxylic acids ChEBI hydroxycarboxylic acid ChEBI hydroxycarboxylic acids ChEBI 0 CH3O 31.03392 31.01839 C(*)O hydroxymethyl chebi_ontology -CH2-OH serine side-chain CHEBI:24712 hydroxymethyl group hydroxymethyl IUPAC -CH2-OH IUPAC serine side-chain ChEBI Any member of the class of pyridines with at least one hydroxy substituent. chebi_ontology hydroxypyridines CHEBI:24745 hydroxypyridine hydroxypyridines ChEBI A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids chebi_ontology oxacids oxiacids oxo acid oxy-acids oxyacids CHEBI:24833 oxoacid oxoacid IUPAC oxoacids IUPAC oxacids ChEBI oxiacids ChEBI oxo acid ChEBI oxy-acids ChEBI oxyacids ChEBI chebi_ontology inorganic anions CHEBI:24834 inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics CHEBI:24835 inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI chebi_ontology inorganic oxides CHEBI:24836 inorganic oxide inorganic oxides ChEBI chebi_ontology anorganisches Salz inorganic salts CHEBI:24839 inorganic salt anorganisches Salz ChEBI inorganic salts ChEBI A salt is an assembly of cations and anions. salt chebi_ontology Salz Salze ionic compound ionic compounds sal sales salts sel sels CHEBI:24866 salt salt IUPAC Salz ChEBI Salze ChEBI ionic compound ChEBI ionic compounds ChEBI sal ChEBI sales ChEBI salts ChEBI sel ChEBI sels ChEBI chebi_ontology monoatomic ions CHEBI:24867 monoatomic ion monoatomic ions ChEBI chebi_ontology organic salts organisches Salz CHEBI:24868 organic salt organic salts ChEBI organisches Salz ChEBI A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions CHEBI:24870 ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI iron molecular entity chebi_ontology iron compounds iron molecular entities CHEBI:24873 iron molecular entity iron molecular entity ChEBI iron compounds ChEBI iron molecular entities ChEBI Fe 55.845 55.93494 iron cation chebi_ontology Fe cation iron cations CHEBI:24875 iron cation iron cation IUPAC Fe cation UniProt iron cations ChEBI A 2-amino-3-methylpentanoic acid having either (2R,3R)- or (2S,3S)-configuration. 0 C6H13NO2 131.175 131.09463 Beilstein:1721790 CAS:443-79-8 PMID:17190852 Reaxys:1721790 isoleucine chebi_ontology Hile rel-(2R,3R)-2-amino-3-methylpentanoic acid CHEBI:24898 isoleucine Beilstein:1721790 Beilstein CAS:443-79-8 ChemIDplus CAS:443-79-8 NIST Chemistry WebBook PMID:17190852 Europe PMC Reaxys:1721790 Reaxys isoleucine IUPAC Hile IUPAC rel-(2R,3R)-2-amino-3-methylpentanoic acid IUPAC Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives. LIPID_MAPS_class:LMPR01 PMID:12769708 PMID:19219049 isoprenoid isoprenoids chebi_ontology isoprenoids CHEBI:24913 isoprenoid LIPID_MAPS_class:LMPR01 LIPID MAPS PMID:12769708 Europe PMC PMID:19219049 Europe PMC isoprenoid ChEBI isoprenoids IUPAC isoprenoids ChEBI ketoaldonate chebi_ontology ketoaldonates CHEBI:24961 ketoaldonate ketoaldonate ChEBI ketoaldonates ChEBI Oxo carboxylic acids formally derived from aldonic acids by replacement of a secondary CHOH group by a carbonyl group. ketoaldonic acid chebi_ontology ketoaldonic acids CHEBI:24963 ketoaldonic acid ketoaldonic acid ChEBI ketoaldonic acids ChEBI Any hexose containing a single ketone group. ketohexose chebi_ontology ketohexoses CHEBI:24973 ketohexose ketohexose ChEBI ketohexoses ChEBI Ketonic parent sugars (polyhydroxy ketones H[CH(OH)]nC(=O)[CH(OH)]mH) and their intramolecular hemiketals. CHEBI:6131 ketose chebi_ontology ketoses CHEBI:24978 ketose ketose ChEBI ketoses ChEBI Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactam lactams chebi_ontology Laktam Laktame lactams CHEBI:24995 lactam lactam IUPAC lactams IUPAC Laktam ChEBI Laktame ChEBI lactams ChEBI Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactone lactones chebi_ontology Lacton Lakton Laktone lactona lactonas CHEBI:25000 lactone lactone IUPAC lactones IUPAC Lacton ChEBI Lakton ChEBI Laktone ChEBI lactona IUPAC lactonas IUPAC A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isobutyl group. 0 C6H13NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9) ROHFNLRQFUQHCH-UHFFFAOYSA-N 131.17296 131.09463 CC(C)CC(N)C(O)=O Beilstein:636005 CAS:328-39-2 Gmelin:50203 KEGG:C16439 LIPID_MAPS_instance:LMFA01100048 PMID:17439666 Reaxys:636005 Wikipedia:Leucine leucine chebi_ontology (+-)-Leucine (RS)-Leucine 2-amino-4-methylpentanoic acid DL-Leucine Hleu L Leu Leucin Leuzin CHEBI:25017 leucine Beilstein:636005 Beilstein CAS:328-39-2 ChemIDplus CAS:328-39-2 NIST Chemistry WebBook Gmelin:50203 Gmelin LIPID_MAPS_instance:LMFA01100048 LIPID MAPS PMID:17439666 Europe PMC Reaxys:636005 Reaxys leucine IUPAC (+-)-Leucine ChemIDplus (RS)-Leucine ChemIDplus 2-amino-4-methylpentanoic acid IUPAC DL-Leucine ChemIDplus Hleu IUPAC L ChEBI Leu ChEBI Leucin ChEBI Leuzin ChEBI chebi_ontology CHEBI:25046 linear tetrapyrrole A diamino acid that is caproic (hexanoic) acid bearing two amino substituents at positions 2 and 6. 0 C6H14N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10) KDXKERNSBIXSRK-UHFFFAOYSA-N 146.18764 146.10553 NCCCCC(N)C(O)=O Beilstein:1616991 CAS:70-54-2 Gmelin:279284 KEGG:C16440 PMID:17439666 PMID:22264337 Reaxys:1616991 Wikipedia:Lysine 2,6-diaminohexanoic acid lysine chebi_ontology K LYS Lysin alpha,epsilon-diaminocaproic acid CHEBI:25094 lysine Beilstein:1616991 Beilstein CAS:70-54-2 ChemIDplus CAS:70-54-2 NIST Chemistry WebBook Gmelin:279284 Gmelin PMID:17439666 Europe PMC PMID:22264337 Europe PMC Reaxys:1616991 Reaxys 2,6-diaminohexanoic acid IUPAC lysine IUPAC K ChEBI LYS ChEBI Lysin ChEBI alpha,epsilon-diaminocaproic acid ChEBI A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. chebi_ontology Makrolidantibiotika macrolide antibiotics CHEBI:25105 macrolide antibiotic Makrolidantibiotika ChEBI macrolide antibiotics ChEBI A macrocyclic lactone with a ring of twelve or more members derived from a polyketide. Wikipedia:Macrolide macrolide macrolides chebi_ontology Makrolid macrolides CHEBI:25106 macrolide macrolide ChEBI macrolides IUPAC Makrolid ChEBI macrolides ChEBI 0 Mg InChI=1S/Mg FYYHWMGAXLPEAU-UHFFFAOYSA-N 24.30500 23.98504 [Mg] CAS:7439-95-4 DrugBank:DB01378 Gmelin:16207 KEGG:C00305 WebElements:Mg magnesium chebi_ontology 12Mg Magnesium Mg magnesio magnesium CHEBI:25107 magnesium atom CAS:7439-95-4 ChemIDplus Gmelin:16207 Gmelin magnesium IUPAC 12Mg IUPAC Magnesium ChEBI Mg IUPAC Mg UniProt magnesio ChEBI magnesium ChEBI Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI chebi_ontology a metal cation metal cations CHEBI:25213 metal cation a metal cation UniProt metal cations ChEBI chebi_ontology metalloporphyrins metaloporphyrins CHEBI:25216 metalloporphyrin metalloporphyrins ChEBI metaloporphyrins ChEBI chebi_ontology methylated amines CHEBI:25274 methylamines methylated amines ChEBI Any member of the class of pyridines that carries at least one methyl substituent. chebi_ontology CHEBI:25340 methylpyridines Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds CHEBI:25367 molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC An oxoacid containing a single carboxy group. chebi_ontology monocarboxylic acids CHEBI:25384 monocarboxylic acid monocarboxylic acids ChEBI +1 0.00000 [*+] chebi_ontology monoatomic monocations monovalent inorganic cations CHEBI:25414 monoatomic monocation monoatomic monocations ChEBI monovalent inorganic cations ChEBI An agent that increases the frequency of mutations above the normal background level, usually by interacting directly with DNA and causing it damage, including base substitution. Wikipedia:Mutagen chebi_ontology mutagene mutagenes mutagenic agent mutageno mutagenos mutagens CHEBI:25435 mutagen mutagene ChEBI mutagenes ChEBI mutagenic agent ChEBI mutageno ChEBI mutagenos ChEBI mutagens ChEBI A polycyclic aromatic ketone metabolite of naphthalene. chebi_ontology naphthoquinones CHEBI:25481 naphthoquinone naphthoquinones ChEBI An endogenous compound that is used to transmit information across the synapse between a neuron and another cell. Wikipedia:Neurotransmitter chebi_ontology neurotransmitters CHEBI:25512 neurotransmitter neurotransmitters ChEBI 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno CHEBI:25555 nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI chebi_ontology organonitrogen heterocyclic antibiotics CHEBI:25558 organonitrogen heterocyclic antibiotic organonitrogen heterocyclic antibiotics ChEBI nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals CHEBI:25585 nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI A family of polyunsaturated fatty acids that have in common a final carbon-carbon double bond in the omega-3 position, i.e., the third bond from the methyl end of the fatty acid. PMID:15129302 PMID:15253883 PMID:15555528 PMID:16741195 PMID:19154523 PMID:19439966 PMID:21975796 PMID:23643471 PMID:24012777 PMID:24122252 PMID:24128563 PMID:24172034 PMID:24211484 PMID:24240437 PMID:24246761 PMID:24281905 PMID:24397938 PMID:24401220 PMID:24418228 Wikipedia:Omega-3_fatty_acid omega-3 fatty acid chebi_ontology n-3 fatty acid n-3 fatty acids omega-3 fatty acids CHEBI:25681 omega-3 fatty acid PMID:15129302 Europe PMC PMID:15253883 Europe PMC PMID:15555528 Europe PMC PMID:16741195 Europe PMC PMID:19154523 Europe PMC PMID:19439966 Europe PMC PMID:21975796 Europe PMC PMID:23643471 Europe PMC PMID:24012777 Europe PMC PMID:24122252 Europe PMC PMID:24128563 Europe PMC PMID:24172034 Europe PMC PMID:24211484 Europe PMC PMID:24240437 Europe PMC PMID:24246761 Europe PMC PMID:24281905 Europe PMC PMID:24397938 Europe PMC PMID:24401220 Europe PMC PMID:24418228 Europe PMC omega-3 fatty acid ChEBI n-3 fatty acid ChEBI n-3 fatty acids ChEBI omega-3 fatty acids ChEBI chebi_ontology organic heteromonocyclic compounds CHEBI:25693 organic heteromonocyclic compound organic heteromonocyclic compounds ChEBI Any organic ion with a net negative charge. chebi_ontology organic anions CHEBI:25696 organic anion organic anions ChEBI Any organic ion with a net positive charge. chebi_ontology organic cations CHEBI:25697 organic cation organic cations ChEBI chebi_ontology organic ions CHEBI:25699 organic ion organic ions ChEBI Wikipedia:Organophosphate organic phosphate chebi_ontology organic phosphate ester organic phosphate esters organic phosphates organophosphate ester organophosphate esters CHEBI:25703 organic phosphate organic phosphate ChEBI organic phosphate ester ChEBI organic phosphate esters ChEBI organic phosphates ChEBI organophosphate ester ChEBI organophosphate esters ChEBI Compounds of the general formula SO3HOR where R is an organyl group chebi_ontology organic sulfates CHEBI:25704 organic sulfate organic sulfates ChEBI An alcohol derived from an aliphatic compound. 0 HOR 17.007 17.00274 O* KEGG:C02525 Aliphatic alcohol chebi_ontology aliphatic alcohols an aliphatic alcohol CHEBI:2571 aliphatic alcohol Aliphatic alcohol KEGG_COMPOUND aliphatic alcohols ChEBI an aliphatic alcohol UniProt An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters. Wikipedia:Organophosphorus_compound organophosphorus compound chebi_ontology organophosphorus compounds CHEBI:25710 organophosphorus compound organophosphorus compound ChEBI organophosphorus compounds ChEBI A solute used by a cell under water stress to maintain cell volume. chebi_ontology osmolytes CHEBI:25728 osmolyte osmolytes ChEBI An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide oxide ChEBI oxides ChEBI Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule. oxo carboxylic acids chebi_ontology oxo acids oxo carboxylic acids CHEBI:25754 oxo carboxylic acid oxo carboxylic acids IUPAC oxo acids IUPAC oxo carboxylic acids ChEBI Any fatty acid anion containing at least one C-C unsaturated bond; formed by deprotonation of the carboxylic acid moiety. chebi_ontology CHEBI:2580 unsaturated fatty acid anion 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] KEGG:C00007 WebElements:O oxygen chebi_ontology 8O O Sauerstoff oxigeno oxygen oxygene CHEBI:25805 oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI A quinone in which the two oxo groups of the quinone are located para to each other on the 6-membered quinonoid ring. chebi_ontology p-quinone para-quinones CHEBI:25830 p-quinones p-quinone ChEBI para-quinones ChEBI A class of amides formed from pantoic acid and beta-alanine and its derivatives. chebi_ontology CHEBI:25848 pantothenic acids chebi_ontology CHEBI:25865 penicillanic acids A five-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldopentose) or a ketone group at position 2 (ketopentose). pentose chebi_ontology pentoses CHEBI:25901 pentose pentose ChEBI pentoses ChEBI Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine. chebi_ontology peptide hormones polypeptide hormone CHEBI:25905 peptide hormone peptide hormones ChEBI polypeptide hormone ChEBI Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. phosphates chebi_ontology phosphates CHEBI:26020 phosphate phosphates IUPAC phosphates ChEBI chebi_ontology phosphoamino acids CHEBI:26051 phosphoamino acid phosphoamino acids ChEBI A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. 0 H3O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N 97.99520 97.97690 [H]OP(=O)(O[H])O[H] Beilstein:1921286 CAS:7664-38-2 Drug_Central:4478 Gmelin:2000 HMDB:HMDB0002142 KEGG:C00009 KEGG:D05467 KNApSAcK:C00007408 PMID:11455380 PMID:15630224 PMID:17439666 PMID:17518491 PMID:22282755 PMID:22333268 PMID:22381614 PMID:22401268 Reaxys:1921286 Wikipedia:Phosphoric_Acid Phosphoric acid phosphoric acid tetraoxophosphoric acid trihydrogen tetraoxophosphate(3-) trihydroxidooxidophosphorus chebi_ontology H3PO4 Orthophosphoric acid Phosphate Phosphorsaeure Phosphorsaeureloesungen [PO(OH)3] acide phosphorique acidum phosphoricum orthophosphoric acid CHEBI:26078 phosphoric acid Beilstein:1921286 Beilstein CAS:7664-38-2 ChemIDplus CAS:7664-38-2 KEGG COMPOUND CAS:7664-38-2 NIST Chemistry WebBook Drug_Central:4478 DrugCentral Gmelin:2000 Gmelin PMID:11455380 Europe PMC PMID:15630224 Europe PMC PMID:17439666 Europe PMC PMID:17518491 Europe PMC PMID:22282755 Europe PMC PMID:22333268 Europe PMC PMID:22381614 Europe PMC PMID:22401268 Europe PMC Reaxys:1921286 Reaxys Phosphoric acid KEGG_COMPOUND phosphoric acid IUPAC tetraoxophosphoric acid IUPAC trihydrogen tetraoxophosphate(3-) IUPAC trihydroxidooxidophosphorus IUPAC H3PO4 IUPAC Orthophosphoric acid KEGG_COMPOUND Phosphate KEGG_COMPOUND Phosphorsaeure ChEBI Phosphorsaeureloesungen ChEBI [PO(OH)3] IUPAC acide phosphorique ChEBI acidum phosphoricum ChEBI orthophosphoric acid NIST_Chemistry_WebBook chebi_ontology CHEBI:26079 phosphoric acid derivative chebi_ontology phosphorus molecular entities CHEBI:26082 phosphorus molecular entity phosphorus molecular entities ChEBI An endogenous molecular entity that results in a colour of an organism as the consequence of the selective absorption of light. chebi_ontology pigments CHEBI:26130 biological pigment pigments ChEBI Any amino acid whose side chain is capable of forming one or more hydrogen bonds. 0 C2H4NO2R 74.059 74.02420 OC(C(*)N)=O CHEBI:8283 MetaCyc:Polar-amino-acids PMID:12016058 polar amino acid chebi_ontology polar amino acids polar amino-acid polar amino-acids CHEBI:26167 polar amino acid PMID:12016058 Europe PMC polar amino acid ChEBI polar amino acids ChEBI polar amino-acid ChEBI polar amino-acids ChEBI Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides. polyketide chebi_ontology polyketides CHEBI:26188 polyketide polyketide ChEBI polyketides ChEBI A compound that contains two or more hydroxy groups. chebi_ontology polyols CHEBI:26191 polyol polyols ChEBI Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome. PMID:14977874 PMID:16380690 PMID:17891522 chebi_ontology PUFA PUFAs polyunsaturated fatty acids CHEBI:26208 polyunsaturated fatty acid PMID:14977874 Europe PMC PMID:16380690 Europe PMC PMID:17891522 Europe PMC PUFA ChEBI PUFAs ChEBI polyunsaturated fatty acids ChEBI Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure. Wikipedia:Porphyrin porphyrins chebi_ontology CHEBI:26214 porphyrins porphyrins IUPAC 0 K InChI=1S/K ZLMJMSJWJFRBEC-UHFFFAOYSA-N 39.09830 38.96371 [K] CAS:7440-09-7 DrugBank:DB01345 KEGG:C00238 WebElements:K potassium chebi_ontology 19K K Kalium kalium potasio potassium CHEBI:26216 potassium atom CAS:7440-09-7 ChemIDplus potassium IUPAC 19K IUPAC K IUPAC Kalium ChemIDplus kalium IUPAC potasio ChEBI potassium ChEBI potassium molecular entity chebi_ontology potassium molecular entities CHEBI:26217 potassium molecular entity potassium molecular entity ChEBI potassium molecular entities ChEBI A quinone substituted by a polyprenyl-derived side-chain. Prenylquinones occur in all living cells. Due to their amphiphilic character, they are mainly located in biological membranes where they function as electron and proton carriers in the photosynthetic and respiratory electron transport chains. Some prenylquinones also perform more specialised roles sucy as antioxidants and enzyme cofactors. Prenylquinones are classified according to ring structure: the main classes are menaquinones, phylloquinones, ubiquinones and plastoquinones. CHEBI:72751 PMID:19928587 PMID:21777468 PMID:21844348 PMID:22371323 PMID:3985624 chebi_ontology polyprenylquinone polyprenylquinones prenylquinones CHEBI:26255 prenylquinone PMID:19928587 Europe PMC PMID:21777468 Europe PMC PMID:21844348 Europe PMC PMID:22371323 Europe PMC PMID:3985624 Europe PMC polyprenylquinone ChEBI polyprenylquinones ChEBI prenylquinones ChEBI A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity. prosthetic group chebi_ontology groupe prosthetique prosthetic groups CHEBI:26348 prosthetic group prosthetic group IUPAC groupe prosthetique IUPAC prosthetic groups ChEBI chebi_ontology CHEBI:26373 pteridines chebi_ontology CHEBI:26375 pterins A class of imidazopyrimidines that consists of purine and its substituted derivatives. 0 C5N4R7 116.080 116.01230 CHEBI:13678 chebi_ontology CHEBI:26401 purines chebi_ontology pyridine alkaloids CHEBI:26416 pyridine alkaloid pyridine alkaloids ChEBI A monocarboxylic acid in which the carboxy group is attached to a pyridine (or substituted pyridine) ring. chebi_ontology pyridinemonocarboxylic acids CHEBI:26420 pyridinemonocarboxylic acid pyridinemonocarboxylic acids ChEBI Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. chebi_ontology CHEBI:26421 pyridines A nucleobase whose skeleton is derived from pyrimidine. 0 C4HN2R4 77.064 77.01397 N1C(=C(C(=NC1=*)*)*)* pyrimidine nucleobase chebi_ontology a pyrimidine nucleobase pyrimidine bases pyrimidine nucleobases CHEBI:26432 pyrimidine nucleobase pyrimidine nucleobase ChEBI a pyrimidine nucleobase UniProt pyrimidine bases ChEBI pyrimidine nucleobases ChEBI KEGG:C03169 chebi_ontology N-D-Ribosylpyrimidine pyrimidine nucleosides CHEBI:26440 pyrimidine nucleoside N-D-Ribosylpyrimidine KEGG_COMPOUND pyrimidine nucleosides ChEBI A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen. chebi_ontology CHEBI:26469 quaternary nitrogen compound Molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers. Wikipedia:Reactive_oxygen_species chebi_ontology ROS CHEBI:26523 reactive oxygen species ROS ChEBI Oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof. retinoid retinoids chebi_ontology retinoids CHEBI:26537 retinoid retinoid ChEBI retinoids IUPAC retinoids ChEBI Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess. PMID:16492686 PMID:19763019 PMID:20237329 saturated fatty acid chebi_ontology SFA SFAs saturated fatty acids CHEBI:26607 saturated fatty acid PMID:16492686 Europe PMC PMID:19763019 Europe PMC PMID:20237329 Europe PMC saturated fatty acid ChEBI SFA ChEBI SFAs ChEBI saturated fatty acids ChEBI An L-alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class. PMID:20709681 chebi_ontology 3-phosphoglycerate family amino acid 3-phosphoglycerate family amino acids serine family amino acids CHEBI:26650 serine family amino acid PMID:20709681 Europe PMC 3-phosphoglycerate family amino acid ChEBI 3-phosphoglycerate family amino acids ChEBI serine family amino acids ChEBI An aliphatic monocarboxylic acid with a chain length of less than C6. If any non-hydrocarbon substituent is present, the compound is not normally regarded as a short-chain fatty acid. 0 CH2OR 45.017 44.99765 OC([*])=O PMID:16633129 PMID:16870803 PMID:18203540 PMID:20148677 chebi_ontology SCFA SCFAs short-chain fatty acids CHEBI:26666 short-chain fatty acid PMID:16633129 Europe PMC PMID:16870803 Europe PMC PMID:18203540 Europe PMC PMID:20148677 Europe PMC SCFA ChEBI SCFAs ChEBI short-chain fatty acids ChEBI 0 Na InChI=1S/Na KEAYESYHFKHZAL-UHFFFAOYSA-N 22.98977 22.98977 [Na] CAS:7440-23-5 Gmelin:16221 KEGG:C01330 WebElements:Na sodium chebi_ontology 11Na Na Natrium natrium sodio sodium CHEBI:26708 sodium atom CAS:7440-23-5 ChemIDplus Gmelin:16221 Gmelin sodium IUPAC 11Na IUPAC Na IUPAC Natrium ChemIDplus natrium IUPAC sodio ChemIDplus sodium ChEBI chebi_ontology sodium compounds sodium molecular entities CHEBI:26712 sodium molecular entity sodium compounds ChEBI sodium molecular entities ChEBI Any alkali metal salt having sodium(1+) as the cation. chebi_ontology Natriumsalz Natriumsalze sodium salts CHEBI:26714 sodium salt Natriumsalz ChEBI Natriumsalze ChEBI sodium salts ChEBI Any steroid that acts as hormone. chebi_ontology Steroidhormon Steroidhormone hormona esteroide hormonas esteroideas hormone steroide hormones steroides steroid hormones CHEBI:26764 steroid hormone Steroidhormon ChEBI Steroidhormone ChEBI hormona esteroide ChEBI hormonas esteroideas ChEBI hormone steroide ChEBI hormones steroides ChEBI steroid hormones ChEBI An ester of an alcohol and sulfuric acid. 0 O4SR2 96.06300 95.95173 [*]OS(=O)(=O)O[*] chebi_ontology sulfate ester sulfuric acid ester sulfuric acid esters CHEBI:26819 sulfuric ester sulfate ester ChEBI sulfuric acid ester ChEBI sulfuric acid esters ChEBI Salts and esters of sulfuric acid sulfates chebi_ontology sulfuric acid derivative sulphates CHEBI:26820 sulfates sulfates ChEBI sulfuric acid derivative ChEBI sulphates ChEBI chebi_ontology CHEBI:26830 sulfonium compound 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] CAS:7704-34-9 KEGG:C00087 KEGG:D06527 PPDB:605 WebElements:S sulfur chebi_ontology 16S Elemental sulfur S Schwefel azufre soufre sulfur sulphur theion CHEBI:26833 sulfur atom CAS:7704-34-9 ChemIDplus CAS:7704-34-9 NIST Chemistry WebBook sulfur IUPAC 16S IUPAC Elemental sulfur KEGG_COMPOUND S IUPAC S KEGG_COMPOUND Schwefel ChEBI azufre ChEBI soufre ChEBI sulfur ChEBI sulfur UniProt sulphur ChEBI theion IUPAC chebi_ontology sulfur-containing amino acids CHEBI:26834 sulfur-containing amino acid sulfur-containing amino acids ChEBI sulfur molecular entity chebi_ontology sulfur molecular entities CHEBI:26835 sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom. 0 H2O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4) QAOWNCQODCNURD-UHFFFAOYSA-N 98.07948 97.96738 [H]OS(=O)(=O)O[H] CAS:7664-93-9 Gmelin:2122 KEGG:C00059 KEGG:D05963 KNApSAcK:C00007530 MolBase:4 PMID:13568755 PMID:16122922 PMID:19397353 PMID:22047659 PMID:22136045 PMID:22204399 PMID:22267186 PMID:22296037 PMID:22364556 PMID:22435616 PPDB:606 Reaxys:2037554 Wikipedia:Sulfuric_acid Sulfuric acid dihydrogen tetraoxosulfate dihydroxidodioxidosulfur hydrogen tetraoxosulfate(2-) hydrogen tetraoxosulfate(VI) sulfuric acid tetraoxosulfuric acid chebi_ontology Acide sulfurique Acido sulfurico Acidum sulfuricum H2SO4 Schwefelsaeureloesungen [S(OH)2O2] [SO2(OH)2] sulphuric acid CHEBI:26836 sulfuric acid CAS:7664-93-9 ChemIDplus CAS:7664-93-9 KEGG COMPOUND CAS:7664-93-9 NIST Chemistry WebBook Gmelin:2122 Gmelin PMID:13568755 Europe PMC PMID:16122922 Europe PMC PMID:19397353 Europe PMC PMID:22047659 Europe PMC PMID:22136045 Europe PMC PMID:22204399 Europe PMC PMID:22267186 Europe PMC PMID:22296037 Europe PMC PMID:22364556 Europe PMC PMID:22435616 Europe PMC Reaxys:2037554 Reaxys Sulfuric acid KEGG_COMPOUND dihydrogen tetraoxosulfate IUPAC dihydroxidodioxidosulfur IUPAC hydrogen tetraoxosulfate(2-) IUPAC hydrogen tetraoxosulfate(VI) IUPAC sulfuric acid ChEBI sulfuric acid IUPAC tetraoxosulfuric acid IUPAC Acide sulfurique ChemIDplus Acido sulfurico ChemIDplus Acidum sulfuricum ChemIDplus H2SO4 IUPAC Schwefelsaeureloesungen ChemIDplus [S(OH)2O2] MolBase [SO2(OH)2] IUPAC sulphuric acid MolBase Any isoprenoid that is a natural product or related compound formally derived from isoprene units. Terpenoids may contain oxygen in various functional groups. This class is subdivided according to the number of carbon atoms in the parent terpene. The skeleton of terpenoids may differ from strict additivity of isoprene units by the loss or shift of a fragment, generally a methyl group. Wikipedia:Terpenoid Terpenoid terpenoids chebi_ontology terpenoide terpenoides CHEBI:26873 terpenoid Terpenoid ChEBI terpenoids IUPAC terpenoide IUPAC terpenoides IUPAC A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it. 0 C4H7OR3 71.09780 71.04969 OC(C[*])(C[*])C[*] tertiary alcohol chebi_ontology tertiary alcohols CHEBI:26878 tertiary alcohol tertiary alcohol ChEBI tertiary alcohols ChEBI A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups. chebi_ontology CHEBI:26895 tetracyclines Any oxacycle having an oxolane (tetrahydrofuran) skeleton. chebi_ontology CHEBI:26912 oxolanes A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole tetrapyrroles chebi_ontology a tetrapyrrole CHEBI:26932 tetrapyrrole tetrapyrrole IUPAC tetrapyrroles IUPAC a tetrapyrrole UniProt Any terpenoid derived from a tetraterpene. The term includes compounds in which the C40 skeleton of the parent tetraterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups). LIPID_MAPS_class:LMPR0107 tetraterpenoids chebi_ontology C40 isoprenoids tetraterpenoides CHEBI:26935 tetraterpenoid LIPID_MAPS_class:LMPR0107 LIPID MAPS tetraterpenoids IUPAC C40 isoprenoids LIPID_MAPS tetraterpenoides ChEBI Any member of the group of 1,3-thiazolium cations that exhibit biological activity against vitamin B1 deficiency in animals. Symptoms of vitamin B1 deficiency include constipation, loss of apetite, fatigue, nausea, delirium, blurry vision and muscle weakness. Severe vitamin B1 deficiency can also lead to a disease known as beriberi. Vitamin B1 consists of the vitamer thiamin and its acid, aldehyde and phosphorylated derivatives (and their corresponding ionized, salt and hydrate forms). PMID:28859374 PMID:32554808 vitamin B1 chebi_ontology thiamine thiamines thiamins vitamin B1 vitamer vitamin B1 vitamers vitamins B1 CHEBI:26948 vitamin B1 PMID:28859374 Europe PMC PMID:32554808 Europe PMC vitamin B1 ChEBI thiamine ChEBI thiamines ChEBI thiamins ChEBI vitamin B1 vitamer ChEBI vitamin B1 vitamers ChEBI vitamins B1 ChEBI An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. chebi_ontology heterotricyclic compounds organic heterotricyclic compounds CHEBI:26979 organic heterotricyclic compound heterotricyclic compounds ChEBI organic heterotricyclic compounds ChEBI Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group. chebi_ontology CHEBI:27024 toluenes Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Wikipedia:Micronutrient chebi_ontology micronutrients trace elements CHEBI:27027 micronutrient micronutrients ChEBI trace elements ChEBI An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. transition element chebi_ontology Uebergangselement Uebergangsmetalle metal de transicion metal de transition metales de transicion metaux de transition transition element transition elements transition metal transition metals CHEBI:27081 transition element atom transition element IUPAC Uebergangselement ChEBI Uebergangsmetalle ChEBI metal de transicion ChEBI metal de transition ChEBI metales de transicion ChEBI metaux de transition ChEBI transition element ChEBI transition elements ChEBI transition metal ChEBI transition metals ChEBI 0 C24H40O5 408.572 408.28757 chebi_ontology trihydroxy-5beta-cholanic acids CHEBI:27114 trihydroxy-5beta-cholanic acid trihydroxy-5beta-cholanic acids ChEBI A chemical compound containing three hydroxy groups. chebi_ontology triols CHEBI:27136 triol triols ChEBI chebi_ontology heterobicyclic compounds organic heterobicyclic compounds CHEBI:27171 organic heterobicyclic compound heterobicyclic compounds ChEBI organic heterobicyclic compounds ChEBI A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. chebi_ontology univalent acyl group univalent carboacyl groups univalent carboxylic acyl groups CHEBI:27207 univalent carboacyl group univalent acyl group ChEBI univalent carboacyl groups ChEBI univalent carboxylic acyl groups ChEBI Any fatty acid containing at least one C=C or C#C bond. LIPID_MAPS_class:LMFA0103 PMID:5322381 chebi_ontology alkene acid olefinic acid unsaturated fatty acids CHEBI:27208 unsaturated fatty acid LIPID_MAPS_class:LMFA0103 LIPID MAPS PMID:5322381 Europe PMC alkene acid ChEBI olefinic acid ChEBI unsaturated fatty acids ChEBI unsaturated fatty acids LIPID_MAPS chebi_ontology CHEBI:27242 uridines A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isopropyl group. 0 C5H11NO2 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8) KZSNJWFQEVHDMF-UHFFFAOYSA-N 117.14638 117.07898 CC(C)C(N)C(O)=O Beilstein:506689 CAS:516-06-3 Gmelin:49877 KEGG:C16436 PMID:17190852 PMID:22770225 Reaxys:506689 Wikipedia:Valine valine chebi_ontology 2-amino-3-methylbutanoic acid DL-valine Hval Valin valina CHEBI:27266 valine Beilstein:506689 Beilstein CAS:516-06-3 ChemIDplus CAS:516-06-3 KEGG COMPOUND CAS:516-06-3 NIST Chemistry WebBook Gmelin:49877 Gmelin PMID:17190852 Europe PMC PMID:22770225 Europe PMC Reaxys:506689 Reaxys valine IUPAC 2-amino-3-methylbutanoic acid IUPAC DL-valine ChEBI Hval IUPAC Valin ChEBI valina ChEBI Any member of a group of fat-soluble hydroxy seco-steroids that exhibit biological activity against vitamin D deficiency. Vitamin D can be obtained from sun exposure, food and supplements and is biologically inactive and converted into the biologically active calcitriol via double hydroxylation in the body. MetaCyc:Vitamin-D Wikipedia:Vitamin_D chebi_ontology D vitamins vitamin D vitamer vitamin D vitamers vitamin Ds vitamins D CHEBI:27300 vitamin D D vitamins ChEBI vitamin D vitamer ChEBI vitamin D vitamers ChEBI vitamin Ds ChEBI vitamins D ChEBI Any member of the group of pyridines that exhibit biological activity against vitamin B6 deficiency. Vitamin B6 deficiency is associated with microcytic anemia, electroencephalographic abnormalities, dermatitis with cheilosis (scaling on the lips and cracks at the corners of the mouth) and glossitis (swollen tongue), depression and confusion, and weakened immune function. Vitamin B6 consists of the vitamers pyridoxine, pyridoxal, and pyridoxamine and their respective 5'-phosphate esters (and includes their corresponding ionized and salt forms). Vitamin B6 chebi_ontology vitamin B-6 vitamin B6 vitamer vitamin B6 vitamers vitamina B6 vitamine B6 vitamins B6 CHEBI:27306 vitamin B6 Vitamin B6 ChEBI vitamin B-6 JCBN vitamin B6 vitamer ChEBI vitamin B6 vitamers ChEBI vitamina B6 ChEBI vitamine B6 ChEBI vitamins B6 ChEBI Any vitamin that dissolves in water and readily absorbed into tissues for immediate use. Unlike the fat-soluble vitamins, they are not stored in the body and need to be replenished regularly in the diet and will rarely accumulate to toxic levels since they are quickly excreted from the body via urine. chebi_ontology wasserloesliche Vitamine water-soluble vitamin water-soluble vitamins CHEBI:27314 water-soluble vitamin (role) wasserloesliche Vitamine ChEBI water-soluble vitamin ChEBI water-soluble vitamins ChEBI A subclass of carotenoids consisting of the oxygenated carotenes. DrugBank:DB00137 xanthophylls chebi_ontology xanthophylls CHEBI:27325 xanthophyll xanthophylls IUPAC xanthophylls ChEBI 0 Zn InChI=1S/Zn HCHKCACWOHOZIP-UHFFFAOYSA-N 65.39000 63.92914 [Zn] CAS:7440-66-6 Gmelin:16321 KEGG:C00038 PDBeChem:ZN WebElements:Zn zinc chebi_ontology 30Zn Zink Zn Zn(II) Zn2+ cinc zinc zincum CHEBI:27363 zinc atom CAS:7440-66-6 ChemIDplus CAS:7440-66-6 KEGG COMPOUND Gmelin:16321 Gmelin zinc IUPAC 30Zn IUPAC Zink ChEBI Zn IUPAC Zn(II) KEGG_COMPOUND Zn2+ KEGG_COMPOUND cinc ChEBI zinc ChEBI zincum ChEBI chebi_ontology zinc compounds zinc molecular entities CHEBI:27364 zinc molecular entity zinc compounds ChEBI zinc molecular entities ChEBI A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer). zwitterion zwitterions chebi_ontology compose zwitterionique compuestos zwitterionicos zwitteriones zwitterionic compounds CHEBI:27369 zwitterion zwitterion IUPAC zwitterions IUPAC compose zwitterionique IUPAC compuestos zwitterionicos IUPAC zwitteriones IUPAC zwitterionic compounds IUPAC An N-acyl-amino acid that is a form of the water-soluble vitamin B9. Its biologically active forms (tetrahydrofolate and others) are essential for nucleotide biosynthesis and homocysteine remethylation. 0 C19H19N7O6 InChI=1S/C19H19N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,8,12,21H,5-7H2,(H,24,29)(H,27,28)(H,31,32)(H3,20,22,25,26,30)/t12-/m0/s1 OVBPIULPVIDEAO-LBPRGKRZSA-N 441.39750 441.13968 Nc1nc2ncc(CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)nc2c(=O)[nH]1 CHEBI:24075 CHEBI:42610 CHEBI:5140 CHEBI:569217 AGR:IND606960789 Beilstein:100781 CAS:59-30-3 Chemspider:5815 DrugBank:DB00158 Drug_Central:1231 FooDB:FDB014504 HMDB:HMDB0000121 KEGG:C00504 KEGG:D00070 KNApSAcK:C00001539 LINCS:LSM-5355 MetaCyc:CPD-12826 PDBeChem:FOL PMID:10138938 PMID:10897644 PMID:10958818 PMID:11261364 PMID:11451208 PMID:11959400 PMID:14387833 PMID:15321809 PMID:15523939 PMID:15754725 PMID:15797531 PMID:15797685 PMID:15831910 PMID:15990733 PMID:16093404 PMID:16277678 PMID:16380297 PMID:16871332 PMID:17784727 PMID:18788725 PMID:19121630 PMID:19335717 PMID:19355913 PMID:24650098 PMID:33624660 PMID:33965562 PMID:33968971 PMID:34207319 PMID:34219855 PMID:7738698 PMID:8235383 PMID:9040515 PMID:9420019 PMID:9565830 PMID:9683174 PMID:9781393 PMID:9808640 PMID:9808641 Reaxys:100781 Wikipedia:Folic_Acid N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid chebi_ontology (2S)-2-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzamido)pentanedioic acid Acfol Folate Folicet Folsaeure N-[(4-{[(2-amino-4-oxo-1,4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid N-pteroyl-L-glutamic acid PGA PteGlu acide folique acido folico acidum folicum folic acid pteroyl-L-glutamic acid pteroyl-L-monoglutamic acid pteroylglutamic acid pteroylmonoglutamic acid vitamin B11 vitamin B9 vitamin Bc vitamin Be vitamin M CHEBI:27470 folic acid AGR:IND606960789 Europe PMC Beilstein:100781 Beilstein CAS:59-30-3 ChemIDplus CAS:59-30-3 KEGG COMPOUND CAS:59-30-3 NIST Chemistry WebBook Drug_Central:1231 DrugCentral PMID:10138938 Europe PMC PMID:10897644 Europe PMC PMID:10958818 Europe PMC PMID:11261364 Europe PMC PMID:11451208 Europe PMC PMID:11959400 Europe PMC PMID:14387833 Europe PMC PMID:15321809 Europe PMC PMID:15523939 Europe PMC PMID:15754725 Europe PMC PMID:15797531 Europe PMC PMID:15797685 Europe PMC PMID:15831910 Europe PMC PMID:15990733 Europe PMC PMID:16093404 Europe PMC PMID:16277678 Europe PMC PMID:16380297 Europe PMC PMID:16871332 Europe PMC PMID:17784727 Europe PMC PMID:18788725 ChEMBL PMID:19121630 Europe PMC PMID:19335717 Europe PMC PMID:19355913 Europe PMC PMID:24650098 Europe PMC PMID:33624660 Europe PMC PMID:33965562 Europe PMC PMID:33968971 Europe PMC PMID:34207319 Europe PMC PMID:34219855 Europe PMC PMID:7738698 Europe PMC PMID:8235383 Europe PMC PMID:9040515 Europe PMC PMID:9420019 Europe PMC PMID:9565830 Europe PMC PMID:9683174 Europe PMC PMID:9781393 Europe PMC PMID:9808640 Europe PMC PMID:9808641 Europe PMC Reaxys:100781 Reaxys N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid IUPAC (2S)-2-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzamido)pentanedioic acid IUPAC Acfol ChemIDplus Folate KEGG_COMPOUND Folicet KEGG_DRUG Folsaeure ChEBI N-[(4-{[(2-amino-4-oxo-1,4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid PDBeChem N-pteroyl-L-glutamic acid ChEBI PGA NIST_Chemistry_WebBook PteGlu NIST_Chemistry_WebBook acide folique WHO_MedNet acido folico WHO_MedNet acidum folicum WHO_MedNet folic acid WHO_MedNet pteroyl-L-glutamic acid ChemIDplus pteroyl-L-monoglutamic acid ChemIDplus pteroylglutamic acid KEGG_COMPOUND pteroylmonoglutamic acid ChemIDplus vitamin B11 ChemIDplus vitamin B9 ChemIDplus vitamin Bc ChemIDplus vitamin Be ChemIDplus vitamin M ChemIDplus 0 Se InChI=1S/Se BUGBHKTXTAQXES-UHFFFAOYSA-N 78.96000 79.91652 [Se] CHEBI:26627 CHEBI:9091 CAS:7782-49-2 DrugBank:DB11135 FooDB:FDB013400 HMDB:HMDB0001349 KEGG:C01529 WebElements:Se Wikipedia:Selenium selenium chebi_ontology 34Se Se Selen Selenium selenio selenium CHEBI:27568 selenium atom CAS:7782-49-2 ChemIDplus CAS:7782-49-2 NIST Chemistry WebBook selenium IUPAC 34Se IUPAC Se IUPAC Selen ChemIDplus Selenium KEGG_COMPOUND selenio ChEBI selenium ChEBI 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] CHEBI:23009 CHEBI:3399 CAS:7440-44-0 KEGG:C06265 WebElements:C carbon chebi_ontology 6C C Carbon Kohlenstoff carbon carbone carbonium carbono CHEBI:27594 carbon atom CAS:7440-44-0 ChemIDplus CAS:7440-44-0 KEGG COMPOUND carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI A cobalt group element atom that has atomic number 27. 0 Co InChI=1S/Co GUTLYIVDDKVIGB-UHFFFAOYSA-N 58.93320 58.93319 [Co] CHEBI:23335 CHEBI:3788 CAS:7440-48-4 KEGG:C00175 KEGG:C19171 PDBeChem:3CO WebElements:Co cobalt chebi_ontology 27Co Co Cobalt Kobalt cobalt cobalto cobaltum CHEBI:27638 cobalt atom CAS:7440-48-4 ChemIDplus CAS:7440-48-4 KEGG COMPOUND CAS:7440-48-4 NIST Chemistry WebBook cobalt IUPAC 27Co IUPAC Co IUPAC Co UniProt Cobalt KEGG_COMPOUND Kobalt NIST_Chemistry_WebBook cobalt ChEBI cobalto ChEBI cobaltum ChEBI A surfactant (or a mixture containing one or more surfactants) having cleaning properties in dilute solutions. CHEBI:23648 CHEBI:4456 KEGG:C01689 detergent chebi_ontology Detergents CHEBI:27780 detergent detergent IUPAC Detergents KEGG_COMPOUND 0 C62H89CoN13O15P InChI=1S/C62H90N13O14P.Co.H2O/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;1H2/q;+3;/p-3/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 YOZNUFWCRFCGIH-WZHZPDAFSA-K 1346.35510 1345.56706 [H]O[Co-3]1234N5C6=C(C)C7=[N+]1C(=CC1=[N+]2C(=C(C)C2=[N+]3[C@@](C)([C@@]5([H])[C@H](CC(N)=O)[C@@]6(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]3[C@@H](O)[C@H](O[C@@H]3CO)n3c[n+]4c4cc(C)c(C)cc34)[C@@](C)(CC(N)=O)[C@@H]2CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]1CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O CHEBI:24652 CHEBI:5795 CHEBI:5803 CAS:13422-51-0 Chemspider:28534326 DrugBank:DB00200 FooDB:FDB003166 Gmelin:5723 HMDB:HMDB0002308 KEGG:C08230 KEGG:D01027 KNApSAcK:C00050467 MetaCyc:CPD0-1256 PMID:11830394 PMID:15815367 PMID:20352539 PMID:31000316 PMID:31864779 PMID:32718732 PMID:32815652 PMID:33005568 PMID:33224611 PMID:33246585 PMID:33283331 PMID:33444605 PMID:33692053 PMID:33754111 PMID:33912838 PMID:34023033 PMID:34176677 PMID:7802338 PMID:8012169 PMID:8440794 PMID:8857117 PMID:9102519 Wikipedia:Hydroxocobalamin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-hydroxocobamide chebi_ontology AlphaRedisol Cyanokit Hydroxycobalamin OH-Cbl hidroxocobalamina hydroxocobalamin hydroxocobalamine hydroxocobalaminum vitamin B-12b CHEBI:27786 hydroxocobalamin CAS:13422-51-0 ChemIDplus CAS:13422-51-0 KEGG COMPOUND Gmelin:5723 Gmelin PMID:11830394 Europe PMC PMID:15815367 Europe PMC PMID:20352539 Europe PMC PMID:31000316 Europe PMC PMID:31864779 Europe PMC PMID:32718732 Europe PMC PMID:32815652 Europe PMC PMID:33005568 Europe PMC PMID:33224611 Europe PMC PMID:33246585 Europe PMC PMID:33283331 Europe PMC PMID:33444605 Europe PMC PMID:33692053 Europe PMC PMID:33754111 Europe PMC PMID:33912838 Europe PMC PMID:34023033 Europe PMC PMID:34176677 Europe PMC PMID:7802338 Europe PMC PMID:8012169 Europe PMC PMID:8440794 Europe PMC PMID:8857117 Europe PMC PMID:9102519 Europe PMC Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-hydroxocobamide IUPAC AlphaRedisol KEGG_DRUG Cyanokit KEGG_DRUG Hydroxycobalamin KEGG_COMPOUND OH-Cbl CBN hidroxocobalamina WHO_MedNet hydroxocobalamin WHO_MedNet hydroxocobalamine WHO_MedNet hydroxocobalaminum WHO_MedNet vitamin B-12b CBN A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. 0 C22H24N2O8 InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/t9-,10-,15-,21+,22-/m0/s1 OFVLGDICTFRJMM-WESIUVDSSA-N 444.43460 444.15327 [H][C@@]12C[C@@]3([H])C(C(=O)c4c(O)cccc4[C@@]3(C)O)=C(O)[C@]1(O)C(=O)C(C(N)=O)=C(O)[C@H]2N(C)C CHEBI:26894 CHEBI:45729 CHEBI:9474 Beilstein:2230417 CAS:60-54-8 DrugBank:DB00759 Drug_Central:2611 Gmelin:1103368 KEGG:C06570 KEGG:D00201 MetaCyc:CPD0-1414 PDBeChem:TAC PMID:11061623 PMID:11550419 PMID:11744940 PMID:12934399 PMID:14585720 PMID:15825421 PMID:15913752 PMID:16443056 PMID:1650428 PMID:16749547 PMID:17251127 PMID:17260506 PMID:18326855 PMID:18406588 PMID:19032078 PMID:19112759 PMID:19136803 PMID:25286144 PMID:26876942 Patent:US2699054 Patent:US2712517 Patent:US2886595 Patent:US3005023 Patent:US3019173 Patent:US3301899 Reaxys:2230417 VSDB:1739 Wikipedia:Tetracycline (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide TETRACYCLINE Tetracycline tetracycline chebi_ontology (4S,4aS,5aS,12aS)-4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide Abramycin Achromycin Anhydrotetracycline Deschlorobiomycin Liquamycin Tetracyclin Tetrazyklin Tsiklomitsin tetracycline tetracyclinum CHEBI:27902 tetracycline Beilstein:2230417 Beilstein CAS:60-54-8 ChemIDplus CAS:60-54-8 KEGG COMPOUND Drug_Central:2611 DrugCentral Gmelin:1103368 Gmelin PMID:11061623 Europe PMC PMID:11550419 Europe PMC PMID:11744940 Europe PMC PMID:12934399 Europe PMC PMID:14585720 Europe PMC PMID:15825421 Europe PMC PMID:15913752 Europe PMC PMID:16443056 Europe PMC PMID:1650428 Europe PMC PMID:16749547 Europe PMC PMID:17251127 Europe PMC PMID:17260506 Europe PMC PMID:18326855 Europe PMC PMID:18406588 Europe PMC PMID:19032078 Europe PMC PMID:19112759 Europe PMC PMID:19136803 Europe PMC PMID:25286144 Europe PMC PMID:26876942 Europe PMC Reaxys:2230417 Reaxys (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide IUPAC TETRACYCLINE PDBeChem Tetracycline KEGG_COMPOUND tetracycline ChEBI (4S,4aS,5aS,12aS)-4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide ChemIDplus Abramycin ChemIDplus Achromycin ChEBI Anhydrotetracycline DrugBank Deschlorobiomycin ChemIDplus Liquamycin ChemIDplus Tetracyclin ChEBI Tetrazyklin ChEBI Tsiklomitsin ChemIDplus tetracycline ChemIDplus tetracyclinum ChemIDplus An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. CHEBI:10427 CHEBI:22844 KEGG:C03438 PMID:19254642 PMID:22594007 Wikipedia:Beta-lactam_antibiotic chebi_ontology beta-Lactam antibiotics beta-lactam antibiotics CHEBI:27933 beta-lactam antibiotic PMID:19254642 Europe PMC PMID:22594007 Europe PMC beta-Lactam antibiotics KEGG_COMPOUND beta-lactam antibiotics ChEBI An aromatic amino acid that is alanine in which one of the methyl hydrogens is substituted by a phenyl group. 0 C9H11NO2 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12) COLNVLDHVKWLRT-UHFFFAOYSA-N 165.18918 165.07898 NC(Cc1ccccc1)C(O)=O CHEBI:25984 CHEBI:8089 Beilstein:1910407 CAS:150-30-1 Gmelin:50836 KEGG:C02057 PMID:17439666 PMID:22264337 Reaxys:1910407 Wikipedia:Phenylalanine 2-amino-3-phenylpropanoic acid Phenylalanine phenylalanine chebi_ontology DL-Phenylalanine F PHE Phenylalanin alpha-Amino-beta-phenylpropionic acid fenilalanina CHEBI:28044 phenylalanine Beilstein:1910407 Beilstein CAS:150-30-1 ChemIDplus CAS:150-30-1 NIST Chemistry WebBook Gmelin:50836 Gmelin PMID:17439666 Europe PMC PMID:22264337 Europe PMC Reaxys:1910407 Reaxys 2-amino-3-phenylpropanoic acid IUPAC Phenylalanine KEGG_COMPOUND phenylalanine ChEBI phenylalanine IUPAC DL-Phenylalanine KEGG_COMPOUND F ChEBI PHE ChEBI Phenylalanin ChEBI alpha-Amino-beta-phenylpropionic acid KEGG_COMPOUND fenilalanina ChEBI 0 C63H91CoN13O14P InChI=1S/C62H90N13O14P.CH3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);1H3;/q;;+2/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 JEWJRMKHSMTXPP-WZHZPDAFSA-L 1344.38230 1343.58780 [H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]4[C@@H](O)[C@H](O[C@@H]4CO)n4c[n+](c5cc(C)c(C)cc45)[Co-3]456(C)N1C3=C(C)C1=[N+]4C(=CC3=[N+]5C(=C(C)C4=[N+]6[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O CHEBI:25291 CHEBI:48831 CHEBI:6869 CAS:13422-55-4 COMe:MOL000085 DrugBank:DB03614 Gmelin:124528 KEGG:C06453 KEGG:D03246 PDBeChem:COB Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-methylcobamide Methylcobalamin methylcobalamin chebi_ontology CO-METHYLCOBALAMIN MeCbl mecobalamin methylcob(III)alamin CHEBI:28115 methylcobalamin CAS:13422-55-4 ChemIDplus CAS:13422-55-4 KEGG COMPOUND Gmelin:124528 Gmelin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-methylcobamide IUPAC Methylcobalamin KEGG_COMPOUND methylcobalamin CBN CO-METHYLCOBALAMIN PDBeChem MeCbl CBN mecobalamin ChEBI methylcob(III)alamin UniProt An aldohexose that is the C-4 epimer of glucose. 0 C6H12O6 180.156 180.06339 CHEBI:24162 CHEBI:33933 CHEBI:5256 CAS:26566-61-0 KEGG:C01582 Wikipedia:Galactose Galactose galacto-hexose galactose chebi_ontology Gal Galaktose CHEBI:28260 galactose CAS:26566-61-0 ChemIDplus CAS:26566-61-0 NIST Chemistry WebBook Galactose KEGG_COMPOUND galacto-hexose IUPAC galactose IUPAC Gal JCBN Galaktose ChEBI CHEBI:10197 CHEBI:13780 CHEBI:22361 KEGG:C04025 alpha,omega-Dicarboxylic acid chebi_ontology alpha(omega)-Dicarboxylic acid alpha,omega-dicarboxylic acids CHEBI:28383 alpha,omega-dicarboxylic acid alpha,omega-Dicarboxylic acid KEGG_COMPOUND alpha(omega)-Dicarboxylic acid KEGG_COMPOUND alpha,omega-dicarboxylic acids ChEBI Any member of a group of fat-soluble 2-methyl-1,4-napthoquinones that exhibit biological activity against vitamin K deficiency. Vitamin K is required for the synthesis of prothrombin and certain other blood coagulation factors. CHEBI:10009 CHEBI:27301 CHEBI:27307 CAS:12001-79-5 KEGG:C01628 MetaCyc:CPD-11501 PMID:26413183 PMID:33255760 PMID:34109217 Wikipedia:Vitamin_K Vitamin K chebi_ontology vitamin K vitamer vitamin K vitamers vitamine K vitamins K CHEBI:28384 vitamin K CAS:12001-79-5 ChemIDplus CAS:12001-79-5 KEGG COMPOUND PMID:26413183 Europe PMC PMID:33255760 Europe PMC PMID:34109217 Europe PMC Vitamin K KEGG_COMPOUND vitamin K vitamer ChEBI vitamin K vitamers ChEBI vitamine K ChEBI vitamins K ChEBI A cyclic carotene with a beta- and an epsilon-ring at opposite ends respectively. 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-23,25-28,37H,15-16,24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+ ANVAOWXLWRTKGA-JLTXGRSLSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\C1C(C)=CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C CHEBI:10215 CHEBI:22447 Beilstein:2067408 Beilstein:3227599 CAS:432-70-2 HMDB:HMDB0003993 KEGG:C05433 KNApSAcK:C00003765 LIPID_MAPS_instance:LMPR01070258 PMID:23620017 PMID:24169341 PMID:9408998 Reaxys:2682045 alpha-Carotene alpha-carotene beta,epsilon-carotene chebi_ontology all-trans-alpha-carotene CHEBI:28425 alpha-carotene Beilstein:2067408 Beilstein Beilstein:3227599 Beilstein CAS:432-70-2 ChemIDplus LIPID_MAPS_instance:LMPR01070258 LIPID MAPS PMID:23620017 Europe PMC PMID:24169341 Europe PMC PMID:9408998 Europe PMC Reaxys:2682045 Reaxys alpha-Carotene KEGG_COMPOUND alpha-carotene UniProt beta,epsilon-carotene IUPAC all-trans-alpha-carotene ChemIDplus A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised. 0 CH3NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) KXDHJXZQYSOELW-UHFFFAOYSA-N 61.04006 61.01638 NC(O)=O CHEBI:22504 CHEBI:23002 CHEBI:3386 CHEBI:44573 Beilstein:1734754 CAS:463-77-4 DrugBank:DB04261 Gmelin:130345 KEGG:C01563 PDBeChem:OUT Wikipedia:Carbamic_acid CARBAMIC ACID Carbamic acid carbamic acid chebi_ontology Aminoameisensaeure Aminoformic acid Carbamate Carbamidsaeure CHEBI:28616 carbamic acid Beilstein:1734754 Beilstein CAS:463-77-4 ChemIDplus CAS:463-77-4 KEGG COMPOUND Gmelin:130345 Gmelin CARBAMIC ACID PDBeChem Carbamic acid KEGG_COMPOUND carbamic acid IUPAC Aminoameisensaeure ChEBI Aminoformic acid KEGG_COMPOUND Carbamate KEGG_COMPOUND Carbamidsaeure ChEBI 0 P InChI=1S/P OAICVXFJPJFONN-UHFFFAOYSA-N 30.97376 30.97376 [P] CHEBI:26080 CHEBI:8168 CAS:7723-14-0 Gmelin:16235 KEGG:C06262 WebElements:P phosphorus chebi_ontology 15P P Phosphor Phosphorus fosforo phosphore phosphorus CHEBI:28659 phosphorus atom CAS:7723-14-0 ChemIDplus CAS:7723-14-0 KEGG COMPOUND Gmelin:16235 Gmelin phosphorus IUPAC 15P IUPAC P IUPAC P KEGG_COMPOUND Phosphor ChEBI Phosphorus KEGG_COMPOUND fosforo ChEBI phosphore ChEBI phosphorus ChEBI A ketohexose that is an isomer of glucose. CHEBI:24104 CHEBI:24110 CHEBI:5172 CAS:30237-26-4 DrugBank:DB04173 KEGG:C01496 Wikipedia:Fructose Fructose arabino-hex-2-ulose fructose chebi_ontology Fru Fruchtzucker Fruktose arabino-Hexulose CHEBI:28757 fructose CAS:30237-26-4 ChemIDplus Fructose KEGG_COMPOUND arabino-hex-2-ulose IUPAC fructose IUPAC Fru JCBN Fruchtzucker ChEBI Fruktose ChEBI arabino-Hexulose KEGG_COMPOUND 0 C40H56O2 InChI=1S/C40H56O2/c1-29(17-13-19-31(3)21-23-37-33(5)25-35(41)27-39(37,7)8)15-11-12-16-30(2)18-14-20-32(4)22-24-38-34(6)26-36(42)28-40(38,9)10/h11-25,35-37,41-42H,26-28H2,1-10H3/b12-11+,17-13+,18-14+,23-21+,24-22+,29-15+,30-16+,31-19+,32-20+/t35-,36+,37-/m0/s1 KBPHJBAIARWVSC-RGZFRNHPSA-N 568.87144 568.42803 CC(\C=C\C=C(C)\C=C\[C@H]1C(C)=C[C@H](O)CC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)C[C@@H](O)CC1(C)C CHEBI:27324 CHEBI:43817 CHEBI:6576 Beilstein:2068550 CAS:127-40-2 DrugBank:DB00137 Drug_Central:4145 HMDB:HMDB0003233 KEGG:C08601 KNApSAcK:C00003776 LIPID_MAPS_instance:LMPR01070274 MetaCyc:CPD1F-119 PDBeChem:LUT PMID:10714278 PMID:14670087 PMID:23543147 PMID:24451312 Reaxys:2068550 Wikipedia:Lutein (3R,3'R,6'R)-beta,epsilon-carotene-3,3'-diol Lutein lutein chebi_ontology (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL Bo-Xan E 161b Xanthophyll CHEBI:28838 lutein Beilstein:2068550 Beilstein CAS:127-40-2 ChemIDplus CAS:127-40-2 KEGG COMPOUND Drug_Central:4145 DrugCentral LIPID_MAPS_instance:LMPR01070274 LIPID MAPS PMID:10714278 Europe PMC PMID:14670087 Europe PMC PMID:23543147 Europe PMC PMID:24451312 Europe PMC Reaxys:2068550 Reaxys (3R,3'R,6'R)-beta,epsilon-carotene-3,3'-diol IUPAC Lutein KEGG_COMPOUND lutein UniProt (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL PDBeChem Bo-Xan ChemIDplus E 161b ChEBI Xanthophyll KEGG_COMPOUND The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13634 CHEBI:24022 CHEBI:4985 KEGG:C02403 PMID:18628202 Fatty acid anion chebi_ontology Alkanate Fettsaeureanion Fettsaeureanionen a fatty acid acido graso anionico acidos grasos anionicos anion de l'acide gras fatty acid anions CHEBI:28868 fatty acid anion PMID:18628202 Europe PMC Fatty acid anion KEGG_COMPOUND Alkanate KEGG_COMPOUND Fettsaeureanion ChEBI Fettsaeureanionen ChEBI a fatty acid UniProt acido graso anionico ChEBI acidos grasos anionicos ChEBI anion de l'acide gras ChEBI fatty acid anions ChEBI An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] CHEBI:22534 CHEBI:49783 CHEBI:7435 CAS:14798-03-9 Gmelin:84 KEGG:C01342 MetaCyc:AMMONIUM MolBase:929 PDBeChem:NH4 PMID:11319011 PMID:11341317 PMID:12096804 PMID:14512268 PMID:14879753 PMID:16345391 PMID:16903292 PMID:17392693 PMID:18515490 PMID:19199063 PMID:19596600 PMID:19682559 PMID:19716251 PMID:21993530 PMID:22265469 PMID:22524020 PMID:22562341 PMID:22631217 Reaxys:16093784 Wikipedia:Ammonium ammonium azanium chebi_ontology Ammonium(1+) NH4(+) NH4+ [NH4](+) ammonium cation ammonium ion CHEBI:28938 ammonium CAS:14798-03-9 ChemIDplus CAS:14798-03-9 NIST Chemistry WebBook Gmelin:84 Gmelin PMID:11319011 Europe PMC PMID:11341317 Europe PMC PMID:12096804 Europe PMC PMID:14512268 Europe PMC PMID:14879753 Europe PMC PMID:16345391 Europe PMC PMID:16903292 Europe PMC PMID:17392693 Europe PMC PMID:18515490 Europe PMC PMID:19199063 Europe PMC PMID:19596600 Europe PMC PMID:19682559 Europe PMC PMID:19716251 Europe PMC PMID:21993530 Europe PMC PMID:22265469 Europe PMC PMID:22524020 Europe PMC PMID:22562341 Europe PMC PMID:22631217 Europe PMC Reaxys:16093784 Reaxys ammonium ChEBI ammonium IUPAC azanium IUPAC Ammonium(1+) ChemIDplus NH4(+) IUPAC NH4(+) UniProt NH4+ KEGG_COMPOUND [NH4](+) MolBase ammonium cation ChemIDplus ammonium ion PDBeChem An N-acetyl-L-amino acid that is the N-acetylated derivative of the natural amino acid L-cysteine. 0 C5H9NO3S InChI=1S/C5H9NO3S/c1-3(7)6-4(2-10)5(8)9/h4,10H,2H2,1H3,(H,6,7)(H,8,9)/t4-/m0/s1 PWKSKIMOESPYIA-BYPYZUCNSA-N 163.19590 163.03031 CC(=O)N[C@@H](CS)C(O)=O CHEBI:21548 CHEBI:2418 CHEBI:45481 Beilstein:1724426 CAS:616-91-1 DrugBank:DB06151 Drug_Central:66 Gmelin:142554 HMDB:HMDB0001890 KEGG:C06809 KEGG:D00221 LINCS:LSM-4672 MetaCyc:CPD-9175 PDBeChem:SC2 PMID:10651166 PMID:11544433 PMID:12057717 PMID:15025780 PMID:15647642 PMID:17174578 PMID:19580823 PMID:2026726 PMID:20819793 PMID:24119926 PMID:25553484 PMID:9624310 PMID:9711192 Reaxys:1724426 Wikipedia:Acetylcysteine N-ACETYL-L-CYSTEINE N-acetyl-L-cysteine chebi_ontology (2R)-2-acetylamino-3-sulfanylpropanoic acid (R)-2-acetylamino-3-mercaptopropanoic acid (R)-mercapturic acid Acetylcysteine L-acetylcysteine L-alpha-acetamido-beta-mercaptopropionic acid N-acetyl-L-(+)-cysteine N-acetylcysteine NAC acetilcisteina acetylcysteinum mercapturic acid CHEBI:28939 N-acetyl-L-cysteine Beilstein:1724426 Beilstein CAS:616-91-1 ChemIDplus CAS:616-91-1 KEGG COMPOUND CAS:616-91-1 NIST Chemistry WebBook Drug_Central:66 DrugCentral Gmelin:142554 Gmelin PMID:10651166 Europe PMC PMID:11544433 Europe PMC PMID:12057717 Europe PMC PMID:15025780 Europe PMC PMID:15647642 Europe PMC PMID:17174578 Europe PMC PMID:19580823 Europe PMC PMID:2026726 Europe PMC PMID:20819793 Europe PMC PMID:24119926 Europe PMC PMID:25553484 Europe PMC PMID:9624310 Europe PMC PMID:9711192 Europe PMC Reaxys:1724426 Reaxys N-ACETYL-L-CYSTEINE PDBeChem N-acetyl-L-cysteine IUPAC (2R)-2-acetylamino-3-sulfanylpropanoic acid IUPAC (R)-2-acetylamino-3-mercaptopropanoic acid ChEBI (R)-mercapturic acid ChemIDplus Acetylcysteine KEGG_COMPOUND L-acetylcysteine ChemIDplus L-alpha-acetamido-beta-mercaptopropionic acid NIST_Chemistry_WebBook N-acetyl-L-(+)-cysteine NIST_Chemistry_WebBook N-acetylcysteine ChemIDplus NAC ChEBI acetilcisteina ChemIDplus acetylcysteinum ChemIDplus mercapturic acid ChemIDplus A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid. -2 C2O4R 88.019 87.97966 [O-]C(=O)[*]C([O-])=O CHEBI:13632 CHEBI:23688 CHEBI:23689 CHEBI:38711 dicarboxylic acid dianion chebi_ontology a dicarboxylate dicarboxylate dicarboxylates dicarboxylic acid dianions CHEBI:28965 dicarboxylic acid dianion dicarboxylic acid dianion ChEBI a dicarboxylate UniProt dicarboxylate ChEBI dicarboxylates ChEBI dicarboxylic acid dianions ChEBI 0 CH2O3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4) BVKZGUZCCUSVTD-UHFFFAOYSA-N 62.02478 62.00039 OC(O)=O CHEBI:13351 CHEBI:23017 CHEBI:23744 CHEBI:3401 CAS:463-79-6 Gmelin:25554 KEGG:C01353 PDBeChem:CO3 Carbonic acid carbonic acid dihydroxidooxidocarbon chebi_ontology Dihydrogen carbonate H2CO3 Koehlensaeure [CO(OH)2] CHEBI:28976 carbonic acid CAS:463-79-6 ChemIDplus CAS:463-79-6 KEGG COMPOUND Gmelin:25554 Gmelin Carbonic acid KEGG_COMPOUND carbonic acid IUPAC dihydroxidooxidocarbon IUPAC Dihydrogen carbonate KEGG_COMPOUND H2CO3 IUPAC H2CO3 KEGG_COMPOUND Koehlensaeure ChEBI [CO(OH)2] IUPAC An alpha-amino acid that is glycine in which the alpha-is substituted by a 3-guanidinopropyl group. 0 C6H14N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10) ODKSFYDXXFIFQN-UHFFFAOYSA-N 174.20112 174.11168 NC(CCCNC(N)=N)C(O)=O CHEBI:22616 CHEBI:2643 Beilstein:1725411 CAS:7200-25-1 KEGG:C02385 PMID:10848923 Reaxys:1725411 Wikipedia:L-Arginine Arginine arginine chebi_ontology 2-Amino-5-guanidinovaleric acid 2-amino-5-(carbamimidamido)pentanoic acid 2-amino-5-guanidinopentanoic acid Arginin Harg CHEBI:29016 arginine Beilstein:1725411 Beilstein CAS:7200-25-1 ChemIDplus PMID:10848923 Europe PMC Reaxys:1725411 Reaxys Arginine KEGG_COMPOUND arginine IUPAC 2-Amino-5-guanidinovaleric acid KEGG_COMPOUND 2-amino-5-(carbamimidamido)pentanoic acid IUPAC 2-amino-5-guanidinopentanoic acid JCBN Arginin ChEBI Harg IUPAC A pantothenate that is the conjugate base of (R)-pantothenic acid, obtained by deprotonation of the carboxy group. -1 C9H16NO5 InChI=1S/C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13)/p-1/t7-/m0/s1 GHOKWGTUZJEAQD-ZETCQYMHSA-M 218.22708 218.10340 CC(C)(CO)[C@@H](O)C(=O)NCCC([O-])=O CHEBI:11008 CHEBI:18700 CAS:20938-62-9 Gmelin:775395 MetaCyc:PANTOTHENATE PMID:15565250 PMID:16042590 Reaxys:3907450 (R)-Pantothenate (R)-pantothenate 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoate chebi_ontology (R)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-beta-alanine, ion(1-) pantothenate CHEBI:29032 (R)-pantothenate CAS:20938-62-9 ChemIDplus Gmelin:775395 Gmelin PMID:15565250 Europe PMC PMID:16042590 Europe PMC Reaxys:3907450 Reaxys (R)-Pantothenate KEGG_COMPOUND (R)-pantothenate UniProt 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoate IUPAC (R)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-beta-alanine, ion(1-) ChemIDplus pantothenate ChemIDplus CHEBI:14490 CHEBI:24954 chebi_ontology CHEBI:29057 keratan The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 chebi_ontology a carboxylate carboxylic acid anions carboxylic anions CHEBI:29067 carboxylic acid anion a carboxylate UniProt carboxylic acid anions ChEBI carboxylic anions ChEBI A monoatomic monocation obtained from sodium. +1 Na InChI=1S/Na/q+1 FKNQFGJONOIPTF-UHFFFAOYSA-N 22.98977 22.98922 [Na+] CHEBI:26717 CHEBI:49766 CHEBI:9175 CAS:17341-25-2 Gmelin:15196 KEGG:C01330 PDBeChem:NA sodium cation sodium(1+) sodium(1+) ion sodium(I) cation chebi_ontology Na(+) Na+ SODIUM ION CHEBI:29101 sodium(1+) CAS:17341-25-2 ChemIDplus CAS:17341-25-2 NIST Chemistry WebBook Gmelin:15196 Gmelin sodium cation IUPAC sodium(1+) IUPAC sodium(1+) ion IUPAC sodium(I) cation IUPAC Na(+) IUPAC Na(+) UniProt Na+ KEGG_COMPOUND SODIUM ION PDBeChem A monoatomic monocation obtained from potassium. +1 K InChI=1S/K/q+1 NPYPAHLBTDXSSS-UHFFFAOYSA-N 39.09830 38.96316 [K+] CHEBI:26219 CHEBI:49685 CHEBI:8345 CAS:24203-36-9 Gmelin:15203 KEGG:C00238 KEGG:D08403 PDBeChem:K potassium cation potassium(1+) potassium(1+) ion potassium(I) cation chebi_ontology K(+) K+ POTASSIUM ION CHEBI:29103 potassium(1+) CAS:24203-36-9 NIST Chemistry WebBook Gmelin:15203 Gmelin potassium cation IUPAC potassium(1+) IUPAC potassium(1+) ion IUPAC potassium(I) cation IUPAC K(+) IUPAC K(+) UniProt K+ KEGG_COMPOUND POTASSIUM ION PDBeChem +2 Ca InChI=1S/Ca/q+2 BHPQYMZQTOCNFJ-UHFFFAOYSA-N 40.07800 39.96149 [Ca++] CHEBI:22988 CHEBI:3308 CHEBI:48760 CAS:14127-61-8 Gmelin:6850 KEGG:C00076 PDBeChem:CA calcium(2+) calcium(2+) ion calcium(II) cation chebi_ontology CALCIUM ION Ca(2+) Ca2+ calcium, doubly charged positive ion CHEBI:29108 calcium(2+) CAS:14127-61-8 ChemIDplus CAS:14127-61-8 NIST Chemistry WebBook Gmelin:6850 Gmelin calcium(2+) IUPAC calcium(2+) ion IUPAC calcium(II) cation IUPAC CALCIUM ION PDBeChem Ca(2+) IUPAC Ca(2+) UniProt Ca2+ KEGG_COMPOUND calcium, doubly charged positive ion NIST_Chemistry_WebBook 0 H2O3S InChI=1S/H2O3S/c1-4(2)3/h4H,(H,1,2,3) BDHFUVZGWQCTTF-UHFFFAOYSA-N 82.08008 81.97247 [H]S(O)(=O)=O Gmelin:1404640 hydridohydroxidodioxidosulfur sulfonic acid chebi_ontology HSHO3 Sulfonsaeure [SHO2(OH)] acide sulfonique sulphonic acid CHEBI:29214 sulfonic acid Gmelin:1404640 Gmelin hydridohydroxidodioxidosulfur IUPAC sulfonic acid IUPAC HSHO3 IUPAC Sulfonsaeure ChEBI [SHO2(OH)] IUPAC acide sulfonique ChEBI sulphonic acid ChEBI A diatomic molecule containing covalently bonded hydrogen and fluorine atoms. 0 FH InChI=1S/FH/h1H KRHYYFGTRYWZRS-UHFFFAOYSA-N 20.00634 20.00623 F[H] CAS:7664-39-3 Drug_Central:4499 Gmelin:166 KEGG:C16487 Hydrogen fluoride fluorane fluoridohydrogen hydrogen fluoride chebi_ontology Fluoride Fluorwasserstoff HF Hydrogenfluorid [HF] fluorure d'hydrogene hydrofluoric acid CHEBI:29228 hydrogen fluoride CAS:7664-39-3 ChemIDplus CAS:7664-39-3 KEGG COMPOUND CAS:7664-39-3 NIST Chemistry WebBook Drug_Central:4499 DrugCentral Gmelin:166 Gmelin Hydrogen fluoride KEGG_COMPOUND fluorane IUPAC fluoridohydrogen IUPAC hydrogen fluoride IUPAC Fluoride KEGG_COMPOUND Fluorwasserstoff ChEBI HF IUPAC Hydrogenfluorid ChEBI [HF] IUPAC fluorure d'hydrogene ChEBI hydrofluoric acid ChemIDplus -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] amide azanide dihydridonitrate(1-) chebi_ontology NH2(-) CHEBI:29337 azanide amide IUPAC azanide IUPAC dihydridonitrate(1-) IUPAC NH2(-) IUPAC A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] azanediide hydridonitrate(2-) chebi_ontology NH(2-) imide CHEBI:29340 hydridonitrate(2-) azanediide IUPAC hydridonitrate(2-) IUPAC NH(2-) IUPAC imide IUPAC A carboxamide derived from a monocarboxylic acid. 0 CNOR3 42.01680 41.99799 [*]N([*])C([*])=O CHEBI:13211 CHEBI:22207 CHEBI:25383 CHEBI:6977 chebi_ontology monocarboxylic acid amides CHEBI:29347 monocarboxylic acid amide monocarboxylic acid amides ChEBI A bile acid anion that is the conjugate base of cholic acid. -1 C24H39O5 InChI=1S/C24H40O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-20,22,25-27H,4-12H2,1-3H3,(H,28,29)/p-1/t13-,14+,15-,16-,17+,18+,19-,20+,22+,23+,24-/m1/s1 BHQCQFFYRZLCQQ-OELDTZBJSA-M 407.56346 407.28030 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])C[C@H](O)[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC([O-])=O CHEBI:11895 CHEBI:13978 CHEBI:20216 CHEBI:23168 CHEBI:57748 Beilstein:3915750 Reaxys:3915750 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oate cholate chebi_ontology 3alpha,7alpha,12alpha-trihydroxy-5beta-cholanate CHEBI:29747 cholate Beilstein:3915750 Beilstein Reaxys:3915750 Reaxys 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oate IUPAC cholate UniProt 3alpha,7alpha,12alpha-trihydroxy-5beta-cholanate ChEBI An alpha-amino-acid anion that is the conjugate base of L-glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-M 146.12136 146.04588 [NH3+][C@@H](CCC([O-])=O)C([O-])=O CHEBI:13107 CHEBI:21301 CAS:11070-68-1 Gmelin:936654 MetaCyc:GLT L-glutamate(1-) hydrogen L-glutamate chebi_ontology (2S)-2-ammoniopentanedioate L-glutamate L-glutamic acid monoanion L-glutamic acid, ion(1-) CHEBI:29985 L-glutamate(1-) CAS:11070-68-1 ChemIDplus Gmelin:936654 Gmelin L-glutamate(1-) JCBN hydrogen L-glutamate IUPAC (2S)-2-ammoniopentanedioate IUPAC L-glutamate ChEBI L-glutamate UniProt L-glutamic acid monoanion JCBN L-glutamic acid, ion(1-) ChemIDplus An alpha-amino-acid anion that is the conjugate base of D-glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-M 146.12136 146.04588 [NH3+][C@H](CCC([O-])=O)C([O-])=O CHEBI:12979 CHEBI:21022 Beilstein:8319427 MetaCyc:D-GLT D-glutamate(1-) hydrogen D-glutamate chebi_ontology (2R)-2-ammoniopentanedioate D-glutamate D-glutamic acid monoanion CHEBI:29986 D-glutamate(1-) Beilstein:8319427 Beilstein D-glutamate(1-) JCBN hydrogen D-glutamate IUPAC (2R)-2-ammoniopentanedioate IUPAC D-glutamate UniProt D-glutamic acid monoanion JCBN A dicarboxylic acid dianion that is the conjugate base of glutamate(1-). -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2 WHUUTDBJXJRKMK-UHFFFAOYSA-L 145.11342 145.03860 NC(CCC([O-])=O)C([O-])=O Beilstein:4134100 Gmelin:327903 Reaxys:4134100 2-aminopentanedioate glutamate glutamate(2-) chebi_ontology glutamic acid dianion CHEBI:29987 glutamate(2-) Beilstein:4134100 Beilstein Gmelin:327903 Gmelin Reaxys:4134100 Reaxys 2-aminopentanedioate IUPAC glutamate IUPAC glutamate(2-) JCBN glutamic acid dianion JCBN An L-alpha-amino acid anion that is the dianion obtained by the deprotonation of the both the carboxy groups of L-glutamic acid. -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-L 145.11342 145.03860 N[C@@H](CCC([O-])=O)C([O-])=O Gmelin:327905 (2S)-2-aminopentanedioate L-glutamate L-glutamate(2-) chebi_ontology L-glutamic acid dianion CHEBI:29988 L-glutamate(2-) Gmelin:327905 Gmelin (2S)-2-aminopentanedioate IUPAC L-glutamate IUPAC L-glutamate(2-) JCBN L-glutamic acid dianion JCBN -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-L 145.11342 145.03860 N[C@H](CCC([O-])=O)C([O-])=O Beilstein:8143000 Gmelin:327904 (2R)-2-aminopentanedioate D-glutamate D-glutamate(2-) chebi_ontology D-glutamic acid dianion CHEBI:29989 D-glutamate(2-) Beilstein:8143000 Beilstein Gmelin:327904 Gmelin (2R)-2-aminopentanedioate IUPAC D-glutamate IUPAC D-glutamate(2-) JCBN D-glutamic acid dianion JCBN A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid. -1 C2H3O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1 QTBSBXVTEAMEQO-UHFFFAOYSA-M 59.04402 59.01385 CC([O-])=O CHEBI:13704 CHEBI:22165 CHEBI:40480 Beilstein:1901470 CAS:71-50-1 DrugBank:DB03166 Gmelin:1379 KEGG:C00033 MetaCyc:ACET PDBeChem:ACT PMID:17190852 PMID:22211106 PMID:22371380 Reaxys:1901470 UM-BBD_compID:c0050 Wikipedia:Acetate acetate chebi_ontology ACETATE ION Azetat CH3-COO(-) Ethanoat MeCO2 anion acetic acid, ion(1-) ethanoate CHEBI:30089 acetate Beilstein:1901470 Beilstein CAS:71-50-1 ChemIDplus CAS:71-50-1 NIST Chemistry WebBook Gmelin:1379 Gmelin PMID:17190852 Europe PMC PMID:22211106 Europe PMC PMID:22371380 Europe PMC Reaxys:1901470 Reaxys UM-BBD_compID:c0050 UM-BBD acetate IUPAC acetate UniProt ACETATE ION PDBeChem Azetat ChEBI CH3-COO(-) IUPAC Ethanoat ChEBI MeCO2 anion NIST_Chemistry_WebBook acetic acid, ion(1-) ChemIDplus ethanoate ChEBI 0 C3H7 43.08768 43.05478 CC(*)C isopropyl propan-2-yl chebi_ontology (CH3)2CH- -CH(CH3)2 1-methylethyl iPr valine side-chain CHEBI:30353 isopropyl group isopropyl IUPAC propan-2-yl IUPAC (CH3)2CH- IUPAC -CH(CH3)2 ChEBI 1-methylethyl IUPAC iPr CBN valine side-chain ChEBI 0 C4H9 57.11426 57.07043 CC(C)C* 2-methylpropan-1-ido 2-methylpropyl isobutyl chebi_ontology (CH3)2CH-CH2- -CH2-CH(CH3)2 iBu leucine side-chain CHEBI:30356 isobutyl group 2-methylpropan-1-ido IUPAC 2-methylpropyl IUPAC isobutyl IUPAC (CH3)2CH-CH2- IUPAC -CH2-CH(CH3)2 ChEBI iBu CBN leucine side-chain ChEBI An alkane that is propane substituted by a methyl group at position 2. 0 C4H10 InChI=1S/C4H10/c1-4(2)3/h4H,1-3H3 NNPPMTNAJDCUHE-UHFFFAOYSA-N 58.12220 58.07825 CC(C)C Beilstein:1730720 CAS:75-28-5 Gmelin:1301 KEGG:D04623 PMID:24179026 PMID:24464945 Reaxys:1730720 Wikipedia:Isobutane 2-methylpropane isobutane chebi_ontology (CH3)2CH-CH3 E943b R-600a CHEBI:30363 isobutane Beilstein:1730720 Beilstein CAS:75-28-5 ChemIDplus CAS:75-28-5 NIST Chemistry WebBook Gmelin:1301 Gmelin PMID:24179026 Europe PMC PMID:24464945 Europe PMC Reaxys:1730720 Reaxys 2-methylpropane IUPAC isobutane IUPAC (CH3)2CH-CH3 IUPAC E943b ChEBI R-600a ChEBI A cobalt-corrinoid hexaamide that is cobalamin with the oxidation state of the central cobalt atom unspecified. COMe:MOL000036 PDBeChem:B12 PMID:11371572 PMID:15181872 COBALAMIN Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide cobalamin chebi_ontology CHEBI:30411 cobalamin PMID:11371572 Europe PMC PMID:15181872 Europe PMC COBALAMIN PDBeChem Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide IUPAC cobalamin IUPAC +2 0.00000 [*++] CHEBI:23856 CHEBI:4665 KEGG:C00572 chebi_ontology Divalent cation divalent inorganic cations monoatomic dications CHEBI:30412 monoatomic dication Divalent cation KEGG_COMPOUND divalent inorganic cations ChEBI monoatomic dications ChEBI A heme is any tetrapyrrolic chelate of iron. CHEBI:14386 CHEBI:24491 COMe:MOL000025 DrugBank:DB03014 KEGG:C00032 heme hemes chebi_ontology Haem haem haeme hem hemos CHEBI:30413 heme heme IUPAC heme IUPAC heme UniProt hemes IUPAC Haem ChEBI haem ChEBI haem IUPAC haeme IUPAC hem IUPAC hemos IUPAC A derivative of the dimethylisoalloxazine (7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione) skeleton, with a substituent on the 10 position. 0 C12H9N4O2R 241.22550 241.07255 Cc1cc2nc3c(nc(=O)[nH]c3=O)n([*])c2cc1C CHEBI:24042 CHEBI:5073 KEGG:C00176 Flavin flavins chebi_ontology CHEBI:30527 flavin Flavin KEGG_COMPOUND flavins IUPAC A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of oxalic acid. -2 C2O4 InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-2 MUBZPKHOEPUJKR-UHFFFAOYSA-L 88.01900 87.98076 [O-]C(=O)C([O-])=O CHEBI:14702 CHEBI:25729 CHEBI:44820 Beilstein:1905970 CAS:338-70-5 Gmelin:2207 KEGG:C00209 PDBeChem:OXL Reaxys:1905970 UM-BBD_compID:c0017 ethanedioate chebi_ontology OXALATE ION ethanedioic acid, ion(2-) ox oxalate CHEBI:30623 oxalate(2-) Beilstein:1905970 Beilstein CAS:338-70-5 ChemIDplus Gmelin:2207 Gmelin Reaxys:1905970 Reaxys UM-BBD_compID:c0017 UM-BBD ethanedioate IUPAC OXALATE ION PDBeChem ethanedioic acid, ion(2-) ChemIDplus ox IUPAC oxalate UniProt The simplest carboxylic acid, containing a single carbon. Occurs naturally in various sources including the venom of bee and ant stings, and is a useful organic synthetic reagent. Principally used as a preservative and antibacterial agent in livestock feed. Induces severe metabolic acidosis and ocular injury in human subjects. 0 CH2O2 InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3) BDAGIHXWWSANSR-UHFFFAOYSA-N 46.02538 46.00548 [H]C(O)=O CHEBI:24082 CHEBI:42460 CHEBI:5145 BPDB:1749 Beilstein:1209246 CAS:64-18-6 DrugBank:DB01942 Gmelin:1008 HMDB:HMDB0000142 KEGG:C00058 KNApSAcK:C00001182 LIPID_MAPS_instance:LMFA01010040 MetaCyc:FORMATE PDBeChem:FMT PMID:12591956 PMID:14637377 PMID:15811469 PMID:16120414 PMID:16185830 PMID:16222862 PMID:16230297 PMID:16445901 PMID:16465784 PMID:18034701 PMID:18397576 PMID:22080171 PMID:22280475 PMID:22304812 PMID:22385261 PMID:22447125 PMID:22483350 PMID:22499553 PMID:22540994 PMID:22606986 PMID:22622393 PMID:3946945 PMID:7361809 Patent:CN101481304 Reaxys:1209246 Wikipedia:Formic_acid FORMIC ACID Formic acid formic acid chebi_ontology Acide formique Ameisensaeure H-COOH HCO2H HCOOH Methanoic acid aminic acid bilorin formylic acid hydrogen carboxylic acid methoic acid CHEBI:30751 formic acid Beilstein:1209246 Beilstein CAS:64-18-6 ChemIDplus CAS:64-18-6 KEGG COMPOUND CAS:64-18-6 NIST Chemistry WebBook Gmelin:1008 Gmelin LIPID_MAPS_instance:LMFA01010040 LIPID MAPS PMID:12591956 Europe PMC PMID:14637377 Europe PMC PMID:15811469 Europe PMC PMID:16120414 Europe PMC PMID:16185830 Europe PMC PMID:16222862 Europe PMC PMID:16230297 Europe PMC PMID:16445901 Europe PMC PMID:16465784 Europe PMC PMID:18034701 Europe PMC PMID:18397576 Europe PMC PMID:22080171 Europe PMC PMID:22280475 Europe PMC PMID:22304812 Europe PMC PMID:22385261 Europe PMC PMID:22447125 Europe PMC PMID:22483350 Europe PMC PMID:22499553 Europe PMC PMID:22540994 Europe PMC PMID:22606986 Europe PMC PMID:22622393 Europe PMC PMID:3946945 Europe PMC PMID:7361809 Europe PMC Reaxys:1209246 Reaxys FORMIC ACID PDBeChem Formic acid KEGG_COMPOUND formic acid IUPAC Acide formique ChemIDplus Ameisensaeure ChemIDplus H-COOH IUPAC HCO2H ChEBI HCOOH NIST_Chemistry_WebBook Methanoic acid KEGG_COMPOUND aminic acid ChemIDplus bilorin ChemIDplus formylic acid ChemIDplus hydrogen carboxylic acid ChemIDplus methoic acid ChEBI A short-chain saturated fatty acid comprising ethane attached to the carbon of a carboxy group. 0 C3H6O2 InChI=1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5) XBDQKXXYIPTUBI-UHFFFAOYSA-N 74.07850 74.03678 CCC(O)=O CHEBI:26304 CHEBI:45227 CHEBI:8476 Beilstein:506071 CAS:79-09-4 DrugBank:DB03766 Gmelin:1821 KEGG:C00163 KEGG:D02310 LIPID_MAPS_instance:LMFA01010003 PDBeChem:PPI PMID:15868474 PMID:1628870 PMID:16763906 PPDB:1341 Propionic acid propanoic acid propionic acid chebi_ontology CH3-CH2-COOH PA PROPANOIC ACID Propanoic acid Propionsaeure acide propanoique acide propionique carboxyethane ethanecarboxylic acid ethylformic acid metacetonic acid methylacetic acid propioic acid propoic acid pseudoacetic acid CHEBI:30768 propionic acid Beilstein:506071 Beilstein CAS:79-09-4 ChemIDplus CAS:79-09-4 KEGG COMPOUND CAS:79-09-4 NIST Chemistry WebBook Gmelin:1821 Gmelin LIPID_MAPS_instance:LMFA01010003 LIPID MAPS PMID:15868474 Europe PMC PMID:1628870 Europe PMC PMID:16763906 Europe PMC Propionic acid KEGG_COMPOUND propanoic acid IUPAC propionic acid IUPAC CH3-CH2-COOH IUPAC PA ChEBI PROPANOIC ACID PDBeChem Propanoic acid KEGG_COMPOUND Propionsaeure ChEBI acide propanoique ChEBI acide propionique NIST_Chemistry_WebBook carboxyethane ChemIDplus ethanecarboxylic acid ChemIDplus ethylformic acid ChemIDplus metacetonic acid ChemIDplus methylacetic acid ChemIDplus propioic acid LIPID_MAPS propoic acid ChEBI pseudoacetic acid ChemIDplus A straight-chain saturated fatty acid that is butane in which one of the terminal methyl groups has been oxidised to a carboxy group. 0 C4H8O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6) FERIUCNNQQJTOY-UHFFFAOYSA-N 88.10510 88.05243 CCCC(O)=O CHEBI:113450 CHEBI:22948 CHEBI:3234 CHEBI:41208 Beilstein:906770 CAS:107-92-6 DrugBank:DB03568 Gmelin:26242 HMDB:HMDB0000039 KEGG:C00246 KNApSAcK:C00001180 LIPID_MAPS_instance:LMFA01010004 MetaCyc:BUTYRIC_ACID PDBeChem:BUA PMID:10736622 PMID:10956204 PMID:11201044 PMID:11208715 PMID:11238216 PMID:11305323 PMID:12068484 PMID:13678314 PMID:14962641 PMID:1542095 PMID:15809727 PMID:15810631 PMID:15938880 PMID:19318247 PMID:19366864 PMID:19703412 PMID:21699495 PMID:22038864 PMID:22194341 PMID:22322557 PMID:22339023 PMID:22466881 Reaxys:906770 Wikipedia:Butyric_acid Butyric acid butanoic acid butyric acid chebi_ontology 1-butanoic acid 1-butyric acid 1-propanecarboxylic acid 4:0 BUTANOIC ACID Butanoate Butanoic acid Buttersaeure C4:0 CH3-[CH2]2-COOH acide butanoique acide butyrique butanic acid butoic acid ethylacetic acid n-butanoic acid n-butyric acid propanecarboxylic acid propylformic acid CHEBI:30772 butyric acid Beilstein:906770 Beilstein CAS:107-92-6 ChemIDplus CAS:107-92-6 KEGG COMPOUND CAS:107-92-6 NIST Chemistry WebBook Gmelin:26242 Gmelin LIPID_MAPS_instance:LMFA01010004 LIPID MAPS PMID:10736622 Europe PMC PMID:10956204 ChEMBL PMID:11201044 Europe PMC PMID:11208715 Europe PMC PMID:11238216 Europe PMC PMID:11305323 Europe PMC PMID:12068484 Europe PMC PMID:13678314 Europe PMC PMID:14962641 Europe PMC PMID:1542095 ChEMBL PMID:15809727 Europe PMC PMID:15810631 Europe PMC PMID:15938880 Europe PMC PMID:19318247 Europe PMC PMID:19366864 Europe PMC PMID:19703412 Europe PMC PMID:21699495 Europe PMC PMID:22038864 Europe PMC PMID:22194341 Europe PMC PMID:22322557 Europe PMC PMID:22339023 Europe PMC PMID:22466881 Europe PMC Reaxys:906770 Reaxys Butyric acid KEGG_COMPOUND butanoic acid IUPAC butyric acid IUPAC 1-butanoic acid HMDB 1-butyric acid HMDB 1-propanecarboxylic acid MetaCyc 4:0 ChEBI BUTANOIC ACID PDBeChem Butanoate KEGG_COMPOUND Butanoic acid KEGG_COMPOUND Buttersaeure ChEBI C4:0 ChEBI CH3-[CH2]2-COOH IUPAC acide butanoique IUPAC acide butyrique ChEBI butanic acid ChEBI butoic acid ChEBI ethylacetic acid NIST_Chemistry_WebBook n-butanoic acid NIST_Chemistry_WebBook n-butyric acid NIST_Chemistry_WebBook propanecarboxylic acid HMDB propylformic acid MetaCyc A C6, straight-chain saturated fatty acid. 0 C6H12O2 InChI=1S/C6H12O2/c1-2-3-4-5-6(7)8/h2-5H2,1H3,(H,7,8) FUZZWVXGSFPDMH-UHFFFAOYSA-N 116.15830 116.08373 CCCCCC(O)=O CHEBI:24571 CHEBI:40213 CHEBI:5702 Beilstein:773837 CAS:142-62-1 ECMDB:ECMDB21229 Gmelin:185066 HMDB:HMDB0000535 KEGG:C01585 KNApSAcK:C00001218 LIPID_MAPS_instance:LMFA01010006 MetaCyc:HEXANOATE PDBeChem:6NA PMID:10685018 PMID:1556177 PMID:24357269 PMID:24924750 Reaxys:773837 Wikipedia:Hexanoic_acid YMDB:YMDB01424 HEXANOIC ACID Hexanoic acid hexanoic acid chebi_ontology 1-hexanoic acid 1-pentanecarboxylic acid 6:0 C6:0 CH3-[CH2]4-COOH Hexanoate Hexylic acid Pentanecarboxylic acid butylacetic acid caproic acid capronic acid hexoic acid n-Caproic acid n-hexanoic acid n-hexoic acid n-hexylic acid pentiformic acid pentylformic acid CHEBI:30776 hexanoic acid Beilstein:773837 Beilstein CAS:142-62-1 ChemIDplus CAS:142-62-1 KEGG COMPOUND CAS:142-62-1 NIST Chemistry WebBook Gmelin:185066 Gmelin LIPID_MAPS_instance:LMFA01010006 LIPID MAPS PMID:10685018 Europe PMC PMID:1556177 Europe PMC PMID:24357269 Europe PMC PMID:24924750 Europe PMC Reaxys:773837 Reaxys HEXANOIC ACID PDBeChem Hexanoic acid KEGG_COMPOUND hexanoic acid IUPAC 1-hexanoic acid ChemIDplus 1-pentanecarboxylic acid ChemIDplus 6:0 ChEBI C6:0 ChEBI CH3-[CH2]4-COOH IUPAC Hexanoate KEGG_COMPOUND Hexylic acid KEGG_COMPOUND Pentanecarboxylic acid ChemIDplus butylacetic acid ChemIDplus caproic acid ChEBI capronic acid NIST_Chemistry_WebBook hexoic acid NIST_Chemistry_WebBook n-Caproic acid KEGG_COMPOUND n-hexanoic acid NIST_Chemistry_WebBook n-hexoic acid ChemIDplus n-hexylic acid ChemIDplus pentiformic acid ChemIDplus pentylformic acid ChemIDplus A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. 0 HOR 17.007 17.00274 O[*] CHEBI:13804 CHEBI:22288 CHEBI:2553 KEGG:C00069 Alcohol alcohols chebi_ontology an alcohol CHEBI:30879 alcohol Alcohol KEGG_COMPOUND alcohols IUPAC an alcohol UniProt -1 C8H11N2O3S InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/p-1/t3-,4+,6-/m1/s1 NGHVIOIJCVXTGV-ALEPSDHESA-M 215.25062 215.04959 [H][C@@]1(N)C(=O)N2[C@]1([H])SC(C)(C)[C@]2([H])C([O-])=O CHEBI:12207 CHEBI:20704 Gmelin:604420 KEGG:C02954 (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate chebi_ontology CHEBI:30938 6-aminopenicillanate Gmelin:604420 Gmelin (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate IUPAC Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration. KEGG:C01558 Bile acid chebi_ontology 5beta-bile acid 5beta-bile acids Bile salt Gallensaeure Gallensaeuren bile acids CHEBI:3098 bile acid Bile acid KEGG_COMPOUND 5beta-bile acid ChEBI 5beta-bile acids ChEBI Bile salt KEGG_COMPOUND Gallensaeure ChEBI Gallensaeuren ChEBI bile acids ChEBI A short-chain fatty acid anion that is the conjugate base of valeric acid; present in ester form as component of many steroid-based pharmaceuticals. -1 C5H9O2 InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)/p-1 NQPDZGIKBAWPEJ-UHFFFAOYSA-M 101.12376 101.06080 CCCCC([O-])=O CHEBI:14751 CHEBI:25890 Beilstein:3903735 CAS:10023-74-2 Gmelin:325619 PMID:17314444 PMID:18783570 Reaxys:3903735 pentanoate chebi_ontology CH3-[CH2]3-COO(-) n-propylacetate pentanoate pentanoic acid, ion(1-) CHEBI:31011 valerate Beilstein:3903735 Beilstein CAS:10023-74-2 ChemIDplus Gmelin:325619 Gmelin PMID:17314444 Europe PMC PMID:18783570 Europe PMC Reaxys:3903735 Reaxys pentanoate IUPAC CH3-[CH2]3-COO(-) IUPAC n-propylacetate ChEBI pentanoate UniProt pentanoic acid, ion(1-) ChemIDplus The L-enantiomer of cysteinate(1-). -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-M 120.15128 120.01247 N[C@@H](CS)C([O-])=O Beilstein:4128886 Gmelin:325857 Reaxys:4128886 L-cysteinate(1-) hydrogen L-cysteinate chebi_ontology (2R)-2-amino-3-mercaptopropanoate (2R)-2-amino-3-sulfanylpropanoate L-cysteine anion L-cysteine monoanion CHEBI:32442 L-cysteinate(1-) Beilstein:4128886 Beilstein Gmelin:325857 Gmelin Reaxys:4128886 Reaxys L-cysteinate(1-) JCBN hydrogen L-cysteinate IUPAC (2R)-2-amino-3-mercaptopropanoate ChEBI (2R)-2-amino-3-sulfanylpropanoate IUPAC L-cysteine anion NIST_Chemistry_WebBook L-cysteine monoanion JCBN The L-enantiomer of cysteinate(2-). -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-L 119.14334 119.00520 N[C@@H](C[S-])C([O-])=O Beilstein:5921923 Gmelin:325856 Reaxys:5921923 L-cysteinate L-cysteinate(2-) chebi_ontology (2R)-2-amino-3-sulfidopropanoate L-cysteine dianion CHEBI:32443 L-cysteinate(2-) Beilstein:5921923 Beilstein Gmelin:325856 Gmelin Reaxys:5921923 Reaxys L-cysteinate IUPAC L-cysteinate(2-) JCBN (2R)-2-amino-3-sulfidopropanoate IUPAC L-cysteine dianion JCBN The L-enantiomer of cysteinium. +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-O 122.16716 122.02703 [NH3+][C@@H](CS)C(O)=O Gmelin:325860 L-cysteinium chebi_ontology (1R)-1-carboxy-2-mercaptoethanaminium (1R)-1-carboxy-2-sulfanylethanaminium L-cysteine cation L-cysteinium(1+) CHEBI:32445 L-cysteinium Gmelin:325860 Gmelin L-cysteinium IUPAC (1R)-1-carboxy-2-mercaptoethanaminium ChEBI (1R)-1-carboxy-2-sulfanylethanaminium IUPAC L-cysteine cation JCBN L-cysteinium(1+) ChEBI The D-enantiomer of cysteinate(1-). -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-M 120.15128 120.01247 N[C@H](CS)C([O-])=O Gmelin:1006156 D-cysteinate(1-) hydrogen D-cysteinate chebi_ontology (2S)-2-amino-3-mercaptopropanoate (2S)-2-amino-3-sulfanylpropanoate D-cysteine monoanion CHEBI:32449 D-cysteinate(1-) Gmelin:1006156 Gmelin D-cysteinate(1-) JCBN hydrogen D-cysteinate IUPAC (2S)-2-amino-3-mercaptopropanoate ChEBI (2S)-2-amino-3-sulfanylpropanoate IUPAC D-cysteine monoanion JCBN The D-enantiomer of cysteinate(2-). -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-L 119.14334 119.00520 N[C@H](C[S-])C([O-])=O Gmelin:1342792 D-cysteinate D-cysteinate(2-) chebi_ontology (2S)-2-amino-3-sulfidopropanoate D-cysteine dianion CHEBI:32450 D-cysteinate(2-) Gmelin:1342792 Gmelin D-cysteinate IUPAC D-cysteinate(2-) JCBN (2S)-2-amino-3-sulfidopropanoate IUPAC D-cysteine dianion JCBN The D-enantiomer of cysteinium. +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-O 122.16716 122.02703 [NH3+][C@H](CS)C(O)=O Gmelin:363237 D-cysteinium chebi_ontology (1S)-1-carboxy-2-mercaptoethanaminium (1S)-1-carboxy-2-sulfanylethanaminium D-cysteine cation CHEBI:32451 D-cysteinium Gmelin:363237 Gmelin D-cysteinium IUPAC (1S)-1-carboxy-2-mercaptoethanaminium ChEBI (1S)-1-carboxy-2-sulfanylethanaminium IUPAC D-cysteine cation JCBN A sulfur-containing amino-acid anion that is the conjugate base of cysteine, obtained by deprotonation of the carboxy group. -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1 XUJNEKJLAYXESH-UHFFFAOYSA-M 120.15128 120.01247 NC(CS)C([O-])=O Beilstein:4128885 Gmelin:363235 Reaxys:4128885 cysteinate(1-) hydrogen cysteinate chebi_ontology 2-amino-3-mercaptopropanoate 2-amino-3-sulfanylpropanoate cys(-) cysteine monoanion CHEBI:32456 cysteinate(1-) Beilstein:4128885 Beilstein Gmelin:363235 Gmelin Reaxys:4128885 Reaxys cysteinate(1-) JCBN hydrogen cysteinate IUPAC 2-amino-3-mercaptopropanoate ChEBI 2-amino-3-sulfanylpropanoate IUPAC cys(-) IUPAC cysteine monoanion JCBN -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2 XUJNEKJLAYXESH-UHFFFAOYSA-L 119.14334 119.00520 NC(C[S-])C([O-])=O Gmelin:49990 cysteinate cysteinate(2-) chebi_ontology 2-amino-3-sulfidopropanoate cysteine dianion CHEBI:32457 cysteinate(2-) Gmelin:49990 Gmelin cysteinate IUPAC cysteinate(2-) JCBN 2-amino-3-sulfidopropanoate IUPAC cysteine dianion JCBN +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1 XUJNEKJLAYXESH-UHFFFAOYSA-O 122.16716 122.02703 [NH3+]C(CS)C(O)=O Gmelin:325859 1-carboxy-2-sulfanylethanaminium cysteinium chebi_ontology 1-carboxy-2-mercaptoethanaminium H2cys(+) cysteine cation CHEBI:32458 cysteinium Gmelin:325859 Gmelin 1-carboxy-2-sulfanylethanaminium IUPAC cysteinium JCBN 1-carboxy-2-mercaptoethanaminium ChEBI H2cys(+) IUPAC cysteine cation JCBN An aromatic amino-acid anion that is the conjugate base of phenylalanine, arising from deprotonation of the carboxy group. -1 C9H10NO2 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/p-1 COLNVLDHVKWLRT-UHFFFAOYSA-M 164.18120 164.07170 NC(Cc1ccccc1)C([O-])=O Gmelin:329083 phenylalaninate chebi_ontology 2-amino-3-phenylpropanoate phenylalanine anion CHEBI:32504 phenylalaninate Gmelin:329083 Gmelin phenylalaninate IUPAC 2-amino-3-phenylpropanoate IUPAC phenylalanine anion JCBN An alpha-amino-acid cation that is the conjugate acid of phenylalanine, arising from protonation of the amino group. +1 C9H12NO2 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/p+1 COLNVLDHVKWLRT-UHFFFAOYSA-O 166.19710 166.08626 [NH3+]C(Cc1ccccc1)C(O)=O phenylalaninium chebi_ontology 1-carboxy-2-phenylethanaminium phenylalanine cation CHEBI:32505 phenylalaninium phenylalaninium IUPAC 1-carboxy-2-phenylethanaminium IUPAC phenylalanine cation JCBN An alpha-amino-acid cation that is the conjugate acid of glycine, arising from protonation of the amino. +1 C2H6NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/p+1 DHMQDGOQFOQNFH-UHFFFAOYSA-O 76.07458 76.03930 [NH3+]CC(O)=O Gmelin:323509 glycinium chebi_ontology H2gly(+) NH3(+)-CH2-COOH carboxymethanaminium glycine cation CHEBI:32507 glycinium Gmelin:323509 Gmelin glycinium IUPAC H2gly(+) IUPAC NH3(+)-CH2-COOH IUPAC carboxymethanaminium IUPAC glycine cation JCBN An alpha-amino-acid anion that is the conjugate base of glycine, arising from deprotonation of the carboxy group. -1 C2H4NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/p-1 DHMQDGOQFOQNFH-UHFFFAOYSA-M 74.05870 74.02475 NCC([O-])=O Beilstein:1852023 Gmelin:81890 Reaxys:1852023 UM-BBD_compID:c0559 glycinate chebi_ontology H2N-CH2-COO(-) aminoacetate gly(-) glycine anion CHEBI:32508 glycinate Beilstein:1852023 Beilstein Gmelin:81890 Gmelin Reaxys:1852023 Reaxys UM-BBD_compID:c0559 UM-BBD glycinate IUPAC H2N-CH2-COO(-) IUPAC aminoacetate IUPAC gly(-) IUPAC glycine anion JCBN A pyridinemonocarboxylate that is the conjugate base of nicotinic acid, arising from deprotonation of the carboxy group; major species at pH 7.3. -1 C6H4NO2 InChI=1S/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9)/p-1 PVNIIMVLHYAWGP-UHFFFAOYSA-M 122.10150 122.02475 [O-]C(=O)c1cccnc1 CHEBI:14650 CHEBI:22851 CHEBI:25530 Beilstein:3539722 Gmelin:327384 KEGG:C00253 MetaCyc:NIACINE PMID:17190852 PMID:21742010 PMID:21953179 Reaxys:3539722 nicotinate pyridine-3-carboxylate chebi_ontology 3-pyridinecarboxylate CHEBI:32544 nicotinate Beilstein:3539722 Beilstein Gmelin:327384 Gmelin PMID:17190852 Europe PMC PMID:21742010 Europe PMC PMID:21953179 Europe PMC Reaxys:3539722 Reaxys nicotinate UniProt pyridine-3-carboxylate IUPAC 3-pyridinecarboxylate ChEBI An alpha-amino-acid anion that is the conjugate base of lysine, arising from deprotonation of the carboxy group. -1 C6H13N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p-1 KDXKERNSBIXSRK-UHFFFAOYSA-M 145.17970 145.09825 NCCCCC(N)C([O-])=O Gmelin:815095 lysinate chebi_ontology 2,6-diaminohexanoate lys(-) lysinate(1-) lysine anion CHEBI:32563 lysinate Gmelin:815095 Gmelin lysinate IUPAC 2,6-diaminohexanoate IUPAC lys(-) IUPAC lysinate(1-) ChEBI lysine anion JCBN An alpha-amino-acid cation that is the conjugate acid of lysine, having two cationic amino groups and an anionic carboxy group. +1 C6H15N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1 KDXKERNSBIXSRK-UHFFFAOYSA-O 147.19558 147.11280 [NH3+]CCCCC([NH3+])C([O-])=O lysinium lysinium(1+) chebi_ontology 2,6-diammoniohexanoate lysine monocation CHEBI:32564 lysinium(1+) lysinium IUPAC lysinium(1+) JCBN 2,6-diammoniohexanoate IUPAC lysine monocation JCBN An alpha-amino-acid cation obtained by protonation of both amino groups of lysine. +2 C6H16N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+2 KDXKERNSBIXSRK-UHFFFAOYSA-P 148.20352 148.12008 [NH3+]CCCCC([NH3+])C(O)=O lysinediium lysinium(2+) chebi_ontology 1-carboxypentane-1,5-diaminium lysine dication CHEBI:32565 lysinium(2+) lysinediium IUPAC lysinium(2+) JCBN 1-carboxypentane-1,5-diaminium IUPAC lysine dication JCBN An acene that consists of four ortho-fused benzene rings in a rectilinear arrangement. 0 C18H12 InChI=1S/C18H12/c1-2-6-14-10-18-12-16-8-4-3-7-15(16)11-17(18)9-13(14)5-1/h1-12H IFLREYGFSNHWGE-UHFFFAOYSA-N 228.28788 228.09390 c1ccc2cc3cc4ccccc4cc3cc2c1 Beilstein:1909299 CAS:92-24-0 Gmelin:306993 PMID:11493061 PMID:24655187 Reaxys:1909299 Wikipedia:Tetracene tetracene chebi_ontology 2,3-benzanthracene benz[b]anthracene naphthacene CHEBI:32600 tetracene Beilstein:1909299 Beilstein CAS:92-24-0 ChemIDplus CAS:92-24-0 NIST Chemistry WebBook Gmelin:306993 Gmelin PMID:11493061 Europe PMC PMID:24655187 Europe PMC Reaxys:1909299 Reaxys tetracene IUPAC 2,3-benzanthracene NIST_Chemistry_WebBook benz[b]anthracene NIST_Chemistry_WebBook naphthacene IUPAC Gmelin:101585 isoleucinate chebi_ontology ile(-) isoleucine anion rel-(2R,3R)-2-amino-3-methylpentanoate CHEBI:32612 isoleucinate Gmelin:101585 Gmelin isoleucinate IUPAC ile(-) IUPAC isoleucine anion JCBN rel-(2R,3R)-2-amino-3-methylpentanoate IUPAC Gmelin:1651827 isoleucinium chebi_ontology H2ile(+) isoleucine cation rel-(1R,2R)-1-carboxy-2-methylbutan-1-aminium CHEBI:32613 isoleucinium Gmelin:1651827 Gmelin isoleucinium IUPAC H2ile(+) IUPAC isoleucine cation JCBN rel-(1R,2R)-1-carboxy-2-methylbutan-1-aminium IUPAC An alpha-amino-acid anion that is the conjugate base of leucine, arising from deprotonation of the carboxy group. -1 C6H12NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/p-1 ROHFNLRQFUQHCH-UHFFFAOYSA-M 130.16502 130.08735 CC(C)CC(N)C([O-])=O Reaxys:5245805 leucinate chebi_ontology 2-amino-4-methylpentanoate leu(-) leucine anion CHEBI:32627 leucinate Reaxys:5245805 Reaxys leucinate IUPAC 2-amino-4-methylpentanoate IUPAC leu(-) IUPAC leucine anion JCBN An alpha-amino-acid cation that is the conjugate acid of leucine, arising from protonation of the amino group. +1 C6H14NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/p+1 ROHFNLRQFUQHCH-UHFFFAOYSA-O 132.18090 132.10191 CC(C)CC([NH3+])C(O)=O Gmelin:1651836 leucinium chebi_ontology 1-carboxy-3-methylbutan-1-aminium H2leu(+) leucine cation CHEBI:32628 leucinium Gmelin:1651836 Gmelin leucinium IUPAC 1-carboxy-3-methylbutan-1-aminium IUPAC H2leu(+) IUPAC leucine cation JCBN The L-enantiomer of methioninate. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-M 148.20444 148.04377 CSCC[C@H](N)C([O-])=O Beilstein:4740675 Gmelin:326566 Reaxys:4740675 L-methioninate chebi_ontology (2S)-2-amino-4-(methylsulfanyl)butanoate L-methionine anion CHEBI:32631 L-methioninate Beilstein:4740675 Beilstein Gmelin:326566 Gmelin Reaxys:4740675 Reaxys L-methioninate IUPAC (2S)-2-amino-4-(methylsulfanyl)butanoate IUPAC L-methionine anion JCBN The L-enantiomer of methioninium. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-O 150.22032 150.05833 CSCC[C@H]([NH3+])C(O)=O Gmelin:1568767 L-methioninium chebi_ontology (1S)-1-carboxy-3-(methylsulfanyl)propan-1-aminium L-methionine cation CHEBI:32632 L-methioninium Gmelin:1568767 Gmelin L-methioninium IUPAC (1S)-1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC L-methionine cation JCBN The D-enantiomer of methioninate. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-M 148.20444 148.04377 CSCC[C@@H](N)C([O-])=O Gmelin:720123 D-methioninate chebi_ontology (2R)-2-amino-4-(methylsulfanyl)butanoate D-methionine anion CHEBI:32637 D-methioninate Gmelin:720123 Gmelin D-methioninate IUPAC (2R)-2-amino-4-(methylsulfanyl)butanoate IUPAC D-methionine anion JCBN The D-enantiomer of methioninium. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-O 150.22032 150.05833 CSCC[C@@H]([NH3+])C(O)=O D-methioninium chebi_ontology (1R)-1-carboxy-3-(methylsulfanyl)propan-1-aminium D-methionine cation CHEBI:32638 D-methioninium D-methioninium IUPAC (1R)-1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC D-methionine cation JCBN A sulfur-containing amino-acid anion that is the conjugate base of methionine, arising from deprotonation of the carboxy group. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1 FFEARJCKVFRZRR-UHFFFAOYSA-M 148.20444 148.04377 CSCCC(N)C([O-])=O Beilstein:3937270 Gmelin:326565 Reaxys:3937270 methioninate chebi_ontology 2-amino-4-(methylsulfanyl)butanoate met(-) methionine anion CHEBI:32644 methioninate Beilstein:3937270 Beilstein Gmelin:326565 Gmelin Reaxys:3937270 Reaxys methioninate IUPAC 2-amino-4-(methylsulfanyl)butanoate IUPAC met(-) IUPAC methionine anion JCBN A sulfur-containing amino-acid cation that is the conjugate acid of methionine, arising from protonation of the amino group. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1 FFEARJCKVFRZRR-UHFFFAOYSA-O 150.22032 150.05833 CSCCC([NH3+])C(O)=O Gmelin:326567 methioninium chebi_ontology 1-carboxy-3-(methylsulfanyl)propan-1-aminium H2met(+) methionine cation CHEBI:32646 methioninium Gmelin:326567 Gmelin methioninium IUPAC 1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC H2met(+) IUPAC methionine cation JCBN -1 C6H13N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p-1 ODKSFYDXXFIFQN-UHFFFAOYSA-M 173.19318 173.10440 NC(CCCNC(N)=N)C([O-])=O Gmelin:603497 argininate chebi_ontology 2-amino-5-(carbamimidamido)pentanoate 2-amino-5-guanidinopentanoate arg(-) arginine anion CHEBI:32695 argininate Gmelin:603497 Gmelin argininate IUPAC 2-amino-5-(carbamimidamido)pentanoate IUPAC 2-amino-5-guanidinopentanoate JCBN arg(-) IUPAC arginine anion JCBN +1 C6H15N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1 ODKSFYDXXFIFQN-UHFFFAOYSA-O 175.20906 175.11895 NC(=[NH2+])NCCCC([NH3+])C([O-])=O Gmelin:1345599 argininium argininium(1+) chebi_ontology 2-ammonio-5-guanidiniopentanoate H2arg(+) arginine arginine monocation CHEBI:32696 argininium(1+) Gmelin:1345599 Gmelin argininium IUPAC argininium(1+) JCBN 2-ammonio-5-guanidiniopentanoate JCBN H2arg(+) IUPAC arginine UniProt arginine monocation JCBN +2 C6H16N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+2 ODKSFYDXXFIFQN-UHFFFAOYSA-P 176.21700 176.12623 NC(=[NH2+])NCCCC([NH3+])C(O)=O argininediium argininium(2+) chebi_ontology (1-carboxy-4-guanidiniobutyl)ammonium H3arg(2+) arginine dication CHEBI:32697 argininium(2+) argininediium IUPAC argininium(2+) JCBN (1-carboxy-4-guanidiniobutyl)ammonium ChEBI H3arg(2+) IUPAC arginine dication JCBN An alpha-amino-acid anion that is the conjugate base of tyrosine, arising from deprotonation of the carboxy group. -1 C9H10NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/p-1 OUYCCCASQSFEME-UHFFFAOYSA-M 180.18064 180.06662 NC(Cc1ccc(O)cc1)C([O-])=O Beilstein:3548387 Beilstein:4139515 Gmelin:329372 hydrogen tyrosinate tyrosinate(1-) chebi_ontology 2-amino-3-(4-hydroxyphenyl)propanoate tyrosine anion CHEBI:32784 tyrosinate(1-) Beilstein:3548387 Beilstein Beilstein:4139515 Beilstein Gmelin:329372 Gmelin hydrogen tyrosinate IUPAC tyrosinate(1-) JCBN 2-amino-3-(4-hydroxyphenyl)propanoate IUPAC tyrosine anion JCBN -2 C9H9NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/p-2 OUYCCCASQSFEME-UHFFFAOYSA-L 179.17270 179.05934 NC(Cc1ccc([O-])cc1)C([O-])=O tyrosinate tyrosinate(2-) chebi_ontology 2-amino-3-(4-oxidophenyl)propanoate tyrosine dianion CHEBI:32785 tyrosinate(2-) tyrosinate IUPAC tyrosinate(2-) JCBN 2-amino-3-(4-oxidophenyl)propanoate IUPAC tyrosine dianion JCBN An alpha-amino-acid cation that is the conjugate acid of tyrosine, arising from protonation of the amino group. +1 C9H12NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/p+1 OUYCCCASQSFEME-UHFFFAOYSA-O 182.19652 182.08117 [NH3+]C(Cc1ccc(O)cc1)C(O)=O tyrosinium chebi_ontology 1-carboxy-2-(4-hydroxyphenyl)ethanaminium tyrosine cation CHEBI:32786 tyrosinium tyrosinium IUPAC 1-carboxy-2-(4-hydroxyphenyl)ethanaminium IUPAC tyrosine cation JCBN A 2-oxo monocarboxylic acid that is the 2-keto derivative of propionic acid. It is a metabolite obtained during glycolysis. 0 C3H4O3 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6) LCTONWCANYUPML-UHFFFAOYSA-N 88.06206 88.01604 CC(=O)C(O)=O CHEBI:26466 CHEBI:45253 CHEBI:8685 Beilstein:506211 CAS:127-17-3 DrugBank:DB00119 ECMDB:ECMDB00243 Gmelin:101087 HMDB:HMDB0000243 KEGG:C00022 KNApSAcK:C00001200 LIPID_MAPS_instance:LMFA01060077 MetaCyc:PYRUVATE PDBeChem:PYR PMID:11762589 PMID:19260671 PMID:22150460 PMID:22233273 PMID:22735334 PMID:22770225 Reaxys:506211 Wikipedia:Pyruvic_acid YMDB:YMDB00175 2-oxopropanoic acid PYRUVIC ACID Pyruvic acid pyruvic acid chebi_ontology 2-Oxopropanoic acid 2-Oxopropansaeure 2-Oxopropionsaeure 2-ketopropionic acid 2-oxopropanoic acid Acetylformic acid BTS Brenztraubensaeure CH3COCOOH Pyroracemic acid acetylformic acid acide pyruvique alpha-Oxopropionsaeure alpha-ketopropionic acid CHEBI:32816 pyruvic acid Beilstein:506211 Beilstein CAS:127-17-3 ChemIDplus CAS:127-17-3 NIST Chemistry WebBook Gmelin:101087 Gmelin LIPID_MAPS_instance:LMFA01060077 LIPID MAPS PMID:11762589 Europe PMC PMID:19260671 Europe PMC PMID:22150460 Europe PMC PMID:22233273 Europe PMC PMID:22735334 Europe PMC PMID:22770225 Europe PMC Reaxys:506211 Reaxys 2-oxopropanoic acid IUPAC PYRUVIC ACID PDBeChem Pyruvic acid KEGG_COMPOUND pyruvic acid ChEBI 2-Oxopropanoic acid KEGG_COMPOUND 2-Oxopropansaeure ChemIDplus 2-Oxopropionsaeure ChemIDplus 2-ketopropionic acid ChemIDplus 2-oxopropanoic acid ChEBI Acetylformic acid HMDB BTS ChemIDplus Brenztraubensaeure ChEBI CH3COCOOH NIST_Chemistry_WebBook Pyroracemic acid KEGG_COMPOUND acetylformic acid NIST_Chemistry_WebBook acide pyruvique ChEBI alpha-Oxopropionsaeure ChemIDplus alpha-ketopropionic acid NIST_Chemistry_WebBook A serinate that is the conjugate base of L-serine, obtained by deprotonation of the carboxy group. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-M 104.08468 104.03532 N[C@@H](CO)C([O-])=O Beilstein:4372751 Gmelin:324693 L-serinate chebi_ontology (2S)-2-amino-3-hydroxypropanoate L-serine anion CHEBI:32836 L-serinate Beilstein:4372751 Beilstein Gmelin:324693 Gmelin L-serinate IUPAC (2S)-2-amino-3-hydroxypropanoate IUPAC L-serine anion JCBN A serinium that is the conjugate acid of L-serine, obtained by protonation of the amino group. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-O 106.10056 106.04987 [NH3+][C@@H](CO)C(O)=O L-serinium chebi_ontology (1S)-1-carboxy-2-hydroxyethanaminium L-serine cation CHEBI:32837 L-serinium L-serinium IUPAC (1S)-1-carboxy-2-hydroxyethanaminium IUPAC L-serine cation JCBN The D-enantiomer of serinate. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-M 104.08468 104.03532 N[C@H](CO)C([O-])=O Gmelin:745975 D-serinate chebi_ontology (2R)-2-amino-3-hydroxypropanoate D-serine anion CHEBI:32840 D-serinate Gmelin:745975 Gmelin D-serinate IUPAC (2R)-2-amino-3-hydroxypropanoate IUPAC D-serine anion JCBN The D-enantiomer of serinium. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-O 106.10056 106.04987 [NH3+][C@H](CO)C(O)=O D-serinium chebi_ontology (1R)-1-carboxy-2-hydroxyethanaminium D-serine cation CHEBI:32841 D-serinium D-serinium IUPAC (1R)-1-carboxy-2-hydroxyethanaminium IUPAC D-serine cation JCBN An alpha-amino-acid anion that is the conjugate base of serine. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1 MTCFGRXMJLQNBG-UHFFFAOYSA-M 104.08468 104.03532 NC(CO)C([O-])=O Gmelin:324692 serinate chebi_ontology 2-amino-3-hydroxypropanoate serine anion CHEBI:32845 serinate Gmelin:324692 Gmelin serinate IUPAC 2-amino-3-hydroxypropanoate IUPAC serine anion JCBN An alpha-amino-acid cation that is the conjugate acid of serine. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1 MTCFGRXMJLQNBG-UHFFFAOYSA-O 106.10056 106.04987 [NH3+]C(CO)C(O)=O Gmelin:1925675 serinium chebi_ontology 1-carboxy-2-hydroxyethanaminium serine cation CHEBI:32846 serinium Gmelin:1925675 Gmelin serinium IUPAC 1-carboxy-2-hydroxyethanaminium IUPAC serine cation JCBN -1 C5H10NO2 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/p-1 KZSNJWFQEVHDMF-UHFFFAOYSA-M 116.13844 116.07170 CC(C)C(N)C([O-])=O Gmelin:49876 valinate chebi_ontology 2-amino-3-methylbutanoate val(-) valine anion CHEBI:32859 valinate Gmelin:49876 Gmelin valinate IUPAC 2-amino-3-methylbutanoate IUPAC val(-) IUPAC valine anion JCBN +1 C5H12NO2 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/p+1 KZSNJWFQEVHDMF-UHFFFAOYSA-O 118.15432 118.08626 CC(C)C([NH3+])C(O)=O Gmelin:1651060 valinium chebi_ontology 1-carboxy-2-methylpropan-1-aminium H2val(+) valine cation CHEBI:32860 valinium Gmelin:1651060 Gmelin valinium IUPAC 1-carboxy-2-methylpropan-1-aminium IUPAC H2val(+) IUPAC valine cation JCBN A compound formally derived from ammonia by replacing three hydrogen atoms by hydrocarbyl groups. 0 NR3 14.00670 14.00307 [*]N([*])[*] CHEBI:26879 CHEBI:9458 KEGG:C02196 Tertiary amine tertiary amines chebi_ontology R3N tertiaeres Amin CHEBI:32876 tertiary amine Tertiary amine KEGG_COMPOUND tertiary amines IUPAC R3N IUPAC tertiaeres Amin ChEBI A compound formally derived from ammonia by replacing one hydrogen atom by a hydrocarbyl group. 0 H2NR 16.02260 16.01872 N[*] CHEBI:26263 CHEBI:26265 CHEBI:8407 CHEBI:8409 KEGG:C00375 KEGG:C00893 KEGG:C02580 Primary amine primary amines chebi_ontology Primary monoamine R-NH2 RCH2NH2 primaeres Amin CHEBI:32877 primary amine Primary amine KEGG_COMPOUND primary amines IUPAC Primary monoamine KEGG_COMPOUND R-NH2 IUPAC RCH2NH2 KEGG_COMPOUND primaeres Amin ChEBI 0 C3H8 InChI=1S/C3H8/c1-3-2/h3H2,1-2H3 ATUOYWHBWRKTHZ-UHFFFAOYSA-N 44.09562 44.06260 CCC Beilstein:1730718 CAS:74-98-6 Gmelin:25044 propane chebi_ontology CH3-CH2-CH3 E944 Propan CHEBI:32879 propane Beilstein:1730718 Beilstein CAS:74-98-6 ChemIDplus CAS:74-98-6 NIST Chemistry WebBook Gmelin:25044 Gmelin propane IUPAC propane UniProt CH3-CH2-CH3 IUPAC E944 ChEBI Propan ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. CHEBI:13814 CHEBI:22474 CHEBI:2641 KEGG:C00706 Amine amines chebi_ontology Amin Substituted amine CHEBI:32952 amine Amine KEGG_COMPOUND amines IUPAC Amin ChEBI Substituted amine KEGG_COMPOUND -1 C5H11N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p-1 AHLPHDHHMVZTML-UHFFFAOYSA-M 131.15312 131.08260 NCCCC(N)C([O-])=O CHEBI:11448 CHEBI:19370 Gmelin:1242186 2,5-diaminopentanoate ornithinate chebi_ontology ornithine anion CHEBI:32964 ornithinate Gmelin:1242186 Gmelin 2,5-diaminopentanoate IUPAC ornithinate IUPAC ornithine anion JCBN An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG:C00241 Amide amides chebi_ontology CHEBI:32988 amide Amide KEGG_COMPOUND amides IUPAC A calcium salt with formula CCaO3. 0 CCaO3 CO3.Ca InChI=1S/CH2O3.Ca/c2-1(3)4;/h(H2,2,3,4);/q;+2/p-2 VTYYLEPIZMXCLO-UHFFFAOYSA-L 100.087 99.94733 [Ca+2].C(=O)([O-])[O-] BPDB:108 CAS:471-34-1 DrugBank:DB06724 KEGG:C08129 KEGG:D00932 PPDB:108 Reaxys:8008338 Wikipedia:Calcium_carbonate Calcium carbonate calcium carbonate calcium trioxidocarbonate chebi_ontology CaCO3 Calciumcarbonat E 170 Kalziumkarbonat Precipitated calcium carbonate calcium carbonate (1:1) carbonate de calcium carbonato de calcio carbonic acid calcium salt (1:1) kohlensaurer Kalk CHEBI:3311 calcium carbonate CAS:471-34-1 ChemIDplus CAS:471-34-1 KEGG COMPOUND CAS:471-34-1 NIST Chemistry WebBook Reaxys:8008338 Reaxys Calcium carbonate KEGG_COMPOUND calcium carbonate IUPAC calcium trioxidocarbonate IUPAC CaCO3 IUPAC Calciumcarbonat ChEBI E 170 ChEBI Kalziumkarbonat ChEBI Precipitated calcium carbonate KEGG_COMPOUND calcium carbonate (1:1) ChemIDplus carbonate de calcium ChEBI carbonato de calcio ChEBI carbonic acid calcium salt (1:1) ChemIDplus kohlensaurer Kalk ChEBI A benzopyran consisting of a pyran ring having a benzene ring ortho-fused across positions 2 and 3. 0 C9H10O InChI=1S/C9H10O/c1-2-6-9-8(4-1)5-3-7-10-9/h1-2,4,6H,3,5,7H2 VZWXIQHBIQLMPN-UHFFFAOYSA-N 134.17510 134.07316 C1COc2ccccc2C1 Beilstein:116150 CAS:493-08-3 Gmelin:122981 Reaxys:116150 3,4-dihydro-2H-chromene chromane chebi_ontology 3,4-dihydro-2H-1-benzopyran 3,4-dihydrobenzo[b]pyran Chroman CHEBI:33224 chromane Beilstein:116150 Beilstein CAS:493-08-3 ChemIDplus CAS:493-08-3 NIST Chemistry WebBook Gmelin:122981 Gmelin Reaxys:116150 Reaxys 3,4-dihydro-2H-chromene IUPAC chromane IUPAC 3,4-dihydro-2H-1-benzopyran NIST_Chemistry_WebBook 3,4-dihydrobenzo[b]pyran ChEBI Chroman NIST_Chemistry_WebBook A biochemical role played by any micronutrient that is an organic compound. Vitamins are present in foods in small amounts and are essential to normal metabolism and biochemical functions, usually as coenzymes. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines. CHEBI:10004 CHEBI:27305 Wikipedia:Vitamin chebi_ontology vitamin vitamina vitaminas vitamine vitamines vitamins vitaminum CHEBI:33229 vitamin (role) vitamin ChEBI vitamina ChEBI vitaminas ChEBI vitamine ChEBI vitamines ChEBI vitamins ChEBI vitaminum ChEBI A substance that kills or slows the growth of Mycobacterium tuberculosis and is used in the treatment of tuberculosis. chebi_ontology antitubercular antitubercular agents antitubercular drug antitubercular drugs tuberculostatic agent CHEBI:33231 antitubercular agent antitubercular ChEBI antitubercular agents ChEBI antitubercular drug ChEBI antitubercular drugs ChEBI tuberculostatic agent ChEBI Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:33232 application A particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle elementary particle IUPAC elementary particles ChEBI Any member of a group of fat-soluble chromanols that exhibit biological activity against vitamin E deficiency. The vitamers in this class consists of a chroman-6-ol core which is substituted at position 2 by a methyl group and (also at position 2) either a saturated or a triply-unsaturated hydrocarbon chain consisting of three isoprenoid units. The major function of vitamin E is to act as a natural antioxidant by scavenging free radicals and molecular oxygen. MetaCyc:Vitamin-E PMID:33684201 PMID:33847203 PMID:33896432 PMID:34277234 PMID:34278890 PMID:7898412 PMID:7901680 Wikipedia:Vitamin_E vitamin E chebi_ontology vitamin E vitamer vitamin E vitamers vitamin-E vitamins E CHEBI:33234 vitamin E PMID:33684201 Europe PMC PMID:33847203 Europe PMC PMID:33896432 Europe PMC PMID:34277234 Europe PMC PMID:34278890 Europe PMC PMID:7898412 Europe PMC PMID:7901680 Europe PMC vitamin E ChemIDplus vitamin E vitamer ChEBI vitamin E vitamers ChEBI vitamin-E ChEBI vitamins E ChEBI A monoatomic entity is a molecular entity consisting of a single atom. chebi_ontology atomic entity monoatomic entities CHEBI:33238 monoatomic entity atomic entity ChEBI monoatomic entities ChEBI An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands). coordination entities coordination entity chebi_ontology coordination compounds CHEBI:33240 coordination entity coordination entities IUPAC coordination entity IUPAC coordination compounds ChEBI chebi_ontology oxoacid derivatives CHEBI:33241 oxoacid derivative oxoacid derivatives ChEBI chebi_ontology inorganic hydrides CHEBI:33242 inorganic hydride inorganic hydrides ChEBI An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system. chebi_ontology organic fundamental parents organic parent hydrides CHEBI:33245 organic fundamental parent organic fundamental parents ChEBI organic parent hydrides ChEBI Any substituent group which does not contain carbon. chebi_ontology inorganic groups CHEBI:33246 inorganic group inorganic groups ChEBI Any substituent group or skeleton containing carbon. chebi_ontology organic groups CHEBI:33247 organic group organic groups ChEBI A univalent group formed by removing a hydrogen atom from a hydrocarbon. hydrocarbyl group hydrocarbyl groups chebi_ontology groupe hydrocarbyle grupo hidrocarbilo grupos hidrocarbilo CHEBI:33248 hydrocarbyl group hydrocarbyl group IUPAC hydrocarbyl groups IUPAC groupe hydrocarbyle IUPAC grupo hidrocarbilo IUPAC grupos hidrocarbilo IUPAC Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group organyl groups chebi_ontology groupe organyle grupo organilo grupos organilo CHEBI:33249 organyl group organyl group IUPAC organyl groups IUPAC groupe organyle IUPAC grupo organilo IUPAC grupos organilo IUPAC A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus chebi_ontology Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi CHEBI:33252 atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons CHEBI:33253 nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide primary amides chebi_ontology CHEBI:33256 primary amide primary amide IUPAC primary amides IUPAC A molecular entity all atoms of which have the same atomic number. chebi_ontology homoatomic entity homoatomic molecular entities homoatomic molecular entity CHEBI:33259 elemental molecular entity homoatomic entity ChEBI homoatomic molecular entities ChEBI homoatomic molecular entity ChEBI An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 Wikipedia:Organosulfur_compounds organosulfur compound chebi_ontology organosulfur compounds CHEBI:33261 organosulfur compound organosulfur compound ChEBI organosulfur compounds ChEBI An anion consisting of more than one atom. chebi_ontology polyatomic anions CHEBI:33273 polyatomic anion polyatomic anions ChEBI chebi_ontology chemical messenger CHEBI:33280 molecular messenger chemical messenger ChEBI A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 PMID:12964249 PMID:22117953 PMID:22439833 PMID:22849268 PMID:22849276 PMID:22958833 chebi_ontology Antibiotika Antibiotikum antibiotic antibiotics antibiotique antimicrobial antimicrobial agents antimicrobials microbicide microbicides CHEBI:33281 antimicrobial agent PMID:12964249 Europe PMC PMID:22117953 Europe PMC PMID:22439833 Europe PMC PMID:22849268 Europe PMC PMID:22849276 Europe PMC PMID:22958833 Europe PMC Antibiotika ChEBI Antibiotikum ChEBI antibiotic ChEBI antibiotics ChEBI antibiotique IUPAC antimicrobial ChEBI antimicrobial agents ChEBI antimicrobials ChEBI microbicide ChEBI microbicides ChEBI A substance (or active part thereof) that kills or slows the growth of bacteria. chebi_ontology antibacterial agents antibacterials bactericide bactericides CHEBI:33282 antibacterial agent antibacterial agents ChEBI antibacterials ChEBI bactericide ChEBI bactericides ChEBI A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI An agrochemical is a substance that is used in agriculture or horticulture. Wikipedia:Agrochemical chebi_ontology agrichemical agrichemicals agricultural chemicals agrochemicals CHEBI:33286 agrochemical agrichemical ChEBI agrichemicals ChEBI agricultural chemicals ChEBI agrochemicals ChEBI A fertilizer is any substance that is added to soil or water to assist the growth of plants. chebi_ontology fertiliser fertilizers CHEBI:33287 fertilizer fertiliser ChEBI fertilizers ChEBI A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. chebi_ontology food material food materials food role foods foodstuff foodstuffs CHEBI:33290 food food material ChEBI food materials ChEBI food role ChEBI foods ChEBI foodstuff ChEBI foodstuffs ChEBI An energy-rich substance that can be transformed with release of usable energy. chebi_ontology CHEBI:33292 fuel A substance administered to aid diagnosis of a disease. chebi_ontology diagnostic aid CHEBI:33295 diagnostic agent diagnostic aid ChEBI A molecular entity containing one or more atoms of an alkali metal. chebi_ontology alkali metal molecular entities CHEBI:33296 alkali metal molecular entity alkali metal molecular entities ChEBI An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal. alkaline earth molecular entity chebi_ontology alkaline earth compounds alkaline earth molecular entities alkaline-earth compounds CHEBI:33299 alkaline earth molecular entity alkaline earth molecular entity ChEBI alkaline earth compounds ChEBI alkaline earth molecular entities ChEBI alkaline-earth compounds ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens chebi_ontology group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes CHEBI:33300 pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities CHEBI:33302 pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. PMID:17084588 chalcogen chalcogens chebi_ontology Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements CHEBI:33303 chalcogen PMID:17084588 Europe PMC chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements CHEBI:33306 carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. 0 CO2R2 44.010 43.98983 [*]C(=O)O[*] CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester Carboxylic ester KEGG_COMPOUND carboxylic esters IUPAC a carboxylic ester UniProt carboxylic acid esters ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements chebi_ontology Hauptgruppenelement Hauptgruppenelemente main group element CHEBI:33318 main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI group 12 elements chebi_ontology zinc group element zinc group elements CHEBI:33340 zinc group element atom group 12 elements IUPAC zinc group element ChEBI zinc group elements ChEBI group 8 elements chebi_ontology iron group element iron group elements CHEBI:33356 iron group element atom group 8 elements IUPAC iron group element ChEBI iron group elements ChEBI group 9 elements chebi_ontology cobalt group element cobalt group elements CHEBI:33358 cobalt group element atom group 9 elements IUPAC cobalt group element ChEBI cobalt group elements ChEBI A serine zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-N 105.09262 105.04259 [NH3+][C@@H](CO)C([O-])=O MetaCyc:SER (2S)-2-ammonio-3-hydroxypropanoate L-serine zwitterion chebi_ontology L-serine CHEBI:33384 L-serine zwitterion (2S)-2-ammonio-3-hydroxypropanoate IUPAC L-serine zwitterion IUPAC L-serine UniProt chebi_ontology oxoacids of sulfur sulfur oxoacids CHEBI:33402 sulfur oxoacid oxoacids of sulfur ChEBI sulfur oxoacids ChEBI A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). hydracid chebi_ontology hydracids CHEBI:33405 hydracid hydracid IUPAC hydracids ChEBI chebi_ontology pnictogen oxoacids CHEBI:33408 pnictogen oxoacid pnictogen oxoacids ChEBI sulfur oxoacid derivative chebi_ontology sulfur oxoacid derivatives CHEBI:33424 sulfur oxoacid derivative sulfur oxoacid derivative ChEBI sulfur oxoacid derivatives ChEBI -1 0.00000 [*-] chebi_ontology monoatomic monoanions CHEBI:33429 monoatomic monoanion monoatomic monoanions ChEBI elemental halogen chebi_ontology elemental halogens CHEBI:33434 elemental halogen elemental halogen ChEBI elemental halogens ChEBI Arylmethyl groups and derivatives formed by substitution: ArCR2-. benzylic group benzylic groups chebi_ontology benzylic groups groupe benzylique CHEBI:33452 benzylic group benzylic group IUPAC benzylic groups IUPAC benzylic groups ChEBI groupe benzylique IUPAC A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons. phosphorus oxoacid chebi_ontology Oxosaeure des Phosphors oxoacids of phosphorus phosphorus oxoacids CHEBI:33457 phosphorus oxoacid phosphorus oxoacid ChEBI Oxosaeure des Phosphors ChEBI oxoacids of phosphorus ChEBI phosphorus oxoacids ChEBI pnictogen oxoanion chebi_ontology pnictogen oxoanions CHEBI:33459 pnictogen oxoanion pnictogen oxoanion ChEBI pnictogen oxoanions ChEBI phosphorus oxoanion chebi_ontology oxoanions of phosphorus phosphorus oxoanions CHEBI:33461 phosphorus oxoanion phosphorus oxoanion ChEBI oxoanions of phosphorus ChEBI phosphorus oxoanions ChEBI sulfur oxoanion chebi_ontology oxoanions of sulfur sulfur oxoanions CHEBI:33482 sulfur oxoanion sulfur oxoanion ChEBI oxoanions of sulfur ChEBI sulfur oxoanions ChEBI chalcogen oxoacid chebi_ontology chalcogen oxoacids CHEBI:33484 chalcogen oxoacid chalcogen oxoacid ChEBI chalcogen oxoacids ChEBI chalcogen oxoanion chebi_ontology chalcogen oxoanions CHEBI:33485 chalcogen oxoanion chalcogen oxoanion ChEBI chalcogen oxoanions ChEBI A molecular entity containing one or more atoms of a transition element. chebi_ontology transition element molecular entities transition metal molecular entity CHEBI:33497 transition element molecular entity transition element molecular entities ChEBI transition metal molecular entity ChEBI chebi_ontology alkali metal cations CHEBI:33504 alkali metal cation alkali metal cations ChEBI chebi_ontology alkaline earth cations alkaline earth metal cation alkaline-earth metal cations CHEBI:33513 alkaline earth cation alkaline earth cations ChEBI alkaline earth metal cation ChEBI alkaline-earth metal cations ChEBI chebi_ontology transition element cations transition metal cation CHEBI:33515 transition element cation transition element cations ChEBI transition metal cation ChEBI An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. CHEBI:25217 CHEBI:6788 KEGG:C00050 PMID:21784043 Wikipedia:Metal chebi_ontology elemental metal elemental metals metal element metal elements metals CHEBI:33521 metal atom PMID:21784043 Europe PMC elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI The sulfur oxoanion formed by deprotonation of sulfonic acid. -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h4H,(H,1,2,3)/p-1 BDHFUVZGWQCTTF-UHFFFAOYSA-M 81.07214 80.96519 [H]S([O-])(=O)=O Gmelin:971569 hydridotrioxidosulfate(1-) chebi_ontology SHO3(-) [SHO3](-) sulfonates CHEBI:33543 sulfonate Gmelin:971569 Gmelin hydridotrioxidosulfate(1-) IUPAC SHO3(-) IUPAC [SHO3](-) IUPAC sulfonates ChEBI sulfonic acid derivative chebi_ontology derivatives of sulfonic acid sulfonic acid derivatives CHEBI:33552 sulfonic acid derivative sulfonic acid derivative ChEBI derivatives of sulfonic acid ChEBI sulfonic acid derivatives ChEBI An amino-acid anion obtained by deprotonation of any alpha-amino acid. alpha-amino-acid anion chebi_ontology alpha-amino acid anions alpha-amino-acid anions CHEBI:33558 alpha-amino-acid anion alpha-amino-acid anion ChEBI alpha-amino acid anions ChEBI alpha-amino-acid anions ChEBI chebi_ontology s-block element s-block elements CHEBI:33559 s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. chebi_ontology p-block element p-block elements CHEBI:33560 p-block element atom p-block element ChEBI p-block elements ChEBI chebi_ontology d-block element d-block elements CHEBI:33561 d-block element atom d-block element ChEBI d-block elements ChEBI A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13428 CHEBI:13627 CHEBI:23027 PMID:17147560 PMID:18433345 Wikipedia:Carboxylic_acid carboxylic acid carboxylic acids chebi_ontology Carbonsaeure Carbonsaeuren Karbonsaeure RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid PMID:17147560 Europe PMC PMID:18433345 Europe PMC carboxylic acid IUPAC carboxylic acids IUPAC Carbonsaeure ChEBI Carbonsaeuren ChEBI Karbonsaeure ChEBI RC(=O)OH IUPAC acide carboxylique IUPAC acides carboxyliques IUPAC acido carboxilico IUPAC acidos carboxilicos IUPAC Any carboxylic acid having a sulfur substituent. chebi_ontology S-containing carboxylic acid S-containing carboxylic acids sulfur-containing carboxylic acids CHEBI:33576 sulfur-containing carboxylic acid S-containing carboxylic acid ChEBI S-containing carboxylic acids ChEBI sulfur-containing carboxylic acids ChEBI A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. chebi_ontology main group compounds main group molecular entities CHEBI:33579 main group molecular entity main group compounds ChEBI main group molecular entities ChEBI carbon group molecular entity chebi_ontology carbon group molecular entities CHEBI:33582 carbon group molecular entity carbon group molecular entity ChEBI carbon group molecular entities ChEBI Any molecule that consists of a series of atoms joined together to form a ring. Wikipedia:Cyclic_compound chebi_ontology cyclic compounds CHEBI:33595 cyclic compound cyclic compounds ChEBI A cyclic compound having as ring members atoms of the same element only. homocyclic compound homocyclic compounds chebi_ontology isocyclic compounds CHEBI:33597 homocyclic compound homocyclic compound IUPAC homocyclic compounds IUPAC isocyclic compounds IUPAC A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound carbocyclic compounds chebi_ontology carbocycle CHEBI:33598 carbocyclic compound carbocyclic compound IUPAC carbocyclic compounds IUPAC carbocycle ChEBI chebi_ontology hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI chebi_ontology polycyclic compounds CHEBI:33635 polycyclic compound polycyclic compounds ChEBI A molecule that features two fused rings. chebi_ontology bicyclic compounds CHEBI:33636 bicyclic compound bicyclic compounds ChEBI A polycyclic compound in which two rings have two, and only two, atoms in common. Such compounds have n common faces and 2n common atoms. ortho-fused polycyclic compounds chebi_ontology ortho-fused compounds CHEBI:33637 ortho-fused compound ortho-fused polycyclic compounds IUPAC ortho-fused compounds ChEBI Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds. aliphatic compounds chebi_ontology CHEBI:33653 aliphatic compound aliphatic compounds IUPAC A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compounds aromatic molecular entity chebi_ontology aromatics aromatische Verbindungen CHEBI:33655 aromatic compound aromatic compounds IUPAC aromatic molecular entity IUPAC aromatics ChEBI aromatische Verbindungen ChEBI Any monocyclic or polycyclic aromatic hydrocarbon. arene arenes chebi_ontology aromatic hydrocarbons CHEBI:33658 arene arene IUPAC arenes IUPAC aromatic hydrocarbons IUPAC chebi_ontology organic aromatic compounds CHEBI:33659 organic aromatic compound organic aromatic compounds ChEBI chebi_ontology monocyclic compounds CHEBI:33661 monocyclic compound monocyclic compounds ChEBI A mancude monocyclic hydrocarbon without side chains of the general formula CnHn (n is an even number) or CnHn+1 (n is an odd number). In systematic nomenclature an annulene with seven or more carbon atoms may be named [n]annulene, where n is the number of carbon atoms. annulene annulenes chebi_ontology CHEBI:33662 annulene annulene IUPAC annulenes IUPAC cyclic hydrocarbon chebi_ontology cyclic hydrocarbons CHEBI:33663 cyclic hydrocarbon cyclic hydrocarbon ChEBI cyclic hydrocarbons ChEBI monocyclic hydrocarbon monocyclic hydrocarbons chebi_ontology monocyclic hydrocarbons CHEBI:33664 monocyclic hydrocarbon monocyclic hydrocarbon ChEBI monocyclic hydrocarbons IUPAC monocyclic hydrocarbons ChEBI polycyclic hydrocarbon polycyclic hydrocarbons chebi_ontology CHEBI:33666 polycyclic hydrocarbon polycyclic hydrocarbon IUPAC polycyclic hydrocarbons IUPAC heteromonocyclic compound heteromonocyclic compounds chebi_ontology CHEBI:33670 heteromonocyclic compound heteromonocyclic compound IUPAC heteromonocyclic compounds IUPAC A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compounds chebi_ontology polyheterocyclic compounds CHEBI:33671 heteropolycyclic compound heteropolycyclic compounds IUPAC polyheterocyclic compounds ChEBI A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compounds chebi_ontology CHEBI:33672 heterobicyclic compound heterobicyclic compounds IUPAC chebi_ontology zinc group molecular entities CHEBI:33673 zinc group molecular entity zinc group molecular entities ChEBI An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity chebi_ontology s-block compounds s-block molecular entities CHEBI:33674 s-block molecular entity s-block molecular entity ChEBI s-block compounds ChEBI s-block molecular entities ChEBI A main group molecular entity that contains one or more atoms of a p-block element. chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity p-block compounds ChEBI p-block molecular entities ChEBI p-block molecular entitiy ChEBI A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element. d-block molecular entity chebi_ontology d-block compounds d-block molecular entities CHEBI:33676 d-block molecular entity d-block molecular entity ChEBI d-block compounds ChEBI d-block molecular entities ChEBI Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology CHEBI:33692 hydrides A macromolecule formed by a living organism. biopolymer chebi_ontology Biopolymere biomacromolecules biopolymers CHEBI:33694 biomacromolecule biopolymer IUPAC Biopolymere ChEBI biomacromolecules ChEBI biopolymers ChEBI chebi_ontology genetically encoded biomacromolecules genetically encoded biopolymers information biomacromolecules information biopolymers information macromolecule information macromolecules CHEBI:33695 information biomacromolecule genetically encoded biomacromolecules ChEBI genetically encoded biopolymers ChEBI information biomacromolecules ChEBI information biopolymers ChEBI information macromolecule ChEBI information macromolecules ChEBI chebi_ontology canonical amino-acid residue canonical amino-acid residues common amino acid residues proteinogenic amino-acid residues standard amino acid residues standard amino-acid residues CHEBI:33700 proteinogenic amino-acid residue canonical amino-acid residue ChEBI canonical amino-acid residues ChEBI common amino acid residues ChEBI proteinogenic amino-acid residues ChEBI standard amino acid residues ChEBI standard amino-acid residues ChEBI A cation consisting of more than one atom. chebi_ontology polyatomic cations CHEBI:33702 polyatomic cation polyatomic cations ChEBI amino-acid cation chebi_ontology amino acid cation amino-acid cations CHEBI:33703 amino-acid cation amino-acid cation ChEBI amino acid cation ChEBI amino-acid cations ChEBI An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group. 0 C2H4NO2R 74.05870 74.02420 NC([*])C(O)=O CHEBI:10208 CHEBI:13779 CHEBI:22442 CHEBI:2642 KEGG:C00045 KEGG:C05167 alpha-amino acid chebi_ontology Amino acid Amino acids alpha-amino acids alpha-amino carboxylic acids CHEBI:33704 alpha-amino acid alpha-amino acid IUPAC Amino acid KEGG_COMPOUND Amino acids KEGG_COMPOUND alpha-amino acids ChEBI alpha-amino acids JCBN alpha-amino carboxylic acids IUPAC A non-proteinogenic amino acid in which the amino group is located on the carbon atom at the position beta to the carboxy group. beta-amino acid chebi_ontology beta-amino acids CHEBI:33706 beta-amino acid beta-amino acid ChEBI beta-amino acids ChEBI A non-proteinogenic amino-acid in which the amino group is located on the carbon atom at the position gamma to the carboxy group. gamma-amino acid chebi_ontology gamma-amino acids CHEBI:33707 gamma-amino acid gamma-amino acid ChEBI gamma-amino acids ChEBI When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. amino-acid residue chebi_ontology amino acid residue amino-acid residues CHEBI:33708 amino-acid residue amino-acid residue IUPAC amino acid residue ChEBI amino-acid residues JCBN A carboxylic acid containing one or more amino groups. CHEBI:13815 CHEBI:22477 Wikipedia:Amino_acid chebi_ontology Aminocarbonsaeure Aminokarbonsaeure Aminosaeure amino acids CHEBI:33709 amino acid Aminocarbonsaeure ChEBI Aminokarbonsaeure ChEBI Aminosaeure ChEBI amino acids ChEBI chebi_ontology alpha-amino-acid residues CHEBI:33710 alpha-amino-acid residue alpha-amino-acid residues ChEBI alpha-amino-acid cation chebi_ontology alpha-amino acid cations alpha-amino-acid cations CHEBI:33719 alpha-amino-acid cation alpha-amino-acid cation ChEBI alpha-amino acid cations ChEBI alpha-amino-acid cations ChEBI carbohydrate acid chebi_ontology carbohydrate acids CHEBI:33720 carbohydrate acid carbohydrate acid ChEBI carbohydrate acids ChEBI carbohydrate acid anion chebi_ontology carbohydrate acid anions CHEBI:33721 carbohydrate acid anion carbohydrate acid anion ChEBI carbohydrate acid anions ChEBI iron group molecular entity chebi_ontology iron group molecular entities CHEBI:33744 iron group molecular entity iron group molecular entity ChEBI iron group molecular entities ChEBI cobalt group molecular entity chebi_ontology cobalt group molecular entities CHEBI:33767 cobalt group molecular entity cobalt group molecular entity ChEBI cobalt group molecular entities ChEBI An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:64710 hydroxy compounds chebi_ontology organic alcohol organic hydroxy compounds CHEBI:33822 organic hydroxy compound hydroxy compounds IUPAC organic alcohol ChEBI organic hydroxy compounds ChEBI Alkenols; the term refers specifically to vinylic alcohols, which have the structure HOCR'=CR2. Enols are tautomeric with aldehydes (R' = H) or ketones (R' =/= H). 0 C2HOR3 41.029 41.00274 OC(=C(*)*)* enol enols chebi_ontology alkenols enols CHEBI:33823 enol enol IUPAC enols IUPAC alkenols IUPAC enols ChEBI Any organic molecule that consists of atoms connected in the form of a ring. chebi_ontology organic cyclic compounds CHEBI:33832 organic cyclic compound organic cyclic compounds ChEBI A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarenes chebi_ontology hetarenes CHEBI:33833 heteroarene heteroarenes IUPAC hetarenes IUPAC chebi_ontology benzenoid aromatic compounds benzenoid compound CHEBI:33836 benzenoid aromatic compound benzenoid aromatic compounds ChEBI benzenoid compound ChEBI Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion. COMe:PRX000001 conjugated proteins chebi_ontology complex protein CHEBI:33837 conjugated protein conjugated proteins IUPAC complex protein COMe An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. 0 C5H8O3R2 116.115 116.04734 [C@H]1([C@H]([C@@H](*)[C@@H](O1)*)O)CO CHEBI:13661 CHEBI:25611 CHEBI:7647 KEGG:C00801 Wikipedia:Nucleoside Nucleoside nucleosides chebi_ontology a nucleoside nucleosides CHEBI:33838 nucleoside Nucleoside KEGG_COMPOUND nucleosides IUPAC a nucleoside UniProt nucleosides ChEBI A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. Wikipedia:Macromolecule macromolecule chebi_ontology macromolecules polymer polymer molecule polymers CHEBI:33839 macromolecule macromolecule IUPAC macromolecules ChEBI polymer ChEBI polymer molecule IUPAC polymers ChEBI chebi_ontology aromatic annulenes CHEBI:33842 aromatic annulene aromatic annulenes ChEBI A monocyclic aromatic hydrocarbon. chebi_ontology monocyclic arenes CHEBI:33847 monocyclic arene monocyclic arenes ChEBI A polycyclic aromatic hydrocarbon. PMID:15198916 PMID:25679824 Wikipedia:Polycyclic_aromatic_hydrocarbon chebi_ontology PAH PAHs polycyclic arenes polycyclic aromatic hydrocarbons CHEBI:33848 polycyclic arene PMID:15198916 Europe PMC PMID:25679824 Europe PMC PAH ChEBI PAHs ChEBI polycyclic arenes ChEBI polycyclic aromatic hydrocarbons ChEBI Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. 0 C6HOR5 89.072 89.00274 C1(=C(C(=C(C(=C1*)*)*)*)*)O CHEBI:13664 CHEBI:13825 CHEBI:25969 CHEBI:2857 KEGG:C15584 MetaCyc:Phenols Wikipedia:Phenols phenols chebi_ontology Aryl alcohol a phenol arenols CHEBI:33853 phenols phenols IUPAC Aryl alcohol KEGG_COMPOUND a phenol UniProt arenols IUPAC An amino acid whose structure includes an aromatic ring. 0 C2H4NO2R 88.085 74.02420 CHEBI:13820 CHEBI:22623 CHEBI:2835 KEGG:C01021 Wikipedia:Aromatic_amino_acid Aromatic amino acid chebi_ontology aromatic amino acids CHEBI:33856 aromatic amino acid Aromatic amino acid KEGG_COMPOUND aromatic amino acids ChEBI Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. CHEBI:13817 CHEBI:13821 CHEBI:2830 chebi_ontology aromatic carboxylic acids CHEBI:33859 aromatic carboxylic acid aromatic carboxylic acids ChEBI An amino compound in which the amino group is linked directly to an aromatic system. CHEBI:13827 CHEBI:22622 CHEBI:22646 CHEBI:2834 CHEBI:2863 chebi_ontology aromatic amines aryl amine aryl amines arylamine arylamines CHEBI:33860 aromatic amine aromatic amines ChEBI aryl amine ChEBI aryl amines ChEBI arylamine ChEBI arylamines ChEBI chebi_ontology transition element coordination entities transition metal coordination compounds transition metal coordination entities CHEBI:33861 transition element coordination entity transition element coordination entities ChEBI transition metal coordination compounds ChEBI transition metal coordination entities ChEBI cobalt molecular entity chebi_ontology cobalt compounds cobalt molecular entities CHEBI:33888 cobalt molecular entity cobalt molecular entity ChEBI cobalt compounds ChEBI cobalt molecular entities ChEBI cobalt coordination entity chebi_ontology cobalt coordination compounds cobalt coordination entities CHEBI:33890 cobalt coordination entity cobalt coordination entity ChEBI cobalt coordination compounds ChEBI cobalt coordination entities ChEBI iron coordination entity chebi_ontology iron coordination compounds iron coordination entities CHEBI:33892 iron coordination entity iron coordination entity ChEBI iron coordination compounds ChEBI iron coordination entities ChEBI A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent chebi_ontology reactif reactivo reagents CHEBI:33893 reagent reagent IUPAC reactif IUPAC reactivo IUPAC reagents ChEBI chebi_ontology cobalt corrinoids cobalt-corrinoids CHEBI:33906 cobalt corrinoid cobalt corrinoids ChEBI cobalt-corrinoids ChEBI chebi_ontology metal-tetrapyrrole metal-tetrapyrrole complex metallotetrapyrroles CHEBI:33909 metallotetrapyrrole metal-tetrapyrrole ChEBI metal-tetrapyrrole complex ChEBI metallotetrapyrroles ChEBI A derivative of the corrin nucleus, which contains four reduced or partly reduced pyrrole rings joined in a macrocycle by three =C- groups and one direct carbon-carbon bond linking alpha positions. 0 C19HN4R21 285.239 285.02012 CHEBI:23391 CHEBI:3890 KEGG:C06021 Corrinoid corrinoid corrinoids chebi_ontology Corrinoid protein Corrinoid protein Co+ Korrinoid corrinoide corrinoides CHEBI:33913 corrinoid Corrinoid KEGG_COMPOUND corrinoid UniProt corrinoids IUPAC Corrinoid protein KEGG_COMPOUND Corrinoid protein Co+ KEGG_COMPOUND Korrinoid ChEBI corrinoide IUPAC corrinoides IUPAC A pentose with a (potential) aldehyde group at one end. PMID:10723607 aldopentose chebi_ontology aldopentoses CHEBI:33916 aldopentose PMID:10723607 Europe PMC aldopentose ChEBI aldopentoses ChEBI A hexose with a (potential) aldehyde group at one end. CHEBI:2558 aldohexose chebi_ontology aldohexoses CHEBI:33917 aldohexose aldohexose ChEBI aldohexoses ChEBI Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals. chebi_ontology macronutrients CHEBI:33937 macronutrient macronutrients ChEBI Any aldopentose where the open-chain form has all the hydroxy groups on the same side in the Fischer projection. Occurrs in two enantiomeric forms, D- and L-ribose, of which only the former is found in nature. 0 C5H10O5 150.130 150.05282 CHEBI:26564 ribo-pentose ribose chebi_ontology Rib CHEBI:33942 ribose ribo-pentose IUPAC ribose IUPAC Rib JCBN A quaternary ammonium ion that is the the conjugate acid of carnitine. +1 C7H16NO3 InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3/p+1 PHIQHXFUZVPYII-UHFFFAOYSA-O 162.20688 162.11247 C[N+](C)(C)CC(O)CC(O)=O CAS:406-76-8 CAS:461-06-3 KEGG:C00487 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium chebi_ontology 3-hydroxy-4-(trimethylammonio)butanoic acid Carnitine CHEBI:3424 carnitinium CAS:406-76-8 KEGG COMPOUND CAS:461-06-3 KEGG COMPOUND 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium IUPAC 3-hydroxy-4-(trimethylammonio)butanoic acid ChEBI Carnitine KEGG_COMPOUND chebi_ontology nitrogen hydrides CHEBI:35106 nitrogen hydride nitrogen hydrides ChEBI Saturated acyclic nitrogen hydrides having the general formula NnHn+2. chebi_ontology azanes CHEBI:35107 azane azanes ChEBI COMe:PRX000002 metalloprotein chebi_ontology metalloproteine metalloproteins CHEBI:35134 metalloprotein metalloprotein COMe metalloproteine ChEBI metalloproteins ChEBI COMe:PRX000004 iron protein chebi_ontology iron proteins iron-containing proteins CHEBI:35136 iron protein iron protein COMe iron proteins ChEBI iron-containing proteins ChEBI Conjugated proteins containing heme as the prosthetic group. COMe:PRX000008 hemoprotein chebi_ontology Haemoprotein Haemprotein haem protein haemoprotein heme protein hemeproteins hemoproteins CHEBI:35137 hemoprotein hemoprotein ChEBI Haemoprotein ChEBI Haemprotein ChEBI haem protein COMe haemoprotein ChEBI heme protein ChEBI hemeproteins IUBMB hemoproteins ChEBI COMe:PRX000321 hemoglobin chebi_ontology haemoglobin vertebrate haemoglobin CHEBI:35143 hemoglobin hemoglobin ChEBI haemoglobin ChEBI vertebrate haemoglobin COMe 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-23,25-28,37H,15-16,24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+/t37-/m0/s1 ANVAOWXLWRTKGA-NTXLUARGSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\[C@H]1C(C)=CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C Beilstein:2067409 CAS:7488-99-5 LIPID_MAPS_instance:LMPR01070011 (6'R)-beta,epsilon-carotene chebi_ontology (+)-alpha-carotene alpha-carotene (natural) CHEBI:35147 (6'R)-beta,epsilon-carotene Beilstein:2067409 Beilstein CAS:7488-99-5 ChemIDplus LIPID_MAPS_instance:LMPR01070011 LIPID MAPS (6'R)-beta,epsilon-carotene IUPAC (+)-alpha-carotene ChemIDplus alpha-carotene (natural) ChemIDplus 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-23,25-28,37H,15-16,24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+/t37-/m1/s1 ANVAOWXLWRTKGA-QTRZAOAUSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\[C@@H]1C(C)=CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C Beilstein:2682045 (6'S)-beta,epsilon-carotene chebi_ontology CHEBI:35148 (6'S)-beta,epsilon-carotene Beilstein:2682045 Beilstein (6'S)-beta,epsilon-carotene IUPAC chebi_ontology CHEBI:35155 elemental calcium chebi_ontology Kalziumsalz Kalziumsalze calcium salts CHEBI:35156 calcium salt Kalziumsalz ChEBI Kalziumsalze ChEBI calcium salts ChEBI cyclic carotene chebi_ontology cyclic carotenes CHEBI:35163 cyclic carotene cyclic carotene ChEBI cyclic carotenes ChEBI An oxo monocarboxylic acid anion in which the oxo group is located at the 2-position. -1 C2O3R 72.020 71.98474 [O-]C(=O)C([*])=O CHEBI:70795 MetaCyc:2-Oxo-carboxylates PMID:10850983 chebi_ontology 2-oxo monocarboxylate 2-oxo monocarboxylic acid anions a 2-oxocarboxylate CHEBI:35179 2-oxo monocarboxylic acid anion MetaCyc:2-Oxo-carboxylates SUBMITTER PMID:10850983 SUBMITTER 2-oxo monocarboxylate ChEBI 2-oxo monocarboxylic acid anions ChEBI a 2-oxocarboxylate UniProt A hydrocarbon of biological origin having carbon skeleton formally derived from isoprene [CH2=C(CH3)CH=CH2]. terpene terpenes chebi_ontology Terpen terpenes terpeno terpenos CHEBI:35186 terpene terpene IUPAC terpenes IUPAC Terpen ChEBI terpenes IUPAC terpeno IUPAC terpenos IUPAC A C20 terpene. diterpenes chebi_ontology Diterpen diterpenes diterpeno diterpenos CHEBI:35190 diterpene diterpenes IUPAC Diterpen ChEBI diterpenes IUPAC diterpeno IUPAC diterpenos IUPAC A C30 terpene. triterpenes chebi_ontology Triterpen triterpenes triterpeno triterpenos CHEBI:35191 triterpene triterpenes IUPAC Triterpen ChEBI triterpenes IUPAC triterpeno IUPAC triterpenos IUPAC A C40 terpene. tetraterpenes chebi_ontology tetraterpenes tetraterpeno tetraterpenos CHEBI:35193 tetraterpene tetraterpenes IUPAC tetraterpenes IUPAC tetraterpeno IUPAC tetraterpenos IUPAC A substance which lowers the surface tension of the medium in which it is dissolved, and/or the interfacial tension with other phases, and, accordingly, is positively adsorbed at the liquid/vapour and/or at other interfaces. surfactant chebi_ontology surface active agent surfactants CHEBI:35195 surfactant surfactant IUPAC surface active agent IUPAC surfactants ChEBI A substance that diminishes the rate of a chemical reaction. inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor inhibitor IUPAC inhibidor ChEBI inhibiteur ChEBI inhibitors ChEBI A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction. catalyst chebi_ontology Katalysator catalizador catalyseur CHEBI:35223 catalyst catalyst IUPAC Katalysator ChEBI catalizador ChEBI catalyseur ChEBI 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-N 121.15922 121.01975 [NH3+][C@@H](CS)C([O-])=O Gmelin:49993 (2R)-2-ammonio-3-sulfanylpropanoate L-cysteine zwitterion chebi_ontology (2R)-2-ammonio-3-mercaptopropanoate L-cysteine CHEBI:35235 L-cysteine zwitterion Gmelin:49993 Gmelin (2R)-2-ammonio-3-sulfanylpropanoate IUPAC L-cysteine zwitterion IUPAC (2R)-2-ammonio-3-mercaptopropanoate ChEBI L-cysteine UniProt 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-N 121.15922 121.01975 [NH3+][C@H](CS)C([O-])=O Gmelin:2352354 (2S)-2-ammonio-3-sulfanylpropanoate D-cysteine zwitterion chebi_ontology (2S)-2-ammonio-3-mercaptopropanoate D-cysteine CHEBI:35236 D-cysteine zwitterion Gmelin:2352354 Gmelin (2S)-2-ammonio-3-sulfanylpropanoate IUPAC D-cysteine zwitterion IUPAC (2S)-2-ammonio-3-mercaptopropanoate ChEBI D-cysteine UniProt 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 [NH3+]C(CS)C([O-])=O Gmelin:49992 2-ammonio-3-sulfanylpropanoate cysteine zwitterion chebi_ontology (+)H3N-CH(CH2SH)-COO(-) 2-ammonio-3-mercaptopropanoate CHEBI:35237 cysteine zwitterion Gmelin:49992 Gmelin 2-ammonio-3-sulfanylpropanoate IUPAC cysteine zwitterion IUPAC (+)H3N-CH(CH2SH)-COO(-) ChEBI 2-ammonio-3-mercaptopropanoate ChEBI The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group. amino acid zwitterion chebi_ontology CHEBI:35238 amino acid zwitterion amino acid zwitterion ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7) MTCFGRXMJLQNBG-UHFFFAOYSA-N 105.09262 105.04259 [NH3+]C(CO)C([O-])=O Beilstein:3935647 Gmelin:2060272 2-ammonio-3-hydroxypropanoate serine zwitterion chebi_ontology CHEBI:35243 serine zwitterion Beilstein:3935647 Beilstein Gmelin:2060272 Gmelin 2-ammonio-3-hydroxypropanoate IUPAC serine zwitterion IUPAC A serine zwitterion obtained by transfer of a proton from the carboxy to the amino group of D-serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-N 105.09262 105.04259 [NH3+][C@H](CO)C([O-])=O MetaCyc:D-SERINE (2R)-2-ammonio-3-hydroxypropanoate D-serine zwitterion chebi_ontology D-serine CHEBI:35247 D-serine zwitterion (2R)-2-ammonio-3-hydroxypropanoate IUPAC D-serine zwitterion IUPAC D-serine UniProt A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups. +1 NR4 14.00670 14.00307 [*][N+]([*])([*])[*] CHEBI:26470 CHEBI:8693 KEGG:C06703 quaternary ammonium ion chebi_ontology Quaternary amine a quaternary ammonium quaternary ammonium ions CHEBI:35267 quaternary ammonium ion quaternary ammonium ion IUPAC Quaternary amine KEGG_COMPOUND a quaternary ammonium UniProt quaternary ammonium ions ChEBI A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc). chebi_ontology ammonium ion derivatives azanium ion derivative azanium ion derivatives CHEBI:35274 ammonium ion derivative ammonium ion derivatives ChEBI azanium ion derivative ChEBI azanium ion derivatives ChEBI Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. betaines chebi_ontology onium betaines CHEBI:35281 onium betaine betaines IUPAC onium betaines ChEBI Neutral molecules having charge-separated forms with an sulfonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. chebi_ontology sulfonium betaines CHEBI:35282 sulfonium betaine sulfonium betaines ChEBI Any neutral molecule having charge-separated forms with a quaternary ammonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. chebi_ontology ammonium betaines CHEBI:35284 ammonium betaine ammonium betaines ChEBI chebi_ontology fused compounds fused polycyclic compounds fused-ring polycyclic compound fused-ring polycyclic compounds polycyclic fused-ring compounds CHEBI:35293 fused compound fused compounds ChEBI fused polycyclic compounds ChEBI fused-ring polycyclic compound ChEBI fused-ring polycyclic compounds ChEBI polycyclic fused-ring compounds ChEBI A polyclic compound in which all of the ring members are carbon atoms. chebi_ontology carbopolycyclic compounds CHEBI:35294 carbopolycyclic compound carbopolycyclic compounds ChEBI chebi_ontology homopolycyclic compounds CHEBI:35295 homopolycyclic compound homopolycyclic compounds ChEBI chebi_ontology ortho-fused polycyclic arenes CHEBI:35296 ortho-fused polycyclic arene ortho-fused polycyclic arenes ChEBI A polycyclic aromatic hydrocarbon consisting of fused benzene rings in a rectilinear arrangement. 0 C10H8.(C4H2)n Wikipedia:Acene acene acenes chebi_ontology Acen Azen polyacenes CHEBI:35297 acene acene IUPAC acenes IUPAC Acen ChEBI Azen ChEBI polyacenes ChEBI Any drug that enhances the activity of the central nervous system. Wikipedia:Central_nervous_system_stimulants central nervous system stimulant chebi_ontology CNS stimulant analeptic analeptic agent analeptic drug analeptics central stimulant CHEBI:35337 central nervous system stimulant central nervous system stimulant ChEBI CNS stimulant ChEBI analeptic ChEBI analeptic agent ChEBI analeptic drug ChEBI analeptics ChEBI central stimulant ChEBI Amines that constitute a class of central nervous system stimulants based on the structure of the parent amphetamine 1-phenylpropan-2-amine. chebi_ontology amphetamine drug CHEBI:35338 amphetamines amphetamine drug ChEBI Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. 0 C19H31R 259.450 259.24258 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C CHEBI:13687 CHEBI:26768 CHEBI:9263 KEGG:C00377 MetaCyc:Steroids Steroid steroids chebi_ontology a steroid CHEBI:35341 steroid Steroid KEGG_COMPOUND steroids IUPAC a steroid UniProt A sterol in which the hydroxy group at position 3 has beta- configuration. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C CHEBI:13609 CHEBI:1725 CHEBI:1726 CHEBI:20248 chebi_ontology 3beta-hydroxysteroids 3beta-sterols CHEBI:35348 3beta-sterol 3beta-hydroxysteroids ChEBI 3beta-sterols ChEBI CHEBI:24748 CHEBI:5814 KEGG:C02159 chebi_ontology Hydroxysteroid hydroxy steroids hydroxysteroids CHEBI:35350 hydroxy steroid Hydroxysteroid KEGG_COMPOUND hydroxy steroids ChEBI hydroxysteroids ChEBI Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens CHEBI:35352 organonitrogen compound organonitrogen compounds IUPAC organonitrogens ChEBI An amide of a sulfonic acid RS(=O)2NR'2. 0 NO2SR3 78.07100 77.96497 [*]S(=O)(=O)N([*])[*] PMID:11498380 PMID:2434548 PMID:26811268 PMID:26832216 Wikipedia:Sulfonamide sulfonamides chebi_ontology sulfonamides CHEBI:35358 sulfonamide PMID:11498380 Europe PMC PMID:2434548 Europe PMC PMID:26811268 Europe PMC PMID:26832216 Europe PMC sulfonamides IUPAC sulfonamides ChEBI Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13633 CHEBI:24024 CHEBI:4984 KEGG:C00162 PMID:14287444 PMID:14300208 PMID:14328676 Wikipedia:Fatty_acid Fatty acid fatty acids chebi_ontology Fettsaeure Fettsaeuren acide gras acides gras acido graso acidos grasos fatty acids CHEBI:35366 fatty acid PMID:14287444 Europe PMC PMID:14300208 Europe PMC PMID:14328676 Europe PMC Fatty acid KEGG_COMPOUND fatty acids IUPAC Fettsaeure ChEBI Fettsaeuren ChEBI acide gras ChEBI acides gras ChemIDplus acido graso ChEBI acidos grasos ChEBI fatty acids ChEBI Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group. CHEBI:25407 CHEBI:6984 KEGG:C06698 Monosaccharide monosaccharides chebi_ontology Monosaccharid Monosacharid monosacarido monosacaridos CHEBI:35381 monosaccharide Monosaccharide KEGG_COMPOUND monosaccharides IUPAC Monosaccharid ChEBI Monosacharid ChEBI monosacarido ChEBI monosacaridos IUPAC An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion chebi_ontology oxoacid anions oxoanions CHEBI:35406 oxoanion oxoanion ChEBI oxoacid anions ChEBI oxoanions ChEBI ortho-fused polycyclic hydrocarbon chebi_ontology ortho-fused polycyclic hydrocarbons CHEBI:35427 ortho-fused polycyclic hydrocarbon ortho-fused polycyclic hydrocarbon ChEBI ortho-fused polycyclic hydrocarbons ChEBI A substance used in the prophylaxis or therapy of infectious diseases. chebi_ontology anti-infective agents anti-infective drugs antiinfective agents antiinfective drug CHEBI:35441 antiinfective agent anti-infective agents ChEBI anti-infective drugs ChEBI antiinfective agents ChEBI antiinfective drug ChEBI A substance used to treat or prevent parasitic infections. Wikipedia:Antiparasitic chebi_ontology antiparasitic drugs antiparasitics parasiticides CHEBI:35442 antiparasitic agent antiparasitic drugs ChEBI antiparasitics ChEBI parasiticides ChEBI An EC 3.4.15.* (peptidyl-dipeptidase) inhibitor that interferes with the action of peptidyl-dipeptidase A (EC 3.4.15.1). Wikipedia:ACE_inhibitor chebi_ontology ACE inhibitor ACE inhibitors DCP inhibitor DCP inhibitors EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitors EC 3.4.15.1 inhibitor EC 3.4.15.1 inhibitors PDH inhibitor PDH inhibitors angiotensin I-converting enzyme inhibitor angiotensin I-converting enzyme inhibitors angiotensin-converting enzyme inhibitor angiotensin-converting enzyme inhibitors carboxycathepsin inhibitor carboxycathepsin inhibitors dipeptidase inhibitor dipeptidase inhibitors dipeptide hydrolase inhibitor dipeptide hydrolase inhibitors dipeptidyl carboxypeptidase I inhibitor dipeptidyl carboxypeptidase I inhibitors dipeptidyl carboxypeptidase inhibitor dipeptidyl carboxypeptidase inhibitors endothelial cell peptidyl dipeptidase inhibitor endothelial cell peptidyl dipeptidase inhibitors kininase II inhibitor kininase II inhibitors peptidase P inhibitor peptidase P inhibitors peptidyl dipeptidase A inhibitor peptidyl dipeptidase A inhibitors peptidyl dipeptidase I inhibitor peptidyl dipeptidase I inhibitors peptidyl dipeptidase-4 inhibitor peptidyl dipeptidase-4 inhibitors peptidyl dipeptide hydrolase inhibitor peptidyl dipeptide hydrolase inhibitors peptidyl-dipeptidase A (EC 3.4.15.1) inhibitor peptidyl-dipeptidase A (EC 3.4.15.1) inhibitors peptidyl-dipeptidase A inhibitor peptidyl-dipeptidase A inhibitors peptidyl-dipeptide hydrolase inhibitor peptidyl-dipeptide hydrolase inhibitors peptidyldipeptide hydrolase inhibitor peptidyldipeptide hydrolase inhibitors CHEBI:35457 EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor ACE inhibitor ChEBI ACE inhibitors ChEBI DCP inhibitor ChEBI DCP inhibitors ChEBI EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitors ChEBI EC 3.4.15.1 inhibitor ChEBI EC 3.4.15.1 inhibitors ChEBI PDH inhibitor ChEBI PDH inhibitors ChEBI angiotensin I-converting enzyme inhibitor ChEBI angiotensin I-converting enzyme inhibitors ChEBI angiotensin-converting enzyme inhibitor ChEBI angiotensin-converting enzyme inhibitors ChEBI carboxycathepsin inhibitor ChEBI carboxycathepsin inhibitors ChEBI dipeptidase inhibitor ChEBI dipeptidase inhibitors ChEBI dipeptide hydrolase inhibitor ChEBI dipeptide hydrolase inhibitors ChEBI dipeptidyl carboxypeptidase I inhibitor ChEBI dipeptidyl carboxypeptidase I inhibitors ChEBI dipeptidyl carboxypeptidase inhibitor ChEBI dipeptidyl carboxypeptidase inhibitors ChEBI endothelial cell peptidyl dipeptidase inhibitor ChEBI endothelial cell peptidyl dipeptidase inhibitors ChEBI kininase II inhibitor ChEBI kininase II inhibitors ChEBI peptidase P inhibitor ChEBI peptidase P inhibitors ChEBI peptidyl dipeptidase A inhibitor ChEBI peptidyl dipeptidase A inhibitors ChEBI peptidyl dipeptidase I inhibitor ChEBI peptidyl dipeptidase I inhibitors ChEBI peptidyl dipeptidase-4 inhibitor ChEBI peptidyl dipeptidase-4 inhibitors ChEBI peptidyl dipeptide hydrolase inhibitor ChEBI peptidyl dipeptide hydrolase inhibitors ChEBI peptidyl-dipeptidase A (EC 3.4.15.1) inhibitor ChEBI peptidyl-dipeptidase A (EC 3.4.15.1) inhibitors ChEBI peptidyl-dipeptidase A inhibitor ChEBI peptidyl-dipeptidase A inhibitors ChEBI peptidyl-dipeptide hydrolase inhibitor ChEBI peptidyl-dipeptide hydrolase inhibitors ChEBI peptidyldipeptide hydrolase inhibitor ChEBI peptidyldipeptide hydrolase inhibitors ChEBI Antidepressants are mood-stimulating drugs used primarily in the treatment of affective disorders and related conditions. chebi_ontology antidepressant drugs antidepressants thymoanaleptics thymoleptic drugs thymoleptics CHEBI:35469 antidepressant antidepressant drugs ChEBI antidepressants ChEBI thymoanaleptics ChEBI thymoleptic drugs ChEBI thymoleptics ChEBI A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. chebi_ontology CNS agent CNS drugs central nervous system agents CHEBI:35470 central nervous system drug CNS agent ChEBI CNS drugs ChEBI central nervous system agents ChEBI A loosely defined grouping of drugs that have effects on psychological function. Wikipedia:Psychotropic_drug chebi_ontology psychoactive agent psychoactive drugs psychopharmaceuticals psychotropic drugs CHEBI:35471 psychotropic drug psychoactive agent ChEBI psychoactive drugs ChEBI psychopharmaceuticals ChEBI psychotropic drugs ChEBI A substance that reduces or suppresses inflammation. chebi_ontology anti-inflammatory drugs antiinflammatory agent antiinflammatory drug antiinflammatory drugs CHEBI:35472 anti-inflammatory drug anti-inflammatory drugs ChEBI antiinflammatory agent ChEBI antiinflammatory drug ChEBI antiinflammatory drugs ChEBI A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour. chebi_ontology ataractics tranquilising drug tranquilizing drugs tranquillising agent tranquillizing agents CHEBI:35473 tranquilizing drug ataractics ChEBI tranquilising drug ChEBI tranquilizing drugs ChEBI tranquillising agent ChEBI tranquillizing agents ChEBI Anxiolytic drugs are agents that alleviate anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting clarity of consciousness or neurologic conditions. chebi_ontology anti-anxiety agents anti-anxiety drugs anxiolytic agents anxiolytics minor tranquilisers minor tranquilizers minor tranquilizing agents CHEBI:35474 anxiolytic drug anti-anxiety agents ChEBI anti-anxiety drugs ChEBI anxiolytic agents ChEBI anxiolytics ChEBI minor tranquilisers ChEBI minor tranquilizers ChEBI minor tranquilizing agents ChEBI An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. Wikipedia:Non-steroidal_anti-inflammatory_drug chebi_ontology NSAID NSAIDs non-steroidal anti-inflammatory agent non-steroidal anti-inflammatory drugs CHEBI:35475 non-steroidal anti-inflammatory drug NSAID ChEBI NSAIDs ChEBI non-steroidal anti-inflammatory agent ChEBI non-steroidal anti-inflammatory drugs ChEBI Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. chebi_ontology Neuroleptikum antipsychotic agents antipsychotic drug antipsychotic drugs antipsychotics antipsychotiques grosser Tranquilizer major tranquilizers major tranquilizing agents neuroleptic neuroleptic agents neuroleptics neuroleptique neuroleptiques CHEBI:35476 antipsychotic agent Neuroleptikum ChEBI antipsychotic agents ChEBI antipsychotic drug ChEBI antipsychotic drugs ChEBI antipsychotics ChEBI antipsychotiques ChEBI grosser Tranquilizer ChEBI major tranquilizers ChEBI major tranquilizing agents ChEBI neuroleptic ChEBI neuroleptic agents ChEBI neuroleptics ChEBI neuroleptique ChEBI neuroleptiques ChEBI Antimanic drugs are agents used to treat bipolar disorders or mania associated with other affective disorders. chebi_ontology antimanic agent antimanic drugs antimanics CHEBI:35477 antimanic drug antimanic agent ChEBI antimanic drugs ChEBI antimanics ChEBI chebi_ontology alkali metal salts CHEBI:35479 alkali metal salt alkali metal salts ChEBI An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms. chebi_ontology CHEBI:35480 analgesic A drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors. chebi_ontology CHEBI:35481 non-narcotic analgesic A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. chebi_ontology narcotic narcotic analgesic narcotic analgesics narcotics opioid analgesics CHEBI:35482 opioid analgesic narcotic ChEBI narcotic analgesic ChEBI narcotic analgesics ChEBI narcotics ChEBI opioid analgesics ChEBI A loosely defined group of drugs that tend to reduce the activity of the central nervous system. chebi_ontology CNS depressants central nervous system depressants CHEBI:35488 central nervous system depressant CNS depressants ChEBI central nervous system depressants ChEBI A compound which inhibits or antagonises the biosynthesis or actions of androgens. Wikipedia:Antiandrogen chebi_ontology antiandrogen CHEBI:35497 androgen antagonist antiandrogen ChEBI An agent that promotes the excretion of urine through its effects on kidney function. chebi_ontology diuretics CHEBI:35498 diuretic diuretics ChEBI natural product fundamental parents chebi_ontology CHEBI:35507 natural product fundamental parent natural product fundamental parents IUPAC chebi_ontology steroid fundamental parents CHEBI:35508 steroid fundamental parent steroid fundamental parents ChEBI 0 C27H48 InChI=1S/C27H48/c1-19(2)9-8-10-20(3)23-14-15-24-22-13-12-21-11-6-7-17-26(21,4)25(22)16-18-27(23,24)5/h19-25H,6-18H2,1-5H3/t20-,21?,22+,23-,24+,25+,26+,27-/m1/s1 XIIAYQZJNBULGD-LDHZKLTISA-N 372.67002 372.37560 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C Beilstein:5334741 CAS:14982-53-7 LIPID_MAPS_instance:LMST01010000 Wikipedia:Cholestane cholestane chebi_ontology CHEBI:35516 cholestane Beilstein:5334741 Beilstein CAS:14982-53-7 ChemIDplus CAS:14982-53-7 NIST Chemistry WebBook LIPID_MAPS_instance:LMST01010000 LIPID MAPS cholestane IUPAC 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18?,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-BRPMRXRMSA-N 330.59028 330.32865 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC cholane chebi_ontology CHEBI:35519 cholane cholane IUPAC An agent that selectively binds to and activates beta-adrenergic receptors. chebi_ontology beta-adrenergic agonists beta-adrenergic receptor agonist beta-adrenoceptor agonists CHEBI:35522 beta-adrenergic agonist beta-adrenergic agonists ChEBI beta-adrenergic receptor agonist ChEBI beta-adrenoceptor agonists IUPHAR An agent that causes an increase in the expansion of a bronchus or bronchial tubes. chebi_ontology bronchodilator bronchodilator agents broncholytic agent CHEBI:35523 bronchodilator agent bronchodilator ChEBI bronchodilator agents ChEBI broncholytic agent ChEBI A drug which lowers the blood glucose level. chebi_ontology antidiabetic antihyperglycemic antihyperglycemic agent antihyperglycemic agents antihyperglycemic drug antihyperglycemic drugs antihyperglycemics hypoglycemic agents hypoglycemic drug hypoglycemic drugs CHEBI:35526 hypoglycemic agent antidiabetic ChEBI antihyperglycemic ChEBI antihyperglycemic agent ChEBI antihyperglycemic agents ChEBI antihyperglycemic drug ChEBI antihyperglycemic drugs ChEBI antihyperglycemics ChEBI hypoglycemic agents ChEBI hypoglycemic drug ChEBI hypoglycemic drugs ChEBI An agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. beta-Adrenergic antagonists are used for treatment of hypertension, cardiac arrhythmias, angina pectoris, glaucoma, migraine headaches and anxiety. chebi_ontology beta-adrenergic antagonists beta-adrenergic blocker beta-adrenergic blockers beta-adrenergic receptor blockaders beta-adrenoceptor antagonists beta-blocker beta-blockers CHEBI:35530 beta-adrenergic antagonist beta-adrenergic antagonists ChEBI beta-adrenergic blocker ChEBI beta-adrenergic blockers ChEBI beta-adrenergic receptor blockaders ChEBI beta-adrenoceptor antagonists IUPHAR beta-blocker ChEBI beta-blockers ChEBI heterocyclic parent hydrides chebi_ontology heterocyclic fundamental parent heterocyclic organic fundamental parents organic heterocyclic fundamental parents CHEBI:35552 heterocyclic organic fundamental parent heterocyclic parent hydrides IUPAC heterocyclic fundamental parent ChEBI heterocyclic organic fundamental parents ChEBI organic heterocyclic fundamental parents ChEBI A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. chebi_ontology cardiovascular agent cardiovascular drugs CHEBI:35554 cardiovascular drug cardiovascular agent ChEBI cardiovascular drugs ChEBI Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds. mancude-ring systems chebi_ontology mancude rings mancunide-ring systems CHEBI:35568 mancude ring mancude-ring systems IUPAC mancude rings ChEBI mancunide-ring systems IUPAC An agent that selectively binds to and activates alpha-adrenergic receptors. chebi_ontology alpha-adrenergic agonists alpha-adrenergic receptor agonist alpha-adrenoceptor agonists CHEBI:35569 alpha-adrenergic agonist alpha-adrenergic agonists ChEBI alpha-adrenergic receptor agonist ChEBI alpha-adrenoceptor agonists IUPHAR chebi_ontology mancude organic heterobicyclic parents mancude-ring organic heterobicyclic parents CHEBI:35570 mancude organic heterobicyclic parent mancude organic heterobicyclic parents ChEBI mancude-ring organic heterobicyclic parents ChEBI chebi_ontology mancude organic heterocyclic parents mancude-ring organic heterocyclic parents CHEBI:35571 mancude organic heterocyclic parent mancude organic heterocyclic parents ChEBI mancude-ring organic heterocyclic parents ChEBI chebi_ontology organic mancude parents organic mancude-ring parents CHEBI:35573 organic mancude parent organic mancude parents ChEBI organic mancude-ring parents ChEBI N-oxide chebi_ontology N-oxides CHEBI:35580 N-oxide N-oxide ChEBI N-oxides ChEBI A heterobicyclic aromatic organic compound comprising a pyrimidine ring fused to an imidazole ring; the parent compound of the purines. 0 C5H4N4 120.112 120.04360 HMDB:HMDB0001366 KEGG:C15587 MetaCyc:PURINE PMID:12865945 PMID:24088627 purine chebi_ontology CHEBI:35584 purine PMID:12865945 Europe PMC PMID:24088627 Europe PMC purine IUPAC A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n. carbon oxoanion chebi_ontology carbon oxoanions oxocarbon anion oxocarbon anions CHEBI:35604 carbon oxoanion carbon oxoanion ChEBI carbon oxoanions ChEBI oxocarbon anion ChEBI oxocarbon anions ChEBI chebi_ontology carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid carbon oxoacids ChEBI oxoacids of carbon ChEBI A substance that inhibits or prevents the proliferation of neoplasms. chebi_ontology anticancer agent anticancer agents antineoplastic antineoplastic agents cytostatic CHEBI:35610 antineoplastic agent anticancer agent ChEBI anticancer agents ChEBI antineoplastic ChEBI antineoplastic agents ChEBI cytostatic ChEBI A food additive that is used to added improve the taste or odour of a food. chebi_ontology flavoring agent flavoring agents flavour enhancer flavour enhancers flavouring agents CHEBI:35617 flavouring agent flavoring agent ChEBI flavoring agents ChEBI flavour enhancer ChEBI flavour enhancers ChEBI flavouring agents ChEBI A drug used to cause dilation of the blood vessels. chebi_ontology vasodilator vasodilator agents CHEBI:35620 vasodilator agent vasodilator ChEBI vasodilator agents ChEBI A drug used to prevent seizures or reduce their severity. chebi_ontology Antiepileptika Antiepileptikum Antikonvulsiva Antikonvulsivum anti-convulsant anti-convulsants anti-convulsive agent anti-convulsive agents anticonvulsants anticonvulsive agent anticonvulsive agents antiepileptic antiepileptics antiepileptique antiepileptiques CHEBI:35623 anticonvulsant Antiepileptika ChEBI Antiepileptikum ChEBI Antikonvulsiva ChEBI Antikonvulsivum ChEBI anti-convulsant ChEBI anti-convulsants ChEBI anti-convulsive agent ChEBI anti-convulsive agents ChEBI anticonvulsants ChEBI anticonvulsive agent ChEBI anticonvulsive agents ChEBI antiepileptic ChEBI antiepileptics ChEBI antiepileptique ChEBI antiepileptiques ChEBI A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. 0 C3H2NOR3 68.054 68.01364 C1(C(N(*)C1*)=O)* CHEBI:10426 CHEBI:13203 CHEBI:22845 KEGG:C01866 Wikipedia:Beta-lactam beta-Lactam chebi_ontology a beta-lactam beta-lactams CHEBI:35627 beta-lactam beta-Lactam KEGG_COMPOUND a beta-lactam UniProt beta-lactams ChEBI An EC 1.17.3.* (oxidoreductase acting on CH or CH2 with oxygen as acceptor) inhibitor that interferes with the action of xanthine oxidase (EC 1.17.3.2). chebi_ontology EC 1.17.3.2 (xanthine oxidase) inhibitors EC 1.17.3.2 inhibitor EC 1.17.3.2 inhibitors Schardinger enzyme inhibitor Schardinger enzyme inhibitors hypoxanthine oxidase inhibitor hypoxanthine oxidase inhibitors hypoxanthine-xanthine oxidase inhibitor hypoxanthine-xanthine oxidase inhibitors hypoxanthine:oxygen oxidoreductase inhibitor hypoxanthine:oxygen oxidoreductase inhibitors xanthine oxidase (EC 1.17.3.2) inhibitor xanthine oxidase (EC 1.17.3.2) inhibitors xanthine oxidase inhibitor xanthine oxidase inhibitors xanthine oxidoreductase inhibitor xanthine oxidoreductase inhibitors xanthine:O2 oxidoreductase inhibitor xanthine:O2 oxidoreductase inhibitors xanthine:oxygen oxidoreductase inhibitor xanthine:oxygen oxidoreductase inhibitors xanthine:xanthine oxidase inhibitor xanthine:xanthine oxidase inhibitors CHEBI:35634 EC 1.17.3.2 (xanthine oxidase) inhibitor EC 1.17.3.2 (xanthine oxidase) inhibitors ChEBI EC 1.17.3.2 inhibitor ChEBI EC 1.17.3.2 inhibitors ChEBI Schardinger enzyme inhibitor ChEBI Schardinger enzyme inhibitors ChEBI hypoxanthine oxidase inhibitor ChEBI hypoxanthine oxidase inhibitors ChEBI hypoxanthine-xanthine oxidase inhibitor ChEBI hypoxanthine-xanthine oxidase inhibitors ChEBI hypoxanthine:oxygen oxidoreductase inhibitor ChEBI hypoxanthine:oxygen oxidoreductase inhibitors ChEBI xanthine oxidase (EC 1.17.3.2) inhibitor ChEBI xanthine oxidase (EC 1.17.3.2) inhibitors ChEBI xanthine oxidase inhibitor ChEBI xanthine oxidase inhibitors ChEBI xanthine oxidoreductase inhibitor ChEBI xanthine oxidoreductase inhibitors ChEBI xanthine:O2 oxidoreductase inhibitor ChEBI xanthine:O2 oxidoreductase inhibitors ChEBI xanthine:oxygen oxidoreductase inhibitor ChEBI xanthine:oxygen oxidoreductase inhibitors ChEBI xanthine:xanthine oxidase inhibitor ChEBI xanthine:xanthine oxidase inhibitors ChEBI An inhibitor of HIV protease, an enzyme required for production of proteins needed for viral assembly. Wikipedia:Protease_inhibitor_(pharmacology) chebi_ontology HIV protease inhibitors CHEBI:35660 HIV protease inhibitor HIV protease inhibitors ChEBI Any EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that inhibits HMG-CoA reductases. Hydroxymethylglutaryl-CoA reductase inhibitors have been shown to lower directly cholesterol synthesis. The Enzyme Commission designation is EC 1.1.1.34 for the NADPH-dependent enzyme and EC 1.1.1.88 for an NADH-dependent enzyme. PMID:1464741 PMID:15531285 PMID:20467214 Wikipedia:HMG-CoA_reductase chebi_ontology HMG-CoA reductase inhibitor HMG-CoA reductase inhibitors hydroxymethylglutaryl-CoA reductase inhibitor hydroxymethylglutaryl-CoA reductase inhibitors CHEBI:35664 EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor PMID:1464741 Europe PMC PMID:15531285 Europe PMC PMID:20467214 Europe PMC HMG-CoA reductase inhibitor ChEBI HMG-CoA reductase inhibitors ChEBI hydroxymethylglutaryl-CoA reductase inhibitor ChEBI hydroxymethylglutaryl-CoA reductase inhibitors ChEBI Any drug used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism. Wikipedia:Antihypertensive_drug chebi_ontology antihypertensive antihypertensive agents antihypertensive drug antihypertensive drugs CHEBI:35674 antihypertensive agent antihypertensive ChEBI antihypertensive agents ChEBI antihypertensive drug ChEBI antihypertensive drugs ChEBI A substance used to treat hyperlipidemia (an excess of lipids in the blood). Wikipedia:Hypolipidemic_agent chebi_ontology antihyperlipemic antihyperlipemics antihyperlipidaemic agent antihyperlipidaemic agents antihyperlipidaemic drug antihyperlipidaemic drugs antihyperlipidemic antihyperlipidemic agent antihyperlipidemic agents antihyperlipidemic drug antihyperlipidemic drugs antihyperlipidemics antilipemic antilipemic drugs antilipemics hypolipidemic agent hypolipidemic agents lipid-lowering agent lipid-lowering agents lipid-lowering drug lipid-lowering drugs CHEBI:35679 antilipemic drug antihyperlipemic ChEBI antihyperlipemics ChEBI antihyperlipidaemic agent ChEBI antihyperlipidaemic agents ChEBI antihyperlipidaemic drug ChEBI antihyperlipidaemic drugs ChEBI antihyperlipidemic ChEBI antihyperlipidemic agent ChEBI antihyperlipidemic agents ChEBI antihyperlipidemic drug ChEBI antihyperlipidemic drugs ChEBI antihyperlipidemics ChEBI antilipemic ChEBI antilipemic drugs ChEBI antilipemics ChEBI hypolipidemic agent ChEBI hypolipidemic agents ChEBI lipid-lowering agent ChEBI lipid-lowering agents ChEBI lipid-lowering drug ChEBI lipid-lowering drugs ChEBI A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it. 0 CH2OR2 30.026 30.01056 *C(*)O CHEBI:13425 CHEBI:13686 CHEBI:26617 CHEBI:58662 CHEBI:8741 CHEBI:9077 KEGG:C00432 KEGG:C01612 Secondary alcohol chebi_ontology R-CHOH-R' a secondary alcohol secondary alcohols CHEBI:35681 secondary alcohol Secondary alcohol KEGG_COMPOUND R-CHOH-R' KEGG_COMPOUND a secondary alcohol UniProt secondary alcohols ChEBI Any carboxylic acid containing two carboxy groups. CHEBI:23692 CHEBI:36172 CHEBI:4501 KEGG:C02028 Dicarboxylic acid chebi_ontology dicarboxylic acids CHEBI:35692 dicarboxylic acid Dicarboxylic acid KEGG_COMPOUND dicarboxylic acids ChEBI dicarboxylic acid anion chebi_ontology dicarboxylic acid anions CHEBI:35693 dicarboxylic acid anion dicarboxylic acid anion ChEBI dicarboxylic acid anions ChEBI Any dicarboxylic acid anion that is a monoanion obtained by the deprotonation of only one of the carboxy groups of the dicarboxylic acid. chebi_ontology dicarboxylic acid monoanions CHEBI:35695 dicarboxylic acid monoanion dicarboxylic acid monoanions ChEBI A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:4859 KEGG:C00287 Wikipedia:Ester Ester chebi_ontology esters CHEBI:35701 ester Ester KEGG_COMPOUND esters ChEBI An agent that suppresses immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. chebi_ontology immunosuppressant immunosuppressive agents inmunosupresor CHEBI:35705 immunosuppressive agent immunosuppressant ChEBI immunosuppressive agents ChEBI inmunosupresor ChEBI A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. chebi_ontology hypnotics hypnotics and sedatives sedative drug sedatives sedatives and hypnotics CHEBI:35717 sedative hypnotics ChEBI hypnotics and sedatives ChEBI sedative drug ChEBI sedatives ChEBI sedatives and hypnotics ChEBI An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce. chebi_ontology antifungal antifungal agents antifungal drug antifungal drugs antifungals CHEBI:35718 antifungal agent antifungal ChEBI antifungal agents ChEBI antifungal drug ChEBI antifungal drugs ChEBI antifungals ChEBI chebi_ontology glycosaminoglycan sulfate glycosaminoglycan sulfates sulfated glycosaminoglycans CHEBI:35722 sulfated glycosaminoglycan glycosaminoglycan sulfate ChEBI glycosaminoglycan sulfates ChEBI sulfated glycosaminoglycans ChEBI chebi_ontology carbohydrate sulfates carbohydrate sulphates CHEBI:35724 carbohydrate sulfate carbohydrate sulfates ChEBI carbohydrate sulphates ChEBI Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acid-derived group is attached. PMID:18606873 chebi_ontology glycerolipids CHEBI:35741 glycerolipid PMID:18606873 Europe PMC glycerolipids ChEBI A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated. -1 CO2R 44.01000 43.98983 [O-]C([*])=O CHEBI:13657 CHEBI:25382 CHEBI:3407 KEGG:C00060 chebi_ontology Carboxylate Monocarboxylate a monocarboxylate monocarboxylates monocarboxylic acid anions CHEBI:35757 monocarboxylic acid anion Carboxylate KEGG_COMPOUND Monocarboxylate KEGG_COMPOUND a monocarboxylate UniProt monocarboxylates ChEBI monocarboxylic acid anions ChEBI A phosphorus oxoanion that is the conjugate base of phosphoric acid. chebi_ontology Pi phosphate phosphate ions CHEBI:35780 phosphate ion Pi ChEBI phosphate ChEBI phosphate ions ChEBI chebi_ontology seco-steroids CHEBI:35788 seco-steroid seco-steroids ChEBI A substance that suppresses Mycobacterium leprae, ameliorates the clinical manifestations of leprosy, and/or reduces the incidence and severity of leprous reactions. chebi_ontology leprostatic leprostatic agent leprostatic drugs CHEBI:35816 leprostatic drug leprostatic ChEBI leprostatic agent ChEBI leprostatic drugs ChEBI Any fatty acid in which the parent hydrocarbon chain has one or more alkyl substituents; a common component in animal and bacterial lipids. The fatty acyl chain is usually saturated and the substituent a methyl group; however, unsaturated BCFAs are found in marine animals, and branches other than methyl are found in microbial lipids. CHEBI:22919 CHEBI:3166 KEGG:C05996 PMID:18318842 chebi_ontology BCFA BCFAs Branched chain fatty acid branched fatty acid branched fatty acids branched-chain fatty acids CHEBI:35819 branched-chain fatty acid PMID:18318842 Europe PMC BCFA ChEBI BCFAs ChEBI Branched chain fatty acid KEGG_COMPOUND branched fatty acid ChEBI branched fatty acids ChEBI branched-chain fatty acids ChEBI Any antimicrobial drug which is used to treat or prevent protozoal infections. Wikipedia:Antiprotozoal_agent chebi_ontology antiprotozoal agent antiprotozoal agents antiprotozoal drugs CHEBI:35820 antiprotozoal drug antiprotozoal agent ChEBI antiprotozoal agents ChEBI antiprotozoal drugs ChEBI A substance used to lower plasma cholesterol levels. CHEBI:64906 chebi_ontology anticholesteremic anticholesteremic agent anticholesteremic drugs antihypercholesterolemic antihypercholesterolemic agent antihypercholesterolemic agents antihypercholesterolemic drug antihypercholesterolemic drugs antihypercholesterolemics cholesterol inhibitor cholesterol-lowering agent cholesterol-lowering agents cholesterol-lowering drug cholesterol-lowering drugs hypocholesteremic agent CHEBI:35821 anticholesteremic drug anticholesteremic ChEBI anticholesteremic agent ChEBI anticholesteremic drugs ChEBI antihypercholesterolemic ChEBI antihypercholesterolemic agent ChEBI antihypercholesterolemic agents ChEBI antihypercholesterolemic drug ChEBI antihypercholesterolemic drugs ChEBI antihypercholesterolemics ChEBI cholesterol inhibitor ChEBI cholesterol-lowering agent ChEBI cholesterol-lowering agents ChEBI cholesterol-lowering drug ChEBI cholesterol-lowering drugs ChEBI hypocholesteremic agent ChEBI A gout suppressant that acts directly on the renal tubule to increase the excretion of uric acid, thus reducing its concentrations in plasma. chebi_ontology uricosuric agent uricosuric drugs CHEBI:35841 uricosuric drug uricosuric agent ChEBI uricosuric drugs ChEBI A drug used to treat rheumatoid arthritis. chebi_ontology anti-rheumatic drugs antirheumatic agent antirheumatic drugs CHEBI:35842 antirheumatic drug anti-rheumatic drugs ChEBI antirheumatic agent ChEBI antirheumatic drugs ChEBI A drug that increases uric acid excretion by the kidney (uricosuric drug), decreases uric acid production (antihyperuricemic), or alleviates the pain and inflammation of acute attacks of gout. chebi_ontology gout suppressants CHEBI:35845 gout suppressant gout suppressants ChEBI A drug used for its effect on the kidneys' regulation of body fluid composition and volume. chebi_ontology renal agents CHEBI:35846 renal agent renal agents ChEBI Any monocarboxylic acid which also contains a separate (alcoholic or phenolic) hydroxy substituent. chebi_ontology hydroxy acid hydroxy monocarboxylic acids CHEBI:35868 hydroxy monocarboxylic acid hydroxy acid ChEBI hydroxy monocarboxylic acids ChEBI Any monocarboxylic acid having at least one additional oxo functional group. chebi_ontology oxo monocarboxylic acids CHEBI:35871 oxo monocarboxylic acid oxo monocarboxylic acids ChEBI chebi_ontology imidazopyrimidines CHEBI:35875 imidazopyrimidine imidazopyrimidines ChEBI pnictogen hydride chebi_ontology pnictogen hydrides CHEBI:35881 pnictogen hydride pnictogen hydride ChEBI pnictogen hydrides ChEBI CHEBI:35178 CHEBI:35901 chebi_ontology oxo monocarboxylic acid anions CHEBI:35902 oxo monocarboxylic acid anion oxo monocarboxylic acid anions ChEBI Any carboxylic acid anion containing at least one oxo group. chebi_ontology oxo carboxylic acid anions CHEBI:35903 oxo carboxylic acid anion oxo carboxylic acid anions ChEBI Any monocarboxylic acid having a 2-oxo substituent. 0 C2HO3R 73.02750 72.99257 OC(=O)C([*])=O CHEBI:11634 CHEBI:1238 CHEBI:13195 CHEBI:13594 CHEBI:19736 CHEBI:35909 KEGG:C00161 2-oxo carboxylic acids chebi_ontology 2-Oxo acid 2-Oxocarboxylate 2-oxo acid 2-oxo monocarboxylic acids CHEBI:35910 2-oxo monocarboxylic acid 2-oxo carboxylic acids IUPAC 2-Oxo acid KEGG_COMPOUND 2-Oxocarboxylate KEGG_COMPOUND 2-oxo acid UniProt 2-oxo monocarboxylic acids ChEBI A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function. chebi_ontology neurotransmitter agents CHEBI:35942 neurotransmitter agent neurotransmitter agents ChEBI A hydroxy monocarboxylic acid that has a hydroxy group beta to the carboxy group. chebi_ontology 3-hydroxy acid 3-hydroxy monocarboxylic acids beta-hydroxy acid beta-hydroxy acids beta-hydroxy carboxylic acid beta-hydroxy carboxylic acids CHEBI:35969 3-hydroxy monocarboxylic acid 3-hydroxy acid ChEBI 3-hydroxy monocarboxylic acids ChEBI beta-hydroxy acid ChEBI beta-hydroxy acids ChEBI beta-hydroxy carboxylic acid ChEBI beta-hydroxy carboxylic acids ChEBI Any amino acid carrying two amino groups. chebi_ontology CHEBI:35987 diamino acid Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified. penams chebi_ontology CHEBI:35992 penams penams IUPAC Any C22 polyunsaturated fatty acid containing six double bonds. 0 C22H32O2 328.489 328.24023 docosahexaenoic acid chebi_ontology DHA docosahexaenoic acids CHEBI:36005 docosahexaenoic acid docosahexaenoic acid IUPAC DHA ChEBI docosahexaenoic acids ChEBI A drug used to treat or prevent microbial infections. chebi_ontology antimicrobial drugs CHEBI:36043 antimicrobial drug antimicrobial drugs ChEBI A substance used in the prophylaxis or therapy of virus diseases. chebi_ontology anti-viral drug anti-virus drug antiviral drugs CHEBI:36044 antiviral drug anti-viral drug ChEBI anti-virus drug ChEBI antiviral drugs ChEBI A drug used to treat or prevent bacterial infections. Wikipedia:Antibacterial chebi_ontology antibacterial drugs CHEBI:36047 antibacterial drug antibacterial drugs ChEBI Any monocarboxylic acid anion carrying at least one hydroxy substituent. chebi_ontology hydroxy monocarboxylic acid anions hydroxymonocarboxylic acid anion hydroxymonocarboxylic acid anions CHEBI:36059 hydroxy monocarboxylic acid anion hydroxy monocarboxylic acid anions ChEBI hydroxymonocarboxylic acid anion ChEBI hydroxymonocarboxylic acid anions ChEBI CHEBI:22867 CHEBI:50419 LIPID_MAPS_class:LMST04 chebi_ontology bile acids and derivatives cholanoids CHEBI:36078 cholanoid LIPID_MAPS_class:LMST04 LIPID MAPS bile acids and derivatives LIPID_MAPS cholanoids ChEBI A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. CHEBI:13677 CHEBI:14911 proteins chebi_ontology CHEBI:36080 protein proteins IUPAC Compounds having a fully conjugated cyclic dione structure, such as that of benzoquinones, derived from aromatic compounds by conversion of an even number of -CH= groups into -C(=O)- groups with any necessary rearrangement of double bonds (polycyclic and heterocyclic analogues are included). CHEBI:13684 CHEBI:26517 Wikipedia:Quinone quinone quinones chebi_ontology Chinon quinones CHEBI:36141 quinone quinone IUPAC quinones IUPAC Chinon ChEBI quinones ChEBI A compound in which two monosaccharides are joined by a glycosidic bond. CHEBI:23844 CHEBI:4654 KEGG:C01911 Disaccharide disaccharides chebi_ontology Disaccharid Disacharid disacarido disacaridos CHEBI:36233 disaccharide Disaccharide KEGG_COMPOUND disaccharides IUPAC Disaccharid ChEBI Disacharid ChEBI disacarido ChEBI disacaridos IUPAC Conjugate base of chenodeoxycholic acid; major species at pH 7.3. -1 C24H39O4 InChI=1S/C24H40O4/c1-14(4-7-21(27)28)17-5-6-18-22-19(9-11-24(17,18)3)23(2)10-8-16(25)12-15(23)13-20(22)26/h14-20,22,25-26H,4-13H2,1-3H3,(H,27,28)/p-1/t14-,15+,16-,17-,18+,19+,20-,22+,23+,24-/m1/s1 RUDATBOHQWOJDD-BSWAIDMHSA-M 391.56406 391.28538 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC([O-])=O CHEBI:13960 CHEBI:23093 CHEBI:57884 Beilstein:3703074 3alpha,7alpha-dihydroxy-5beta-cholan-24-oate chenodeoxycholate chebi_ontology chenodeoxycholate anion chenodeoxycholate(1-) CHEBI:36234 chenodeoxycholate Beilstein:3703074 Beilstein 3alpha,7alpha-dihydroxy-5beta-cholan-24-oate IUPAC chenodeoxycholate UniProt chenodeoxycholate anion ChEBI chenodeoxycholate(1-) ChEBI chebi_ontology bile acid anions CHEBI:36235 bile acid anion bile acid anions ChEBI A steroid acid that consists of cholane having a carboxy group in place of the methyl group at position 24. 0 C24H40O2 InChI=1S/C24H40O2/c1-16(7-12-22(25)26)19-10-11-20-18-9-8-17-6-4-5-14-23(17,2)21(18)13-15-24(19,20)3/h16-21H,4-15H2,1-3H3,(H,25,26)/t16-,17?,18+,19-,20+,21+,23+,24-/m1/s1 RPKLZQLYODPWTM-KBMWBBLPSA-N 360.57320 360.30283 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC(O)=O CAS:25312-65-6 Patent:JP2008069152 Reaxys:13246008 cholan-24-oic acid chebi_ontology CHEBI:36237 cholanic acid CAS:25312-65-6 ChemIDplus Reaxys:13246008 Reaxys cholan-24-oic acid IUPAC 0 C24H40O2 InChI=1S/C24H40O2/c1-16(7-12-22(25)26)19-10-11-20-18-9-8-17-6-4-5-14-23(17,2)21(18)13-15-24(19,20)3/h16-21H,4-15H2,1-3H3,(H,25,26)/t16-,17+,18+,19-,20+,21+,23+,24-/m1/s1 RPKLZQLYODPWTM-LVVAJZGHSA-N 360.57320 360.30283 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC(O)=O Beilstein:3214794 CAS:546-18-9 LIPID_MAPS_instance:LMST04010441 5beta-cholan-24-oic acid 5beta-cholanic acid chebi_ontology (5beta)-cholan-24-oic acid (5beta,17beta)-gamma-methylandrostane-17-butanoic acid 5beta-cholanoic acid ursocholanic acid CHEBI:36238 5beta-cholanic acid Beilstein:3214794 Beilstein CAS:546-18-9 ChemIDplus LIPID_MAPS_instance:LMST04010441 LIPID MAPS 5beta-cholan-24-oic acid IUPAC 5beta-cholanic acid ChemIDplus (5beta)-cholan-24-oic acid ChemIDplus (5beta,17beta)-gamma-methylandrostane-17-butanoic acid ChemIDplus 5beta-cholanoic acid ChemIDplus ursocholanic acid ChemIDplus Members of the class of cholanic acids based on a 5beta-cholane skeleton. chebi_ontology CHEBI:36248 5beta-cholanic acids A salt of a bile acid. chebi_ontology bile acid salts CHEBI:36277 bile acid salt bile acid salts ChEBI CHEBI:23166 CHEBI:23211 chebi_ontology CHEBI:36278 cholanic acids macrocyclic tetrapyrroles chebi_ontology cyclic tetrapyrroles macrocyclic tetrapyrrole CHEBI:36309 cyclic tetrapyrrole macrocyclic tetrapyrroles IUPAC cyclic tetrapyrroles ChEBI macrocyclic tetrapyrrole ChEBI The glycerol phosphate ester of a phosphocholine. A nutrient with many different roles in human health. CHEBI:26698 CHEBI:35763 PMID:8467564 chebi_ontology glycerophosphocholines CHEBI:36313 glycerophosphocholine PMID:8467564 Europe PMC glycerophosphocholines ChEBI Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. local anaesthetic chebi_ontology Lokalanaesthetikum anesthesique local local anaesthetics local anesthetics CHEBI:36333 local anaesthetic local anaesthetic IUPAC Lokalanaesthetikum ChEBI anesthesique local ChEBI local anaesthetics ChEBI local anesthetics ChEBI Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). chebi_ontology leptons CHEBI:36338 lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). chebi_ontology baryons CHEBI:36339 baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion chebi_ontology fermions CHEBI:36340 fermion fermion IUPAC fermions ChEBI A particle smaller than an atom. Wikipedia:Subatomic_particle chebi_ontology subatomic particles CHEBI:36342 subatomic particle subatomic particles ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). chebi_ontology composite particles CHEBI:36343 composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. chebi_ontology hadrons CHEBI:36344 hadron hadrons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology CHEBI:36347 nuclear particle nuclear particle IUPAC Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity polyatomic entities ChEBI An ion consisting of more than one atom. chebi_ontology polyatomic ions CHEBI:36358 polyatomic ion polyatomic ions ChEBI phosphorus oxoacid derivative chebi_ontology CHEBI:36359 phosphorus oxoacid derivative phosphorus oxoacid derivative ChEBI chebi_ontology CHEBI:36360 phosphorus oxoacids and derivatives chebi_ontology alkaline earth salts CHEBI:36364 alkaline earth salt alkaline earth salts ChEBI Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compounds chebi_ontology CHEBI:36586 carbonyl compound carbonyl compounds IUPAC Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. oxo compounds chebi_ontology organic oxo compounds CHEBI:36587 organic oxo compound oxo compounds IUPAC organic oxo compounds ChEBI heterotricyclic compound heterotricyclic compounds chebi_ontology heterotricyclic compounds CHEBI:36688 heterotricyclic compound heterotricyclic compound ChEBI heterotricyclic compounds IUPAC heterotricyclic compounds ChEBI Any of a class of steroid hormones that are produced in the adrenal cortex. chebi_ontology adrenal cortex hormones corticosteroid hormones CHEBI:36699 corticosteroid hormone adrenal cortex hormones ChEBI corticosteroid hormones ChEBI Any compound having phosphocholine as part of its structure. chebi_ontology O-phosphocholines choline phosphates phosphorylcholines CHEBI:36700 phosphocholines O-phosphocholines ChEBI choline phosphates ChEBI phosphorylcholines ChEBI Compounds based on a biladiene skeleton. chebi_ontology CHEBI:36735 biladienes -1 chebi_ontology monoanions CHEBI:36830 monoanion monoanions ChEBI Any hydroxy steroid carrying a hydroxy group at position 3. chebi_ontology 3-hydroxy steroids CHEBI:36834 3-hydroxy steroid 3-hydroxy steroids ChEBI A 3-hydroxy steroid in which the 3-hydroxy substituent is in the alpha-position. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@H](C4)O)C CHEBI:71194 MetaCyc:3-alpha-Hydroxysteroids PMID:11514561 chebi_ontology 3alpha-hydroxy steroids 3alpha-hydroxysteroid 3alpha-hydroxysteroids a 3alpha-hydroxysteroid CHEBI:36835 3alpha-hydroxy steroid PMID:11514561 SUBMITTER 3alpha-hydroxy steroids ChEBI 3alpha-hydroxysteroid ChEBI 3alpha-hydroxysteroids ChEBI a 3alpha-hydroxysteroid UniProt A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C CHEBI:71195 KEGG:C02945 MetaCyc:3-Beta-Hydroxysterols PMID:10535978 PMID:12829805 chebi_ontology 3beta-hydroxy steroids a 3beta-hydroxysteroid CHEBI:36836 3beta-hydroxy steroid PMID:10535978 SUBMITTER PMID:12829805 SUBMITTER 3beta-hydroxy steroids ChEBI a 3beta-hydroxysteroid UniProt A 7-hydroxy steroid in which the hydroxy group at position 7 has an alpha-configuration. chebi_ontology 7alpha-hydroxy steroids CHEBI:36843 7alpha-hydroxy steroid 7alpha-hydroxy steroids ChEBI A hydroxy steroid carrying a hydroxy substituent at position 7. chebi_ontology 7-hydroxy steroids CHEBI:36844 7-hydroxy steroid 7-hydroxy steroids ChEBI chebi_ontology 12-hydroxy steroids CHEBI:36845 12-hydroxy steroid 12-hydroxy steroids ChEBI chebi_ontology 12alpha-hydroxy steroids CHEBI:36846 12alpha-hydroxy steroid 12alpha-hydroxy steroids ChEBI chebi_ontology hydroxy seco-steroids CHEBI:36853 hydroxy seco-steroid hydroxy seco-steroids ChEBI chebi_ontology CHEBI:36892 elemental fluorine 0 F 18.998 18.99840 chebi_ontology atomic fluorine CHEBI:36895 monoatomic fluorine atomic fluorine ChEBI chebi_ontology inorganic ions CHEBI:36914 inorganic ion inorganic ions ChEBI chebi_ontology inorganic cations CHEBI:36915 inorganic cation inorganic cations ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. CHEBI:23058 CHEBI:3473 KEGG:C01373 Cation cation chebi_ontology Kation Kationen cationes cations CHEBI:36916 cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI chalcocarbonic acid chalcocarbonic acids chebi_ontology chalcocarbonic acids CHEBI:36961 chalcocarbonic acid chalcocarbonic acid ChEBI chalcocarbonic acids IUPAC chalcocarbonic acids ChEBI An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds CHEBI:36962 organochalcogen compound organochalcogen compound ChEBI organochalcogen compounds ChEBI An organochalcogen compound containing at least one carbon-oxygen bond. PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds CHEBI:36963 organooxygen compound PMID:17586126 Europe PMC organooxygen compound ChEBI organooxygen compounds ChEBI chebi_ontology vitamin B-6 phosphates vitamin B6 phosphates CHEBI:36970 vitamin B6 phosphate vitamin B-6 phosphates JCBN vitamin B6 phosphates ChEBI amino-acid anion chebi_ontology amino acid anions amino-acid anions CHEBI:37022 amino-acid anion amino-acid anion ChEBI amino acid anions ChEBI amino-acid anions ChEBI chebi_ontology organic hydrides CHEBI:37175 organic hydride organic hydrides ChEBI mononuclear parent hydrides chebi_ontology mononuclear hydride mononuclear hydrides CHEBI:37176 mononuclear parent hydride mononuclear parent hydrides IUPAC mononuclear hydride ChEBI mononuclear hydrides IUPAC chebi_ontology CHEBI:37246 elemental sodium chebi_ontology CHEBI:37247 elemental potassium chebi_ontology CHEBI:37253 elemental zinc A branched-chain saturated fatty acid anion that is the conjugate base of phytanic acid, arising from deprotonation of the carboxylic acid group. -1 C20H39O2 InChI=1S/C20H40O2/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)15-20(21)22/h16-19H,6-15H2,1-5H3,(H,21,22)/p-1 RLCKHJSFHOZMDR-UHFFFAOYSA-M 311.52246 311.29555 CC(C)CCCC(C)CCCC(C)CCCC(C)CC([O-])=O CHEBI:14834 CHEBI:26109 Beilstein:3669982 KEGG:C01607 PMID:5130448 Reaxys:3669982 3,7,11,15-tetramethylhexadecanoate chebi_ontology 3,7,11,15-tetramethylhexadecanoate 3,7,11,15-tetramethylpalmitate phytanate anion CHEBI:37257 phytanate Beilstein:3669982 Beilstein PMID:5130448 Europe PMC Reaxys:3669982 Reaxys 3,7,11,15-tetramethylhexadecanoate IUPAC 3,7,11,15-tetramethylhexadecanoate UniProt 3,7,11,15-tetramethylpalmitate ChEBI phytanate anion ChEBI A 7,8-dimethylbenzo[g]pteridine-2,4-dione that is isoalloxazine substituted by methyl groups at positions 7 and 8. 0 C12H10N4O2 InChI=1S/C12H10N4O2/c1-5-3-7-8(4-6(5)2)14-10-9(13-7)11(17)16-12(18)15-10/h3-4H,1-2H3,(H2,14,15,16,17,18) ZJTJUVIJVLLGSP-UHFFFAOYSA-N 242.23356 242.08038 Cc1cc2nc3c(nc(=O)[nH]c3=O)[nH]c2cc1C Beilstein:539579 PMID:16128574 Reaxys:539579 7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione chebi_ontology dimethylisoalloxazine CHEBI:37323 7,8-dimethylisoalloxazine Beilstein:539579 Beilstein PMID:16128574 Europe PMC Reaxys:539579 Reaxys 7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione IUPAC dimethylisoalloxazine IUPAC 0 C12H10N4O2 242.234 242.08038 7,8-dimethylbenzo[g]pteridine-2,4-dione chebi_ontology CHEBI:37324 7,8-dimethylbenzo[g]pteridine-2,4-dione 7,8-dimethylbenzo[g]pteridine-2,4-dione IUPAC 0 C10H6N4O2 InChI=1S/C10H6N4O2/c15-9-7-8(13-10(16)14-9)12-6-4-2-1-3-5(6)11-7/h1-4H,(H2,12,13,14,15,16) HAUGRYOERYOXHX-UHFFFAOYSA-N 214.18040 214.04908 O=c1[nH]c2nc3ccccc3nc2c(=O)[nH]1 Beilstein:85819 CAS:490-59-5 LINCS:LSM-2889 alloxazine benzo[g]pteridine-2,4(1H,3H)-dione chebi_ontology Alloxazin CHEBI:37325 alloxazine Beilstein:85819 Beilstein CAS:490-59-5 NIST Chemistry WebBook alloxazine NIST_Chemistry_WebBook benzo[g]pteridine-2,4(1H,3H)-dione IUPAC Alloxazin NIST_Chemistry_WebBook 0 C10H6N4O2 214.181 214.04908 benzo[g]pteridine-2,4-dione chebi_ontology CHEBI:37326 benzo[g]pteridine-2,4-dione benzo[g]pteridine-2,4-dione IUPAC 0 C10H6N4O2 InChI=1S/C10H6N4O2/c15-9-7-8(13-10(16)14-9)12-6-4-2-1-3-5(6)11-7/h1-4H,(H2,12,13,14,15,16) HAUGRYOERYOXHX-UHFFFAOYSA-N 214.18040 214.04908 O=c1nc2[nH]c3ccccc3nc2c(=O)[nH]1 Beilstein:991206 benzo[g]pteridine-2,4(3H,10H)-dione chebi_ontology CHEBI:37327 isoalloxazine Beilstein:991206 Beilstein benzo[g]pteridine-2,4(3H,10H)-dione IUPAC A substance administered to enhance contrast in images of the inside of the body obtained using X-rays, gamma-rays, sound waves, radio waves (MRI), or radioactive particles in order to diagnose disease. chebi_ontology CHEBI:37334 diagnostic imaging agent Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid. CHEBI:25425 CHEBI:7011 KEGG:C05114 Mucopolysaccharide mucopolysaccharides chebi_ontology Mucopolysaccharid Mukopolysaccharid mucopolisacarido mucopolisacaridos CHEBI:37395 mucopolysaccharide Mucopolysaccharide KEGG_COMPOUND mucopolysaccharides IUPAC Mucopolysaccharid ChEBI Mukopolysaccharid ChEBI mucopolisacarido ChEBI mucopolisacaridos IUPAC Any of a class of 10--60 kDa glycosaminoglycan sulfates, widely distributed in cartilage and other mammalian connective tissues. CHEBI:23224 CHEBI:3676 CAS:9007-28-7 KEGG:C00607 PMID:11514091 PMID:7538297 Chondroitin sulfate chebi_ontology Chondroitinsulfat chondroitin polysulfate chondroitin sulfates chondroitin sulfuric acid chondroitin sulphate CHEBI:37397 chondroitin sulfate CAS:9007-28-7 ChemIDplus CAS:9007-28-7 KEGG COMPOUND PMID:11514091 Europe PMC PMID:7538297 Europe PMC Chondroitin sulfate KEGG_COMPOUND Chondroitinsulfat ChEBI chondroitin polysulfate ChemIDplus chondroitin sulfates ChemIDplus chondroitin sulfuric acid ChemIDplus chondroitin sulphate ChemIDplus A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. CHEBI:24074 CHEBI:24076 folates chebi_ontology folate folates CHEBI:37445 folic acids folates IUPAC folate ChEBI folates ChEBI An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). CHEBI:13800 CHEBI:13801 CHEBI:22209 CHEBI:2426 KEGG:C00174 Acid acid chebi_ontology Saeure Saeuren acide acido acids CHEBI:37527 acid Acid KEGG_COMPOUND acid IUPAC Saeure ChEBI Saeuren ChEBI acide IUPAC acido ChEBI acids ChEBI A molecular entity consisting of two or more chemical elements. chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI A lactone having a five-membered lactone ring. 0 C4H3O2R3 83.066 83.01330 O1C(C(C(C1=O)*)*)* CHEBI:13194 CHEBI:18937 CHEBI:22971 CHEBI:541 PMID:18789684 chebi_ontology 1,4-Lactone 1,4-lactones a 1,4-lactone butyrolactones gamma-Laktone gamma-lactona gamma-lactonas gamma-lactones CHEBI:37581 gamma-lactone PMID:18789684 Europe PMC 1,4-Lactone KEGG_COMPOUND 1,4-lactones ChEBI a 1,4-lactone UniProt butyrolactones ChEBI gamma-Laktone ChEBI gamma-lactona ChEBI gamma-lactonas ChEBI gamma-lactones ChEBI An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. 0 CNOR3 42.01680 41.99799 [*]C(=O)N([*])[*] CHEBI:35354 CHEBI:35355 carboxamides chebi_ontology carboxamides primary carboxamide CHEBI:37622 carboxamide carboxamides IUPAC carboxamides ChEBI primary carboxamide ChEBI A compound which inhibits or antagonizes the biosynthesis or actions of proteases (endopeptidases). Wikipedia:Protease_inhibitor_(biology) chebi_ontology protease inhibitors CHEBI:37670 protease inhibitor protease inhibitors ChEBI An EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that interferes with the action of cholinesterase (EC 3.1.1.8). chebi_ontology BChE inhibitor BChE inhibitors BtChoEase inhibitor BtChoEase inhibitors EC 3.1.1.8 (cholinesterase) inhibitors EC 3.1.1.8 inhibitor EC 3.1.1.8 inhibitors anticholineesterase inhibitor anticholineesterase inhibitors anticholinesterase anticholinesterases benzoylcholinesterase inhibitor benzoylcholinesterase inhibitors butyrylcholine esterase inhibitor butyrylcholine esterase inhibitors butyrylcholinesterase inhibitor butyrylcholinesterase inhibitors choline esterase II (unspecific) inhibitor choline esterase II (unspecific) inhibitors choline esterase inhibitor choline esterase inhibitors cholinesterase (EC 3.1.1.8) inhibitor cholinesterase (EC 3.1.1.8) inhibitors cholinesterase inhibitor non-specific cholinesterase inhibitor non-specific cholinesterase inhibitors propionylcholinesterase inhibitor propionylcholinesterase inhibitors pseudocholinesterase inhibitor pseudocholinesterase inhibitors CHEBI:37733 EC 3.1.1.8 (cholinesterase) inhibitor BChE inhibitor ChEBI BChE inhibitors ChEBI BtChoEase inhibitor ChEBI BtChoEase inhibitors ChEBI EC 3.1.1.8 (cholinesterase) inhibitors ChEBI EC 3.1.1.8 inhibitor ChEBI EC 3.1.1.8 inhibitors ChEBI anticholineesterase inhibitor ChEBI anticholineesterase inhibitors ChEBI anticholinesterase ChEBI anticholinesterases ChEBI benzoylcholinesterase inhibitor ChEBI benzoylcholinesterase inhibitors ChEBI butyrylcholine esterase inhibitor ChEBI butyrylcholine esterase inhibitors ChEBI butyrylcholinesterase inhibitor ChEBI butyrylcholinesterase inhibitors ChEBI choline esterase II (unspecific) inhibitor ChEBI choline esterase II (unspecific) inhibitors ChEBI choline esterase inhibitor ChEBI choline esterase inhibitors ChEBI cholinesterase (EC 3.1.1.8) inhibitor ChEBI cholinesterase (EC 3.1.1.8) inhibitors ChEBI cholinesterase inhibitor ChEBI non-specific cholinesterase inhibitor ChEBI non-specific cholinesterase inhibitors ChEBI propionylcholinesterase inhibitor ChEBI propionylcholinesterase inhibitors ChEBI pseudocholinesterase inhibitor ChEBI pseudocholinesterase inhibitors ChEBI CHEBI:26019 chebi_ontology CHEBI:37734 phosphoric ester Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone. CHEBI:24362 CHEBI:5456 PMID:17393491 chebi_ontology glycerophospholipids phosphatide phosphatides phosphoglyceride phosphoglycerides CHEBI:37739 glycerophospholipid PMID:17393491 Europe PMC glycerophospholipids ChEBI phosphatide ChEBI phosphatides ChEBI phosphoglyceride ChEBI phosphoglycerides ChEBI A penam that consists of 3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane bearing a carboxy group at position 2 and having (2S,5R)-configuration. 0 C8H11NO3S InChI=1S/C8H11NO3S/c1-8(2)6(7(11)12)9-4(10)3-5(9)13-8/h5-6H,3H2,1-2H3,(H,11,12)/t5-,6+/m1/s1 RBKMMJSQKNKNEV-RITPCOANSA-N 201.24388 201.04596 [H][C@@]12CC(=O)N1[C@@H](C(O)=O)C(C)(C)S2 Beilstein:4677775 CAS:87-53-6 Reaxys:4677775 2,2-dimethylpenam-3alpha-carboxylic acid penicillanic acid chebi_ontology (2S,5R)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid CHEBI:37806 penicillanic acid Beilstein:4677775 Beilstein CAS:87-53-6 ChemIDplus Reaxys:4677775 Reaxys 2,2-dimethylpenam-3alpha-carboxylic acid IUPAC penicillanic acid ChemIDplus (2S,5R)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid IUPAC A straight chain alkane composed of 4 carbon atoms. 0 C4H10 InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3 IJDNQMDRQITEOD-UHFFFAOYSA-N 58.12220 58.07825 CCCC CHEBI:22945 CHEBI:25462 CHEBI:44430 Beilstein:969129 CAS:106-97-8 Gmelin:1148 PDBeChem:NBU PMID:24179026 Reaxys:969129 Wikipedia:Butane butane chebi_ontology E 943a E-943a E943a N-BUTANE R-600 n-Butan n-C4H10 n-butane CHEBI:37808 butane Beilstein:969129 Beilstein CAS:106-97-8 ChemIDplus CAS:106-97-8 NIST Chemistry WebBook Gmelin:1148 Gmelin PMID:24179026 Europe PMC Reaxys:969129 Reaxys butane IUPAC butane UniProt E 943a ChEBI E-943a ChEBI E943a ChEBI N-BUTANE PDBeChem R-600 ChEBI n-Butan ChEBI n-C4H10 NIST_Chemistry_WebBook n-butane NIST_Chemistry_WebBook sulfuric acid derivative chebi_ontology sulfuric acid derivatives CHEBI:37826 sulfuric acid derivative sulfuric acid derivative ChEBI sulfuric acid derivatives ChEBI A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. carboacyl groups carboxylic acyl group chebi_ontology carboxylic acyl groups CHEBI:37838 carboacyl group carboacyl groups IUPAC carboxylic acyl group IUPAC carboxylic acyl groups IUPAC An agent that selectively binds to and activates adrenergic receptors. chebi_ontology adrenergic agonists adrenergic receptor agonist adrenoceptor agonists adrenomimetic adrenomimetics CHEBI:37886 adrenergic agonist adrenergic agonists ChEBI adrenergic receptor agonist ChEBI adrenoceptor agonists IUPHAR adrenomimetic ChEBI adrenomimetics ChEBI An agent that binds to but does not activate adrenergic receptors thereby blocking the actions of endogenous or exogenous adrenergic agonists. chebi_ontology adrenergic antagonists adrenergic blockaders adrenergic blocker adrenergic blockers adrenergic receptor blockaders adrenoceptor antagonists CHEBI:37887 adrenergic antagonist adrenergic antagonists ChEBI adrenergic blockaders ChEBI adrenergic blocker ChEBI adrenergic blockers ChEBI adrenergic receptor blockaders ChEBI adrenoceptor antagonists IUPHAR An agent that binds to but does not activate alpha-adrenergic receptors thereby blocking the actions of endogenous or exogenous alpha-adrenergic agonists. alpha-Adrenergic antagonists are used in the treatment of hypertension, vasospasm, peripheral vascular disease, shock, and pheochromocytoma. chebi_ontology alpha-adrenergic antagonists alpha-adrenergic blocker alpha-adrenergic blockers alpha-adrenergic receptor blockaders alpha-adrenoceptor antagonists CHEBI:37890 alpha-adrenergic antagonist alpha-adrenergic antagonists ChEBI alpha-adrenergic blocker ChEBI alpha-adrenergic blockers ChEBI alpha-adrenergic receptor blockaders ChEBI alpha-adrenoceptor antagonists IUPHAR Histamine antagonists are the drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. PMID:22035879 Wikipedia:Antihistamines chebi_ontology antihistamine antihistamines antihistaminico antihistaminics histamine receptor blocker histamine receptor blockers CHEBI:37956 histamine antagonist PMID:22035879 Europe PMC antihistamine ChEBI antihistamines ChEBI antihistaminico ChEBI antihistaminics ChEBI histamine receptor blocker ChEBI histamine receptor blockers ChEBI Drugs used for their actions on histaminergic systems. chebi_ontology histamine agents histamine drugs histaminergic agent histaminergic agents histaminergic drugs CHEBI:37957 histaminergic drug histamine agents ChEBI histamine drugs ChEBI histaminergic agent ChEBI histaminergic agents ChEBI histaminergic drugs ChEBI Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter. chebi_ontology adrenergic agents adrenergic drug adrenergic drugs adrenergic neuron agents adrenergics CHEBI:37962 adrenergic agent adrenergic agents ChEBI adrenergic drug ChEBI adrenergic drugs ChEBI adrenergic neuron agents ChEBI adrenergics ChEBI A drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres. chebi_ontology anti-arrhythmia agent antiarrhythmic agent CHEBI:38070 anti-arrhythmia drug anti-arrhythmia agent ChEBI antiarrhythmic agent ChEBI A compound composed of two or more pyrrole units. Beilstein:8538310 chebi_ontology PPys poly(pyrrole)s polypyrroles CHEBI:38077 polypyrrole Beilstein:8538310 Beilstein PPys ChEBI poly(pyrrole)s ChEBI polypyrroles ChEBI Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. chebi_ontology heterocyclic organonitrogen compounds organonitrogen heterocyclic compounds CHEBI:38101 organonitrogen heterocyclic compound heterocyclic organonitrogen compounds ChEBI organonitrogen heterocyclic compounds ChEBI Any organic heterocyclic compound containing at least one ring oxygen atom. PMID:17134300 chebi_ontology heterocyclic organooxygen compounds organooxygen heterocyclic compounds oxacycles CHEBI:38104 oxacycle PMID:17134300 Europe PMC heterocyclic organooxygen compounds ChEBI organooxygen heterocyclic compounds ChEBI oxacycles ChEBI chebi_ontology heterocyclic organosulfur compounds organosulfur heterocyclic compounds CHEBI:38106 organosulfur heterocyclic compound heterocyclic organosulfur compounds ChEBI organosulfur heterocyclic compounds ChEBI chebi_ontology iron chelating agents iron chelators CHEBI:38157 iron chelator iron chelating agents ChEBI iron chelators ChEBI A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate. CHEBI:23090 CHEBI:3585 CHEBI:6789 KEGG:C00917 KEGG:C02169 chebi_ontology Chelating agent Metal chelator chelating agents chelators complexon CHEBI:38161 chelator Chelating agent KEGG_COMPOUND Metal chelator KEGG_COMPOUND chelating agents ChEBI chelators ChEBI complexon ChEBI CHEBI:25429 CHEBI:38075 chebi_ontology organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound organic heteropolycyclic compounds ChEBI chebi_ontology monocyclic heteroarenes CHEBI:38179 monocyclic heteroarene monocyclic heteroarenes ChEBI A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of a pyridinemonocarboxylic acid. A 'closed class'. chebi_ontology pyridinemonocarboxylates CHEBI:38181 pyridinemonocarboxylate pyridinemonocarboxylates ChEBI A hydroxypyridine carrying a single hydroxy substituent. chebi_ontology monohydroxypyridines CHEBI:38182 monohydroxypyridine monohydroxypyridines ChEBI chebi_ontology pyridinecarbaldehydes CHEBI:38187 pyridinecarbaldehyde pyridinecarbaldehydes ChEBI Any member of the class of pyridines carrying a hydroxymethyl substituent at unspecified position. chebi_ontology hydroxymethylpyridines CHEBI:38196 hydroxymethylpyridine hydroxymethylpyridines ChEBI One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. chebi_ontology calcium channel antagonist calcium channel antagonists calcium channel blockers CHEBI:38215 calcium channel blocker calcium channel antagonist ChEBI calcium channel antagonists ChEBI calcium channel blockers ChEBI Any inhibitor of a DNA polymerase. chebi_ontology CHEBI:38234 DNA polymerase inhibitor A branched chain amino acid that consists of 3-methylpentanoic acid bearing an amino substituent at position 2. 0 C6H13NO2 InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9) AGPKZVBTJJNPAG-UHFFFAOYSA-N 131.17296 131.09463 CCC(C)C(N)C(O)=O CAS:443-79-8 KEGG:C16434 PMID:10944265 Reaxys:1721790 2-amino-3-methylpentanoic acid chebi_ontology CHEBI:38264 2-amino-3-methylpentanoic acid CAS:443-79-8 ChemIDplus CAS:443-79-8 KEGG COMPOUND PMID:10944265 Europe PMC Reaxys:1721790 Reaxys 2-amino-3-methylpentanoic acid IUPAC chebi_ontology azabicycloalkanes CHEBI:38295 azabicycloalkane azabicycloalkanes ChEBI chebi_ontology thiabicycloalkanes CHEBI:38297 thiabicycloalkane thiabicycloalkanes ChEBI chebi_ontology cephems CHEBI:38311 cephem cephems ChEBI Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). chebi_ontology CHEBI:38313 diazines An EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitor that interferes with the activity of 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27). CHEBI:50380 chebi_ontology 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) inhibitor 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) inhibitors 4-hydroxyphenylpyruvate dioxygenase inhibitor 4-hydroxyphenylpyruvate dioxygenase inhibitors 4-hydroxyphenylpyruvate hydroxylase inhibitor 4-hydroxyphenylpyruvate hydroxylase inhibitors 4-hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating) inhibitor 4-hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating) inhibitors 4-hydroxyphenylpyruvic acid dioxygenase inhibitor 4-hydroxyphenylpyruvic acid dioxygenase inhibitors EC 1.13.11.27 (4-hydroxyphenylpyruvate dioxygenase) inhibitors EC 1.13.11.27 inhibitor EC 1.13.11.27 inhibitors HPPD inhibitor HPPD inhibitors p-hydroxyphenylpyruvate dioxygenase inhibitor p-hydroxyphenylpyruvate dioxygenase inhibitors p-hydroxyphenylpyruvate hydroxylase inhibitor p-hydroxyphenylpyruvate hydroxylase inhibitors p-hydroxyphenylpyruvate oxidase inhibitor p-hydroxyphenylpyruvate oxidase inhibitors p-hydroxyphenylpyruvic acid hydroxylase inhibitor p-hydroxyphenylpyruvic acid hydroxylase inhibitors p-hydroxyphenylpyruvic hydroxylase inhibitor p-hydroxyphenylpyruvic hydroxylase inhibitors p-hydroxyphenylpyruvic oxidase inhibitor p-hydroxyphenylpyruvic oxidase inhibitors CHEBI:38317 EC 1.13.11.27 (4-hydroxyphenylpyruvate dioxygenase) inhibitor 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) inhibitor ChEBI 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) inhibitors ChEBI 4-hydroxyphenylpyruvate dioxygenase inhibitor ChEBI 4-hydroxyphenylpyruvate dioxygenase inhibitors ChEBI 4-hydroxyphenylpyruvate hydroxylase inhibitor ChEBI 4-hydroxyphenylpyruvate hydroxylase inhibitors ChEBI 4-hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating) inhibitor ChEBI 4-hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating) inhibitors ChEBI 4-hydroxyphenylpyruvic acid dioxygenase inhibitor ChEBI 4-hydroxyphenylpyruvic acid dioxygenase inhibitors ChEBI EC 1.13.11.27 (4-hydroxyphenylpyruvate dioxygenase) inhibitors ChEBI EC 1.13.11.27 inhibitor ChEBI EC 1.13.11.27 inhibitors ChEBI HPPD inhibitor ChEBI HPPD inhibitors ChEBI p-hydroxyphenylpyruvate dioxygenase inhibitor ChEBI p-hydroxyphenylpyruvate dioxygenase inhibitors ChEBI p-hydroxyphenylpyruvate hydroxylase inhibitor ChEBI p-hydroxyphenylpyruvate hydroxylase inhibitors ChEBI p-hydroxyphenylpyruvate oxidase inhibitor ChEBI p-hydroxyphenylpyruvate oxidase inhibitors ChEBI p-hydroxyphenylpyruvic acid hydroxylase inhibitor ChEBI p-hydroxyphenylpyruvic acid hydroxylase inhibitors ChEBI p-hydroxyphenylpyruvic hydroxylase inhibitor ChEBI p-hydroxyphenylpyruvic hydroxylase inhibitors ChEBI p-hydroxyphenylpyruvic oxidase inhibitor ChEBI p-hydroxyphenylpyruvic oxidase inhibitors ChEBI Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons. chebi_ontology cholinergic agent cholinergic drugs cholinomimetic CHEBI:38323 cholinergic drug cholinergic agent ChEBI cholinergic drugs ChEBI cholinomimetic ChEBI Any drug that binds to and activates cholinergic receptors. chebi_ontology acetylcholine agonist acetylcholine agonists acetylcholine receptor agonist cholinergic agonists cholinomimetic cholinomimetics CHEBI:38324 cholinergic agonist acetylcholine agonist ChEBI acetylcholine agonists ChEBI acetylcholine receptor agonist IUPHAR cholinergic agonists ChEBI cholinomimetic ChEBI cholinomimetics ChEBI Any drug that binds to and activates a muscarinic cholinergic receptor. chebi_ontology muscarinic acetylcholine receptor agonist muscarinic agonists muscarinic cholinergic agonist muscarinic cholinergic agonists CHEBI:38325 muscarinic agonist muscarinic acetylcholine receptor agonist ChEBI muscarinic agonists ChEBI muscarinic cholinergic agonist ChEBI muscarinic cholinergic agonists ChEBI A pyrimidine carrying one or more oxo substituents. chebi_ontology pyrimidones CHEBI:38337 pyrimidone pyrimidones ChEBI A member of the class of pyrimidines that is pyrimidine substituted by at least one amino group and its derivatives. chebi_ontology aminopyrimidines CHEBI:38338 aminopyrimidine aminopyrimidines ChEBI CHEBI:26949 CHEBI:38417 1,3-thiazoles chebi_ontology CHEBI:38418 1,3-thiazoles 1,3-thiazoles ChEBI chebi_ontology 1-benzopyrans CHEBI:38443 1-benzopyran 1-benzopyrans ChEBI An EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that interferes with the action of enzyme acetylcholinesterase (EC 3.1.1.7), which helps breaking down of acetylcholine into choline and acetic acid. Wikipedia:Acetylcholinesterase_inhibitor chebi_ontology AChEI AcCholE inhibitor AcCholE inhibitors EC 3.1.1.7 (acetylcholinesterase) inhibitors EC 3.1.1.7 inhibitor EC 3.1.1.7 inhibitors acetyl.beta-methylcholinesterase inhibitor acetyl.beta-methylcholinesterase inhibitors acetylcholine acetylhydrolase inhibitor acetylcholine acetylhydrolase inhibitors acetylcholine esterase inhibitor acetylcholine hydrolase inhibitor acetylcholine hydrolase inhibitors acetylcholinesterase (EC 3.1.1.7) inhibitor acetylcholinesterase (EC 3.1.1.7) inhibitors acetylcholinesterase inhibitor acetylcholinesterase inhibitors acetylthiocholinesterase inhibitor acetylthiocholinesterase inhibitors choline esterase I inhibitor choline esterase I inhibitors cholinesterase inhibitor cholinesterase inhibitors true cholinesterase inhibitor true cholinesterase inhibitors CHEBI:38462 EC 3.1.1.7 (acetylcholinesterase) inhibitor AChEI ChEBI AcCholE inhibitor ChEBI AcCholE inhibitors ChEBI EC 3.1.1.7 (acetylcholinesterase) inhibitors ChEBI EC 3.1.1.7 inhibitor ChEBI EC 3.1.1.7 inhibitors ChEBI acetyl.beta-methylcholinesterase inhibitor ChEBI acetyl.beta-methylcholinesterase inhibitors ChEBI acetylcholine acetylhydrolase inhibitor ChEBI acetylcholine acetylhydrolase inhibitors ChEBI acetylcholine esterase inhibitor ChEBI acetylcholine hydrolase inhibitor ChEBI acetylcholine hydrolase inhibitors ChEBI acetylcholinesterase (EC 3.1.1.7) inhibitor ChEBI acetylcholinesterase (EC 3.1.1.7) inhibitors ChEBI acetylcholinesterase inhibitor ChEBI acetylcholinesterase inhibitors ChEBI acetylthiocholinesterase inhibitor ChEBI acetylthiocholinesterase inhibitors ChEBI choline esterase I inhibitor ChEBI choline esterase I inhibitors ChEBI cholinesterase inhibitor ChEBI cholinesterase inhibitors ChEBI true cholinesterase inhibitor ChEBI true cholinesterase inhibitors ChEBI An EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitor that interferes with the action of monoamine oxidase (EC 1.4.3.4). Wikipedia:Monoamine_oxidase_inhibitor chebi_ontology EC 1.4.3.4 (monoamine oxidase) inhibitors EC 1.4.3.4 inhibitor EC 1.4.3.4 inhibitors MAO A inhibitor MAO A inhibitors MAO B inhibitor MAO B inhibitors MAO inhibitor MAO inhibitors MAO-A inhibitor MAO-A inhibitors MAO-B inhibitor MAO-B inhibitors adrenalin oxidase inhibitor adrenalin oxidase inhibitors adrenaline oxidase inhibitor adrenaline oxidase inhibitors amine oxidase (flavin-containing) inhibitor amine oxidase (flavin-containing) inhibitors amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitor amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitors amine:oxygen oxidoreductase (deaminating) inhibitor amine:oxygen oxidoreductase (deaminating) inhibitors epinephrine oxidase inhibitor epinephrine oxidase inhibitors monoamine oxidase (EC 1.4.3.4) inhibitor monoamine oxidase (EC 1.4.3.4) inhibitors monoamine oxidase A inhibitor monoamine oxidase A inhibitors monoamine oxidase B inhibitor monoamine oxidase B inhibitors monoamine oxidase inhibitor monoamine oxidase inhibitors monoamine:O2 oxidoreductase (deaminating) inhibitor monoamine:O2 oxidoreductase (deaminating) inhibitors serotonin deaminase inhibitor serotonin deaminase inhibitors tyraminase inhibitor tyraminase inhibitors tyramine oxidase inhibitor tyramine oxidase inhibitors CHEBI:38623 EC 1.4.3.4 (monoamine oxidase) inhibitor EC 1.4.3.4 (monoamine oxidase) inhibitors ChEBI EC 1.4.3.4 inhibitor ChEBI EC 1.4.3.4 inhibitors ChEBI MAO A inhibitor ChEBI MAO A inhibitors ChEBI MAO B inhibitor ChEBI MAO B inhibitors ChEBI MAO inhibitor ChEBI MAO inhibitors ChEBI MAO-A inhibitor ChEBI MAO-A inhibitors ChEBI MAO-B inhibitor ChEBI MAO-B inhibitors ChEBI adrenalin oxidase inhibitor ChEBI adrenalin oxidase inhibitors ChEBI adrenaline oxidase inhibitor ChEBI adrenaline oxidase inhibitors ChEBI amine oxidase (flavin-containing) inhibitor ChEBI amine oxidase (flavin-containing) inhibitors ChEBI amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitor ChEBI amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitors ChEBI amine:oxygen oxidoreductase (deaminating) inhibitor ChEBI amine:oxygen oxidoreductase (deaminating) inhibitors ChEBI epinephrine oxidase inhibitor ChEBI epinephrine oxidase inhibitors ChEBI monoamine oxidase (EC 1.4.3.4) inhibitor ChEBI monoamine oxidase (EC 1.4.3.4) inhibitors ChEBI monoamine oxidase A inhibitor ChEBI monoamine oxidase A inhibitors ChEBI monoamine oxidase B inhibitor ChEBI monoamine oxidase B inhibitors ChEBI monoamine oxidase inhibitor ChEBI monoamine oxidase inhibitors ChEBI monoamine:O2 oxidoreductase (deaminating) inhibitor ChEBI monoamine:O2 oxidoreductase (deaminating) inhibitors ChEBI serotonin deaminase inhibitor ChEBI serotonin deaminase inhibitors ChEBI tyraminase inhibitor ChEBI tyraminase inhibitors ChEBI tyramine oxidase inhibitor ChEBI tyramine oxidase inhibitors ChEBI Any agent that affects the transport of molecular entities across a biological membrane. chebi_ontology membrane transport modulators CHEBI:38632 membrane transport modulator membrane transport modulators ChEBI An agent that inhibits sodium influx through cell membranes. chebi_ontology Na channel blocker sodium channel blockers CHEBI:38633 sodium channel blocker Na channel blocker ChEBI sodium channel blockers ChEBI organic sodium salt chebi_ontology organic sodium salts CHEBI:38700 organic sodium salt organic sodium salt ChEBI organic sodium salts ChEBI Any dianion containing at least one carboxy group. carboxylic acid dianion chebi_ontology carboxylic acid dianions CHEBI:38716 carboxylic acid dianion carboxylic acid dianion ChEBI carboxylic acid dianions ChEBI 0 C14H11N6O3 311.276 311.08926 CHEBI:37074 chebi_ontology CHEBI:38793 pteroate 0 C14H12N6O3 312.284 312.09709 CHEBI:26378 CAS:119-24-4 DrugBank:DB04196 Pteroic acid chebi_ontology Pteroinsaeure CHEBI:38794 pteroic acid CAS:119-24-4 ChemIDplus Pteroic acid ChemIDplus Pteroinsaeure ChEBI chebi_ontology CHEBI:38795 pteroic acids chebi_ontology CHEBI:38796 pteroates A membrane transport modulator that is able to regulate intracellular calcium levels. chebi_ontology calcium channel modulators CHEBI:38808 calcium channel modulator calcium channel modulators ChEBI Substance which produces loss of feeling or sensation. anaesthetic chebi_ontology Anaesthetika Anaesthetikum anaesthetics anesthetic agent anesthetic drug anesthetics CHEBI:38867 anaesthetic anaesthetic IUPAC Anaesthetika ChEBI Anaesthetikum ChEBI anaesthetics ChEBI anesthetic agent ChEBI anesthetic drug ChEBI anesthetics ChEBI Substance that produces loss of consciousness. general anaesthetic chebi_ontology Allgemeinanaesthetika Allgemeinanaesthetikum general anaesthetics general anesthetics CHEBI:38869 general anaesthetic general anaesthetic IUPAC Allgemeinanaesthetika ChEBI Allgemeinanaesthetikum ChEBI general anaesthetics ChEBI general anesthetics ChEBI chebi_ontology Inhalationsanaesthetika Inhalationsanaesthetikum Inhalationsnarkotika Inhalationsnarkotikum anesthetic gases inhalation anesthetics CHEBI:38870 inhalation anaesthetic Inhalationsanaesthetika ChEBI Inhalationsanaesthetikum ChEBI Inhalationsnarkotika ChEBI Inhalationsnarkotikum ChEBI anesthetic gases ChEBI inhalation anesthetics ChEBI chebi_ontology i.v.-Anaesthetika i.v.-Anaesthetikum intravenous anesthetics CHEBI:38877 intravenous anaesthetic i.v.-Anaesthetika ChEBI i.v.-Anaesthetikum ChEBI intravenous anesthetics ChEBI chebi_ontology benzopteridines CHEBI:38925 benzopteridine benzopteridines ChEBI Any alkylbenzene that is benzene substituted with one or more methyl groups. chebi_ontology methylbenzenes CHEBI:38975 methylbenzene methylbenzenes ChEBI A monocyclic arene that is benzene substituted with one or more alkyl groups. alkylbenzene chebi_ontology Alkylbenzol alkylbenzenes CHEBI:38976 alkylbenzene alkylbenzene ChEBI Alkylbenzol ChEBI alkylbenzenes ChEBI chebi_ontology sodium channel modulators CHEBI:39000 sodium channel modulator sodium channel modulators ChEBI Ca 40.078 39.96259 calcium cation chebi_ontology calcium cations CHEBI:39123 calcium cation calcium cation ChEBI calcium cations ChEBI 0 Ca 40.078 39.96259 calcium ion chebi_ontology calcium ions CHEBI:39124 calcium ion calcium ion ChEBI calcium ions ChEBI A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid chebi_ontology Bronsted-Saeure acide de Bronsted donneur d'hydron hydron donor CHEBI:39141 Bronsted acid Bronsted acid IUPAC Bronsted-Saeure ChEBI acide de Bronsted IUPAC donneur d'hydron IUPAC hydron donor IUPAC A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base chebi_ontology Bronsted-Base accepteur d'hydron base de Bronsted hydron acceptor CHEBI:39142 Bronsted base Bronsted base IUPAC Bronsted-Base ChEBI accepteur d'hydron IUPAC base de Bronsted IUPAC hydron acceptor IUPAC A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct. Lewis base chebi_ontology Lewis-Base base de Lewis donneur d'une paire d'electrons electron donor CHEBI:39144 Lewis base Lewis base IUPAC Lewis-Base ChEBI base de Lewis IUPAC donneur d'une paire d'electrons ChEBI electron donor ChEBI Any saturated fatty acid with a carbon side-chain or isopropyl termination. branched-chain saturated fatty acid chebi_ontology branched saturated fatty acid branched saturated fatty acids branched-chain saturated fatty acids CHEBI:39417 branched-chain saturated fatty acid branched-chain saturated fatty acid ChEBI branched saturated fatty acid ChEBI branched saturated fatty acids ChEBI branched-chain saturated fatty acids ChEBI Any saturated fatty acid lacking a side-chain. PMID:15644336 straight-chain saturated fatty acid chebi_ontology straight-chain saturated fatty acids CHEBI:39418 straight-chain saturated fatty acid PMID:15644336 Europe PMC straight-chain saturated fatty acid ChEBI straight-chain saturated fatty acids ChEBI CHEBI:13784 CHEBI:26445 CHEBI:7263 chebi_ontology CHEBI:39446 pyrimidine ribonucleosides Any compound having a pyrimidine as part of its structure. CHEBI:13681 CHEBI:26448 chebi_ontology CHEBI:39447 pyrimidines Any drug which can be used to prevent or alleviate glaucoma, a disease in which the optic nerve is damaged, resulting in progressive, irreversible loss of vision. It is often, though not always, associated with increased pressure of the fluid in the eye. chebi_ontology anti-glaucoma agent anti-glaucoma agents anti-glaucoma drug anti-glaucoma drugs antiglaucoma agent antiglaucoma drugs CHEBI:39456 antiglaucoma drug anti-glaucoma agent ChEBI anti-glaucoma agents ChEBI anti-glaucoma drug ChEBI anti-glaucoma drugs ChEBI antiglaucoma agent ChEBI antiglaucoma drugs ChEBI A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated. -1 H2O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1 NBIIXXVUZAFLBC-UHFFFAOYSA-M 96.98724 96.96962 [H]OP([O-])(=O)O[H] CHEBI:29137 CHEBI:39739 DrugBank:DB02831 Gmelin:1999 PDBeChem:2HP dihydrogen(tetraoxidophosphate)(1-) dihydrogenphosphate dihydrogentetraoxophosphate(1-) dihydrogentetraoxophosphate(V) dihydroxidodioxidophosphate(1-) chebi_ontology DIHYDROGENPHOSPHATE ION H2PO4(-) [PO2(OH)2](-) CHEBI:39745 dihydrogenphosphate Gmelin:1999 Gmelin dihydrogen(tetraoxidophosphate)(1-) IUPAC dihydrogenphosphate IUPAC dihydrogentetraoxophosphate(1-) IUPAC dihydrogentetraoxophosphate(V) IUPAC dihydroxidodioxidophosphate(1-) IUPAC DIHYDROGENPHOSPHATE ION PDBeChem H2PO4(-) IUPAC [PO2(OH)2](-) IUPAC KEGG:C02019 Cyclic ketone cyclic ketones chebi_ontology CHEBI:3992 cyclic ketone Cyclic ketone KEGG_COMPOUND cyclic ketones IUPAC -2 CO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-2 BVKZGUZCCUSVTD-UHFFFAOYSA-L 60.00890 59.98584 [O-]C([O-])=O CHEBI:29201 CHEBI:41605 Beilstein:3600898 CAS:3812-32-6 Gmelin:1559 PDBeChem:CO3 carbonate trioxidocarbonate(2-) chebi_ontology CARBONATE ION CO3(2-) Karbonat [CO3](2-) CHEBI:41609 carbonate Beilstein:3600898 Beilstein CAS:3812-32-6 ChemIDplus Gmelin:1559 Gmelin carbonate IUPAC trioxidocarbonate(2-) IUPAC CARBONATE ION PDBeChem CO3(2-) ChEBI Karbonat ChEBI [CO3](2-) IUPAC 0 CHO 29.01804 29.00274 [H]C(*)=O CHEBI:24089 CHEBI:42480 PDBeChem:FOR FORMYL GROUP aldehyde group carbaldehyde formyl chebi_ontology -CH(O) -CHO Fo H-CO- methanoyl CHEBI:42485 formyl group FORMYL GROUP PDBeChem aldehyde group IUPAC carbaldehyde IUPAC formyl IUPAC -CH(O) IUPAC -CHO IUPAC Fo CBN H-CO- IUPAC methanoyl IUPAC 0 HO 17.00734 17.00274 *O[H] CHEBI:24706 CHEBI:43171 PDBeChem:OH HYDROXY GROUP hydroxy hydroxy group chebi_ontology -OH hydroxyl hydroxyl group CHEBI:43176 hydroxy group HYDROXY GROUP PDBeChem hydroxy IUPAC hydroxy group UniProt -OH IUPAC hydroxyl ChEBI hydroxyl group ChEBI chebi_ontology CHEBI:43254 (4S)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one A phosphate ion that is the conjugate base of dihydrogenphosphate. -2 HO4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2 NBIIXXVUZAFLBC-UHFFFAOYSA-L 95.97930 95.96234 OP([O-])([O-])=O CHEBI:29139 CHEBI:43470 Gmelin:1998 MolBase:1628 PDBeChem:PI PDBeChem:PO4 hydrogen(tetraoxidophosphate)(2-) hydrogenphosphate hydrogentetraoxophosphate(2-) hydrogentetraoxophosphate(V) hydroxidotrioxidophosphate(2-) chebi_ontology HPO4(2-) HYDROGENPHOSPHATE ION INORGANIC PHOSPHATE GROUP [P(OH)O3](2-) [PO3(OH)](2-) hydrogen phosphate phosphate CHEBI:43474 hydrogenphosphate Gmelin:1998 Gmelin hydrogen(tetraoxidophosphate)(2-) IUPAC hydrogenphosphate IUPAC hydrogentetraoxophosphate(2-) IUPAC hydrogentetraoxophosphate(V) IUPAC hydroxidotrioxidophosphate(2-) IUPAC HPO4(2-) IUPAC HYDROGENPHOSPHATE ION PDBeChem INORGANIC PHOSPHATE GROUP PDBeChem [P(OH)O3](2-) MolBase [PO3(OH)](2-) IUPAC hydrogen phosphate ChEBI phosphate UniProt A primary aliphatic amine that is butane substituted by an amino group at position 1. 0 C4H11N InChI=1S/C4H11N/c1-2-3-4-5/h2-5H2,1H3 HQABUPZFAYXKJW-UHFFFAOYSA-N 73.13680 73.08915 CCCCN Beilstein:605269 CAS:109-73-9 DrugBank:DB03659 Gmelin:1784 MetaCyc:BUTYLAMINE PDBeChem:LYT PMID:16387436 PMID:23470444 PMID:23734590 Reaxys:605269 Wikipedia:N-Butylamine butan-1-amine chebi_ontology 1-Aminobutan 1-aminobutane 1-butanamine 1-butylamine BUTYLAMINE butanamine butylamine mono-n-butylamine monobutylamine n-Butylamin n-C4H9NH2 n-butylamine CHEBI:43799 butan-1-amine Beilstein:605269 Beilstein CAS:109-73-9 ChemIDplus CAS:109-73-9 NIST Chemistry WebBook Gmelin:1784 Gmelin PMID:16387436 Europe PMC PMID:23470444 Europe PMC PMID:23734590 Europe PMC Reaxys:605269 Reaxys butan-1-amine IUPAC 1-Aminobutan ChemIDplus 1-aminobutane ChemIDplus 1-butanamine NIST_Chemistry_WebBook 1-butylamine NIST_Chemistry_WebBook BUTYLAMINE PDBeChem butanamine NIST_Chemistry_WebBook butylamine ChemIDplus mono-n-butylamine ChemIDplus monobutylamine NIST_Chemistry_WebBook n-Butylamin ChemIDplus n-C4H9NH2 NIST_Chemistry_WebBook n-butylamine ChemIDplus 0 C4H9 57.11426 57.07043 CC(*)CC CHEBI:30352 CHEBI:45554 PDBeChem:NBU 1-methylpropyl SEC-BUTYL GROUP butan-2-ido butan-2-yl sec-butyl chebi_ontology -CH(CH3)-CH2-CH3 CH3-CH2-CH(CH3)- but-2-yl isoleucine side-chain s-butyl CHEBI:45557 sec-butyl group 1-methylpropyl IUPAC SEC-BUTYL GROUP PDBeChem butan-2-ido IUPAC butan-2-yl IUPAC sec-butyl IUPAC -CH(CH3)-CH2-CH3 ChEBI CH3-CH2-CH(CH3)- IUPAC but-2-yl ChEBI isoleucine side-chain ChEBI s-butyl ChEBI -1 HO4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-1 QAOWNCQODCNURD-UHFFFAOYSA-M 97.07154 96.96010 [H]OS([O-])(=O)=O CHEBI:29199 CHEBI:45693 Gmelin:2121 hydrogen(tetraoxidosulfate)(1-) hydrogensulfate hydrogensulfate(1-) hydrogentetraoxosulfate(1-) hydrogentetraoxosulfate(VI) hydroxidotrioxidosulfate(1-) chebi_ontology HSO4(-) HYDROGEN SULFATE [SO3(OH)](-) CHEBI:45696 hydrogensulfate Gmelin:2121 Gmelin hydrogen(tetraoxidosulfate)(1-) IUPAC hydrogensulfate IUPAC hydrogensulfate(1-) IUPAC hydrogentetraoxosulfate(1-) IUPAC hydrogentetraoxosulfate(VI) IUPAC hydroxidotrioxidosulfate(1-) IUPAC HSO4(-) IUPAC HYDROGEN SULFATE PDBeChem [SO3(OH)](-) IUPAC A ubiquinone having a side chain of 10 isoprenoid units. In the naturally occurring isomer, all isoprenyl double bonds are in the E- configuration. 0 C59H90O4 InChI=1S/C59H90O4/c1-44(2)24-15-25-45(3)26-16-27-46(4)28-17-29-47(5)30-18-31-48(6)32-19-33-49(7)34-20-35-50(8)36-21-37-51(9)38-22-39-52(10)40-23-41-53(11)42-43-55-54(12)56(60)58(62-13)59(63-14)57(55)61/h24,26,28,30,32,34,36,38,40,42H,15-23,25,27,29,31,33,35,37,39,41,43H2,1-14H3/b45-26+,46-28+,47-30+,48-32+,49-34+,50-36+,51-38+,52-40+,53-42+ ACTIUHUUMQJHFO-UPTCCGCDSA-N 863.34350 862.68391 COC1=C(OC)C(=O)C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)=C(C)C1=O CHEBI:46241 CHEBI:9854 Beilstein:1900141 CAS:303-98-0 Chemspider:4445197 Drug_Central:4607 FooDB:FDB013228 HMDB:HMDB0001072 KEGG:C11378 KEGG:D01065 KNApSAcK:C00002866 LIPID_MAPS_instance:LMPR02010001 MetaCyc:UBIQUINONE-10 PDBeChem:U10 PMID:10953455 PMID:13445756 PMID:17192765 PMID:17605305 PMID:18787645 PMID:18843432 PMID:20367194 PMID:25544601 PMID:26741866 PMID:27012265 PMID:7599208 PMID:7718355 Reaxys:1900141 Wikipedia:Coenzyme_Q10 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione Coenzyme Q10 coenzyme Q10 chebi_ontology 2-((all-E)-3,7,11,15,19,23,27,31,35,39-decamethyl-2,6,10,14,18,22,26,30,34,38-tetracontadecaenyl)-5,6-dimethoxy-3-methyl-p-benzoquinone 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methyl-1,4-benzoquinone Adelir CoQ CoQ10 Q Q 199 Q10 UBIQUINONE-10 Ubidecarenone Ubiquinone-10 all-trans-ubiquinone ubiquinone ubiquinone 10 ubiquinone 50 ubiquinone-10 CHEBI:46245 coenzyme Q10 Beilstein:1900141 Beilstein CAS:303-98-0 ChemIDplus CAS:303-98-0 NIST Chemistry WebBook Drug_Central:4607 DrugCentral LIPID_MAPS_instance:LMPR02010001 LIPID MAPS PMID:10953455 Europe PMC PMID:13445756 Europe PMC PMID:17192765 Europe PMC PMID:17605305 Europe PMC PMID:18787645 Europe PMC PMID:18843432 Europe PMC PMID:20367194 Europe PMC PMID:25544601 Europe PMC PMID:26741866 Europe PMC PMID:27012265 Europe PMC PMID:7599208 Europe PMC PMID:7718355 Europe PMC Reaxys:1900141 Reaxys 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione IUPAC Coenzyme Q10 KEGG_COMPOUND coenzyme Q10 ChemIDplus 2-((all-E)-3,7,11,15,19,23,27,31,35,39-decamethyl-2,6,10,14,18,22,26,30,34,38-tetracontadecaenyl)-5,6-dimethoxy-3-methyl-p-benzoquinone ChemIDplus 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methyl-1,4-benzoquinone ChEBI Adelir KEGG_DRUG CoQ ChEBI CoQ10 ChEBI Q ChEBI Q 199 ChemIDplus Q10 ChEBI UBIQUINONE-10 PDBeChem Ubidecarenone KEGG_COMPOUND Ubiquinone-10 KEGG_COMPOUND all-trans-ubiquinone ChEBI ubiquinone ChEBI ubiquinone 10 ChemIDplus ubiquinone 50 ChemIDplus ubiquinone-10 UniProt 0 O 15.99940 15.99491 O=* CHEBI:29353 CHEBI:44607 PDBeChem:O OXO GROUP oxo chebi_ontology =O CHEBI:46629 oxo group OXO GROUP PDBeChem oxo IUPAC =O IUPAC In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals'). Wikipedia:Mineral mineral chebi_ontology Minerale minerales minerals mineraux CHEBI:46662 mineral mineral ChEBI Minerale ChEBI minerales ChEBI minerals ChEBI mineraux ChEBI 0 C7H6O4 InChI=1S/C7H6O4/c1-3-2-4(8)6(10)7(11)5(3)9/h2,10-11H,1H3 DUPLFIFGNDSGBB-UHFFFAOYSA-N 154.12014 154.02661 CC1=CC(=O)C(O)=C(O)C1=O Beilstein:2254950 2,3-dihydroxy-5-methylcyclohexa-2,5-diene-1,4-dione chebi_ontology CHEBI:46691 2,3-dihydroxy-5-methyl-1,4-benzoquinone Beilstein:2254950 Beilstein 2,3-dihydroxy-5-methylcyclohexa-2,5-diene-1,4-dione IUPAC chebi_ontology carbonate salts CHEBI:46721 carbonate salt carbonate salts ChEBI chebi_ontology phosphate minerals CHEBI:46723 phosphate mineral phosphate minerals ChEBI A liquid that can dissolve other substances (solutes) without any change in their chemical composition. Wikipedia:Solvent chebi_ontology Loesungsmittel solvant solvents CHEBI:46787 solvent Loesungsmittel ChEBI solvant ChEBI solvents ChEBI 0 CHO2 45.01744 44.99765 *C(=O)O CHEBI:23025 CHEBI:41420 PDBeChem:FMT CARBOXY GROUP carboxy chebi_ontology -C(O)OH -CO2H -COOH carboxyl group CHEBI:46883 carboxy group CARBOXY GROUP PDBeChem carboxy IUPAC -C(O)OH IUPAC -CO2H ChEBI -COOH IUPAC carboxyl group ChEBI A dicarboxylic acid monoanion that is the conjugate base of oxalic acid. -1 C2HO4 InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-1 MUBZPKHOEPUJKR-UHFFFAOYSA-M 89.02694 88.98803 OC(=O)C([O-])=O Beilstein:3601755 Gmelin:49515 carboxyformate chebi_ontology Hox hydrogen ethanedioate hydrogen oxalate CHEBI:46904 oxalate(1-) Beilstein:3601755 Beilstein Gmelin:49515 Gmelin carboxyformate IUPAC Hox IUPAC hydrogen ethanedioate IUPAC hydrogen oxalate ChEBI A pantothenic acid having R-configuration. 0 C9H17NO5 InChI=1S/C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13)/t7-/m0/s1 GHOKWGTUZJEAQD-ZETCQYMHSA-N 219.23502 219.11067 CC(C)(CO)[C@@H](O)C(=O)NCCC(O)=O CHEBI:18701 CHEBI:44679 Beilstein:1727064 CAS:79-83-4 DrugBank:DB01783 Drug_Central:2055 FooDB:FDB008322 HMDB:HMDB0000210 KEGG:C00864 KEGG:D07413 KNApSAcK:C00001550 MetaCyc:PANTOTHENATE PDBeChem:PAU PMID:12664639 PMID:13614445 PMID:14675432 PMID:15065769 PMID:15136582 PMID:15912738 PMID:16042590 PMID:17023940 PMID:17439666 PMID:17913047 PMID:18186650 PMID:19307712 PMID:19959891 PMID:20451532 PMID:21904030 PMID:22052867 PMID:22468352 PMID:23727638 PMID:27555321 PMID:32416962 PMID:32979277 PMID:5352084 Reaxys:1727064 Wikipedia:Pantothenic_Acid 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoic acid chebi_ontology (+)-Pantothenic acid (R)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-beta-alanine D(+)-N-(2,4-dihydroxy-3,3-dimethylbutyryl)-beta-alanine D-(+)-pantothenic acid D-pantothenic acid N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanine PANTOTHENOIC ACID Pantothenic acid chick antidermatitis factor vitamin B5 CHEBI:46905 (R)-pantothenic acid Beilstein:1727064 ChemIDplus CAS:79-83-4 ChemIDplus CAS:79-83-4 NIST Chemistry WebBook Drug_Central:2055 DrugCentral PMID:12664639 Europe PMC PMID:13614445 Europe PMC PMID:14675432 Europe PMC PMID:15065769 Europe PMC PMID:15136582 Europe PMC PMID:15912738 Europe PMC PMID:16042590 Europe PMC PMID:17023940 Europe PMC PMID:17439666 Europe PMC PMID:17913047 Europe PMC PMID:18186650 Europe PMC PMID:19307712 Europe PMC PMID:19959891 Europe PMC PMID:20451532 Europe PMC PMID:21904030 Europe PMC PMID:22052867 Europe PMC PMID:22468352 Europe PMC PMID:23727638 Europe PMC PMID:27555321 Europe PMC PMID:32416962 Europe PMC PMID:32979277 Europe PMC PMID:5352084 Europe PMC Reaxys:1727064 Reaxys 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoic acid IUPAC (+)-Pantothenic acid HMDB (R)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-beta-alanine ChemIDplus D(+)-N-(2,4-dihydroxy-3,3-dimethylbutyryl)-beta-alanine ChemIDplus D-(+)-pantothenic acid ChEBI D-pantothenic acid ChemIDplus N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanine PDBeChem PANTOTHENOIC ACID PDBeChem Pantothenic acid KEGG_COMPOUND chick antidermatitis factor ChemIDplus vitamin B5 ChemIDplus +1 C5H13N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+1 AHLPHDHHMVZTML-UHFFFAOYSA-O 133.16900 133.09715 [NH3+]CCCC([NH3+])C([O-])=O 2,5-diammoniopentanoate ornithinium ornithinium(1+) chebi_ontology ornithine monocation CHEBI:46912 ornithinium(1+) 2,5-diammoniopentanoate IUPAC ornithinium IUPAC ornithinium(1+) JCBN ornithine monocation JCBN +2 C5H14N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+2 AHLPHDHHMVZTML-UHFFFAOYSA-P 134.17694 134.10443 [NH3+]CCCC([NH3+])C(O)=O 1-carboxybutane-1,4-diaminium ornithinediium ornithinium(2+) chebi_ontology ornithine dication CHEBI:46913 ornithinium(2+) 1-carboxybutane-1,4-diaminium IUPAC ornithinediium IUPAC ornithinium(2+) JCBN ornithine dication JCBN chebi_ontology tetrahydrofuranols CHEBI:47017 tetrahydrofuranol tetrahydrofuranols ChEBI chebi_ontology dihydroxytetrahydrofurans CHEBI:47019 dihydroxytetrahydrofuran dihydroxytetrahydrofurans ChEBI Any ester resulting from the condensation of one or more of the hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. CHEBI:13730 CHEBI:22230 glyceride glycerides chebi_ontology acylglycerols glycerides CHEBI:47778 glyceride glyceride ChEBI glycerides IUPAC acylglycerols ChEBI glycerides ChEBI chebi_ontology penamcarboxylates CHEBI:47811 penamcarboxylate penamcarboxylates ChEBI CHEBI:27220 CHEBI:36947 chebi_ontology urea derivatives CHEBI:47857 ureas urea derivatives ChEBI A chemical compound that can be excited by light of a specific wavelength and subsequently transfer energy to a chosen reactant. This is commonly molecular oxygen within a cancer tissue, which is converted to (highly rective) singlet state oxygen. This rapidly reacts with any nearby biomolecules, ultimately killing the cancer cells. chebi_ontology photosensitising agent CHEBI:47868 photosensitizing agent photosensitising agent ChEBI macrocyclic polypyrroles chebi_ontology cyclic polypyrroles polypyrrole macrocycles CHEBI:47882 cyclic polypyrrole macrocyclic polypyrroles IUPAC cyclic polypyrroles ChEBI polypyrrole macrocycles ChEBI Any steroid substituted by at least one carboxy group. chebi_ontology steroid acids CHEBI:47891 steroid acid steroid acids ChEBI An agonist that selectively binds to and activates a nicotinic acetylcholine receptor. CHEBI:82738 Wikipedia:Nicotinic_acetylcholine_receptor chebi_ontology muscarinic agonists nicotinic acetylcholine receptor agonists nicotinic agonist nicotinic agonists CHEBI:47958 nicotinic acetylcholine receptor agonist muscarinic agonists ChEBI nicotinic acetylcholine receptor agonists ChEBI nicotinic agonist ChEBI nicotinic agonists ChEBI A compound, usually an anti-bacterial agent or a toxin, which inhibits the synthesis of a protein. chebi_ontology protein synthesis antagonist protein synthesis antagonists protein synthesis inhibitors CHEBI:48001 protein synthesis inhibitor protein synthesis antagonist ChEBI protein synthesis antagonists ChEBI protein synthesis inhibitors ChEBI chebi_ontology Schwefeloxide oxides of sulfur sulfur oxides CHEBI:48154 sulfur oxide Schwefeloxide ChEBI oxides of sulfur ChEBI sulfur oxides ChEBI chebi_ontology serotonergic agents serotonergic drugs serotonin drugs CHEBI:48278 serotonergic drug serotonergic agents ChEBI serotonergic drugs ChEBI serotonin drugs ChEBI A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. polar solvent chebi_ontology polar solvents CHEBI:48354 polar solvent polar solvent IUPAC polar solvents ChEBI chebi_ontology CHEBI:48355 non-polar solvent A polar solvent that is capable of acting as a hydron (proton) donor. protogenic solvent chebi_ontology CHEBI:48356 protic solvent protogenic solvent IUPAC Solvent that is capable of acting as a hydron (proton) acceptor. protophilic solvent chebi_ontology HBA solvent hydrogen bond acceptor solvent CHEBI:48359 protophilic solvent protophilic solvent IUPAC HBA solvent ChEBI hydrogen bond acceptor solvent ChEBI Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. amphiprotic solvent chebi_ontology CHEBI:48360 amphiprotic solvent amphiprotic solvent IUPAC 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(O)=N Beilstein:773698 CAS:4744-36-9 carbamimidic acid chebi_ontology H2N-C(=NH)-OH H2N-C(OH)=NH HO-C(=NH)-NH2 Isoharnstoff carbamimic acid carbonamidimidic acid isourea pseudourea CHEBI:48376 carbamimidic acid Beilstein:773698 Beilstein CAS:4744-36-9 ChemIDplus carbamimidic acid IUPAC H2N-C(=NH)-OH IUPAC H2N-C(OH)=NH IUPAC HO-C(=NH)-NH2 IUPAC Isoharnstoff ChEBI carbamimic acid ChemIDplus carbonamidimidic acid IUPAC isourea ChemIDplus pseudourea ChemIDplus Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing =O by =NR; thus tautomers of amides. In organic chemistry an unspecified imidic acid is generally a carboximidic acid, RC(=NR)(OH). imidic acid imidic acids chebi_ontology imidic acids imino acids CHEBI:48377 imidic acid imidic acid ChEBI imidic acids IUPAC imidic acids ChEBI imino acids IUPAC carboximidic acid carboximidic acids chebi_ontology carboximidic acids CHEBI:48378 carboximidic acid carboximidic acid ChEBI carboximidic acids IUPAC carboximidic acids ChEBI A carboximidic acid that is the imidic acid tautomer of urea, H2NC(=NH)OH, and its hydrocarbyl derivatives. isoureas chebi_ontology isoureas CHEBI:48379 isourea isoureas IUPAC isoureas ChEBI A drug used in the treatment of Parkinson's disease. Wikipedia:Antiparkinson chebi_ontology antiparkinson agent CHEBI:48407 antiparkinson drug antiparkinson agent ChEBI An agent and endogenous substances that antagonize or inhibit the development of new blood vessels. CHEBI:67170 Wikipedia:Angiogenesis_inhibitor chebi_ontology angiogenesis antagonist angiostatic agents anti-angiogenic agent CHEBI:48422 angiogenesis inhibitor angiogenesis antagonist ChEBI angiostatic agents ChEBI anti-angiogenic agent ChEBI A local anesthetic that is used to numb the surface of a body part. chebi_ontology topical anaesthetics topical anesthetic CHEBI:48425 topical anaesthetic topical anaesthetics ChEBI topical anesthetic ChEBI Any drug that acts on an alpha-adrenergic receptor. chebi_ontology alpha-adrenergic drugs CHEBI:48539 alpha-adrenergic drug alpha-adrenergic drugs ChEBI Any of the drugs that act on beta-adrenergic receptors. chebi_ontology beta-adrenergic drugs CHEBI:48540 beta-adrenergic drug beta-adrenergic drugs ChEBI A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons. chebi_ontology dopamine agent dopamine agents dopamine drug dopamine drugs dopaminergic agents CHEBI:48560 dopaminergic agent dopamine agent ChEBI dopamine agents ChEBI dopamine drug ChEBI dopamine drugs ChEBI dopaminergic agents ChEBI A drug that binds to but does not activate dopamine receptors, thereby blocking the actions of dopamine or exogenous agonists. chebi_ontology dopamine antagonist dopamine blocker dopamine receptor antagonist dopaminergic antagonists CHEBI:48561 dopaminergic antagonist dopamine antagonist ChEBI dopamine blocker ChEBI dopamine receptor antagonist ChEBI dopaminergic antagonists ChEBI A role played by a substance that can react readily with, and thereby eliminate, radicals. chebi_ontology free radical scavengers free-radical scavenger CHEBI:48578 radical scavenger free radical scavengers ChEBI free-radical scavenger ChEBI Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own. agonist chebi_ontology agonista agoniste agonists CHEBI:48705 agonist agonist IUPAC agonista ChEBI agoniste ChEBI agonists ChEBI Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances. antagonist chebi_ontology antagonista antagoniste antagonists CHEBI:48706 antagonist antagonist IUPAC antagonista ChEBI antagoniste ChEBI antagonists ChEBI 0 H2O3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3) LSNNMFCWUKXFEE-UHFFFAOYSA-N 82.08008 81.97247 OS(O)=O CHEBI:26837 CHEBI:9344 CAS:7782-99-2 Gmelin:1458 KEGG:C00094 KNApSAcK:C00019662 PDBeChem:SO3 UM-BBD_compID:c0348 Sulfurous acid dihydrogen trioxosulfate dihydroxidooxidosulfur sulfurous acid trioxosulfuric acid chebi_ontology H2SO3 S(O)(OH)2 Sulfite [SO(OH)2] acide sulfureux acido sulfuroso schweflige Saeure sulphurous acid CHEBI:48854 sulfurous acid CAS:7782-99-2 ChemIDplus Gmelin:1458 Gmelin UM-BBD_compID:c0348 UM-BBD Sulfurous acid KEGG_COMPOUND dihydrogen trioxosulfate IUPAC dihydroxidooxidosulfur IUPAC sulfurous acid IUPAC trioxosulfuric acid IUPAC H2SO3 IUPAC S(O)(OH)2 IUPAC Sulfite KEGG_COMPOUND [SO(OH)2] IUPAC acide sulfureux ChEBI acido sulfuroso ChEBI schweflige Saeure ChemIDplus sulphurous acid ChemIDplus Any drug that binds to but does not activate cholinergic receptors, thereby blocking the actions of acetylcholine or cholinergic agonists. chebi_ontology Anticholinergika Anticholinergikum acetylcholine antagonists acetylcholine receptor antagonist agent anticholinergique agente anticolinergico agentes anticolinergicos anticholinergic agents anticholinergics anticholinergiques anticolinergicos cholinergic-blocking agents CHEBI:48873 cholinergic antagonist Anticholinergika ChEBI Anticholinergikum ChEBI acetylcholine antagonists ChEBI acetylcholine receptor antagonist IUPHAR agent anticholinergique ChEBI agente anticolinergico ChEBI agentes anticolinergicos ChEBI anticholinergic agents ChEBI anticholinergics ChEBI anticholinergiques ChEBI anticolinergicos ChEBI cholinergic-blocking agents ChEBI A drug that binds to but does not activate muscarinic cholinergic receptors, thereby blocking the actions of endogenous acetylcholine or exogenous agonists. chebi_ontology Antimuskarinika Antimuskarinikum agente antimuscarinico agentes antimuscarinicos agents antimuscariniques antimuscarinic agents antimuscarinicos muscarinic acetylcholine receptor antagonist muscarinic antagonists CHEBI:48876 muscarinic antagonist Antimuskarinika ChEBI Antimuskarinikum ChEBI agente antimuscarinico ChEBI agentes antimuscarinicos ChEBI agents antimuscariniques ChEBI antimuscarinic agents ChEBI antimuscarinicos ChEBI muscarinic acetylcholine receptor antagonist ChEBI muscarinic antagonists ChEBI An antagonist at the nicotinic cholinergic receptor. Wikipedia:Nicotinic_antagonist chebi_ontology agente antinicotinico agentes antinicotinicos agents antinicotiniques antinicotinicos nicotinic acetylcholine receptor antagonist nicotinic acetylcholine receptor antagonists nicotinic antagonists nicotinic cholinergic antagonist nicotinic cholinergic antagonists CHEBI:48878 nicotinic antagonist agente antinicotinico ChEBI agentes antinicotinicos ChEBI agents antinicotiniques ChEBI antinicotinicos ChEBI nicotinic acetylcholine receptor antagonist ChEBI nicotinic acetylcholine receptor antagonists ChEBI nicotinic antagonists ChEBI nicotinic cholinergic antagonist ChEBI nicotinic cholinergic antagonists ChEBI An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom. chebi_ontology thiazole CHEBI:48901 thiazoles thiazole ChEBI Any L-alpha-amino acid carrying an N-acyl substituent. 0 C3H3NO3R2 101.061 101.01129 CHEBI:13240 CHEBI:7232 KEGG:C02850 chebi_ontology N-Acyl-L-amino acid CHEBI:48927 N-acyl-L-alpha-amino acid N-Acyl-L-amino acid KEGG_COMPOUND 0 C20H42 InChI=1S/C20H42/c1-7-18(4)12-9-14-20(6)16-10-15-19(5)13-8-11-17(2)3/h17-20H,7-16H2,1-6H3 GGYKPYDKXLHNTI-UHFFFAOYSA-N 282.54748 282.32865 CCC(C)CCCC(C)CCCC(C)CCCC(C)C Beilstein:1744639 CAS:638-36-8 2,6,10,14-tetramethylhexadecane chebi_ontology Phytan CHEBI:48937 phytane Beilstein:1744639 Beilstein CAS:638-36-8 NIST Chemistry WebBook 2,6,10,14-tetramethylhexadecane IUPAC Phytan NIST_Chemistry_WebBook A chemical substance which inhibits the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites. chebi_ontology hormone antagonists CHEBI:49020 hormone antagonist hormone antagonists ChEBI chebi_ontology CHEBI:49095 beta-amino-acid anion chebi_ontology drug metabolites CHEBI:49103 drug metabolite drug metabolites ChEBI An aldehyde in which a formyl group is located on a heteroarene. chebi_ontology CHEBI:49104 heteroarenecarbaldehyde A drug designed to prevent leukotriene synthesis or activity by blocking binding at the receptor level. chebi_ontology LTRA leukotriene antagonists leukotriene receptor antagonist leukotriene receptor antagonists CHEBI:49159 leukotriene antagonist LTRA DrugBank leukotriene antagonists ChEBI leukotriene receptor antagonist ChEBI leukotriene receptor antagonists ChEBI A drug used to treat asthma. chebi_ontology anti-asthmatic agent anti-asthmatic agents anti-asthmatic drugs CHEBI:49167 anti-asthmatic drug anti-asthmatic agent ChEBI anti-asthmatic agents ChEBI anti-asthmatic drugs ChEBI One of various classes of drugs with different action mechanisms used to treat or ameliorate peptic ulcer or irritation of the gastrointestinal tract. chebi_ontology anti-ulcer agent anti-ulcer agents anti-ulcer drugs CHEBI:49201 anti-ulcer drug anti-ulcer agent ChEBI anti-ulcer agents ChEBI anti-ulcer drugs ChEBI A chemical substance that prevents or reduces the probability of conception. chebi_ontology contraceptive agent contraceptive drugs CHEBI:49323 contraceptive drug contraceptive agent ChEBI contraceptive drugs ChEBI A chemical substance or agent with contraceptive activity in females. chebi_ontology female contraceptive agent female contraceptive drugs CHEBI:49324 female contraceptive drug female contraceptive agent ChEBI female contraceptive drugs ChEBI A compound, usually hormonal, taken orally in order to block ovulation and prevent the occurrence of pregnancy. chebi_ontology oral contraceptives CHEBI:49325 oral contraceptive oral contraceptives ChEBI 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] CHEBI:24634 CHEBI:49636 WebElements:H hydrogen chebi_ontology 1H H Wasserstoff hidrogeno hydrogen hydrogene CHEBI:49637 hydrogen atom hydrogen IUPAC 1H IUPAC H IUPAC Wasserstoff ChEBI hidrogeno ChEBI hydrogen ChEBI hydrogene ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. chebi_ontology organic amino compounds CHEBI:50047 organic amino compound organic amino compounds ChEBI An agent that binds to and activates excitatory amino acid receptors. chebi_ontology excitatory amino acid agonists excitatory amino acid receptor agonist excitatory amino acid receptor agonists CHEBI:50103 excitatory amino acid agonist excitatory amino acid agonists ChEBI excitatory amino acid receptor agonist ChEBI excitatory amino acid receptor agonists ChEBI 0 C3H3NaO3 InChI=1S/C3H4O3.Na/c1-2(4)3(5)6;/h1H3,(H,5,6);/q;+1/p-1 DAEPDZWVDSPTHF-UHFFFAOYSA-M 110.04389 109.99799 [Na+].CC(=O)C([O-])=O Beilstein:3568341 CAS:113-24-6 Gmelin:97013 sodium 2-oxopropanoate chebi_ontology Natriumpyruvat pyruvic acid, sodium salt CHEBI:50144 sodium pyruvate Beilstein:3568341 Beilstein CAS:113-24-6 ChemIDplus Gmelin:97013 Gmelin sodium 2-oxopropanoate IUPAC Natriumpyruvat ChEBI pyruvic acid, sodium salt ChemIDplus Any anion formed by loss of a proton from a steroid acid. chebi_ontology steroid acid anions CHEBI:50160 steroid acid anion steroid acid anions ChEBI A drug that softens, separates, and causes desquamation of the cornified epithelium or horny layer of skin. Keratolytic drugs are used to expose mycelia of infecting fungi or to treat corns, warts, and certain other skin diseases. chebi_ontology desquamating agent keratolytic agent keratolytic drugs skin-peeling agent CHEBI:50176 keratolytic drug desquamating agent ChEBI keratolytic agent ChEBI keratolytic drugs ChEBI skin-peeling agent ChEBI A drug used to treat or prevent skin disorders or for the routine care of skin. chebi_ontology dermatologic agent dermatologic drugs dermatological agent CHEBI:50177 dermatologic drug dermatologic agent ChEBI dermatologic drugs ChEBI dermatological agent ChEBI A substance that can be converted into a vitamin by animal tissues. Wikipedia:Provitamin chebi_ontology provitamins CHEBI:50188 provitamin provitamins ChEBI Any protective agent counteracting or neutralizing the action of poisons. chebi_ontology antidotes CHEBI:50247 antidote antidotes ChEBI Drug that acts on blood and blood-forming organs and those that affect the hemostatic system. chebi_ontology hematologic agents CHEBI:50248 hematologic agent hematologic agents ChEBI An agent that prevents blood clotting. chebi_ontology anticoagulante anticoagulants CHEBI:50249 anticoagulant anticoagulante ChEBI anticoagulants ChEBI Heterocyclic compound with sulfur and nitrogen in the ring. chebi_ontology Thiazides tiazidas CHEBI:50264 thiazide Thiazides ChEBI tiazidas ChEBI Heterocyclic compound of a ring with sulfur and two nitrogen atoms fused to a benzene ring. Members inhibit sodium-potassium-chloride symporters and are used as diuretics. chebi_ontology Benzothiadiazines benzothiadiazines CHEBI:50265 benzothiadiazine Benzothiadiazines ChEBI benzothiadiazines ChEBI A compound that, on administration, must undergo chemical conversion by metabolic processes before becoming the pharmacologically active drug for which it is a prodrug. PMID:23993918 PMID:23998799 PMID:24329110 PMID:24628402 PMID:24709544 PMID:25144792 PMID:25157234 PMID:25269430 PMID:25391982 PMID:25591121 PMID:25620096 PMID:25795057 PMID:26028253 PMID:26184144 PMID:28070577 PMID:28215138 PMID:28219047 PMID:28259775 PMID:28319647 PMID:28329729 PMID:28334528 Wikipedia:Prodrug chebi_ontology Prodrugs CHEBI:50266 prodrug PMID:23993918 Europe PMC PMID:23998799 Europe PMC PMID:24329110 Europe PMC PMID:24628402 Europe PMC PMID:24709544 Europe PMC PMID:25144792 Europe PMC PMID:25157234 Europe PMC PMID:25269430 Europe PMC PMID:25391982 Europe PMC PMID:25591121 Europe PMC PMID:25620096 Europe PMC PMID:25795057 Europe PMC PMID:26028253 Europe PMC PMID:26184144 Europe PMC PMID:28070577 Europe PMC PMID:28215138 Europe PMC PMID:28219047 Europe PMC PMID:28259775 Europe PMC PMID:28319647 Europe PMC PMID:28329729 Europe PMC PMID:28334528 Europe PMC Prodrugs ChEBI Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent. chebi_ontology chemoprotectant chemoprotectants chemoprotective agent chemoprotective agents protective agents CHEBI:50267 protective agent chemoprotectant ChEBI chemoprotectants ChEBI chemoprotective agent ChEBI chemoprotective agents ChEBI protective agents ChEBI A substance that does not act as agonist or antagonist but does affect the gamma-aminobutyric acid receptor-ionophore complex. GABA-A receptors appear to have at least three allosteric sites at which modulators act: a site at which benzodiazepines act by increasing the opening frequency of gamma-aminobutyric acid-activated chloride channels; a site at which barbiturates act to prolong the duration of channel opening; and a site at which some steroids may act. chebi_ontology GABA modulators CHEBI:50268 GABA modulator GABA modulators ChEBI chebi_ontology CHEBI:50312 onium compound Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cations chebi_ontology onium cations onium ion onium ions CHEBI:50313 onium cation onium cations IUPAC onium cations ChEBI onium ion ChEBI onium ions ChEBI +1 FH2 InChI=1S/FH2/h1H2/q+1 YNESUKSMQODWNS-UHFFFAOYSA-N 21.01428 21.01350 [H][F+][H] fluoranium fluoronium chebi_ontology H2F(+) [FH2](+) CHEBI:50314 fluoronium fluoranium IUPAC fluoronium IUPAC H2F(+) IUPAC [FH2](+) ChEBI A univalent organyl group obtained by cleaving the bond from C-2 to the side chain of a proteinogenic amino-acid. chebi_ontology canonical amino-acid side-chain canonical amino-acid side-chains proteinogenic amino-acid side-chain proteinogenic amino-acid side-chain groups proteinogenic amino-acid side-chains CHEBI:50325 proteinogenic amino-acid side-chain group canonical amino-acid side-chain ChEBI canonical amino-acid side-chains ChEBI proteinogenic amino-acid side-chain ChEBI proteinogenic amino-acid side-chain groups ChEBI proteinogenic amino-acid side-chains ChEBI 0 CH3S 47.10052 46.99555 SC* sulfanylmethyl chebi_ontology -CH2-SH HS-CH2- cysteine side-chain CHEBI:50326 sulfanylmethyl group sulfanylmethyl IUPAC -CH2-SH IUPAC HS-CH2- IUPAC cysteine side-chain ChEBI 0 C3H5O2 73.07060 73.02895 C(CC(=O)O)* 2-carboxyethyl chebi_ontology glutamic acid side-chain CHEBI:50329 2-carboxyethyl group 2-carboxyethyl IUPAC glutamic acid side-chain ChEBI chebi_ontology pyridinium ions CHEBI:50334 pyridinium ion pyridinium ions ChEBI 0 C7H7O 107.12988 107.04969 C1=C(C*)C=CC(=C1)O 4-hydroxybenzyl chebi_ontology tyrosine side-chain CHEBI:50336 4-hydroxybenzyl group 4-hydroxybenzyl IUPAC tyrosine side-chain ChEBI 0 C4H10N 72.12894 72.08132 NCCCC* 4-aminobutyl chebi_ontology lysine side-chain CHEBI:50339 4-aminobutyl group 4-aminobutyl IUPAC lysine side-chain ChEBI 0 C4H10N3 100.14242 100.08747 NC(=N)NCCC* 3-carbamimidamidopropyl chebi_ontology 3-(carbamimidoylamino)propyl 3-guanidinopropyl arginine side-chain CHEBI:50340 3-carbamimidamidopropyl group 3-carbamimidamidopropyl IUPAC 3-(carbamimidoylamino)propyl IUPAC 3-guanidinopropyl ChEBI arginine side-chain ChEBI Any cholinergic antagonist that inhibits the actions of the parasympathetic nervous system. The major group of drugs used therapeutically for this purpose is the muscarinic antagonists. chebi_ontology parasympatholytics CHEBI:50370 parasympatholytic parasympatholytics ChEBI Any steroid based on a cholestane skeleton and its derivatives. chebi_ontology cholestanoids CHEBI:50401 cholestanoid cholestanoids ChEBI A drug or agent which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system. chebi_ontology platelet aggregation inhibitors CHEBI:50427 platelet aggregation inhibitor platelet aggregation inhibitors ChEBI Substance that sweeten food, beverages, medications, etc. chebi_ontology sweetener sweeteners CHEBI:50505 sweetening agent sweetener ChEBI sweeteners ChEBI An agent that inhibits cell membrane glycoproteins that are selectively permeable to potassium ions. chebi_ontology CHEBI:50509 potassium channel blocker chebi_ontology CHEBI:50510 potassium channel modulator A gamma-lactone that consists of a 2-furanone skeleton and its substituted derivatives. 0 C4H4O2 84.074 84.02113 CHEBI:22960 CHEBI:38121 Wikipedia:Butenolide furan-2-one chebi_ontology 2-furanone butenolides CHEBI:50523 butenolide furan-2-one IUPAC 2-furanone ChEBI butenolides ChEBI An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position. CHEBI:22937 CHEBI:50581 chebi_ontology alkyl alcohols hydroxyalkane hydroxyalkanes CHEBI:50584 alkyl alcohol alkyl alcohols ChEBI hydroxyalkane ChEBI hydroxyalkanes ChEBI A substance used either in the prevention or facilitation of pregnancy. chebi_ontology reproductive control agent reproductive control drugs CHEBI:50689 reproductive control drug reproductive control agent ChEBI reproductive control drugs ChEBI A chemical substance that interrupts pregnancy after implantation. Wikipedia:Abortifacient chebi_ontology abortifacient agent abortifacient agents abortifacient drug abortifacient drugs abortifacients CHEBI:50691 abortifacient abortifacient agent ChEBI abortifacient agents ChEBI abortifacient drug ChEBI abortifacient drugs ChEBI abortifacients ChEBI A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. CHEBI:25679 CHEBI:35319 CHEBI:7758 KEGG:C00930 Oligosaccharide oligosaccharides chebi_ontology O-glycosylglycoside O-glycosylglycosides oligosacarido oligosacaridos CHEBI:50699 oligosaccharide Oligosaccharide KEGG_COMPOUND oligosaccharides IUPAC O-glycosylglycoside ChEBI O-glycosylglycosides ChEBI oligosacarido ChEBI oligosacaridos IUPAC A product in capsule, tablet or liquid form that provide essential nutrients, such as a vitamin, an essential mineral, a protein, an herb, or similar nutritional substance. chebi_ontology Dietary Supplement Food Supplementation Nutritional supplement CHEBI:50733 nutraceutical Dietary Supplement ChEBI Food Supplementation ChEBI Nutritional supplement ChEBI A substance that possess antiestrogenic actions but can also produce estrogenic effects as well. It acts as complete or partial agonist or as antagonist. It can be either steroidal or nonsteroidal in structure. chebi_ontology CHEBI:50739 estrogen receptor modulator An EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor which interferes with the action of aromatase (EC 1.14.14.14) and so reduces production of estrogenic steroid hormones. Wikipedia:Aromatase_inhibitor chebi_ontology EC 1.14.14.14 (aromatase) inhibitors EC 1.14.14.14 inhibitor EC 1.14.14.14 inhibitors aromatase (EC 1.14.14.14) inhibitor aromatase (EC 1.14.14.14) inhibitors aromatase inhibitor aromatase inhibitors estrogen synthase inhibitor estrogen synthase inhibitors estrogen synthetase inhibitor estrogen synthetase inhibitors oestrogen synthase inhibitor oestrogen synthase inhibitors oestrogen synthetase inhibitor oestrogen synthetase inhibitors CHEBI:50790 EC 1.14.14.14 (aromatase) inhibitor EC 1.14.14.14 (aromatase) inhibitors ChEBI EC 1.14.14.14 inhibitor ChEBI EC 1.14.14.14 inhibitors ChEBI aromatase (EC 1.14.14.14) inhibitor ChEBI aromatase (EC 1.14.14.14) inhibitors ChEBI aromatase inhibitor ChEBI aromatase inhibitors ChEBI estrogen synthase inhibitor ChEBI estrogen synthase inhibitors ChEBI estrogen synthetase inhibitor ChEBI estrogen synthetase inhibitors ChEBI oestrogen synthase inhibitor ChEBI oestrogen synthase inhibitors ChEBI oestrogen synthetase inhibitor ChEBI oestrogen synthetase inhibitors ChEBI A drug used to treat hyperparathyroidism by reducing the excessive production of parathyroid hormones. chebi_ontology antiparathyroid agent antiparathyroid agents antiparathyroid drugs CHEBI:50827 antiparathyroid drug antiparathyroid agent ChEBI antiparathyroid agents ChEBI antiparathyroid drugs ChEBI A compound which inhibits or antagonises the biosynthesis or actions of estrogens. chebi_ontology oestrogen antagonist CHEBI:50837 estrogen antagonist oestrogen antagonist ChEBI Biologically active substance whose activity affects or plays a role in the functioning of the immune system. Wikipedia:Immunotherapy chebi_ontology Biomodulator Immune factor Immunologic factor Immunological factor immunomodulators CHEBI:50846 immunomodulator Biomodulator ChEBI Immune factor ChEBI Immunologic factor ChEBI Immunological factor ChEBI immunomodulators ChEBI A substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. Wikipedia:Immunologic_adjuvant chebi_ontology Immunoactivator Immunoadjuvant Immunologic adjuvant Immunopotentiator Immunostimulant CHEBI:50847 immunological adjuvant Immunoactivator ChEBI Immunoadjuvant ChEBI Immunologic adjuvant ChEBI Immunopotentiator ChEBI Immunostimulant ChEBI A cardiovascular drug that prevents atherogenesis, the accumulation of lipid-containing plaques on the innermost layers of the arteries. Compare with antiatherosclerotic agent. PMID:14592471 PMID:16366593 PMID:17990280 PMID:20222342 PMID:21074432 PMID:21172387 PMID:21649483 PMID:3288054 PMID:9796331 antiatherogenic agent chebi_ontology anti-atherogenic agent anti-atherogenic agents anti-atherogenic drug anti-atherogenic drugs antiatherogenic agents antiatherogenic drug antiatherogenic drugs CHEBI:50855 antiatherogenic agent PMID:14592471 Europe PMC PMID:16366593 Europe PMC PMID:17990280 Europe PMC PMID:20222342 Europe PMC PMID:21074432 Europe PMC PMID:21172387 Europe PMC PMID:21649483 Europe PMC PMID:3288054 Europe PMC PMID:9796331 Europe PMC antiatherogenic agent ChEBI anti-atherogenic agent ChEBI anti-atherogenic agents ChEBI anti-atherogenic drug ChEBI anti-atherogenic drugs ChEBI antiatherogenic agents ChEBI antiatherogenic drug ChEBI antiatherogenic drugs ChEBI A drug used to treat allergic reactions. chebi_ontology anti-allergic agents anti-allergic drug anti-allergic drugs CHEBI:50857 anti-allergic agent anti-allergic agents ChEBI anti-allergic drug ChEBI anti-allergic drugs ChEBI A natural or synthetic analogue of the hormones secreted by the adrenal gland. chebi_ontology corticoides corticosteroides corticosteroids CHEBI:50858 corticosteroid corticoides ChEBI corticosteroides ChEBI corticosteroids ChEBI Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 chebi_ontology organic compounds organic entity organic molecular entities CHEBI:50860 organic molecular entity organic compounds ChEBI organic entity ChEBI organic molecular entities ChEBI A role played by a chemical compound to induce direct or indirect DNA damage. Such damage can potentially lead to the formation of a malignant tumour, but DNA damage does not lead inevitably to the creation of cancerous cells. Wikipedia:Genotoxicity chebi_ontology genotoxic agent genotoxic agents genotoxins CHEBI:50902 genotoxin genotoxic agent ChEBI genotoxic agents ChEBI genotoxins ChEBI A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities. chebi_ontology agente carcinogeno cancerigene cancerogene carcinogen carcinogene carcinogenic agents carcinogeno carcinogens CHEBI:50903 carcinogenic agent agente carcinogeno ChEBI cancerigene ChEBI cancerogene ChEBI carcinogen ChEBI carcinogene ChEBI carcinogenic agents ChEBI carcinogeno ChEBI carcinogens ChEBI A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy. Wikipedia:Allergen chebi_ontology alergeno allergene allergenic agent CHEBI:50904 allergen alergeno ChEBI allergene ChEBI allergenic agent ChEBI A role is particular behaviour which a material entity may exhibit. chebi_ontology CHEBI:50906 role A poison that interferes with the functions of the nervous system. CHEBI:50911 Wikipedia:Neurotoxin chebi_ontology agente neurotoxico nerve poison nerve poisons neurotoxic agent neurotoxic agents neurotoxicant neurotoxins CHEBI:50910 neurotoxin agente neurotoxico ChEBI nerve poison ChEBI nerve poisons ChEBI neurotoxic agent ChEBI neurotoxic agents ChEBI neurotoxicant ChEBI neurotoxins ChEBI A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors. Wikipedia:Antiemetic chebi_ontology anti-emetic anti-emetics antiemetico antiemetics CHEBI:50919 antiemetic anti-emetic ChEBI anti-emetics ChEBI antiemetico ChEBI antiemetics ChEBI An agent that modulates the physiologic angiogenesis process. This is accomplished by endogenous angiogenic proteins and a variety of other chemicals and pharmaceutical agents. chebi_ontology CHEBI:50926 angiogenesis modulating agent true A compound that specifically inhibits the reuptake of serotonin in the brain. This increases the serotonin concentration in the synaptic cleft which then activates serotonin receptors to a greater extent. Wikipedia:Selective_serotonin_reuptake_inhibitor chebi_ontology SSRI serotonin reuptake inhibitor CHEBI:50949 serotonin uptake inhibitor SSRI ChEBI serotonin reuptake inhibitor ChEBI A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group. chebi_ontology primary amino compounds CHEBI:50994 primary amino compound primary amino compounds ChEBI A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. chebi_ontology tertiary amino compounds CHEBI:50996 tertiary amino compound tertiary amino compounds ChEBI A cyclic compound containing nine or more atoms as part of the cyclic system. Wikipedia:Macrocycle macrocycle chebi_ontology Makrocyclen Makrozyklen macrocycles makrocyclische Verbindungen makrozyklische Verbindungen CHEBI:51026 macrocycle macrocycle IUPAC Makrocyclen ChEBI Makrozyklen ChEBI macrocycles ChEBI makrocyclische Verbindungen ChEBI makrozyklische Verbindungen ChEBI A dopaminergic agent that blocks the transport of dopamine into axon terminals or into storage vesicles within terminals. Most of the adrenergic uptake inhibitors also inhibit dopamine uptake. Wikipedia:Dopamine_uptake_inhibitor chebi_ontology DARI DRI dopamine reuptake inhibitor dopamine reuptake inhibitors dopamine uptake inhibitors CHEBI:51039 dopamine uptake inhibitor DARI ChEBI DRI ChEBI dopamine reuptake inhibitor ChEBI dopamine reuptake inhibitors ChEBI dopamine uptake inhibitors ChEBI A drug that modulates the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites. chebi_ontology hormone receptor modulators CHEBI:51061 hormone receptor modulator hormone receptor modulators ChEBI A role played by the molecular entity or part thereof within a chemical context. chebi_ontology CHEBI:51086 chemical role CHEBI:25556 CHEBI:7594 KEGG:C06061 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities CHEBI:51143 nitrogen molecular entity Nitrogenous compounds KEGG_COMPOUND nitrogen compounds ChEBI nitrogen molecular entities ChEBI An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case. chebi_ontology dipolar compounds CHEBI:51151 dipolar compound dipolar compounds ChEBI Polycyclic aromatic hydrocarbons consisting of fused benzene rings in a rectilinear arrangement and their substitution derivatives. chebi_ontology CHEBI:51269 acenes Compounds containing a tetracene skeleton. chebi_ontology naphthacenes CHEBI:51270 tetracenes naphthacenes ChEBI Any anion formed by loss of a proton from the carboxy group of a penicillin. -1 C9H10N2O4SR 242.25200 242.03613 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C([O-])=O CHEBI:58108 chebi_ontology a penicillin penicillin anion penicillin anions CHEBI:51356 penicillinate anion a penicillin UniProt penicillin anion ChEBI penicillin anions ChEBI A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. chebi_ontology muscle relaxants CHEBI:51371 muscle relaxant muscle relaxants ChEBI A drug used for its actions on skeletal muscle. chebi_ontology CHEBI:51372 neuromuscular agent A drug that binds to and activates gamma-aminobutyric acid receptors. chebi_ontology GABA agonists GABA receptor agonist GABA receptor agonists gamma-aminobutyric acid receptor agonist gamma-aminobutyric acid receptor agonists CHEBI:51373 GABA agonist GABA agonists ChEBI GABA receptor agonist ChEBI GABA receptor agonists ChEBI gamma-aminobutyric acid receptor agonist ChEBI gamma-aminobutyric acid receptor agonists ChEBI A substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems. chebi_ontology CHEBI:51374 GABA agent Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). chebi_ontology organodiyl groups CHEBI:51422 organodiyl group organodiyl groups ChEBI chebi_ontology CHEBI:51446 organic divalent group chebi_ontology CHEBI:51447 organic univalent group A carboxamide resulting from the formal condensation of a carboxylic acid with the amino group of an amino acid. CHEBI:21653 CHEBI:22226 chebi_ontology N-acyl amino acid N-acyl amino acids N-acyl-amino-acid N-acyl-amino-acids N-acylamino acid N-acylamino acids acyl-amino-acid acyl-amino-acids acylamino acids CHEBI:51569 N-acyl-amino acid N-acyl amino acid ChEBI N-acyl amino acids ChEBI N-acyl-amino-acid ChEBI N-acyl-amino-acids ChEBI N-acylamino acid ChEBI N-acylamino acids ChEBI acyl-amino-acid ChEBI acyl-amino-acids ChEBI acylamino acids ChEBI Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. chebi_ontology CHEBI:51570 biotins chebi_ontology organic polycyclic compounds CHEBI:51958 organic polycyclic compound organic polycyclic compounds ChEBI chebi_ontology organic tricyclic compounds CHEBI:51959 organic tricyclic compound organic tricyclic compounds ChEBI An organic anion that is the conjugate base of methanol. -1 CH3O InChI=1S/CH3O/c1-2/h1H3/q-1 NBTOZLQBSIZIKS-UHFFFAOYSA-N 31.03390 31.01894 C[O-] Reaxys:1839368 chebi_ontology methoxide ion CHEBI:52090 methoxide Reaxys:1839368 Reaxys methoxide ion ChEBI A biological role played by the molecular entity or part thereof within a biochemical context. chebi_ontology CHEBI:52206 biochemical role chebi_ontology CHEBI:52208 biophysical role A role played by the molecular entity or part thereof which causes the development of a pathological process. chebi_ontology etiopathogenetic agent etiopathogenetic role CHEBI:52209 aetiopathogenetic role etiopathogenetic agent ChEBI etiopathogenetic role ChEBI A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties. chebi_ontology CHEBI:52210 pharmacological role chebi_ontology CHEBI:52211 physiological role Any molecule or ion capable of binding to a central metal atom to form coordination complexes. Wikipedia:Ligand chebi_ontology ligands CHEBI:52214 ligand ligands ChEBI Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:33293 CHEBI:33294 chebi_ontology farmaco medicament pharmaceuticals CHEBI:52217 pharmaceutical farmaco ChEBI medicament ChEBI pharmaceuticals ChEBI A phosphate mineral with the general formula Ca5(PO4)3X where X = OH, F or Cl. HMDB:HMDB0033610 chebi_ontology hydroxyapatite CHEBI:52254 apatite hydroxyapatite ChEBI A phosphate mineral with the formula Ca5(PO4)3(OH). 0 Ca5HO13P3 502.312 501.67595 chebi_ontology CHEBI:52255 hydroxylapatite A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group. chebi_ontology oxyketones CHEBI:52395 oxyketone oxyketones ChEBI An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom. chebi_ontology alpha-oxyketones CHEBI:52396 alpha-oxyketone alpha-oxyketones ChEBI The biological role played by a material entity when bound by a receptor of the adaptive immune system. Specific site on an antigen to which an antibody binds. chebi_ontology antigenic determinant epitope function epitope role CHEBI:53000 epitope antigenic determinant ChEBI epitope function ChEBI epitope role ChEBI A polymer carrying multiple negative charges. chebi_ontology polyanion polyanions CHEBI:53309 polyanionic macromolecule polyanion ChEBI polyanions SUBMITTER Any fatty acid containing at least one C=C double bond. PMID:832335 chebi_ontology CHEBI:53339 olefinic fatty acid PMID:832335 Europe PMC A macromolecule containing ionic groups. chebi_ontology ionic polymer polyionic macromolecule CHEBI:53368 ionic macromolecule ionic polymer ChEBI polyionic macromolecule ChEBI COMe:PRX000257 KEGG:C06258 Globin chebi_ontology globins pentacoordinate globin CHEBI:5386 globin Globin KEGG_COMPOUND globins ChEBI pentacoordinate globin COMe Any drug found useful in the symptomatic treatment of diarrhoea. chebi_ontology antidiarrheal antidiarrheal agent antidiarrheal agents antidiarrheal drug antidiarrheal drugs antidiarrheals antidiarrhoeal antidiarrhoeal agent antidiarrhoeal agents antidiarrhoeal drugs antidiarrhoeals antiperistaltic antiperistaltic agent antiperistaltic agents antiperistaltic drug antiperistaltic drugs antiperistaltics CHEBI:55323 antidiarrhoeal drug antidiarrheal ChEBI antidiarrheal agent ChEBI antidiarrheal agents ChEBI antidiarrheal drug ChEBI antidiarrheal drugs ChEBI antidiarrheals ChEBI antidiarrhoeal ChEBI antidiarrhoeal agent ChEBI antidiarrhoeal agents ChEBI antidiarrhoeal drugs ChEBI antidiarrhoeals ChEBI antiperistaltic ChEBI antiperistaltic agent ChEBI antiperistaltic agents ChEBI antiperistaltic drug ChEBI antiperistaltic drugs ChEBI antiperistaltics ChEBI A drug used for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion. chebi_ontology gastrointestinal agent gastrointestinal agents gastrointestinal drugs CHEBI:55324 gastrointestinal drug gastrointestinal agent ChEBI gastrointestinal agents ChEBI gastrointestinal drugs ChEBI A cyclic compound having as ring members atoms of at least two different elements. Heterocyclic compound chebi_ontology compuesto heterociclico compuestos heterociclicos heterocycle heterocyclic compounds CHEBI:5686 heterocyclic compound Heterocyclic compound KEGG_COMPOUND compuesto heterociclico IUPAC compuestos heterociclicos IUPAC heterocycle ChEBI heterocyclic compounds ChEBI An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of glycine. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06660 75.03203 [NH3+]CC([O-])=O Gmelin:1807 MetaCyc:GLY 2-azaniumylacetate chebi_ontology glycine CHEBI:57305 glycine zwitterion Gmelin:1807 Gmelin 2-azaniumylacetate IUPAC glycine UniProt A fatty acid anion with a chain length of C13 to C22. -1 CO2R 44.010 43.98983 [O-]C([*])=O CHEBI:13652 chebi_ontology a long-chain carboxylate a long-chain fatty acid long-chain fatty acid anions CHEBI:57560 long-chain fatty acid anion a long-chain carboxylate ChEBI a long-chain fatty acid UniProt long-chain fatty acid anions ChEBI Conjugate base of biotin arising from deprotonation of the carboxy group. -1 C10H15N2O3S InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/p-1/t6-,7-,9-/m0/s1 YBJHBAHKTGYVGT-ZKWXMUAHSA-M 243.30300 243.08034 [H][C@]12CS[C@@H](CCCCC([O-])=O)[C@@]1([H])NC(=O)N2 Beilstein:10186323 MetaCyc:BIOTIN 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate chebi_ontology biotin biotin anion CHEBI:57586 biotinate Beilstein:10186323 Beilstein 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate IUPAC biotin UniProt biotin anion ChEBI Zwitterionic form of gamma-amino-beta-hydroxybutyric acid having an anionic carboxy group and a protonated amino group. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8) YQGDEPYYFWUPGO-UHFFFAOYSA-N 119.11920 119.05824 [NH3+]CC(O)CC([O-])=O 4-azaniumyl-3-hydroxybutanoate chebi_ontology 4-amino-3-hydroxybutanoate 4-ammonio-3-hydroxybutanoate CHEBI:57630 gamma-amino-beta-hydroxybutyric acid zwitterion 4-azaniumyl-3-hydroxybutanoate IUPAC 4-amino-3-hydroxybutanoate UniProt 4-ammonio-3-hydroxybutanoate ChEBI Anionic form of chondroitin D-glucuronate arising from deprotonation of the carboxylic acid groups of the repeating units; major species at pH 7.3. H2O(C14H20NO11)n chebi_ontology chondroitin D-glucuronate chondroitin D-glucuronate polyanion CHEBI:57652 chondroitin D-glucuronate anion chondroitin D-glucuronate UniProt chondroitin D-glucuronate polyanion ChEBI Zwitterionic form of L-methionine having a anionic carboxy group and a cationic amino group; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-N 149.21100 149.05105 CSCC[C@H]([NH3+])C([O-])=O Gmelin:560248 MetaCyc:MET (2S)-2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology (2S)-2-ammonio-4-(methylsulfanyl)butanoate L-methionine CHEBI:57844 L-methionine zwitterion Gmelin:560248 Gmelin (2S)-2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC (2S)-2-ammonio-4-(methylsulfanyl)butanoate ChEBI L-methionine UniProt Zwitterionic form of 6-aminopenicillanic acid arising from migration of a proton from the carboxy group to the 6-amino group; major species at pH 7.3. 0 C8H12N2O3S InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1 NGHVIOIJCVXTGV-ALEPSDHESA-N 216.25700 216.05686 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2[NH3+])C([O-])=O 6-azaniumyl-2,2-dimethylpenam-3alpha-carboxylate chebi_ontology (2S,5R,6R)-6-azaniumyl-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate 6-aminopenicillanate CHEBI:57869 6-aminopenicillanic acid zwitterion 6-azaniumyl-2,2-dimethylpenam-3alpha-carboxylate IUPAC (2S,5R,6R)-6-azaniumyl-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate ChEBI 6-aminopenicillanate UniProt Zwitterionic form of D-methionine arising from transfer of a proton from the carboxy to the amino group; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-N 149.21100 149.05105 CSCC[C@@H]([NH3+])C([O-])=O MetaCyc:CPD-218 (2R)-2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology (2R)-2-ammonio-4-(methylsulfanyl)butanoate D-methionine CHEBI:57932 D-methionine zwitterion (2R)-2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC (2R)-2-ammonio-4-(methylsulfanyl)butanoate IUPAC D-methionine UniProt Zwitterionic form of creatine arising from transfer of a proton from the carboxy to the guanidino group; major species at pH 7.3. 0 C4H9N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) CVSVTCORWBXHQV-UHFFFAOYSA-N 131.13320 131.06948 CN(CC([O-])=O)C(N)=[NH2+] MetaCyc:CREATINE {[amino(iminio)methyl](methyl)amino}acetate chebi_ontology creatine CHEBI:57947 creatine zwitterion {[amino(iminio)methyl](methyl)amino}acetate IUPAC creatine UniProt Zwitterionic form of beta-alanine arising from transfer of a proton from the carboxy to the amino group; major species at pH 7.3. 0 C3H7NO2 InChI=1S/C3H7NO2/c4-2-1-3(5)6/h1-2,4H2,(H,5,6) UCMIRNVEIXFBKS-UHFFFAOYSA-N 89.09320 89.04768 [NH3+]CCC([O-])=O Gmelin:454332 3-azaniumylpropanoate chebi_ontology 3-ammoniopropanoate beta-alanine CHEBI:57966 beta-alanine zwitterion Gmelin:454332 Gmelin 3-azaniumylpropanoate IUPAC 3-ammoniopropanoate IUPAC beta-alanine UniProt A dicarboxylic acid dianion obtained by deprotonation of the two carboxy groups of bilirubin; major species at pH 7.3. -2 C33H34N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/p-2/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-L 582.64630 582.24893 CC1=C(C=C)\C(NC1=O)=C\c1[nH]c(Cc2[nH]c(\C=C3NC(=O)C(C=C)=C/3C)c(C)c2CCC([O-])=O)c(CCC([O-])=O)c1C Beilstein:4083310 chebi_ontology 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoate bilirubin IXalpha bilirubin dianion CHEBI:57977 bilirubin(2-) Beilstein:4083310 Beilstein 2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoate ChEBI bilirubin IXalpha UniProt bilirubin dianion ChEBI An organic anion that is the conjugate base of riboflavin resulting from the removal of a proton from the nitrogen at position 3 (between the two carbonyl groups). Major microspecies at pH 7.3. -1 C17H19N4O6 InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/p-1/t11-,12+,14-/m0/s1 AUNGANRZJHBGPY-SCRDCRAPSA-M 375.35600 375.13101 Cc1cc2nc3c(nc(=O)[n-]c3=O)n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C Beilstein:4924198 Chemspider:26330994 MetaCyc:RIBOFLAVIN 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol chebi_ontology 7,8-dimethyl-2,4-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2H,3H,4H,10H-benzo[g]pteridin-3-ide riboflavin riboflavin anion vitamin B2(1-) CHEBI:57986 riboflavin(1-) Beilstein:4924198 Beilstein 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol IUPAC 7,8-dimethyl-2,4-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2H,3H,4H,10H-benzo[g]pteridin-3-ide ChEBI riboflavin UniProt riboflavin anion ChEBI vitamin B2(1-) ChEBI The conjugate acid of a primary aliphatic amine. +1 CH5NR 31.05710 31.04220 [NH3+]C[*] chebi_ontology an aliphatic amine primary aliphatic ammonium cation primary aliphatic ammonium cations primary aliphatic ammonium ions CHEBI:58001 primary aliphatic ammonium ion an aliphatic amine UniProt primary aliphatic ammonium cation ChEBI primary aliphatic ammonium cations ChEBI primary aliphatic ammonium ions ChEBI Dianion of N-phosphocreatine arising from deprotonation of the phospho and carboxy groups and protonation of the guanidino group; major species at pH 7.3. -2 C4H8N3O5P InChI=1S/C4H10N3O5P/c1-7(2-3(8)9)4(5)6-13(10,11)12/h2H2,1H3,(H,8,9)(H4,5,6,10,11,12)/p-2 DRBBFCLWYRJSJZ-UHFFFAOYSA-L 209.09720 209.02125 CN(CC([O-])=O)C(=[NH2+])NP([O-])([O-])=O MetaCyc:CREATINE-P {[iminio(phosphonatoamino)methyl](methyl)amino}acetate chebi_ontology N-phosphocreatinate N-phosphocreatine N-phosphocreatine dianion CHEBI:58092 N-phosphocreatinate(2-) {[iminio(phosphonatoamino)methyl](methyl)amino}acetate IUPAC N-phosphocreatinate ChEBI N-phosphocreatine UniProt N-phosphocreatine dianion ChEBI An ammonium ion that is the conjugate acid of trimethylamine, obtained via protonation of the nitrogen; major species at pH 7.3. +1 C3H10N InChI=1S/C3H9N/c1-4(2)3/h1-3H3/p+1 GETQZCLCWQTVFV-UHFFFAOYSA-O 60.11820 60.08078 C[NH+](C)C MetaCyc:TRIMETHYLAMINE Reaxys:16709444 N,N-dimethylmethanaminium chebi_ontology trimethylamine trimethylammonium cation trimethylazanium trimethylazanium cation CHEBI:58389 trimethylammonium Reaxys:16709444 Reaxys N,N-dimethylmethanaminium IUPAC trimethylamine UniProt trimethylammonium cation ChEBI trimethylazanium ChEBI trimethylazanium cation ChEBI The conjugate base of an N-acetyl-D-amino acid. -1 C4H5NO3R 115.08740 115.02694 CC(=O)N[C@H]([*])C([O-])=O chebi_ontology N-acetyl-D-amino acetate(1-) N-acetyl-D-amino acid anions N-acetyl-D-amino carboxylate anions an N-acetyl-D-amino acid CHEBI:58496 N-acetyl-D-amino acid anion N-acetyl-D-amino acetate(1-) ChEBI N-acetyl-D-amino acid anions ChEBI N-acetyl-D-amino carboxylate anions ChEBI an N-acetyl-D-amino acid UniProt An organic phosphoric acid derivative in which one or more oxygen atoms of the phosphate group(s) has been deprotonated. chebi_ontology organophosphate oxoanions CHEBI:58945 organophosphate oxoanion organophosphate oxoanions ChEBI Any fatty acid anion obtained by removal of a proton from the carboxy group of a short-chain fatty acid (chain length of less than C6). -1 CO2R 44.010 43.98983 [O-]C([*])=O chebi_ontology a short-chain fatty acid short-chain fatty acid anions CHEBI:58951 short-chain fatty acid anion a short-chain fatty acid UniProt short-chain fatty acid anions ChEBI Any fatty acid anion in which there is no C-C unsaturation. chebi_ontology saturated fatty acid anions CHEBI:58953 saturated fatty acid anion saturated fatty acid anions ChEBI Any saturated fatty acid anion lacking a carbon side-chain. chebi_ontology straight-chain saturated fatty acid anions CHEBI:58954 straight-chain saturated fatty acid anion straight-chain saturated fatty acid anions ChEBI Any fatty acid anion with a carbon side-chain or isopropyl termination. chebi_ontology branched-chain fatty acid anions CHEBI:58955 branched-chain fatty acid anion branched-chain fatty acid anions ChEBI Any saturated fatty acid anion with a carbon side-chain or isopropyl termination. chebi_ontology branched-chain saturated fatty acid anions CHEBI:58956 branched-chain saturated fatty acid anion branched-chain saturated fatty acid anions ChEBI An organic anion of general formula RS(=O)2O(-) where R is an organyl group. -1 O4SR 96.06300 95.95173 [O-]S(=O)(=O)O[*] chebi_ontology organosulfate oxoanions CHEBI:58958 organosulfate oxoanion organosulfate oxoanions ChEBI Any substance capable of eliciting an immune response only when attached to a large carrier such as a protein. Examples include dinitrophenols; oligosaccharides; peptides; and heavy metals. PMID:17875790 PMID:17986299 PMID:19101624 PMID:291959 PMID:3782019 chebi_ontology haptens CHEBI:59174 hapten PMID:17875790 Europe PMC PMID:17986299 Europe PMC PMID:19101624 Europe PMC PMID:291959 Europe PMC PMID:3782019 Europe PMC haptens ChEBI Any fatty acid whose skeletal carbon atoms form an unbranched open chain. chebi_ontology straight-chain fatty acids CHEBI:59202 straight-chain fatty acid straight-chain fatty acids ChEBI A fatty acid anion formed by deprotonation of the carboxylic acid functional group of a straight-chain fatty acid. chebi_ontology straight-chain FA anion straight-chain FA anions straight-chain fatty acid anions CHEBI:59203 straight-chain fatty acid anion straight-chain FA anion ChEBI straight-chain FA anions ChEBI straight-chain fatty acid anions ChEBI An organic anion arising from deprotonation of a acyclic tetrapyrrole compound. chebi_ontology acyclic tetrapyrrole anion acyclic tetrapyrrole anions linear tetrapyrrole anions CHEBI:59252 linear tetrapyrrole anion acyclic tetrapyrrole anion ChEBI acyclic tetrapyrrole anions ChEBI linear tetrapyrrole anions ChEBI Any member of the sub-set of polyunsaturated fatty acid for which there is an absolute dietary requirement. PMID:1745654 PMID:19034351 PMID:7609665 chebi_ontology EFA EFAs EFS acides gras indispensables acidos grasos esenciales essential fatty acids essentielle Fettsaeuren CHEBI:59549 essential fatty acid PMID:1745654 Europe PMC PMID:19034351 Europe PMC PMID:7609665 Europe PMC EFA ChEBI EFAs ChEBI EFS ChEBI acides gras indispensables ChEBI acidos grasos esenciales ChEBI essential fatty acids ChEBI essentielle Fettsaeuren ChEBI Any fatty acid with a chain length of between C6 and C12. 0 CHO2R 45.01740 44.99765 OC([*])=O chebi_ontology MCFA MCFAs medium-chain fatty acids CHEBI:59554 medium-chain fatty acid MCFA ChEBI MCFAs ChEBI medium-chain fatty acids ChEBI A fatty acid anion resulting from the deprotonation of the carboxylic acid moiety of a medium-chain fatty acid. -1 CO2R 44.010 43.98983 [O-]C([*])=O chebi_ontology MCFA anion MCFA anions a medium chain fatty acid medium-chain FA anion medium-chain FA anions medium-chain fatty acid anions CHEBI:59558 medium-chain fatty acid anion MCFA anion ChEBI MCFA anions ChEBI a medium chain fatty acid UniProt medium-chain FA anion ChEBI medium-chain FA anions ChEBI medium-chain fatty acid anions ChEBI An organic anion that is the conjugate base of diamino acid. chebi_ontology diamino acid anions CHEBI:59561 diamino acid anion diamino acid anions ChEBI Compounds containing one or more phosphoric acid units. chebi_ontology CHEBI:59698 phosphoric acids The dianion resulting from the removal of two protons from the phosphate group of pyridoxal 5'-phosphate. -2 C8H8NO6P InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)/p-2 NGVDGCNFYWLIFO-UHFFFAOYSA-L 245.12600 245.01002 [H]C(=O)c1c(COP([O-])([O-])=O)cnc(C)c1O PMID:19144516 (4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl phosphate chebi_ontology 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate dianion 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate(2-) pyridoxal 5'-phosphate pyridoxal 5'-phosphate dianion CHEBI:597326 pyridoxal 5'-phosphate(2-) PMID:19144516 ChEMBL (4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl phosphate IUPAC 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate dianion ChEBI 3-hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate(2-) ChEBI pyridoxal 5'-phosphate UniProt pyridoxal 5'-phosphate dianion ChEBI A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. chebi_ontology nucleophile nucleophiles nucleophilic reagents CHEBI:59740 nucleophilic reagent nucleophile ChEBI nucleophiles ChEBI nucleophilic reagents ChEBI A zwitterionic tautomer of S-adenosyl-L-methionine arising from shift of the proton from the carboxy group to the amino group. +1 C15H23N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-O 399.44500 399.14452 C[S+](CC[C@H]([NH3+])C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 [(3S)-3-azaniumyl-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium chebi_ontology S-adenosyl-L-methionine CHEBI:59789 S-adenosyl-L-methionine zwitterion [(3S)-3-azaniumyl-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium IUPAC S-adenosyl-L-methionine SUBMITTER S-adenosyl-L-methionine UniProt Conjugate base of an L-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C2H3NO2R 73.051 73.01638 [C@H](C(=O)[O-])(N)* chebi_ontology L-alpha-amino carboxylate CHEBI:59814 L-alpha-amino acid anion L-alpha-amino carboxylate ChEBI Zwitterionic form of an L-alpha-amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 [NH3+][C@@H]([*])C([O-])=O chebi_ontology L-alpha-amino acid zwitterions an L-alpha-amino acid CHEBI:59869 L-alpha-amino acid zwitterion L-alpha-amino acid zwitterions ChEBI an L-alpha-amino acid UniProt Zwitterionic form of a D-alpha-amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 [NH3+][C@H]([*])C([O-])=O chebi_ontology D-alpha-amino acid zwitterions a D-alpha-amino acid CHEBI:59871 D-alpha-amino acid zwitterion D-alpha-amino acid zwitterions ChEBI a D-alpha-amino acid UniProt A carboxylic acid anion that is the conjugate base of an N-acyl-L-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C3H2NO3R2 100.05290 100.00347 [O-]C(=O)[C@H]([*])NC([*])=O chebi_ontology N-acyl-L-alpha-amino acid(1-) an N-acyl-L-amino acid CHEBI:59874 N-acyl-L-alpha-amino acid anion N-acyl-L-alpha-amino acid(1-) ChEBI an N-acyl-L-amino acid UniProt The conjugate base of an N-acyl-D-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C3H2NO3R2 100.05290 100.00347 [O-]C(=O)[C@@H]([*])NC([*])=O chebi_ontology N-acyl-D-alpha-amino acid(1-) an N-acyl-D-amino acid CHEBI:59876 N-acyl-D-alpha-amino acid anion N-acyl-D-alpha-amino acid(1-) ChEBI an N-acyl-D-amino acid UniProt A drug which interferes with the binding, fusion and entry of an HIV virion to a human cell. By blocking this step in HIV's replication cycle, such agents slow the progression from HIV infection to AIDS. PMID:22470838 Wikipedia:Entry_inhibitor chebi_ontology HIV entry inhibitor HIV entry inhibitors HIV fusion inhibitors CHEBI:59886 HIV fusion inhibitor PMID:22470838 Europe PMC HIV entry inhibitor ChEBI HIV entry inhibitors ChEBI HIV fusion inhibitors ChEBI A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chebi_ontology Chemische Substanz CHEBI:59999 chemical substance Chemische Substanz ChEBI A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. chebi_ontology Mischung CHEBI:60004 mixture Mischung ChEBI A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc.. Wikipedia:Polymer Polymer chebi_ontology Kunststoff CHEBI:60027 polymer Polymer ChEBI Kunststoff ChEBI An ionic polymer is a polymer, composed of ionic macromolecules. chebi_ontology polyionic polymer CHEBI:60164 ionic polymer polyionic polymer ChEBI A metal cation with a valence of two. chebi_ontology a divalent metal cation CHEBI:60240 divalent metal cation a divalent metal cation UniProt An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. chebi_ontology a monovalent cation CHEBI:60242 monovalent inorganic cation a monovalent cation UniProt A hydrolase inhibitor that interferes with the action of any hydrolase acting on peptide bonds (peptidase), EC 3.4.*.*). CHEBI:76763 chebi_ontology EC 3.4.* (hydrolase acting on peptide bond) inhibitor EC 3.4.* (hydrolase acting on peptide bonds) inhibitors EC 3.4.* (hydrolases acting on peptide bond) inhibitors EC 3.4.* (peptidase) inhibitor EC 3.4.* (peptidase) inhibitors EC 3.4.* inhibitor EC 3.4.* inhibitors inhibitor of hydrolases acting on peptide bond (EC 3.4.*) inhibitors of hydrolases acting on peptide bond (EC 3.4.*) peptidase inhibitors protease inhibitor protease inhibitors CHEBI:60258 EC 3.4.* (hydrolases acting on peptide bond) inhibitor EC 3.4.* (hydrolase acting on peptide bond) inhibitor ChEBI EC 3.4.* (hydrolase acting on peptide bonds) inhibitors ChEBI EC 3.4.* (hydrolases acting on peptide bond) inhibitors ChEBI EC 3.4.* (peptidase) inhibitor ChEBI EC 3.4.* (peptidase) inhibitors ChEBI EC 3.4.* inhibitor ChEBI EC 3.4.* inhibitors ChEBI inhibitor of hydrolases acting on peptide bond (EC 3.4.*) ChEBI inhibitors of hydrolases acting on peptide bond (EC 3.4.*) ChEBI peptidase inhibitors ChEBI protease inhibitor ChEBI protease inhibitors ChEBI Any hormone produced by the thyroid gland chebi_ontology thyroid hormones CHEBI:60311 thyroid hormone thyroid hormones ChEBI chebi_ontology CHEBI:60345 organic phosphoramidate anion Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged. 0 C2H4NO2R(C2H2NOR)n chebi_ontology a peptide peptide zwitterions CHEBI:60466 peptide zwitterion a peptide UniProt peptide zwitterions ChEBI Flavin protonated to pH 7.3 -1 C12H8N4O2R 240.21750 240.06473 Cc1cc2nc3c(nc(=O)[n-]c3=O)n([*])c2cc1C chebi_ontology an oxidized flavin CHEBI:60531 flavin(1-) an oxidized flavin UniProt Any substance that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. CHEBI:60797 chebi_ontology N-methyl-D-aspartate receptor antagonist N-methyl-D-aspartate receptor antagonists NMDA receptor antagonists NMDAR antagonist NMDAR antagonists CHEBI:60643 NMDA receptor antagonist N-methyl-D-aspartate receptor antagonist ChEBI N-methyl-D-aspartate receptor antagonists ChEBI NMDA receptor antagonists ChEBI NMDAR antagonist ChEBI NMDAR antagonists ChEBI Any substance which inhibits the action of receptors for excitatory amino acids. chebi_ontology EAA receptor antagonist EAA receptor antagonists excitatory amino acid antagonists excitatory amino acid receptor antagonist excitatory amino acid receptor antagonists CHEBI:60798 excitatory amino acid antagonist EAA receptor antagonist ChEBI EAA receptor antagonists ChEBI excitatory amino acid antagonists ChEBI excitatory amino acid receptor antagonist ChEBI excitatory amino acid receptor antagonists ChEBI Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself. chebi_ontology adjuvants CHEBI:60809 adjuvant adjuvants ChEBI Any alpha-amino acid anion in which the parent amino acid has D-configuration. -1 C2H3NO2R 73.051 73.01638 [C@@H](C(=O)[O-])(N)* chebi_ontology D-alpha-amino acid anions D-alpha-amino carboxylate CHEBI:60895 D-alpha-amino acid anion D-alpha-amino acid anions ChEBI D-alpha-amino carboxylate ChEBI A sulfated glycosaminoglycan, a linear polymer that consists of the repeating disaccharide [3)-beta-Gal-(1->4)-beta-GlcNAc-(1->] and containing sulfo groups located at random positions. chebi_ontology keratan sulfates keratosulfate CHEBI:60924 keratan sulfate keratan sulfates ChEBI keratosulfate SUBMITTER A hormone antagonist that blocks angiotensin receptors. chebi_ontology angiotensin receptor antagonists CHEBI:61016 angiotensin receptor antagonist angiotensin receptor antagonists ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the function of histone deacetylase (EC 3.5.1.98). Wikipedia:Histone_deacetylase_inhibitor chebi_ontology EC 3.5.1.98 (histone deacetylase) inhibitors EC 3.5.1.98 inhibitor EC 3.5.1.98 inhibitors HDAC inhibitor HDAC inhibitors HDACi HDACis HDI HDIs histone amidohydrolase inhibitor histone amidohydrolase inhibitors histone deacetylase (EC 3.5.1.98) inhibitor histone deacetylase (EC 3.5.1.98) inhibitors histone deacetylase inhibitor histone deacetylase inhibitors CHEBI:61115 EC 3.5.1.98 (histone deacetylase) inhibitor EC 3.5.1.98 (histone deacetylase) inhibitors ChEBI EC 3.5.1.98 inhibitor ChEBI EC 3.5.1.98 inhibitors ChEBI HDAC inhibitor ChEBI HDAC inhibitors ChEBI HDACi ChEBI HDACis ChEBI HDI ChEBI HDIs ChEBI histone amidohydrolase inhibitor ChEBI histone amidohydrolase inhibitors ChEBI histone deacetylase (EC 3.5.1.98) inhibitor ChEBI histone deacetylase (EC 3.5.1.98) inhibitors ChEBI histone deacetylase inhibitor ChEBI histone deacetylase inhibitors ChEBI Any compound that has a nucleobase as a part. chebi_ontology nucleobase-containing compound nucleobase-containing compounds nucleobase-containing molecular entities CHEBI:61120 nucleobase-containing molecular entity nucleobase-containing compound SUBMITTER nucleobase-containing compounds ChEBI nucleobase-containing molecular entities ChEBI Any hydroxy carboxylic acid which contains a hydroxy group located beta- to the carboxylic acid group. chebi_ontology 3-hydroxy carboxylic acids 3-hydroxycarboxylic acid 3-hydroxycarboxylic acids beta-hydroxy carboxylic acid beta-hydroxy carboxylic acids beta-hydroxycarboxylic acid beta-hydroxycarboxylic acids CHEBI:61355 3-hydroxy carboxylic acid 3-hydroxy carboxylic acids ChEBI 3-hydroxycarboxylic acid ChEBI 3-hydroxycarboxylic acids ChEBI beta-hydroxy carboxylic acid ChEBI beta-hydroxy carboxylic acids ChEBI beta-hydroxycarboxylic acid ChEBI beta-hydroxycarboxylic acids ChEBI A polymer, composed of polyanion macromolecules. chebi_ontology polyanion polyanions CHEBI:61469 polyanionic polymer polyanion ChEBI polyanions ChEBI A lipid-rich mixture containing glycerol, fatty acids, phosphoric acid and other components. PMID:12545497 PMID:17288433 chebi_ontology CHEBI:61995 lecithin PMID:12545497 Europe PMC PMID:17288433 Europe PMC Zwitterionic form of a polar amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 C(C([O-])=O)(*)[NH3+] MetaCyc:Polar-amino-acids chebi_ontology a polar amino acid CHEBI:62031 polar amino acid zwitterion MetaCyc:Polar-amino-acids SUBMITTER a polar amino acid UniProt Any branched-chain fatty acid containing methyl branches only. PMID:17030019 PMID:19747846 PMID:19933331 chebi_ontology methyl-branched fatty acids CHEBI:62499 methyl-branched fatty acid PMID:17030019 Europe PMC PMID:19747846 Europe PMC PMID:19933331 SUBMITTER methyl-branched fatty acids ChEBI The dicarboxylic acid dianion formed from folic acid by loss of a proton from each of the two carboxy groups in the glutamic acid moiety. -2 C19H17N7O6 InChI=1S/C19H19N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,8,12,21H,5-7H2,(H,24,29)(H,27,28)(H,31,32)(H3,20,22,25,26,30)/p-2/t12-/m0/s1 OVBPIULPVIDEAO-LBPRGKRZSA-L 439.38160 439.12513 Nc1nc2ncc(CNc3ccc(cc3)C(=O)N[C@@H](CCC([O-])=O)C([O-])=O)nc2c(=O)[nH]1 MetaCyc:CPD-12826 PMCID:PMC8181341 PMID:34051149 N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamate(2-) chebi_ontology folate pteroyl-L-glutamate pteroyl-L-monoglutamate pteroylglutamate CHEBI:62501 folate(2-) MetaCyc:CPD-12826 SUBMITTER PMCID:PMC8181341 Europe PMC PMID:34051149 Europe PMC N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamate(2-) IUPAC folate MetaCyc folate UniProt pteroyl-L-glutamate ChEBI pteroyl-L-monoglutamate ChEBI pteroylglutamate ChEBI Any organophosphate oxoanion that is a negatively charged phospholipid, e.g. phosphatidylserine(1-), phosphatidate(2-), phosphatidylglycerol(1-). chebi_ontology anionic phospholipids phospholipid anion phospholipid anions CHEBI:62643 anionic phospholipid anionic phospholipids ChEBI phospholipid anion ChEBI phospholipid anions ChEBI Any additive that enhances the efficiency of fuel. chebi_ontology fuel additives fuel enhancer CHEBI:62803 fuel additive fuel additives ChEBI fuel enhancer ChEBI Any compound that is able to prevent damage to the liver. chebi_ontology antihepatotoxic agent hepatoprotective agents hepatoprotector CHEBI:62868 hepatoprotective agent antihepatotoxic agent ChEBI hepatoprotective agents ChEBI hepatoprotector ChEBI The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability. chebi_ontology emulgent emulgents emulsifiers CHEBI:63046 emulsifier emulgent ChEBI emulgents ChEBI emulsifiers ChEBI An organic cation resulting from protonation or quaternisation at the 3-position of any 1,3-thiazole. chebi_ontology 1,3-thiazolium cations CHEBI:63048 1,3-thiazolium cation 1,3-thiazolium cations ChEBI A beta-amino-acid anion that is the conjugate base of beta-alanine. -1 C3H6NO2 InChI=1S/C3H7NO2/c4-2-1-3(5)6/h1-2,4H2,(H,5,6)/p-1 UCMIRNVEIXFBKS-UHFFFAOYSA-M 88.08520 88.04040 NCCC([O-])=O Reaxys:3536336 3-aminopropanoate chebi_ontology beta-alaninate anion beta-alaninate(1-) CHEBI:63070 beta-alaninate Reaxys:3536336 Reaxys 3-aminopropanoate IUPAC beta-alaninate anion ChEBI beta-alaninate(1-) ChEBI A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity. chebi_ontology glycosyl compounds CHEBI:63161 glycosyl compound glycosyl compounds ChEBI Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. chebi_ontology carbohydrate derivatives derivatised carbohydrate derivatised carbohydrates derivatized carbohydrate derivatized carbohydrates CHEBI:63299 carbohydrate derivative carbohydrate derivatives ChEBI derivatised carbohydrate ChEBI derivatised carbohydrates ChEBI derivatized carbohydrate ChEBI derivatized carbohydrates ChEBI A carbohydrate derivative that is formally obtained from a carbohydrate acid. chebi_ontology carbohydrate acid derivatives CHEBI:63436 carbohydrate acid derivative carbohydrate acid derivatives ChEBI A sulfur-containing amino acid whose alpha-carboxylic acid group is ionized (not protonated). chebi_ontology sulfur-containing amino-acid anions CHEBI:63470 sulfur-containing amino-acid anion sulfur-containing amino-acid anions ChEBI A branched-chain amino acid whose alpha-carboxylic acid group is ionized. chebi_ontology branched-chain amino-acid anions CHEBI:63471 branched-chain amino-acid anion branched-chain amino-acid anions ChEBI An aromatic amino acid whose alpha-carboxylic acid group is ionized (non-protonated). chebi_ontology aromatic amino-acid anions CHEBI:63473 aromatic amino-acid anion aromatic amino-acid anions ChEBI A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative. chebi_ontology carbohydrate acid anion derivative carbohydrate acid anion derivatives carbohydrate acid derivative anions CHEBI:63551 carbohydrate acid derivative anion carbohydrate acid anion derivative ChEBI carbohydrate acid anion derivatives ChEBI carbohydrate acid derivative anions ChEBI An EC 2.6.1.* (transaminase) inhibitor that interferes with the action of 4-aminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.19). Wikipedia:4-aminobutyrate_transaminase chebi_ontology 4-aminobutanoate:2-oxoglutarate aminotransferase inhibitor 4-aminobutanoate:2-oxoglutarate aminotransferase inhibitors 4-aminobutyrate aminotransferase inhibitor 4-aminobutyrate aminotransferase inhibitors 4-aminobutyrate transaminase inhibitor 4-aminobutyrate transaminase inhibitors 4-aminobutyrate--2-ketoglutarate aminotransferase inhibitor 4-aminobutyrate--2-ketoglutarate aminotransferase inhibitors 4-aminobutyrate--2-oxoglutarate aminotransferase inhibitor 4-aminobutyrate--2-oxoglutarate aminotransferase inhibitors 4-aminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.19) inhibitor 4-aminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.19) inhibitors 4-aminobutyrate--2-oxoglutarate transaminase inhibitor 4-aminobutyrate--2-oxoglutarate transaminase inhibitors 4-aminobutyrate-2-oxoglutarate transaminase inhibitor 4-aminobutyrate-2-oxoglutarate transaminase inhibitors 4-aminobutyric acid 2-ketoglutaric acid aminotransferase inhibitor 4-aminobutyric acid 2-ketoglutaric acid aminotransferase inhibitors 4-aminobutyric acid aminotransferase inhibitor 4-aminobutyric acid aminotransferase inhibitors EC 2.6.1.19 (4-aminobutyrate--2-oxoglutarate transaminase) inhibitors EC 2.6.1.19 inhibitor EC 2.6.1.19 inhibitors GABA aminotransferase inhibitor GABA aminotransferase inhibitors GABA transaminase inhibitor GABA transaminase inhibitors GABA transferase inhibitor GABA transferase inhibitors GABA--2-oxoglutarate aminotransferase inhibitor GABA--2-oxoglutarate aminotransferase inhibitors GABA--2-oxoglutarate transaminase inhibitor GABA--2-oxoglutarate transaminase inhibitors GABA--alpha-ketoglutarate aminotransferase inhibitors GABA--alpha-ketoglutarate transaminase inhibitor GABA--alpha-ketoglutarate transaminase inhibitors GABA--alpha-ketoglutaric acid transaminase inhibitor GABA--alpha-ketoglutaric acid transaminase inhibitors GABA--alpha-oxoglutarate aminotransferase inhibitor GABA--alpha-oxoglutarate aminotransferase inhibitors GABA--oxoglutarate aminotransferase inhibitor GABA--oxoglutarate aminotransferase inhibitors GABA--oxoglutarate transaminase inhibitor GABA--oxoglutarate transaminase inhibitors GabT inhibitor GabT inhibitors aminobutyrate aminotransferase inhibitor aminobutyrate aminotransferase inhibitors aminobutyrate transaminase inhibitor aminobutyrate transaminase inhibitors beta-alanine aminotransferase inhibitor beta-alanine aminotransferase inhibitors beta-alanine--oxoglutarate aminotransferase inhibitor beta-alanine--oxoglutarate aminotransferase inhibitors beta-alanine--oxoglutarate transaminase inhibitor beta-alanine--oxoglutarate transaminase inhibitors gamma-amino-N-butyrate transaminase inhibitor gamma-amino-N-butyrate transaminase inhibitors gamma-aminobutyrate aminotransaminase inhibitor gamma-aminobutyrate aminotransaminase inhibitors gamma-aminobutyrate transaminase inhibitor gamma-aminobutyrate transaminase inhibitors gamma-aminobutyrate--alpha-ketoglutarate aminotransferase inhibitor gamma-aminobutyrate--alpha-ketoglutarate aminotransferase inhibitors gamma-aminobutyrate--alpha-ketoglutarate transaminase inhibitor gamma-aminobutyrate--alpha-ketoglutarate transaminase inhibitors gamma-aminobutyrate:alpha-oxoglutarate aminotransferase inhibitor gamma-aminobutyrate:alpha-oxoglutarate aminotransferase inhibitors gamma-aminobutyric acid aminotransferase inhibitor gamma-aminobutyric acid aminotransferase inhibitors gamma-aminobutyric acid pyruvate transaminase inhibitor gamma-aminobutyric acid pyruvate transaminase inhibitors gamma-aminobutyric acid transaminase inhibitor gamma-aminobutyric acid transaminase inhibitors gamma-aminobutyric acid--2-oxoglutarate transaminase inhibitor gamma-aminobutyric acid--2-oxoglutarate transaminase inhibitors gamma-aminobutyric acid--alpha-ketoglutarate transaminase inhibitor gamma-aminobutyric acid--alpha-ketoglutarate transaminase inhibitors gamma-aminobutyric acid--alpha-ketoglutaric acid aminotransferase inhibitor gamma-aminobutyric acid--alpha-ketoglutaric acid aminotransferase inhibitors gamma-aminobutyric transaminase inhibitor gamma-aminobutyric transaminase inhibitors glutamate--succinic semialdehyde transaminase inhibitor glutamate--succinic semialdehyde transaminase inhibitors CHEBI:63674 EC 2.6.1.19 (4-aminobutyrate--2-oxoglutarate transaminase) inhibitor 4-aminobutanoate:2-oxoglutarate aminotransferase inhibitor ChEBI 4-aminobutanoate:2-oxoglutarate aminotransferase inhibitors ChEBI 4-aminobutyrate aminotransferase inhibitor ChEBI 4-aminobutyrate aminotransferase inhibitors ChEBI 4-aminobutyrate transaminase inhibitor ChEBI 4-aminobutyrate transaminase inhibitors ChEBI 4-aminobutyrate--2-ketoglutarate aminotransferase inhibitor ChEBI 4-aminobutyrate--2-ketoglutarate aminotransferase inhibitors ChEBI 4-aminobutyrate--2-oxoglutarate aminotransferase inhibitor ChEBI 4-aminobutyrate--2-oxoglutarate aminotransferase inhibitors ChEBI 4-aminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.19) inhibitor ChEBI 4-aminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.19) inhibitors ChEBI 4-aminobutyrate--2-oxoglutarate transaminase inhibitor ChEBI 4-aminobutyrate--2-oxoglutarate transaminase inhibitors ChEBI 4-aminobutyrate-2-oxoglutarate transaminase inhibitor ChEBI 4-aminobutyrate-2-oxoglutarate transaminase inhibitors ChEBI 4-aminobutyric acid 2-ketoglutaric acid aminotransferase inhibitor ChEBI 4-aminobutyric acid 2-ketoglutaric acid aminotransferase inhibitors ChEBI 4-aminobutyric acid aminotransferase inhibitor ChEBI 4-aminobutyric acid aminotransferase inhibitors ChEBI EC 2.6.1.19 (4-aminobutyrate--2-oxoglutarate transaminase) inhibitors ChEBI EC 2.6.1.19 inhibitor ChEBI EC 2.6.1.19 inhibitors ChEBI GABA aminotransferase inhibitor ChEBI GABA aminotransferase inhibitors ChEBI GABA transaminase inhibitor ChEBI GABA transaminase inhibitors ChEBI GABA transferase inhibitor ChEBI GABA transferase inhibitors ChEBI GABA--2-oxoglutarate aminotransferase inhibitor ChEBI GABA--2-oxoglutarate aminotransferase inhibitors ChEBI GABA--2-oxoglutarate transaminase inhibitor ChEBI GABA--2-oxoglutarate transaminase inhibitors ChEBI GABA--alpha-ketoglutarate aminotransferase inhibitors ChEBI GABA--alpha-ketoglutarate transaminase inhibitor ChEBI GABA--alpha-ketoglutarate transaminase inhibitors ChEBI GABA--alpha-ketoglutaric acid transaminase inhibitor ChEBI GABA--alpha-ketoglutaric acid transaminase inhibitors ChEBI GABA--alpha-oxoglutarate aminotransferase inhibitor ChEBI GABA--alpha-oxoglutarate aminotransferase inhibitors ChEBI GABA--oxoglutarate aminotransferase inhibitor ChEBI GABA--oxoglutarate aminotransferase inhibitors ChEBI GABA--oxoglutarate transaminase inhibitor ChEBI GABA--oxoglutarate transaminase inhibitors ChEBI GabT inhibitor ChEBI GabT inhibitors ChEBI aminobutyrate aminotransferase inhibitor ChEBI aminobutyrate aminotransferase inhibitors ChEBI aminobutyrate transaminase inhibitor ChEBI aminobutyrate transaminase inhibitors ChEBI beta-alanine aminotransferase inhibitor ChEBI beta-alanine aminotransferase inhibitors ChEBI beta-alanine--oxoglutarate aminotransferase inhibitor ChEBI beta-alanine--oxoglutarate aminotransferase inhibitors ChEBI beta-alanine--oxoglutarate transaminase inhibitor ChEBI beta-alanine--oxoglutarate transaminase inhibitors ChEBI gamma-amino-N-butyrate transaminase inhibitor ChEBI gamma-amino-N-butyrate transaminase inhibitors ChEBI gamma-aminobutyrate aminotransaminase inhibitor ChEBI gamma-aminobutyrate aminotransaminase inhibitors ChEBI gamma-aminobutyrate transaminase inhibitor ChEBI gamma-aminobutyrate transaminase inhibitors ChEBI gamma-aminobutyrate--alpha-ketoglutarate aminotransferase inhibitor ChEBI gamma-aminobutyrate--alpha-ketoglutarate aminotransferase inhibitors ChEBI gamma-aminobutyrate--alpha-ketoglutarate transaminase inhibitor ChEBI gamma-aminobutyrate--alpha-ketoglutarate transaminase inhibitors ChEBI gamma-aminobutyrate:alpha-oxoglutarate aminotransferase inhibitor ChEBI gamma-aminobutyrate:alpha-oxoglutarate aminotransferase inhibitors ChEBI gamma-aminobutyric acid aminotransferase inhibitor ChEBI gamma-aminobutyric acid aminotransferase inhibitors ChEBI gamma-aminobutyric acid pyruvate transaminase inhibitor ChEBI gamma-aminobutyric acid pyruvate transaminase inhibitors ChEBI gamma-aminobutyric acid transaminase inhibitor ChEBI gamma-aminobutyric acid transaminase inhibitors ChEBI gamma-aminobutyric acid--2-oxoglutarate transaminase inhibitor ChEBI gamma-aminobutyric acid--2-oxoglutarate transaminase inhibitors ChEBI gamma-aminobutyric acid--alpha-ketoglutarate transaminase inhibitor ChEBI gamma-aminobutyric acid--alpha-ketoglutarate transaminase inhibitors ChEBI gamma-aminobutyric acid--alpha-ketoglutaric acid aminotransferase inhibitor ChEBI gamma-aminobutyric acid--alpha-ketoglutaric acid aminotransferase inhibitors ChEBI gamma-aminobutyric transaminase inhibitor ChEBI gamma-aminobutyric transaminase inhibitors ChEBI glutamate--succinic semialdehyde transaminase inhibitor ChEBI glutamate--succinic semialdehyde transaminase inhibitors ChEBI Any compound that can be used for the treatment of neurodegenerative disorders. chebi_ontology neuroprotectant neuroprotectants neuroprotective agents CHEBI:63726 neuroprotective agent neuroprotectant ChEBI neuroprotectants ChEBI neuroprotective agents ChEBI Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule. CHEBI:50333 chebi_ontology macrocyclic lactones CHEBI:63944 macrocyclic lactone macrocyclic lactones ChEBI An antagonist at the metabotropic glutamate receptor. chebi_ontology mGluR antagonist mGluR antagonists metabotropic glutamate receptor antagonists CHEBI:63963 metabotropic glutamate receptor antagonist mGluR antagonist ChEBI mGluR antagonists ChEBI metabotropic glutamate receptor antagonists ChEBI Any substance which is added to food to preserve or enhance its flavour and/or appearance. Wikipedia:Food_additive chebi_ontology food additives CHEBI:64047 food additive food additives ChEBI A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents. Wikipedia:Acidity_regulator chebi_ontology acidity regulator acidity regulators food acidity regulators pH control agent pH control agents CHEBI:64049 food acidity regulator acidity regulator ChEBI acidity regulators ChEBI food acidity regulators ChEBI pH control agent ChEBI pH control agents ChEBI An agonist that selectively binds to and activates AMPA receptors. Wikipedia:AMPA_receptor chebi_ontology AMPA receptor agonists AMPAR agonist alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor agonist quisqualate receptor agonist CHEBI:64102 AMPA receptor agonist AMPA receptor agonists ChEBI AMPAR agonist ChEBI alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor agonist ChEBI quisqualate receptor agonist ChEBI An EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitor that interferes with the action of protein farnesyltransferase (EC 2.5.1.58), one of the three enzymes in the prenyltransferase group. Wikipedia:Farnesyltransferase chebi_ontology EC 2.5.1.58 (protein farnesyltransferase) inhibitors EC 2.5.1.58 inhibitor EC 2.5.1.58 inhibitors FTase inhibitor FTase inhibitors farnesyl transferase inhibitor farnesyl transferase inhibitors farnesyl-diphosphate:protein-cysteine farnesyltransferase inhibitor farnesyl-diphosphate:protein-cysteine farnesyltransferase inhibitors farnesyltransferase inhibitor farnesyltransferase inhibitors protein farnesyltransferase (EC 2.5.1.58) inhibitor protein farnesyltransferase (EC 2.5.1.58) inhibitors protein farnesyltransferase inhibitor protein farnesyltransferase inhibitors CHEBI:64133 EC 2.5.1.58 (protein farnesyltransferase) inhibitor EC 2.5.1.58 (protein farnesyltransferase) inhibitors ChEBI EC 2.5.1.58 inhibitor ChEBI EC 2.5.1.58 inhibitors ChEBI FTase inhibitor ChEBI FTase inhibitors ChEBI farnesyl transferase inhibitor ChEBI farnesyl transferase inhibitors ChEBI farnesyl-diphosphate:protein-cysteine farnesyltransferase inhibitor ChEBI farnesyl-diphosphate:protein-cysteine farnesyltransferase inhibitors ChEBI farnesyltransferase inhibitor ChEBI farnesyltransferase inhibitors ChEBI protein farnesyltransferase (EC 2.5.1.58) inhibitor ChEBI protein farnesyltransferase (EC 2.5.1.58) inhibitors ChEBI protein farnesyltransferase inhibitor ChEBI protein farnesyltransferase inhibitors ChEBI An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of methionine; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8) FFEARJCKVFRZRR-UHFFFAOYSA-N 149.21100 149.05105 CSCCC([NH3+])C([O-])=O 2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology 2-ammonio-4-(methylsulfanyl)butanoate methionine CHEBI:64558 methionine zwitterion 2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC 2-ammonio-4-(methylsulfanyl)butanoate IUPAC methionine UniProt An EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor that interferes with the action of glycine hydroxymethyltransferase (EC 2.1.2.1). Wikipedia:Glycine_hydroxymethyltransferase chebi_ontology 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors EC 2.1.2.1 inhibitor EC 2.1.2.1 inhibitors L-serine hydroxymethyltransferase inhibitor L-serine hydroxymethyltransferase inhibitors L-threonine aldolase inhibitor L-threonine aldolase inhibitors allothreonine aldolase inhibitor allothreonine aldolase inhibitors glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors glycine hydroxymethyltransferase inhibitor glycine hydroxymethyltransferase inhibitors serine aldolase inhibitor serine aldolase inhibitors serine hydroxymethylase inhibitor serine hydroxymethylase inhibitors serine hydroxymethyltransferase inhibitor serine hydroxymethyltransferase inhibitors serine transhydroxymethylase inhibitor serine transhydroxymethylase inhibitors threonine aldolase inhibitor threonine aldolase inhibitors CHEBI:64570 EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitor 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor ChEBI 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors ChEBI EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors ChEBI EC 2.1.2.1 inhibitor ChEBI EC 2.1.2.1 inhibitors ChEBI L-serine hydroxymethyltransferase inhibitor ChEBI L-serine hydroxymethyltransferase inhibitors ChEBI L-threonine aldolase inhibitor ChEBI L-threonine aldolase inhibitors ChEBI allothreonine aldolase inhibitor ChEBI allothreonine aldolase inhibitors ChEBI glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor ChEBI glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors ChEBI glycine hydroxymethyltransferase inhibitor ChEBI glycine hydroxymethyltransferase inhibitors ChEBI serine aldolase inhibitor ChEBI serine aldolase inhibitors ChEBI serine hydroxymethylase inhibitor ChEBI serine hydroxymethylase inhibitors ChEBI serine hydroxymethyltransferase inhibitor ChEBI serine hydroxymethyltransferase inhibitors ChEBI serine transhydroxymethylase inhibitor ChEBI serine transhydroxymethylase inhibitors ChEBI threonine aldolase inhibitor ChEBI threonine aldolase inhibitors ChEBI An excitatory amino acid agonist which binds to NMDA receptors and triggers a response. chebi_ontology N-methyl-D-aspartate receptor agonist N-methyl-D-aspartate receptor agonists NMDA receptor agonists NMDAR agonist NMDAR agonists CHEBI:64571 NMDA receptor agonist N-methyl-D-aspartate receptor agonist ChEBI N-methyl-D-aspartate receptor agonists ChEBI NMDA receptor agonists ChEBI NMDAR agonist ChEBI NMDAR agonists ChEBI A food additive which is added to flour or dough to improve baking quality and/or colour. Wikipedia:Flour_treatment_agent flour treatment agent chebi_ontology dough improver dough improvers improving agent improving agents CHEBI:64577 flour treatment agent flour treatment agent ChEBI dough improver ChEBI dough improvers ChEBI improving agent ChEBI improving agents ChEBI Any of a group of guanidine or amidine phosphates that function as storage depots for high-energy phosphate in muscle with the purpose of regenerating ATP from ADP during muscular contraction. Wikipedia:Phosphagen chebi_ontology CHEBI:64618 phosphagen An inorganic cation with a valency of two. chebi_ontology CHEBI:64641 divalent inorganic cation An organic molecular entity containing a single carbon atom (C1). chebi_ontology one-carbon compounds CHEBI:64708 one-carbon compound one-carbon compounds ChEBI Any organic molecular entity that is acidic and contains carbon in covalent linkage. chebi_ontology organic acids CHEBI:64709 organic acid organic acids ChEBI Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism. Wikipedia:Poison chebi_ontology poisonous agent poisonous agents poisonous substance poisonous substances poisons toxic agent toxic agents toxic substance toxic substances CHEBI:64909 poison poisonous agent ChEBI poisonous agents ChEBI poisonous substance ChEBI poisonous substances ChEBI poisons ChEBI toxic agent ChEBI toxic agents ChEBI toxic substance ChEBI toxic substances ChEBI A drug used to treat or prevent infections caused by Mycobacteria, a genus of actinobacteria. Aerobic and nonmotile, members of the genus include the pathogens responsible for causing tuberculosis and leprosy. chebi_ontology antimycobacterial agent antimycobacterial agents antimycobacterial drugs antimycobacterials antimycobacterium CHEBI:64912 antimycobacterial drug antimycobacterial agent ChEBI antimycobacterial agents ChEBI antimycobacterial drugs ChEBI antimycobacterials ChEBI antimycobacterium ChEBI An antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus. chebi_ontology anti-AIDS agent anti-AIDS agents anti-HIV agents CHEBI:64946 anti-HIV agent anti-AIDS agent ChEBI anti-AIDS agents ChEBI anti-HIV agents ChEBI An antiviral agent that destroys or inhibits the replication of the herpes simplex virus (also known as the human herpes virus). Wikipedia:Herpes_simplex_virus chebi_ontology anti-HHV agent anti-HHV agents anti-HSV agents anti-herpes simplex virus agent anti-herpes simplex virus agents anti-human herpes virus agent anti-human herpes virus agents CHEBI:64952 anti-HSV agent anti-HHV agent ChEBI anti-HHV agents ChEBI anti-HSV agents ChEBI anti-herpes simplex virus agent ChEBI anti-herpes simplex virus agents ChEBI anti-human herpes virus agent ChEBI anti-human herpes virus agents ChEBI An anti-HSV agent agent that destroys or inhibits the replication of herpes simplex virus-1. chebi_ontology anti-HHV-1 agent anti-HHV-1 agents anti-HHV-I agent anti-HHV-I agents anti-HSV-1 agents anti-HSV-I agent anti-HSV-I agents anti-human herpes virus-1 agent anti-human herpes virus-1 agents anti-human herpes virus-I agent anti-human herpes virus-I agents CHEBI:64953 anti-HSV-1 agent anti-HHV-1 agent ChEBI anti-HHV-1 agents ChEBI anti-HHV-I agent ChEBI anti-HHV-I agents ChEBI anti-HSV-1 agents ChEBI anti-HSV-I agent ChEBI anti-HSV-I agents ChEBI anti-human herpes virus-1 agent ChEBI anti-human herpes virus-1 agents ChEBI anti-human herpes virus-I agent ChEBI anti-human herpes virus-I agents ChEBI An anti-HSV agent agent that destroys or inhibits the replication of herpes simplex virus-2. chebi_ontology anti-HHV-2 agent anti-HHV-2 agents anti-HHV-II agent anti-HHV-II agents anti-HSV-2 agents anti-HSV-II agent anti-HSV-II agents anti-human herpes virus-2 agent anti-human herpes virus-2 agents anti-human herpes virus-II agent anti-human herpes virus-II agents CHEBI:64954 anti-HSV-2 agent anti-HHV-2 agent ChEBI anti-HHV-2 agents ChEBI anti-HHV-II agent ChEBI anti-HHV-II agents ChEBI anti-HSV-2 agents ChEBI anti-HSV-II agent ChEBI anti-HSV-II agents ChEBI anti-human herpes virus-2 agent ChEBI anti-human herpes virus-2 agents ChEBI anti-human herpes virus-II agent ChEBI anti-human herpes virus-II agents ChEBI Any compound that has anti-asthmatic effects. chebi_ontology anti-asthmatic agents antiasthmatic agent antiasthmatic agents CHEBI:65023 anti-asthmatic agent anti-asthmatic agents ChEBI antiasthmatic agent ChEBI antiasthmatic agents ChEBI Antipsychotic drugs which can have different modes of action but which tend to be more likely than second generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements; such body movements can become permanent even after treatment has ceased. Wikipedia:Typical_antipsychotic chebi_ontology first generation antipsychotic agent first generation antipsychotic agents first generation antipsychotic drug first generation antipsychotic drugs first generation antipsychotics typical antipsychotic typical antipsychotic agent typical antipsychotic agents typical antipsychotic drug typical antipsychotic drugs typical antipsychotics CHEBI:65190 first generation antipsychotic first generation antipsychotic agent ChEBI first generation antipsychotic agents ChEBI first generation antipsychotic drug ChEBI first generation antipsychotic drugs ChEBI first generation antipsychotics ChEBI typical antipsychotic ChEBI typical antipsychotic agent ChEBI typical antipsychotic agents ChEBI typical antipsychotic drug ChEBI typical antipsychotic drugs ChEBI typical antipsychotics ChEBI Antipsychotic drugs which can have different modes of action but which tend to be less likely than first generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements. chebi_ontology atypical antipsychotic atypical antipsychotic agent atypical antipsychotic agents atypical antipsychotic drug atypical antipsychotic drugs atypical antipsychotics second generation antipsychotic agent second generation antipsychotic agents second generation antipsychotic drug second generation antipsychotic drugs second generation antipsychotics CHEBI:65191 second generation antipsychotic atypical antipsychotic ChEBI atypical antipsychotic agent ChEBI atypical antipsychotic agents ChEBI atypical antipsychotic drug ChEBI atypical antipsychotic drugs ChEBI atypical antipsychotics ChEBI second generation antipsychotic agent ChEBI second generation antipsychotic agents ChEBI second generation antipsychotic drug ChEBI second generation antipsychotic drugs ChEBI second generation antipsychotics ChEBI A carbohydrate derivative that is any derivative of a polysaccharide. chebi_ontology polysaccharide derivatives CHEBI:65212 polysaccharide derivative polysaccharide derivatives ChEBI Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes. chebi_ontology food preservatives CHEBI:65255 food preservative food preservatives ChEBI A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299). chebi_ontology antimicrobial food preservatives antimicrobial preservative antimicrobial preservatives CHEBI:65256 antimicrobial food preservative antimicrobial food preservatives ChEBI antimicrobial preservative ChEBI antimicrobial preservatives ChEBI A compound that inhibits the action of gamma-aminobutyric acid. Wikipedia:GABA_antagonist chebi_ontology GABA antagonists gamma-aminobutyric acid receptor antagonist gamma-aminobutyric acid receptor antagonists CHEBI:65259 GABA antagonist GABA antagonists ChEBI gamma-aminobutyric acid receptor antagonist ChEBI gamma-aminobutyric acid receptor antagonists ChEBI Any substance which is used to neutralise stomach acidity. Wikipedia:Antacid chebi_ontology antacids CHEBI:65265 antacid antacids ChEBI An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3. +1 H3NR 17.031 17.02655 [NH3+][*] chebi_ontology a primary amine substituted ammonium CHEBI:65296 primary ammonium ion a primary amine UniProt substituted ammonium ChEBI An alpha-amino acid anion that is the conjugate base of citrulline, obtained by deprotonation of the carboxy group. -1 C6H12N3O3 InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/p-1 RHGKLRLOHDJJDR-UHFFFAOYSA-M 174.17780 174.08841 NC(CCCNC(N)=O)C([O-])=O 2-amino-5-(carbamoylamino)pentanoate chebi_ontology CHEBI:66922 citrullinate 2-amino-5-(carbamoylamino)pentanoate IUPAC A monocarboxylic acid anion that is the conjugate base of creatine, obtained by deprotonation of the carboxy group. -1 C4H8N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)/p-1 CVSVTCORWBXHQV-UHFFFAOYSA-M 130.12520 130.06220 CN(CC([O-])=O)C(N)=N {[imino(amino)methyl](methyl)amino}acetate chebi_ontology (N-methylcarbamimidamido)acetate N-[amino(imino)methyl]-N-methylglycinate CHEBI:66924 creatinate {[imino(amino)methyl](methyl)amino}acetate IUPAC (N-methylcarbamimidamido)acetate ChEBI N-[amino(imino)methyl]-N-methylglycinate ChEBI Any compound which can be used to treat or alleviate the symptoms of dyskinesia. chebi_ontology antidyskinesia agents antidyskinesia drug antidyskinesia drugs antidyskinetic agent antidyskinetic agents antidyskinetic drug antidyskinetic drugs CHEBI:66956 antidyskinesia agent antidyskinesia agents ChEBI antidyskinesia drug ChEBI antidyskinesia drugs ChEBI antidyskinetic agent ChEBI antidyskinetic agents ChEBI antidyskinetic drug ChEBI antidyskinetic drugs ChEBI Any compound used for the treatment of eye conditions or eye diseases. chebi_ontology ophthalmic ophthalmic agent ophthalmic agents ophthalmics ophthalmological ophthalmologicals ophthalmology agent ophthalmology agents ophthalmology drugs CHEBI:66981 ophthalmology drug ophthalmic ChEBI ophthalmic agent ChEBI ophthalmic agents ChEBI ophthalmics ChEBI ophthalmological ChEBI ophthalmologicals ChEBI ophthalmology agent ChEBI ophthalmology agents ChEBI ophthalmology drugs ChEBI Any compound used to suppress premature labour and immature birth by suppressing uterine contractions. Wikipedia:Tocolytic chebi_ontology anti-contraction drug anti-contraction drugs anti-contraction medication anti-contraction medications labour repressant labour repressants tocolytic tocolytic agents tocolytic drug tocolytic drugs tocolytics CHEBI:66993 tocolytic agent anti-contraction drug ChEBI anti-contraction drugs ChEBI anti-contraction medication ChEBI anti-contraction medications ChEBI labour repressant ChEBI labour repressants ChEBI tocolytic ChEBI tocolytic agents ChEBI tocolytic drug ChEBI tocolytic drugs ChEBI tocolytics ChEBI An N-acyl-L-alpha-amino acid anion obtained by deprotonation of any folic acid. chebi_ontology folate folate anion folate anions CHEBI:67011 folates folate ChEBI folate anion ChEBI folate anions ChEBI Any branched-chain fatty acid anion containing methyl branches only. chebi_ontology methyl-branched fatty acid anions CHEBI:67013 methyl-branched fatty acid anion methyl-branched fatty acid anions ChEBI A sulfonium betaine that is a conjugate base of S-adenosyl-L-methionine obtained by the deprotonation of the carboxy group. 0 C15H22N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-N 398.43700 398.13724 C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 CAS:29908-03-0 Drug_Central:2414 KEGG:C00019 KNApSAcK:C00007347 PDBeChem:SAM PMID:25628954 [(3S)-3-amino-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonioacetate chebi_ontology AdoMet S-Adenosylmethionine SAM CHEBI:67040 S-adenosyl-L-methioninate CAS:29908-03-0 KEGG COMPOUND Drug_Central:2414 DrugCentral PMID:25628954 Europe PMC [(3S)-3-amino-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonioacetate IUPAC AdoMet KEGG_COMPOUND S-Adenosylmethionine KEGG_COMPOUND SAM KEGG_COMPOUND Any compound that has anti-inflammatory effects. chebi_ontology anti-inflammatory agents antiinflammatory agent antiinflammatory agents CHEBI:67079 anti-inflammatory agent anti-inflammatory agents ChEBI antiinflammatory agent ChEBI antiinflammatory agents ChEBI A provitamin that can be converted into vitamin A by enzymes from animal tissues. chebi_ontology provitamin As CHEBI:67200 provitamin A provitamin As ChEBI Any 1,4-benzoquinone carrying a single hydroxy substituent. 0 C6HO3R3 121.07030 120.99257 OC1=C([*])C(=O)C([*])=C([*])C1=O chebi_ontology 2-hydroxy-1,4-benzoquinones hydroxy-1,4-benzoquinone hydroxy-1,4-benzoquinones hydroxybenzoquinone hydroxybenzoquinones monohydroxybenzoquinones CHEBI:67273 monohydroxy-1,4-benzoquinones 2-hydroxy-1,4-benzoquinones ChEBI hydroxy-1,4-benzoquinone ChEBI hydroxy-1,4-benzoquinones ChEBI hydroxybenzoquinone ChEBI hydroxybenzoquinones ChEBI monohydroxybenzoquinones ChEBI Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. Wikipedia:Azole chebi_ontology azoles CHEBI:68452 azole azoles ChEBI An antagonist at the P2Y12 receptor Wikipedia:P2Y12 chebi_ontology ADP receptor subtype P2Y12 antagonist ADP receptor subtype P2Y12 antagonists P2Y12 receptor antagonists purinergic receptor subtype P2Y12 antagonist purinergic receptor subtype P2Y12 antagonists CHEBI:68563 P2Y12 receptor antagonist ADP receptor subtype P2Y12 antagonist ChEBI ADP receptor subtype P2Y12 antagonists ChEBI P2Y12 receptor antagonists ChEBI purinergic receptor subtype P2Y12 antagonist ChEBI purinergic receptor subtype P2Y12 antagonists ChEBI An antagonist at the AMPA receptor. Wikipedia:AMPA_receptor chebi_ontology AMPA receptor antagonists alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonist alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonists CHEBI:71014 AMPA receptor antagonist AMPA receptor antagonists ChEBI alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonist ChEBI alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonists ChEBI Any drug that has been developed specifically for treatment of a rare medical condition, the condition itself being known as an orphan disease. PMID:20036435 PMID:20800761 PMID:21180460 PMID:21682893 PMID:21947805 PMID:22363762 PMID:22366309 PMID:22371464 PMID:22731105 PMID:22739138 PMID:22747423 PMID:22814659 PMID:22814660 PMID:22973866 PMID:22981668 PMID:22989856 PMID:23013790 PMID:23090701 PMID:23109143 PMID:23129684 Wikipedia:Orphan_drug chebi_ontology orphan drugs CHEBI:71031 orphan drug PMID:20036435 Europe PMC PMID:20800761 Europe PMC PMID:21180460 Europe PMC PMID:21682893 Europe PMC PMID:21947805 Europe PMC PMID:22363762 Europe PMC PMID:22366309 Europe PMC PMID:22371464 Europe PMC PMID:22731105 Europe PMC PMID:22739138 Europe PMC PMID:22747423 Europe PMC PMID:22814659 Europe PMC PMID:22814660 Europe PMC PMID:22973866 Europe PMC PMID:22981668 Europe PMC PMID:22989856 Europe PMC PMID:23013790 Europe PMC PMID:23090701 Europe PMC PMID:23109143 Europe PMC PMID:23129684 Europe PMC orphan drugs ChEBI An enzyme inhibitor that inhibits the action of a transferase (EC 2.*) Wikipedia:Transferase chebi_ontology EC 2 inhibitor EC 2 inhibitors EC 2.* (transferase) inhibitors EC 2.* inhibitor EC 2.* inhibitors transferase inhibitor transferase inhibitors CHEBI:71300 EC 2.* (transferase) inhibitor EC 2 inhibitor ChEBI EC 2 inhibitors ChEBI EC 2.* (transferase) inhibitors ChEBI EC 2.* inhibitor ChEBI EC 2.* inhibitors ChEBI transferase inhibitor ChEBI transferase inhibitors ChEBI An organic anion that is the conjugate base of tetracycline obtained by deprotonation of the two enolic hydroxy groups and protonation of the tertiary amino group. -1 C22H23N2O8 InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/p-1/t9-,10-,15-,21+,22-/m0/s1 OFVLGDICTFRJMM-WESIUVDSSA-M 443.42660 443.14599 [H][C@@]12C[C@@]3([H])C(C(=O)c4c(O)cccc4[C@@]3(C)O)=C([O-])[C@]1(O)C(=O)C(C(N)=O)=C([O-])[C@H]2[NH+](C)C (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,7,11-trihydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracene-2,5-diolate chebi_ontology tetracycline anion CHEBI:71392 tetracycline(1-) (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,7,11-trihydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracene-2,5-diolate IUPAC tetracycline anion ChEBI Benzoquinones with at least one hydroxy substituent. chebi_ontology hydroxybenzoquinones CHEBI:71648 hydroxybenzoquinone hydroxybenzoquinones ChEBI An amino-acid anion in which the amino group is situated gamma- to the carboxylate group. chebi_ontology gamma-amino acid anions CHEBI:71666 gamma-amino acid anion gamma-amino acid anions ChEBI Any compound that promotes the growth of new blood vessels from pre-existing vessels. CHEBI:50927 chebi_ontology angiogenesis inducing agent angiogenesis inducing agents pro-angiogenic agents proangiogenic agent proangiogenic agents CHEBI:72571 pro-angiogenic agent angiogenesis inducing agent ChEBI angiogenesis inducing agents ChEBI pro-angiogenic agents ChEBI proangiogenic agent ChEBI proangiogenic agents ChEBI Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. chebi_ontology organic compound organic compounds organic molecules CHEBI:72695 organic molecule organic compound ChEBI organic compounds ChEBI organic molecules ChEBI A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment. MetaCyc:Exopolysaccharides PMID:11160795 PMID:11785425 PMID:1444258 PMID:15738217 PMID:16075348 PMID:17440912 PMID:18097339 PMID:19453747 PMID:20172021 PMID:20631870 PMID:20718297 PMID:2688547 PMID:6354590 Wikipedia:Exopolysaccharide Wikipedia:Extracellular_polymeric_substance chebi_ontology exopolysaccharides extracellular polymeric substance extracellular polymeric substances CHEBI:72813 exopolysaccharide PMID:11160795 Europe PMC PMID:11785425 Europe PMC PMID:1444258 Europe PMC PMID:15738217 Europe PMC PMID:16075348 Europe PMC PMID:17440912 Europe PMC PMID:18097339 Europe PMC PMID:19453747 Europe PMC PMID:20172021 Europe PMC PMID:20631870 Europe PMC PMID:20718297 Europe PMC PMID:2688547 Europe PMC PMID:6354590 Europe PMC exopolysaccharides ChEBI extracellular polymeric substance ChEBI extracellular polymeric substances ChEBI A drug used in treating and healing of wounds. Wikipedia:Wound_healing chebi_ontology vulneraries wound-healing agent wound-healing agents wound-healing drug wound-healing drugs CHEBI:73336 vulnerary vulneraries ChEBI wound-healing agent ChEBI wound-healing agents ChEBI wound-healing drug ChEBI wound-healing drugs ChEBI A role borne by a molecule that acts to counteract or neutralize the deleterious effects of paracetamol (acetaminophen). PMID:16354242 PMID:16573399 PMID:16575097 PMID:22348679 PMID:22352734 PMID:22353666 PMID:22835053 PMID:22998987 PMID:7112203 chebi_ontology Tylenol poisoning antidote Tylenol poisoning antidotes acetaminophen poisoning antidote acetaminophen poisoning antidotes antidote to Tylenol poisoning antidote to acetaminophen poisoning antidotes to Tylenol poisoning antidotes to acetaminophen poisoning antidotes to paracetamol poisoning paracetamol poisoning antidote paracetamol poisoning antidotes CHEBI:74529 antidote to paracetamol poisoning PMID:16354242 Europe PMC PMID:16573399 Europe PMC PMID:16575097 Europe PMC PMID:22348679 Europe PMC PMID:22352734 Europe PMC PMID:22353666 Europe PMC PMID:22835053 Europe PMC PMID:22998987 Europe PMC PMID:7112203 Europe PMC Tylenol poisoning antidote ChEBI Tylenol poisoning antidotes ChEBI acetaminophen poisoning antidote ChEBI acetaminophen poisoning antidotes ChEBI antidote to Tylenol poisoning ChEBI antidote to acetaminophen poisoning ChEBI antidotes to Tylenol poisoning ChEBI antidotes to acetaminophen poisoning ChEBI antidotes to paracetamol poisoning ChEBI paracetamol poisoning antidote ChEBI paracetamol poisoning antidotes ChEBI A role borne by a molecule that acts to counteract or neutralize the deleterious effects of curare. PMID:13358565 PMID:13386996 PMID:14128111 PMID:1579914 PMID:3896015 PMID:5333582 PMID:5352084 PMID:7720787 chebi_ontology antidote to curare antidote to tubocurarine antidote to tubocurarine poisoning antidotes to curare antidotes to curare poisoning antidotes to tubocurarine antidotes to tubocurarine poisoning curare antidote curare antidotes curare poisoning antidote curare poisoning antidotes tubocurarine antidote tubocurarine antidotes CHEBI:74530 antidote to curare poisoning PMID:13358565 Europe PMC PMID:13386996 Europe PMC PMID:14128111 Europe PMC PMID:1579914 Europe PMC PMID:3896015 Europe PMC PMID:5333582 Europe PMC PMID:5352084 Europe PMC PMID:7720787 Europe PMC antidote to curare ChEBI antidote to tubocurarine ChEBI antidote to tubocurarine poisoning ChEBI antidotes to curare ChEBI antidotes to curare poisoning ChEBI antidotes to tubocurarine ChEBI antidotes to tubocurarine poisoning ChEBI curare antidote ChEBI curare antidotes ChEBI curare poisoning antidote ChEBI curare poisoning antidotes ChEBI tubocurarine antidote ChEBI tubocurarine antidotes ChEBI A compound that causes the contraction of body tissues, typically used to reduce bleeding from minor abrasions. Wikipedia:Astringent chebi_ontology adstringent adstringents astringents CHEBI:74783 astringent adstringent ChEBI adstringents ChEBI astringents ChEBI Any organic aromatic compound having one or more hydroxy groups attached to a heteroarene ring. chebi_ontology hetaryl hydroxy compound hetaryl hydroxy compounds heteroaromatic hydroxy compound heteroaromatic hydroxy compounds heteroaryl hydroxy compounds CHEBI:74818 heteroaryl hydroxy compound hetaryl hydroxy compound ChEBI hetaryl hydroxy compounds ChEBI heteroaromatic hydroxy compound ChEBI heteroaromatic hydroxy compounds ChEBI heteroaryl hydroxy compounds ChEBI A ligase inhibitor that interferes with the action of a C-N bond-forming ligase (EC 6.3.*.*). chebi_ontology C--N bond-forming ligase inhibitor C--N bond-forming ligase inhibitors C-N bond-forming ligase (EC 6.3.*) inhibitor C-N bond-forming ligase (EC 6.3.*) inhibitors C-N bond-forming ligase inhibitor C-N bond-forming ligase inhibitors EC 6.3.* (C-N bond-forming ligase) inhibitorS EC 6.3.* inhibitor EC 6.3.* inhibitors EC 6.3.*.* inhibitor EC 6.3.*.* inhibitors CHEBI:75600 EC 6.3.* (C-N bond-forming ligase) inhibitor C--N bond-forming ligase inhibitor ChEBI C--N bond-forming ligase inhibitors ChEBI C-N bond-forming ligase (EC 6.3.*) inhibitor ChEBI C-N bond-forming ligase (EC 6.3.*) inhibitors ChEBI C-N bond-forming ligase inhibitor ChEBI C-N bond-forming ligase inhibitors ChEBI EC 6.3.* (C-N bond-forming ligase) inhibitorS ChEBI EC 6.3.* inhibitor ChEBI EC 6.3.* inhibitors ChEBI EC 6.3.*.* inhibitor ChEBI EC 6.3.*.* inhibitors ChEBI Any enzyme inhibitor that interferes with the action of a ligase (EC 6.*.*.*). Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. Wikipedia:Ligase chebi_ontology EC 6.* (ligase) inhibitors EC 6.* inhibitor EC 6.* inhibitors EC 6.*.*.* inhibitor EC 6.*.*.* inhibitors ligase inhibitor ligase inhibitors CHEBI:75603 EC 6.* (ligase) inhibitor EC 6.* (ligase) inhibitors ChEBI EC 6.* inhibitor ChEBI EC 6.* inhibitors ChEBI EC 6.*.*.* inhibitor ChEBI EC 6.*.*.* inhibitors ChEBI ligase inhibitor ChEBI ligase inhibitors ChEBI Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. chebi_ontology eukaryotic metabolites CHEBI:75763 eukaryotic metabolite eukaryotic metabolites ChEBI Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. CHEBI:77721 CHEBI:77743 chebi_ontology animal metabolites CHEBI:75767 animal metabolite animal metabolites ChEBI Any animal metabolite produced during a metabolic reaction in mammals. CHEBI:77464 CHEBI:77744 chebi_ontology mammalian metabolites CHEBI:75768 mammalian metabolite mammalian metabolites ChEBI Any member of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such). MetaCyc:B-vitamins PMID:22743781 PMID:23093174 PMID:23238962 PMID:23449527 PMID:23462586 PMID:23690582 Wikipedia:B_vitamin chebi_ontology B vitamins B-group vitamin B-group vitamins vitamin B CHEBI:75769 B vitamin PMID:22743781 Europe PMC PMID:23093174 Europe PMC PMID:23238962 Europe PMC PMID:23449527 Europe PMC PMID:23462586 Europe PMC PMID:23690582 Europe PMC B vitamins ChEBI B-group vitamin ChEBI B-group vitamins ChEBI vitamin B ChEBI Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). chebi_ontology Mus musculus metabolite Mus musculus metabolites mouse metabolites CHEBI:75771 mouse metabolite Mus musculus metabolite ChEBI Mus musculus metabolites ChEBI mouse metabolites ChEBI Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). CHEBI:76949 CHEBI:76951 chebi_ontology S. cerevisiae metabolite S. cerevisiae metabolites S. cerevisiae secondary metabolite S. cerevisiae secondary metabolites Saccharomyces cerevisiae metabolites Saccharomyces cerevisiae secondary metabolites baker's yeast metabolite baker's yeast metabolites baker's yeast secondary metabolite baker's yeast secondary metabolites CHEBI:75772 Saccharomyces cerevisiae metabolite S. cerevisiae metabolite ChEBI S. cerevisiae metabolites ChEBI S. cerevisiae secondary metabolite ChEBI S. cerevisiae secondary metabolites ChEBI Saccharomyces cerevisiae metabolites ChEBI Saccharomyces cerevisiae secondary metabolites ChEBI baker's yeast metabolite ChEBI baker's yeast metabolites ChEBI baker's yeast secondary metabolite ChEBI baker's yeast secondary metabolites ChEBI A mixture containing all eight of the B vitamins (B1, B2, B3, B5, B6, B7, B9, and B12). It is used as a dietary supplement and as a component of growth media for microorganisms. Wikipedia:B_vitamin chebi_ontology vitamin B mixture CHEBI:75782 vitamin B complex vitamin B mixture ChEBI Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. chebi_ontology prokaryotic metabolites CHEBI:75787 prokaryotic metabolite prokaryotic metabolites ChEBI A compound which increases either the number of red cells or the amount of haemoglobin in the blood. chebi_ontology anti-anaemic agents anti-anaemic drug anti-anaemic drugs anti-anemia agent anti-anemia agents anti-anemia drug anti-anemia drugs anti-anemic agent anti-anemic agents anti-anemic drug anti-anemic drugs antianaemia agent antianaemia agents antianaemia drug antianaemia drugs antianaemic agent antianaemic agents antianaemic drug antianaemic drugs antianemia drug antianemia drugs CHEBI:75835 anti-anaemic agent anti-anaemic agents ChEBI anti-anaemic drug ChEBI anti-anaemic drugs ChEBI anti-anemia agent ChEBI anti-anemia agents ChEBI anti-anemia drug ChEBI anti-anemia drugs ChEBI anti-anemic agent ChEBI anti-anemic agents ChEBI anti-anemic drug ChEBI anti-anemic drugs ChEBI antianaemia agent ChEBI antianaemia agents ChEBI antianaemia drug ChEBI antianaemia drugs ChEBI antianaemic agent ChEBI antianaemic agents ChEBI antianaemic drug ChEBI antianaemic drugs ChEBI antianemia drug ChEBI antianemia drugs ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any aromatic amino-acid. 0 C2H4NO2R 74.059 74.02420 [NH3+]C([*])C([O-])=O MetaCyc:Aromatic-Amino-Acids chebi_ontology an aromatic amino-acid aromatic amino-acid zwitterions CHEBI:76042 aromatic amino-acid zwitterion MetaCyc:Aromatic-Amino-Acids SUBMITTER an aromatic amino-acid UniProt aromatic amino-acid zwitterions ChEBI Any metabolite produced by metabolism of a xenobiotic compound. chebi_ontology xenobiotic metabolites CHEBI:76206 xenobiotic metabolite xenobiotic metabolites ChEBI A compressed gas or liquid with a boiling point lower than room temperature which to used to propel and dispense liquids such as deodorants, insecticides, paints, etc. from aerosol cans. PMID:22519407 PMID:24001847 chebi_ontology propellants CHEBI:76414 propellant PMID:22519407 Europe PMC PMID:24001847 Europe PMC propellants ChEBI Any metabolite produced during a metabolic reaction in marine macro- and microorganisms. CHEBI:77078 chebi_ontology marine metabolites CHEBI:76507 marine metabolite marine metabolites ChEBI Any unsaturated fatty acid anion containing more than one C-C unsaturated bond. Major species at pH 7.3. chebi_ontology PUFA polyunsaturated fatty acid anions CHEBI:76567 polyunsaturated fatty acid anion PUFA SUBMITTER polyunsaturated fatty acid anions ChEBI A glycerol compound having one of three possible substituent groups - either acyl, alkyl, or alk-1-enyl - at each of the three possible positions sn-1, sn-2 or sn-3. has functional parent glycerol (CHEBI:17754), children: triglyceride (CHEBI:17855). Parent: is_a glycerolipid (CHEBI:35741) LIPID_MAPS_class:LMGL0301 chebi_ontology triradylglycerols CHEBI:76579 triradylglycerol LIPID_MAPS_class:LMGL0301 SUBMITTER triradylglycerols ChEBI A fatty acid anion obtained by deprotonation of the carboxy group of any omega-methyl fatty acid; major species at pH 7.3. -1 C2H3O2R 59.044 59.01330 C[*]C([O-])=O chebi_ontology an omega-methyl fatty acid CHEBI:76619 omega-methyl fatty acid anion an omega-methyl fatty acid UniProt A transferase inhibitor inhibiting the action of transferase of a one-carbon-containing group (EC 2.1.*.*). chebi_ontology C1-transferase (EC 2.1.*) inhibitor C1-transferase (EC 2.1.*) inhibitors C1-transferase inhibitor C1-transferase inhibitors EC 2.1.* (C1-transferase) inhibitors EC 2.1.* inhibitor EC 2.1.* inhibitors one-carbon-containing group transferase inhibitor one-carbon-containing group transferase inhibitors CHEBI:76655 EC 2.1.* (C1-transferase) inhibitor C1-transferase (EC 2.1.*) inhibitor ChEBI C1-transferase (EC 2.1.*) inhibitors ChEBI C1-transferase inhibitor ChEBI C1-transferase inhibitors ChEBI EC 2.1.* (C1-transferase) inhibitors ChEBI EC 2.1.* inhibitor ChEBI EC 2.1.* inhibitors ChEBI one-carbon-containing group transferase inhibitor ChEBI one-carbon-containing group transferase inhibitors ChEBI A transferase inhibitor that inhibits the transfer of an alkyl (other than methyl) or aryl group (EC 2.5.1.*). chebi_ontology EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitors EC 2.5.1.* inhibitor EC 2.5.1.* inhibitors alkyl/aryl (non-methyl) transferase inhibitor alkyl/aryl (non-methyl) transferase inhibitors non-methyl alkyl/aryl transferase (EC 2.5.1.*) inhibitor non-methyl alkyl/aryl transferase (EC 2.5.1.*) inhibitors non-methyl alkyl/aryl transferase inhibitor non-methyl alkyl/aryl transferase inhibitors non-methyl-alkyl or aryl transferase inhibitor non-methyl-alkyl or aryl transferase inhibitors CHEBI:76663 EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitor EC 2.5.1.* (non-methyl-alkyl or aryl transferase) inhibitors ChEBI EC 2.5.1.* inhibitor ChEBI EC 2.5.1.* inhibitors ChEBI alkyl/aryl (non-methyl) transferase inhibitor ChEBI alkyl/aryl (non-methyl) transferase inhibitors ChEBI non-methyl alkyl/aryl transferase (EC 2.5.1.*) inhibitor ChEBI non-methyl alkyl/aryl transferase (EC 2.5.1.*) inhibitors ChEBI non-methyl alkyl/aryl transferase inhibitor ChEBI non-methyl alkyl/aryl transferase inhibitors ChEBI non-methyl-alkyl or aryl transferase inhibitor ChEBI non-methyl-alkyl or aryl transferase inhibitors ChEBI A transferase inhibitor that inhibits a nitrogenous group transferase (EC 2.6.*.*). chebi_ontology EC 2.6.* inhibitor EC 2.6.* inhibitors nitrogenous group transferase (EC 2.6.*) inhibitor nitrogenous group transferase (EC 2.6.*) inhibitors nitrogenous group transferase inhibitor nitrogenous group transferase inhibitors CHEBI:76665 EC 2.6.* (nitrogenous group transferase) inhibitor EC 2.6.* inhibitor ChEBI EC 2.6.* inhibitors ChEBI nitrogenous group transferase (EC 2.6.*) inhibitor ChEBI nitrogenous group transferase (EC 2.6.*) inhibitors ChEBI nitrogenous group transferase inhibitor ChEBI nitrogenous group transferase inhibitors ChEBI A transferase inhibitor that inhibits the action of a phosphorus-containing group transferase (EC 2.7.*.*). chebi_ontology EC 2.7.* (P-containing group transferase) inhibitors EC 2.7.* (phosphorus-containing group transferase) inhibitor EC 2.7.* (phosphorus-containing group transferase) inhibitors EC 2.7.* inhibitor EC 2.7.* inhibitors phosphorus-containing group transferase (EC 2.7.*) inhibitor phosphorus-containing group transferase (EC 2.7.*) inhibitors phosphorus-containing group transferase inhibitor phosphorus-containing group transferase inhibitors CHEBI:76668 EC 2.7.* (P-containing group transferase) inhibitor EC 2.7.* (P-containing group transferase) inhibitors ChEBI EC 2.7.* (phosphorus-containing group transferase) inhibitor ChEBI EC 2.7.* (phosphorus-containing group transferase) inhibitors ChEBI EC 2.7.* inhibitor ChEBI EC 2.7.* inhibitors ChEBI phosphorus-containing group transferase (EC 2.7.*) inhibitor ChEBI phosphorus-containing group transferase (EC 2.7.*) inhibitors ChEBI phosphorus-containing group transferase inhibitor ChEBI phosphorus-containing group transferase inhibitors ChEBI An enzyme inhibitor which interferes with the action of a lyase (EC 4.*.*.*). Lyases are enzymes cleaving C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation. Wikipedia:Lyase chebi_ontology EC 4.* (lyase) inhibitors EC 4.* inhibitor EC 4.* inhibitors EC 4.*.*.* inhibitor EC 4.*.*.* inhibitors lyase (EC 4.*) inhibitor lyase (EC 4.*) inhibitorS lyase inhibitor lyase inhibitors CHEBI:76710 EC 4.* (lyase) inhibitor EC 4.* (lyase) inhibitors ChEBI EC 4.* inhibitor ChEBI EC 4.* inhibitors ChEBI EC 4.*.*.* inhibitor ChEBI EC 4.*.*.* inhibitors ChEBI lyase (EC 4.*) inhibitor ChEBI lyase (EC 4.*) inhibitorS ChEBI lyase inhibitor ChEBI lyase inhibitors ChEBI A lyase inhibitor which inhibits the action of a C-N lyase (EC 4.3.*.*). chebi_ontology C-N lyase (EC 4.3.*) inhibitor C-N lyase (EC 4.3.*) inhibitors C-N lyase inhibitor C-N lyase inhibitors EC 4.3.* (C-N lyase) inhibitors EC 4.3.* inhibitor EC 4.3.* inhibitors CHEBI:76713 EC 4.3.* (C-N lyase) inhibitor C-N lyase (EC 4.3.*) inhibitor ChEBI C-N lyase (EC 4.3.*) inhibitors ChEBI C-N lyase inhibitor ChEBI C-N lyase inhibitors ChEBI EC 4.3.* (C-N lyase) inhibitors ChEBI EC 4.3.* inhibitor ChEBI EC 4.3.* inhibitors ChEBI An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*). Wikipedia:Oxidoreductase chebi_ontology EC 1.* (oxidoreductase) inhibitors EC 1.* inhibitor EC 1.* inhibitors oxidoreductase (EC 1.*) inhibitor oxidoreductase (EC 1.*) inhibitors oxidoreductase inhibitor oxidoreductase inhibitors CHEBI:76725 EC 1.* (oxidoreductase) inhibitor EC 1.* (oxidoreductase) inhibitors ChEBI EC 1.* inhibitor ChEBI EC 1.* inhibitors ChEBI oxidoreductase (EC 1.*) inhibitor ChEBI oxidoreductase (EC 1.*) inhibitors ChEBI oxidoreductase inhibitor ChEBI oxidoreductase inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the CH-OH group of donors (EC 1.1.*.*). chebi_ontology EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitors EC 1.1.* inhibitor EC 1.1.* inhibitors inhibitor of oxidoreductase acting on CH-OH group of donor inhibitor of oxidoreductase acting on CH-OH group of donors inhibitors of oxidoreductase acting on CH-OH group of donor inhibitors of oxidoreductase acting on CH-OH group of donors oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitor oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitors oxidoreductase acting on donor CH-OH group inhibitor oxidoreductase acting on donor CH-OH group inhibitors CHEBI:76726 EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitor EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitors ChEBI EC 1.1.* inhibitor ChEBI EC 1.1.* inhibitors ChEBI inhibitor of oxidoreductase acting on CH-OH group of donor ChEBI inhibitor of oxidoreductase acting on CH-OH group of donors ChEBI inhibitors of oxidoreductase acting on CH-OH group of donor ChEBI inhibitors of oxidoreductase acting on CH-OH group of donors ChEBI oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitor ChEBI oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitors ChEBI oxidoreductase acting on donor CH-OH group inhibitor ChEBI oxidoreductase acting on donor CH-OH group inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the CH-NH2 group of donors (EC 1.4.*.*). EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor chebi_ontology EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitors EC 1.4.* inhibitor EC 1.4.* inhibitors inhibitor of oxidoreductase acting on CH-NH2 group of donor inhibitor of oxidoreductase acting on CH-NH2 group of donors inhibitors of oxidoreductase acting on CH-NH2 group of donor inhibitors of oxidoreductase acting on CH-NH2 group of donors oxidoreductase acting on CH-NH2 group of donor inhibitor oxidoreductase acting on CH-NH2 group of donor inhibitors oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitor oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitors CHEBI:76730 EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor ChEBI EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitors ChEBI EC 1.4.* inhibitor ChEBI EC 1.4.* inhibitors ChEBI inhibitor of oxidoreductase acting on CH-NH2 group of donor ChEBI inhibitor of oxidoreductase acting on CH-NH2 group of donors ChEBI inhibitors of oxidoreductase acting on CH-NH2 group of donor ChEBI inhibitors of oxidoreductase acting on CH-NH2 group of donors ChEBI oxidoreductase acting on CH-NH2 group of donor inhibitor ChEBI oxidoreductase acting on CH-NH2 group of donor inhibitors ChEBI oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitor ChEBI oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases), EC 1.13.*.*. chebi_ontology EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitors EC 1.13.* inhibitor EC 1.13.* inhibitors oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) (EC 1.13.*) inhibitor oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) (EC 1.13.*) inhibitors oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) inhibitor oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) inhibitors CHEBI:76740 EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitor EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitors ChEBI EC 1.13.* inhibitor ChEBI EC 1.13.* inhibitors ChEBI oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) (EC 1.13.*) inhibitor ChEBI oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) (EC 1.13.*) inhibitors ChEBI oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) inhibitor ChEBI oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases) inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on hydrogen as donors (EC 1.14.*.*). chebi_ontology EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors EC 1.14.* inhibitor EC 1.14.* inhibitors inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors CHEBI:76741 EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors ChEBI EC 1.14.* inhibitor ChEBI EC 1.14.* inhibitors ChEBI inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on CH or CH2 (EC 1.17.*.*). chebi_ontology EC 1.17.* (oxidoreductase acting on CH or CH2) inhibitors EC 1.17.* inhibitor EC 1.17.* inhibitors oxidoreductase acting on CH or CH2 (EC 1.17.*) inhibitor oxidoreductase acting on CH or CH2 (EC 1.17.*) inhibitors oxidoreductase acting on CH or CH2 inhibitor oxidoreductase acting on CH or CH2 inhibitors CHEBI:76744 EC 1.17.* (oxidoreductase acting on CH or CH2) inhibitor EC 1.17.* (oxidoreductase acting on CH or CH2) inhibitors ChEBI EC 1.17.* inhibitor ChEBI EC 1.17.* inhibitors ChEBI oxidoreductase acting on CH or CH2 (EC 1.17.*) inhibitor ChEBI oxidoreductase acting on CH or CH2 (EC 1.17.*) inhibitors ChEBI oxidoreductase acting on CH or CH2 inhibitor ChEBI oxidoreductase acting on CH or CH2 inhibitors ChEBI Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). Wikipedia:Hydrolase chebi_ontology EC 3.* (hydrolase) inhibitors EC 3.* inhibitor EC 3.* inhibitors EC 3.*.*.* inhibitor EC 3.*.*.* inhibitors hydrolase (EC 3.*) inhibitor hydrolase (EC 3.*) inhibitors hydrolase inhibitor hydrolase inhibitors CHEBI:76759 EC 3.* (hydrolase) inhibitor EC 3.* (hydrolase) inhibitors ChEBI EC 3.* inhibitor ChEBI EC 3.* inhibitors ChEBI EC 3.*.*.* inhibitor ChEBI EC 3.*.*.* inhibitors ChEBI hydrolase (EC 3.*) inhibitor ChEBI hydrolase (EC 3.*) inhibitors ChEBI hydrolase inhibitor ChEBI hydrolase inhibitors ChEBI A hydrolase inhibitor that interferes with the action of any ester hydrolase (EC 3.1.*.*). chebi_ontology EC 3.1.* (ester hydrolase) inhibitors EC 3.1.* inhibitor EC 3.1.* inhibitors ester hydrolase (EC 3.1.*) inhibitor ester hydrolase (EC 3.1.*) inhibitors ester hydrolase inhibitor ester hydrolase inhibitors CHEBI:76760 EC 3.1.* (ester hydrolase) inhibitor EC 3.1.* (ester hydrolase) inhibitors ChEBI EC 3.1.* inhibitor ChEBI EC 3.1.* inhibitors ChEBI ester hydrolase (EC 3.1.*) inhibitor ChEBI ester hydrolase (EC 3.1.*) inhibitors ChEBI ester hydrolase inhibitor ChEBI ester hydrolase inhibitors ChEBI Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*). chebi_ontology EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors EC 3.5.* inhibitor EC 3.5.* inhibitors CHEBI:76764 EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor ChEBI EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors ChEBI EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors ChEBI EC 3.5.* inhibitor ChEBI EC 3.5.* inhibitors ChEBI An EC 3.1.* (ester hydrolase) inhibitor that interferes with the action of a carboxylic ester hydrolase (EC 3.1.1.*). chebi_ontology EC 3.1.1.* (carboxylic ester hydrolase) inhibitors EC 3.1.1.* inhibitor EC 3.1.1.* inhibitors carboxylic ester hydrolase (EC 3.1.1.*) inhibitor carboxylic ester hydrolase (EC 3.1.1.*) inhibitors CHEBI:76773 EC 3.1.1.* (carboxylic ester hydrolase) inhibitor EC 3.1.1.* (carboxylic ester hydrolase) inhibitors ChEBI EC 3.1.1.* inhibitor ChEBI EC 3.1.1.* inhibitors ChEBI carboxylic ester hydrolase (EC 3.1.1.*) inhibitor ChEBI carboxylic ester hydrolase (EC 3.1.1.*) inhibitors ChEBI Any EC 3.4.* (hydrolases acting on peptide bond) inhibitor that interferes with the activity of a peptidyl dipeptidase (EC 3.4.15.*). chebi_ontology EC 3.4.15.* (peptidyl-dipeptidase) inhibitors EC 3.4.15.* inhibitor EC 3.4.15.* inhibitors inhibitor of peptidyl-dipeptidases inhibitor of peptidyl-dipeptidases (EC 3.4.15.*) inhibitors of peptidyl-dipeptidases inhibitors of peptidyl-dipeptidases (EC 3.4.15.*) peptidyl-dipeptidase (EC 3.4.15.*) inhibitor peptidyl-dipeptidase (EC 3.4.15.*) inhibitors peptidyl-dipeptidase inhibitor peptidyl-dipeptidase inhibitors CHEBI:76782 EC 3.4.15.* (peptidyl-dipeptidase) inhibitor EC 3.4.15.* (peptidyl-dipeptidase) inhibitors ChEBI EC 3.4.15.* inhibitor ChEBI EC 3.4.15.* inhibitors ChEBI inhibitor of peptidyl-dipeptidases ChEBI inhibitor of peptidyl-dipeptidases (EC 3.4.15.*) ChEBI inhibitors of peptidyl-dipeptidases ChEBI inhibitors of peptidyl-dipeptidases (EC 3.4.15.*) ChEBI peptidyl-dipeptidase (EC 3.4.15.*) inhibitor ChEBI peptidyl-dipeptidase (EC 3.4.15.*) inhibitors ChEBI peptidyl-dipeptidase inhibitor ChEBI peptidyl-dipeptidase inhibitors ChEBI An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*). chebi_ontology EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors EC 3.5.1.* inhibitor EC 3.5.1.* inhibitors non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors CHEBI:76807 EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors ChEBI EC 3.5.1.* inhibitor ChEBI EC 3.5.1.* inhibitors ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors ChEBI An EC 2.7.* (P-containing group transferase) inhibitor that interferes with the action of any nucleotidyltransferase (EC 2.7.7.*). chebi_ontology EC 2.7.7.* (nucleotidyltransferase) inhibitors inhibitor of nucleotidyltransferases inhibitor of nucleotidyltransferases (EC 2.7.7.*) inhibitors of nucleotidyltransferases inhibitors of nucleotidyltransferases (EC 2.7.7.*) nucleotidyltransferase (EC 2.7.7.*) inhibitor nucleotidyltransferase (EC 2.7.7.*) inhibitors nucleotidyltransferase inhibitor nucleotidyltransferase inhibitors CHEBI:76815 EC 2.7.7.* (nucleotidyltransferase) inhibitor EC 2.7.7.* (nucleotidyltransferase) inhibitors ChEBI inhibitor of nucleotidyltransferases ChEBI inhibitor of nucleotidyltransferases (EC 2.7.7.*) ChEBI inhibitors of nucleotidyltransferases ChEBI inhibitors of nucleotidyltransferases (EC 2.7.7.*) ChEBI nucleotidyltransferase (EC 2.7.7.*) inhibitor ChEBI nucleotidyltransferase (EC 2.7.7.*) inhibitors ChEBI nucleotidyltransferase inhibitor ChEBI nucleotidyltransferase inhibitors ChEBI An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of any acid-ammonia (or amine) ligase (EC 6.3.1.*). chebi_ontology EC 6.3.1.* (acid-ammonia/amine ligase) inhibitors EC 6.3.1.* inhibitor EC 6.3.1.* inhibitors acid-ammonia (or amine) ligase inhibitor acid-ammonia (or amine) ligase inhibitors CHEBI:76823 EC 6.3.1.* (acid-ammonia/amine ligase) inhibitor EC 6.3.1.* (acid-ammonia/amine ligase) inhibitors ChEBI EC 6.3.1.* inhibitor ChEBI EC 6.3.1.* inhibitors ChEBI acid-ammonia (or amine) ligase inhibitor ChEBI acid-ammonia (or amine) ligase inhibitors ChEBI An EC 4.3.* (C-N lyase) inhibitor that interferes with the action of any ammonia-lyase (EC 4.3.1.*). chebi_ontology EC 4.3.1.* (ammonia-lyase) inhibitors EC 4.3.1.* (ammonia-lyases) inhibitor EC 4.3.1.* (ammonia-lyases) inhibitors EC 4.3.1.* inhibitor EC 4.3.1.* inhibitors ammonia-lyase (EC 4.3.1.*) inhibitor ammonia-lyase (EC 4.3.1.*) inhibitors ammonia-lyase inhibitor ammonia-lyase inhibitors CHEBI:76832 EC 4.3.1.* (ammonia-lyase) inhibitor EC 4.3.1.* (ammonia-lyase) inhibitors ChEBI EC 4.3.1.* (ammonia-lyases) inhibitor ChEBI EC 4.3.1.* (ammonia-lyases) inhibitors ChEBI EC 4.3.1.* inhibitor ChEBI EC 4.3.1.* inhibitors ChEBI ammonia-lyase (EC 4.3.1.*) inhibitor ChEBI ammonia-lyase (EC 4.3.1.*) inhibitors ChEBI ammonia-lyase inhibitor ChEBI ammonia-lyase inhibitors ChEBI An EC 2.5.* (transferase) inhibitor that inhibits the action of any transferase that transfers an alkyl (other than methyl) or aryl group (EC 2.5.*). chebi_ontology EC 2.5.* (non-methyl-alkyl or aryl transferase) inhibitors EC 2.5.* inhibitor EC 2.5.* inhibitors non-methyl-alkyl or aryl transferase (EC 2.5.*) inhibitor non-methyl-alkyl or aryl transferase (EC 2.5.*) inhibitors CHEBI:76834 EC 2.5.* (non-methyl-alkyl or aryl transferase) inhibitor EC 2.5.* (non-methyl-alkyl or aryl transferase) inhibitors ChEBI EC 2.5.* inhibitor ChEBI EC 2.5.* inhibitors ChEBI non-methyl-alkyl or aryl transferase (EC 2.5.*) inhibitor ChEBI non-methyl-alkyl or aryl transferase (EC 2.5.*) inhibitors ChEBI An EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitor that uses NAD(+) or NADP(+) as acceptor (EC 1.1.1.*). chebi_ontology EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+)acceptor) inhibitors EC 1.1.1.* inhibitor EC 1.1.1.* inhibitors oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitor oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitors CHEBI:76835 EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+)acceptor) inhibitors ChEBI EC 1.1.1.* inhibitor ChEBI EC 1.1.1.* inhibitors ChEBI oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitor ChEBI oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitors ChEBI An EC 1.13.* [oxidoreductase acting on single donors with incorporation of molecular oxygen (oxygenases)] inhibitor that inhibits the action of any oxidoreductase incorporating 2 atoms of oxygen (EC 1.13.11.*). chebi_ontology EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 O atoms) inhibitors EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitor EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitors EC 1.13.11.* inhibitor EC 1.13.11.* inhibitors oxidoreductase acting on single donors and incorporating 2 atoms of oxygen (EC 1.13.11.*) inhibitor oxidoreductase acting on single donors and incorporating 2 atoms of oxygen (EC 1.13.11.*) inhibitors CHEBI:76837 EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 O atoms) inhibitor EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 O atoms) inhibitors ChEBI EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitor ChEBI EC 1.13.11.* (oxidoreductase acting on single donors and incorporating 2 atoms of oxygen) inhibitors ChEBI EC 1.13.11.* inhibitor ChEBI EC 1.13.11.* inhibitors ChEBI oxidoreductase acting on single donors and incorporating 2 atoms of oxygen (EC 1.13.11.*) inhibitor ChEBI oxidoreductase acting on single donors and incorporating 2 atoms of oxygen (EC 1.13.11.*) inhibitors ChEBI An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the action of any such enzyme incorporating one atom of oxygen and using reduced flavin or flavoprotein as donor (EC 1.14.14.*). chebi_ontology EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors EC 1.14.14.* inhibitor EC 1.14.14.* inhibitors oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitor oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitors CHEBI:76838 EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors ChEBI EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor ChEBI EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors ChEBI EC 1.14.14.* inhibitor ChEBI EC 1.14.14.* inhibitors ChEBI oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitor ChEBI oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitors ChEBI An EC 1.17.* (oxidoreductase acting on CH or CH2) inhibitor that interferes with the function of any such enzyme that uses oxygen as acceptor (EC 1.17.3.*). chebi_ontology EC 1.17.3.* (oxidoreductase acting on CH or CH2 with oxygen as acceptor) inhibitors EC 1.17.3.* inhibitor EC 1.17.3.* inhibitors oxidoreductase acting on CH or CH2 with oxygen as acceptor (EC 1.17.3.*) inhibitor oxidoreductase acting on CH or CH2 with oxygen as acceptor (EC 1.17.3.*) inhibitors CHEBI:76850 EC 1.17.3.* (oxidoreductase acting on CH or CH2 with oxygen as acceptor) inhibitor EC 1.17.3.* (oxidoreductase acting on CH or CH2 with oxygen as acceptor) inhibitors ChEBI EC 1.17.3.* inhibitor ChEBI EC 1.17.3.* inhibitors ChEBI oxidoreductase acting on CH or CH2 with oxygen as acceptor (EC 1.17.3.*) inhibitor ChEBI oxidoreductase acting on CH or CH2 with oxygen as acceptor (EC 1.17.3.*) inhibitors ChEBI An EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.4.3.*). chebi_ontology EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitors EC 1.4.3.* inhibitor EC 1.4.3.* inhibitors oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitor oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitors CHEBI:76861 EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitor EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitors ChEBI EC 1.4.3.* inhibitor ChEBI EC 1.4.3.* inhibitors ChEBI oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitor ChEBI oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitors ChEBI An EC 2.1.* (C1-transferase) inhibitor that interferes with the action of any hydroxymethyl-, formyl- and related transferase (EC 2.1.2.*). chebi_ontology EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors EC 2.1.2.* inhibitor EC 2.1.2.* inhibitors hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitors CHEBI:76874 EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors ChEBI EC 2.1.2.* inhibitor ChEBI EC 2.1.2.* inhibitors ChEBI hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor ChEBI hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitors ChEBI An EC 2.6.* (nitrogenous group transferase) inhibitor that inhibits the action of any transaminase (EC 2.6.1.*). chebi_ontology EC 2.6.1.* (transaminase) inhibitors EC 2.6.1.* inhibitor EC 2.6.1.* inhibitors transaminase (EC 2.6.1.*) inhibitor transaminase (EC 2.6.1.*) inhibitors CHEBI:76879 EC 2.6.1.* (transaminase) inhibitor EC 2.6.1.* (transaminase) inhibitors ChEBI EC 2.6.1.* inhibitor ChEBI EC 2.6.1.* inhibitors ChEBI transaminase (EC 2.6.1.*) inhibitor ChEBI transaminase (EC 2.6.1.*) inhibitors ChEBI A drug which increases the blood glucose level. chebi_ontology diabetes inducer hyperglycemic agents CHEBI:76916 hyperglycemic agent diabetes inducer ChEBI hyperglycemic agents ChEBI Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms. CHEBI:75766 CHEBI:76925 chebi_ontology plant metabolites plant secondary metabolites CHEBI:76924 plant metabolite plant metabolites ChEBI plant secondary metabolites ChEBI An enzyme inhibitor that interferes with one or more steps in a metabolic pathway. chebi_ontology metabolic pathway inhibitor metabolic pathway inhibitors pathway inhibitors CHEBI:76932 pathway inhibitor metabolic pathway inhibitor ChEBI metabolic pathway inhibitors ChEBI pathway inhibitors ChEBI Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. CHEBI:75765 CHEBI:76947 chebi_ontology fungal metabolites CHEBI:76946 fungal metabolite fungal metabolites ChEBI Any human metabolite produced by metabolism of a xenobiotic compound in humans. chebi_ontology human xenobiotic metabolites CHEBI:76967 human xenobiotic metabolite human xenobiotic metabolites ChEBI Any prokaryotic metabolite produced during a metabolic reaction in bacteria. CHEBI:75760 CHEBI:76970 chebi_ontology CHEBI:76969 bacterial metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. chebi_ontology E.coli metabolite E.coli metabolites Escherichia coli metabolites CHEBI:76971 Escherichia coli metabolite E.coli metabolite ChEBI E.coli metabolites ChEBI Escherichia coli metabolites ChEBI A compound that alters the structure of mucus so as to decrease its viscosity and thereby facilitate its removal by ciliary action and expectoration. Compare with antitussives, which suppress the cough reflex, and expectorants, which are considered to increase the volume of secretions in the respiratory tract, so facilitating their removal by ciliary action and coughing. PMID:17419975 PMID:17594730 PMID:20031934 PMID:2117172 PMID:22895919 chebi_ontology mucolytics CHEBI:77034 mucolytic PMID:17419975 Europe PMC PMID:17594730 Europe PMC PMID:20031934 Europe PMC PMID:2117172 Europe PMC PMID:22895919 Europe PMC mucolytics ChEBI An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of prostaglandin-E2 9-reductase (EC 1.1.1.189). Wikipedia:Prostaglandin-E2_9-reductase chebi_ontology (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitor (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitors 9-keto-prostaglandin E2 reductase inhibitor 9-keto-prostaglandin E2 reductase inhibitors 9-ketoprostaglandin reductase inhibitor 9-ketoprostaglandin reductase inhibitors EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitors EC 1.1.1.189 inhibitor EC 1.1.1.189 inhibitors PGE-9-ketoreductase inhibitor PGE-9-ketoreductase inhibitors PGE2 9-oxoreductase inhibitor PGE2 9-oxoreductase inhibitors PGE2-9-OR inhibitor PGE2-9-OR inhibitors PGE2-9-ketoreductase inhibitor PGE2-9-ketoreductase inhibitors prostaglandin 9-ketoreductase inhibitor prostaglandin 9-ketoreductase inhibitors prostaglandin E 9-ketoreductase inhibitor prostaglandin E 9-ketoreductase inhibitors prostaglandin E2-9-oxoreductase inhibitor prostaglandin E2-9-oxoreductase inhibitors prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitor prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitors reductase, 15-hydroxy-9-oxoprostaglandin inhibitor reductase, 15-hydroxy-9-oxoprostaglandin inhibitors CHEBI:77119 EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitor (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitor ChEBI (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitors ChEBI 9-keto-prostaglandin E2 reductase inhibitor ChEBI 9-keto-prostaglandin E2 reductase inhibitors ChEBI 9-ketoprostaglandin reductase inhibitor ChEBI 9-ketoprostaglandin reductase inhibitors ChEBI EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitors ChEBI EC 1.1.1.189 inhibitor ChEBI EC 1.1.1.189 inhibitors ChEBI PGE-9-ketoreductase inhibitor ChEBI PGE-9-ketoreductase inhibitors ChEBI PGE2 9-oxoreductase inhibitor ChEBI PGE2 9-oxoreductase inhibitors ChEBI PGE2-9-OR inhibitor ChEBI PGE2-9-OR inhibitors ChEBI PGE2-9-ketoreductase inhibitor ChEBI PGE2-9-ketoreductase inhibitors ChEBI prostaglandin 9-ketoreductase inhibitor ChEBI prostaglandin 9-ketoreductase inhibitors ChEBI prostaglandin E 9-ketoreductase inhibitor ChEBI prostaglandin E 9-ketoreductase inhibitors ChEBI prostaglandin E2-9-oxoreductase inhibitor ChEBI prostaglandin E2-9-oxoreductase inhibitors ChEBI prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitor ChEBI prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitors ChEBI reductase, 15-hydroxy-9-oxoprostaglandin inhibitor ChEBI reductase, 15-hydroxy-9-oxoprostaglandin inhibitors ChEBI A food additive that imparts colour to food. In European countries, E-numbers for permitted food colours are from E 100 to E 199, divided into yellows (E 100-109), oranges (E 110-119), reds (E 120-129), blues and violets (E 130-139), greens (E 140-149), browns and blacks (E 150-159), and others (E 160-199). Wikipedia:Food_coloring chebi_ontology food coloring food colorings food colourings CHEBI:77182 food colouring food coloring ChEBI food colorings ChEBI food colourings ChEBI A diuretic that acts on the ascending loop of Henle in the kidney. Wikipedia:Loop_diuretic chebi_ontology loop diuretics CHEBI:77608 loop diuretic loop diuretics ChEBI An EC 4.3.1.* (ammonia-lyase) inhibitor that interferes with the action of histidine ammonia-lyase (EC 4.3.1.3). Wikipedia:Histidine_ammonia-lyase chebi_ontology EC 4.3.1.3 (histidine ammonia-lyase) inhibitors EC 4.3.1.3 inhibitor EC 4.3.1.3 inhibitors L-histidine ammonia-lyase (urocanate-forming) inhibitor L-histidine ammonia-lyase (urocanate-forming) inhibitors L-histidine ammonia-lyase inhibitor L-histidine ammonia-lyase inhibitors histidase inhibitor histidase inhibitors histidinase inhibitor histidinase inhibitors histidine alpha-deaminase inhibitor histidine alpha-deaminase inhibitors histidine ammonia-lyase (EC 4.3.1.3) inhibitor histidine ammonia-lyase (EC 4.3.1.3) inhibitors histidine ammonia-lyase inhibitor histidine ammonia-lyase inhibitors CHEBI:77703 EC 4.3.1.3 (histidine ammonia-lyase) inhibitor EC 4.3.1.3 (histidine ammonia-lyase) inhibitors ChEBI EC 4.3.1.3 inhibitor ChEBI EC 4.3.1.3 inhibitors ChEBI L-histidine ammonia-lyase (urocanate-forming) inhibitor ChEBI L-histidine ammonia-lyase (urocanate-forming) inhibitors ChEBI L-histidine ammonia-lyase inhibitor ChEBI L-histidine ammonia-lyase inhibitors ChEBI histidase inhibitor ChEBI histidase inhibitors ChEBI histidinase inhibitor ChEBI histidinase inhibitors ChEBI histidine alpha-deaminase inhibitor ChEBI histidine alpha-deaminase inhibitors ChEBI histidine ammonia-lyase (EC 4.3.1.3) inhibitor ChEBI histidine ammonia-lyase (EC 4.3.1.3) inhibitors ChEBI histidine ammonia-lyase inhibitor ChEBI histidine ammonia-lyase inhibitors ChEBI Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). CHEBI:75770 CHEBI:77123 chebi_ontology H. sapiens metabolite H. sapiens metabolites Homo sapiens metabolite Homo sapiens metabolites CHEBI:77746 human metabolite H. sapiens metabolite ChEBI H. sapiens metabolites ChEBI Homo sapiens metabolite ChEBI Homo sapiens metabolites ChEBI A zwitterion obtained by transfer of a proton from the 2-hydroxy group to the 1-amino group of tetracycline. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). 0 C22H24N2O8 InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/t9-,10-,15-,21+,22-/m0/s1 OFVLGDICTFRJMM-WESIUVDSSA-N 444.43460 444.15327 C[NH+](C)[C@H]1[C@@H]2C[C@H]3C(=C(O)[C@]2(O)C(=O)C(C(N)=O)=C1[O-])C(=O)c1c(O)cccc1[C@@]3(C)O (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,5,7,11-tetrahydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracen-2-olate chebi_ontology tetracycline CHEBI:77932 tetracycline zwitterion (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,5,7,11-tetrahydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracen-2-olate IUPAC tetracycline UniProt An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4). Wikipedia:Amidase chebi_ontology EC 3.5.1.4 (amidase) inhibitors EC 3.5.1.4 inhibitor EC 3.5.1.4 inhibitors N-acetylaminohydrolase inhibitor N-acetylaminohydrolase inhibitors acylamidase inhibitor acylamidase inhibitors acylamide amidohydrolase inhibitor acylamide amidohydrolase inhibitors amidase (EC 3.5.1.4) inhibitor amidase (EC 3.5.1.4) inhibitors amidase inhibitor amidase inhibitors amidohydrolase inhibitor amidohydrolase inhibitors deaminase inhibitor deaminase inhibitors fatty acylamidase inhibitor fatty acylamidase inhibitors CHEBI:77941 EC 3.5.1.4 (amidase) inhibitor EC 3.5.1.4 (amidase) inhibitors ChEBI EC 3.5.1.4 inhibitor ChEBI EC 3.5.1.4 inhibitors ChEBI N-acetylaminohydrolase inhibitor ChEBI N-acetylaminohydrolase inhibitors ChEBI acylamidase inhibitor ChEBI acylamidase inhibitors ChEBI acylamide amidohydrolase inhibitor ChEBI acylamide amidohydrolase inhibitors ChEBI amidase (EC 3.5.1.4) inhibitor ChEBI amidase (EC 3.5.1.4) inhibitors ChEBI amidase inhibitor ChEBI amidase inhibitors ChEBI amidohydrolase inhibitor ChEBI amidohydrolase inhibitors ChEBI deaminase inhibitor ChEBI deaminase inhibitors ChEBI fatty acylamidase inhibitor ChEBI fatty acylamidase inhibitors ChEBI A food additive that is used to make or keep fruit or vegetable tissues firm and crisp. or which interacts with gelling agents such as pectin to produce or strengthen a gel. Wikipedia:Firming_agent chebi_ontology firming agent firming agents food firming agents CHEBI:77960 food firming agent firming agent ChEBI firming agents ChEBI food firming agents ChEBI An antioxidant that used as a food additives to help guard against food deterioration. chebi_ontology food antioxidants CHEBI:77962 food antioxidant food antioxidants ChEBI A food preservative that acts by chelating with metal cations (particularly those of copper, iron and nickel) that catalyse the oxidation of fats in food. Wikipedia:Sequestrant chebi_ontology sequestrants CHEBI:77963 sequestrant sequestrants ChEBI A propellant that is used to expel foods from an aerosol container. chebi_ontology food propellants CHEBI:78017 food propellant food propellants ChEBI A polyunsaturated fatty acid anion that is the conjugate base of docosahexaenoic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C22H31O2 327.4803 327.23241 [O-]C([*])=O chebi_ontology CHEBI:78060 docosahexaenoate Any saturated fatty acid anion containing 3 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C3H5O2 73.07060 73.02895 [O-]C([*])=O chebi_ontology fatty acid 3:0 CHEBI:78113 fatty acid anion 3:0 fatty acid 3:0 UniProt Any saturated fatty acid anion containing 4 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C4H7O2 87.09718 87.04460 [O-]C([*])=O chebi_ontology fatty acid 4:0 CHEBI:78115 fatty acid anion 4:0 fatty acid 4:0 UniProt Any saturated fatty acid anion containing 6 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C6H11O2 115.15034 115.07590 [O-]C([*])=O chebi_ontology fatty acid 6:0 CHEBI:78116 fatty acid anion 6:0 fatty acid 6:0 UniProt Any saturated fatty acid anion containing 16 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C16H31O2 255.41610 255.23241 [O-]C([*])=O chebi_ontology fatty acid 16:0 CHEBI:78123 fatty acid anion 16:0 fatty acid 16:0 UniProt A monocarboxylic acid anion that is the conjugate base of N-acetyl-L-cysteine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C5H8NO3S InChI=1S/C5H9NO3S/c1-3(7)6-4(2-10)5(8)9/h4,10H,2H2,1H3,(H,6,7)(H,8,9)/p-1/t4-/m0/s1 PWKSKIMOESPYIA-BYPYZUCNSA-M 162.18700 162.02304 CC(=O)N[C@@H](CS)C([O-])=O MetaCyc:CPD-9175 PMID:19268377 Reaxys:6327823 (2R)-2-acetamido-3-sulfanylpropanoate chebi_ontology N-acetyl-L-cysteine CHEBI:78236 N-acetyl-L-cysteinate MetaCyc:CPD-9175 SUBMITTER PMID:19268377 SUBMITTER Reaxys:6327823 Reaxys (2R)-2-acetamido-3-sulfanylpropanoate IUPAC N-acetyl-L-cysteine UniProt A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. chebi_ontology dietary component dietary components food components CHEBI:78295 food component dietary component ChEBI dietary components ChEBI food components ChEBI Any minor or unwanted substance introduced into the environment that can have undesired effects. chebi_ontology environmental contaminants CHEBI:78298 environmental contaminant environmental contaminants ChEBI A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure. Wikipedia:Refrigerant chebi_ontology refrigerants CHEBI:78433 refrigerant refrigerants ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3. 0 C2H4NO2R 74.059 74.02420 [NH3+]C([*])C([O-])=O CHEBI:83409 MetaCyc:Alpha-Amino-Acids chebi_ontology an alpha-amino acid CHEBI:78608 alpha-amino acid zwitterion MetaCyc:Alpha-Amino-Acids SUBMITTER an alpha-amino acid UniProt Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. chebi_ontology carbohydrates and derivatives carbohydrates and their derivatives CHEBI:78616 carbohydrates and carbohydrate derivatives carbohydrates and derivatives ChEBI carbohydrates and their derivatives ChEBI A chromanol that is chromane in which the hydrogen at position 6 is replaced by a hydroxy group. 0 C9H10O2 InChI=1S/C9H10O2/c10-8-3-4-9-7(6-8)2-1-5-11-9/h3-4,6,10H,1-2,5H2 GZCJJOLJSBCUNR-UHFFFAOYSA-N 150.17450 150.06808 Oc1ccc2OCCCc2c1 Reaxys:1283166 3,4-dihydro-2H-chromen-6-ol chebi_ontology 3,4-dihydrobenzopyran-6-ol CHEBI:78631 chroman-6-ol Reaxys:1283166 Reaxys 3,4-dihydro-2H-chromen-6-ol IUPAC 3,4-dihydrobenzopyran-6-ol ChEBI Any metabolite produced by all living cells. chebi_ontology essential metabolite essential metabolites fundamental metabolites CHEBI:78675 fundamental metabolite essential metabolite ChEBI essential metabolites ChEBI fundamental metabolites ChEBI Any organic molecular entity that contains at least one C=C bond. chebi_ontology olefinic compounds CHEBI:78840 olefinic compound olefinic compounds ChEBI A long-chain fatty acid anion that is the conjugate base of hexadecanoic acid (palmitic acid); major species at pH 7.3. -1 C16H31O2 InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18)/p-1 IPCSVZSSVZVIGE-UHFFFAOYSA-M 255.41610 255.23295 CCCCCCCCCCCCCCCC([O-])=O CHEBI:231736 Beilstein:3589907 CAS:143-20-4 Gmelin:344266 HMDB:HMDB0000220 MetaCyc:PALMITATE Reaxys:3589907 hexadecanoate chebi_ontology (16:0) 1-hexyldecanoate 1-pentadecanecarboxylate CH3-[CH2]14-COO(-) Hexadecanoic acid, ion(1-) n-hexadecanoate n-hexadecoate palmitate pentadecanecarboxylate CHEBI:7896 hexadecanoate Beilstein:3589907 Beilstein CAS:143-20-4 ChemIDplus Gmelin:344266 Gmelin Reaxys:3589907 Reaxys hexadecanoate IUPAC hexadecanoate UniProt (16:0) ChEBI 1-hexyldecanoate HMDB 1-pentadecanecarboxylate ChEBI CH3-[CH2]14-COO(-) ChEBI Hexadecanoic acid, ion(1-) ChemIDplus n-hexadecanoate ChEBI n-hexadecoate ChEBI palmitate ChEBI pentadecanecarboxylate ChEBI A member of the class of pantothenic acids that is an amide formed from pantoic acid and beta-alanine. 0 C9H17NO5 InChI=1S/C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13) GHOKWGTUZJEAQD-UHFFFAOYSA-N 219.23502 219.11067 CC(C)(CO)C(O)C(=O)NCCC(O)=O Beilstein:1727062 CAS:599-54-2 DrugBank:DB01783 HMDB:HMDB0000210 KEGG:C00864 KEGG:D07413 PMID:24727172 Reaxys:1727062 Wikipedia:Pantothenic_acid 3-(2,4-dihydroxy-3,3-dimethylbutanamido)propanoic acid Pantothenic acid chebi_ontology N-(2,4-dihydroxy-3,3-dimethylbutanoyl)-beta-alanine CHEBI:7916 pantothenic acid Beilstein:1727062 Beilstein CAS:599-54-2 ChemIDplus PMID:24727172 Europe PMC Reaxys:1727062 Reaxys 3-(2,4-dihydroxy-3,3-dimethylbutanamido)propanoic acid IUPAC Pantothenic acid KEGG_COMPOUND N-(2,4-dihydroxy-3,3-dimethylbutanoyl)-beta-alanine ChEBI Any inorganic anion with a valency of three. chebi_ontology trivalent inorganic anions CHEBI:79387 trivalent inorganic anion trivalent inorganic anions ChEBI Any inorganic anion with a valency of two. chebi_ontology divalent inorganic anions CHEBI:79388 divalent inorganic anion divalent inorganic anions ChEBI Any inorganic anion with a valency of one. chebi_ontology monovalent inorganic anions CHEBI:79389 monovalent inorganic anion monovalent inorganic anions ChEBI A member of the class of monohydroxy-1,4-benzoquinones that is 2-hydroxy-1,4-benzoquinone carrying an additional methyl substituent at position 5. 0 C7H6O3 InChI=1S/C7H6O3/c1-4-2-6(9)7(10)3-5(4)8/h2-3,10H,1H3 BMBZVGUSOUAIMK-UHFFFAOYSA-N 138.121 138.03169 C=1C(C(=CC(C1C)=O)O)=O CAS:615-91-8 KEGG:C18316 MetaCyc:CPD-9135 Reaxys:1861302 2-hydroxy-5-methylcyclohexa-2,5-diene-1,4-dione chebi_ontology 2-Hydroxy-5-methyl-1,4-benzoquinone 2-Hydroxy-5-methyl-p-benzoquinone CHEBI:81667 2-hydroxy-5-methylquinone CAS:615-91-8 ChemIDplus CAS:615-91-8 KEGG COMPOUND Reaxys:1861302 Reaxys 2-hydroxy-5-methylcyclohexa-2,5-diene-1,4-dione IUPAC 2-Hydroxy-5-methyl-1,4-benzoquinone KEGG_COMPOUND 2-Hydroxy-5-methyl-p-benzoquinone ChemIDplus An elemental molecular entity in which all of the atoms have atomic number 26. chebi_ontology CHEBI:82663 elemental iron A Daphnia metabolite produced by the species Daphnia galeata. chebi_ontology Daphnia galeata metabolites CHEBI:83038 Daphnia galeata metabolite Daphnia galeata metabolites ChEBI An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill. chebi_ontology crustacean metabolites CHEBI:83039 crustacean metabolite crustacean metabolites ChEBI A Daphnia metabolite produced by the species Daphnia magna. chebi_ontology Daphnia magna metabolites CHEBI:83056 Daphnia magna metabolite Daphnia magna metabolites ChEBI A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia Wikipedia:Daphnia chebi_ontology Daphnia metabolites CHEBI:83057 Daphnia metabolite Daphnia metabolites ChEBI Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom. chebi_ontology canonical amino acid derivative canonical amino acid derivatives canonical amino-acid derivative canonical amino-acid derivatives proteinogenic amino acid derivatives proteinogenic amino-acid derivative proteinogenic amino-acid derivatives CHEBI:83811 proteinogenic amino acid derivative canonical amino acid derivative ChEBI canonical amino acid derivatives ChEBI canonical amino-acid derivative ChEBI canonical amino-acid derivatives ChEBI proteinogenic amino acid derivatives ChEBI proteinogenic amino-acid derivative ChEBI proteinogenic amino-acid derivatives ChEBI Any derivative of a non-proteinogenic amino acid resulting from reaction at an amino group or carboxy group, or from the replacement of any hydrogen by a heteroatom. chebi_ontology non-canonical amino acid derivative non-canonical amino-acid derivatives non-proteinogenic amino-acid derivatives CHEBI:83812 non-proteinogenic amino acid derivative non-canonical amino acid derivative ChEBI non-canonical amino-acid derivatives ChEBI non-proteinogenic amino-acid derivatives ChEBI Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration. Wikipedia:Proteinogenic_amino_acid chebi_ontology canonical amino acid canonical amino acids proteinogenic amino acids CHEBI:83813 proteinogenic amino acid canonical amino acid ChEBI canonical amino acids ChEBI proteinogenic amino acids ChEBI Any amino-acid that is not naturally encoded in the genetic code of any organism. Wikipedia:Non-proteinogenic_amino_acids chebi_ontology non-canonical amino acid non-canonical amino acids non-canonical amino-acid non-canonical amino-acids non-coded amino acid non-coded amino acids non-coded amino-acid non-coded amino-acids non-proteinogenic amino acids non-proteinogenic amino-acid non-proteinogenic amino-acids CHEBI:83820 non-proteinogenic amino acid non-canonical amino acid ChEBI non-canonical amino acids ChEBI non-canonical amino-acid ChEBI non-canonical amino-acids ChEBI non-coded amino acid ChEBI non-coded amino acids ChEBI non-coded amino-acid ChEBI non-coded amino-acids ChEBI non-proteinogenic amino acids ChEBI non-proteinogenic amino-acid ChEBI non-proteinogenic amino-acids ChEBI Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues. CHEBI:25359 chebi_ontology amino acid derivatives modified amino acids CHEBI:83821 amino acid derivative amino acid derivatives ChEBI modified amino acids ChEBI A proteinogenic amino acid derivative resulting from the formal reaction of L-cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of L-cysteine by a heteroatom. chebi_ontology L-cysteine derivatives CHEBI:83824 L-cysteine derivative L-cysteine derivatives ChEBI Any alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. chebi_ontology non-proteinogenic alpha-amino acids non-proteinogenic alpha-amino-acid non-proteinogenic alpha-amino-acids CHEBI:83925 non-proteinogenic alpha-amino acid non-proteinogenic alpha-amino acids ChEBI non-proteinogenic alpha-amino-acid ChEBI non-proteinogenic alpha-amino-acids ChEBI A fatty acid anion obtained by deprotonation of the carboxy group of any 2-saturated fatty acid. -1 C2H2O2R 58.036 58.00548 [O-]C(=O)C[*] chebi_ontology 1,2-saturated fatty acid anion a 1,2-saturated fatty acid CHEBI:83955 2-saturated fatty acid anion 1,2-saturated fatty acid anion ChEBI a 1,2-saturated fatty acid UniProt A methyl-branched fatty acid anion obtained by deprotonation of the carboxy group of any 3-methyl fatty acid; major species at pH 7.3. -1 C4H6O2R 86.089 86.03678 CC([*])CC([O-])=O chebi_ontology 3-methyl fatty acid 3-methyl-branched fatty acid anion 3-methyl-branched fatty acid(1-) CHEBI:83972 3-methyl fatty acid anion 3-methyl fatty acid UniProt 3-methyl-branched fatty acid anion ChEBI 3-methyl-branched fatty acid(1-) SUBMITTER A proteinogenic amino acid derivative resulting from reaction of L-glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen of L-glutamic acid by a heteroatom. chebi_ontology L-glutamic acid derivatives CHEBI:83982 L-glutamic acid derivative L-glutamic acid derivatives ChEBI Any metabolite (endogenous or exogenous) found in human urine samples. chebi_ontology human urinary metabolites CHEBI:84087 human urinary metabolite human urinary metabolites ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of nicotinamidase (EC 3.5.1.19). Wikipedia:Nicotinamidase chebi_ontology EC 3.5.1.19 (nicotinamidase) inhibitors EC 3.5.1.19 inhibitor EC 3.5.1.19 inhibitors YNDase inhibitor YNDase inhibitors nicotinamidase (EC 3.5.1.19) inhibitor nicotinamidase (EC 3.5.1.19) inhibitors nicotinamidase inhibitor nicotinamidase inhibitors nicotinamide amidase inhibitor nicotinamide amidase inhibitors nicotinamide amidohydrolase inhibitor nicotinamide amidohydrolase inhibitors nicotinamide deaminase inhibitor nicotinamide deaminase inhibitors CHEBI:84264 EC 3.5.1.19 (nicotinamidase) inhibitor EC 3.5.1.19 (nicotinamidase) inhibitors ChEBI EC 3.5.1.19 inhibitor ChEBI EC 3.5.1.19 inhibitors ChEBI YNDase inhibitor ChEBI YNDase inhibitors ChEBI nicotinamidase (EC 3.5.1.19) inhibitor ChEBI nicotinamidase (EC 3.5.1.19) inhibitors ChEBI nicotinamidase inhibitor ChEBI nicotinamidase inhibitors ChEBI nicotinamide amidase inhibitor ChEBI nicotinamide amidase inhibitors ChEBI nicotinamide amidohydrolase inhibitor ChEBI nicotinamide amidohydrolase inhibitors ChEBI nicotinamide deaminase inhibitor ChEBI nicotinamide deaminase inhibitors ChEBI Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae. chebi_ontology algal metabolites CHEBI:84735 algal metabolite algal metabolites ChEBI Any member of the class of cholanic acids carrying two hydroxy substituents at unspecified positions. chebi_ontology dihydroxycholanic acids CHEBI:85184 dihydroxycholanic acid dihydroxycholanic acids ChEBI Any metabolite (endogenous or exogenous) found in human blood serum samples. chebi_ontology human blood serum metabolites CHEBI:85234 human blood serum metabolite human blood serum metabolites ChEBI An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. chebi_ontology quinolone antibiotics CHEBI:86324 quinolone antibiotic quinolone antibiotics ChEBI Any antifungal agent used to prevent or treat fungal infections in humans or animals. Wikipedia:Antifungal chebi_ontology anti-fungal drug anti-fungal drugs anti-fungal medication anti-fungal medications antifungal drugs antifungal medication antifungal medications pharmaceutical fungicide pharmaceutical fungicides CHEBI:86327 antifungal drug anti-fungal drug ChEBI anti-fungal drugs ChEBI anti-fungal medication ChEBI anti-fungal medications ChEBI antifungal drugs ChEBI antifungal medication ChEBI antifungal medications ChEBI pharmaceutical fungicide ChEBI pharmaceutical fungicides ChEBI A class of sulfonamides whose members generally have bacteriostatic antibiotic properties. PMID:24443047 PMID:24928456 PMID:25064257 PMID:25796473 PMID:26177406 Wikipedia:Sulfonamide_(medicine) chebi_ontology sulfonamide antibiotics sulfonamide antimicrobial agent sulfonamide antimicrobial agents sulphonamide antibiotic sulphonamide antibiotics CHEBI:87228 sulfonamide antibiotic PMID:24443047 Europe PMC PMID:24928456 Europe PMC PMID:25064257 Europe PMC PMID:25796473 Europe PMC PMID:26177406 Europe PMC sulfonamide antibiotics ChEBI sulfonamide antimicrobial agent ChEBI sulfonamide antimicrobial agents ChEBI sulphonamide antibiotic ChEBI sulphonamide antibiotics ChEBI Any metal which causes the onset of an allergic reaction. chebi_ontology allergenic metal allergenic metals metal allergens CHEBI:88184 metal allergen allergenic metal ChEBI allergenic metals ChEBI metal allergens ChEBI Any drug which causes the onset of an allergic reaction. chebi_ontology allergenic drug CHEBI:88188 drug allergen allergenic drug ChEBI An organic anion obtained by deprotonation of the hydroxy group of 2-hydroxy-5-methylquinone. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). -1 C7H5O3 InChI=1S/C7H6O3/c1-4-2-6(9)7(10)3-5(4)8/h2-3,10H,1H3/p-1 BMBZVGUSOUAIMK-UHFFFAOYSA-M 137.113 137.02442 C1(C=C(C(C=C1C)=O)[O-])=O MetaCyc:CPD-9135 4-methyl-3,6-dioxocyclohexa-1,4-dien-1-olate chebi_ontology 2-hydroxy-5-methylquinone 2-hydroxy-5-methylquinone(1-) CHEBI:88190 2-oxido-5-methylquinone MetaCyc:CPD-9135 SUBMITTER 4-methyl-3,6-dioxocyclohexa-1,4-dien-1-olate IUPAC 2-hydroxy-5-methylquinone UniProt 2-hydroxy-5-methylquinone(1-) ChEBI A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors. CHEBI:189678 Wikipedia:Receptor_modulator chebi_ontology receptor modulators CHEBI:90710 receptor modulator receptor modulators ChEBI A role borne by a molecule that acts to counteract or neutralize the deleterious effects of cyanide. chebi_ontology CHEBI:90749 antidote to cyanide poisoning A carboxylic acic anion obtained by deprotonation of the carboxy group of any aromatic carboxylic acid. Major species at pH 7.3. -1 CO2R 44.010 43.98983 *C([O-])=O chebi_ontology an aromatic carboxylate CHEBI:91007 aromatic carboxylate an aromatic carboxylate UniProt Any inhibitor of erythropoietin, a glycoprotein hormone that controls erythropoiesis (red blood cell production). chebi_ontology EPO inhibitor EPO inhibitors erythropoietin inhibitors CHEBI:91025 erythropoietin inhibitor EPO inhibitor ChEBI EPO inhibitors ChEBI erythropoietin inhibitors ChEBI An antagonist at purinergic P2 receptors Wikipedia:Purinergic_receptor chebi_ontology P2 antagonist P2 antagonists non-selective P2 purinergic antagonist non-selective P2 purinergic antagonists purinergic receptor P2 antagonists CHEBI:91079 purinergic receptor P2 antagonist P2 antagonist ChEBI P2 antagonists ChEBI non-selective P2 purinergic antagonist ChEBI non-selective P2 purinergic antagonists ChEBI purinergic receptor P2 antagonists ChEBI A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:mah OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 cell in vivo https://github.com/obophenotype/cell-ontology/issues/2124 obsolete native cell true OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:mah Any fibroblast that is deriived from the neural crest. fibroblast neural crest derived Any fibroblast that is deriived from the neural crest. https://orcid.org/0000-0001-5208-3432 neuronal receptor cell (sensu Animalia) neuronal receptor cell A cell found in the embryo before the formation of all the gem layers is complete. early embryonic cell (metazoa) A cell found in the embryo before the formation of all the gem layers is complete. GOC:tfm Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. migratory cranial neural crest cell Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007091 https://orcid.org/0000-0001-5208-3432 Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. migratory trunk neural crest cell Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. ZFA:0007095 https://orcid.org/0000-0001-5208-3432 A stem cell that is the precursor of gametes. FBbt:00004861 germline stem cell germ line stem cell true A stem cell that is the precursor of gametes. doi:10.1016/j.stem.2012.05.016 A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis. FMA:72290 MA:0002765 VHOG:0001531 ncithesaurus:Spermatogenic_Cell male germ cell https://github.com/obophenotype/cell-ontology/issues/574 true A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis. PMID:29462262 https://orcid.org/0000-0001-5208-3432 A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. BTO:0001275 CALOHA:TS-0951 EMAPA:31484 FBbt:00004936 FMA:84049 WBbt:0006799 spermatocyte A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. GOC:tfm MESH:D013090 A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. BTO:0001274 CALOHA:TS-0950 EMAPA:31486 FBbt:00004942 FMA:72294 WBbt:0006800 nematoblast spermatid A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. MESH:D013087 A mature male germ cell that develops from a spermatid. BTO:0001277 BTO:0002046 CALOHA:TS-0949 FBbt:00004954 FMA:67338 WBbt:0006798 sperm cell spermatozoid spermatozoon sperm true A mature male germ cell that develops from a spermatid. GOC:tfm MESH:D013094 An euploid male germ cell of an early stage of spermatogenesis. BTO:0000958 CALOHA:TS-2193 EMAPA:31482 FBbt:00004934 FBbt:00004935 FMA:72291 spermatogonial cell spermatogonium An euploid male germ cell of an early stage of spermatogenesis. MESH:D013093 Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 ncithesaurus:Egg female germ cell true Female germ cell is a germ cell that supports female gamete production. GOC:tfm PMID:11023867 PMID:20454446 A stem cell that is the precursor of female gametes. FBbt:00004873 female germ line stem cell true true A stem cell that is the precursor of female gametes. doi:10.1016/j.stem.2012.05.016 A female germ cell that has entered meiosis. BTO:0000964 CALOHA:TS-0711 FBbt:00004886 FMA:18644 MESH:D009865 WBbt:0006797 oogonium oocyte true A female germ cell that has entered meiosis. GOC:tfm ISBN:0721662544 An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 oogonial cell true An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. GOC:tfm ISBN:0721662544 A smooth muscle cell derived from the neural crest. smooth muscle cell neural crest derived true A smooth muscle cell derived from the neural crest. https://orcid.org/0000-0001-5208-3432 neuron neural crest derived neural crest derived neuron true A cell that will develop into a neuron often after a migration phase. BTO:0000930 FMA:70563 neuroblast neuroblast (sensu Vertebrata) A cell that will develop into a neuron often after a migration phase. GOC:NV http://en.wikipedia.org/wiki/Neuroblast A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 animal stem cell This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’. stem cell A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. GOC:tfm MESH:D013234 A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell unipotential stem cell single fate stem cell A stem cell that self-renews as well as give rise to a single mature cell type. GOC:tfm A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:86475 MESH:D006412 VHOG:0001485 blood forming stem cell hemopoietic stem cell HSC colony forming unit hematopoietic Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. GOC:add GOC:dsd GOC:tfm PMID:19022770 http://en.wikipedia.org/wiki/Hematopoietic_stem_cell HSC A progenitor cell committed to the erythroid lineage. BTO:0004911 BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell true A progenitor cell committed to the erythroid lineage. GOC:add ISBN:0721601464 BFU-E CFU-E A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. Originally this term had some plant germ line cell children. germ line cell A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. GOC:tfm ISBN:0721662544 A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. CALOHA:TS-1195 FMA:83553 CFU-M colony forming unit macrophage colony forming unit monocyte monocyte stem cell Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. monoblast true A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus. GOC:add PMID:1104740 http://en.wikipedia.org/wiki/Monoblast http://www.copewithcytokines.de CFU-M A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell multi fate stem cell A stem cell that can give rise to multiple lineages of cells. GOC:add A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. BTO:0004730 common myeloid precursor CFU-GEMM CFU-S CMP colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor true A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. GOC:add ISBN:0878932437 MESH:D023461 CFU-GEMM ISBN:0878932437 CFU-S ISBN:0878932437 CMP ISBN:0878932437 colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte ISBN:0878932437 multipotential myeloid stem cell ISBN:0878932437 myeloid stem cell ISBN:0878932437 pluripotent stem cell (bone marrow) ISBN:0878932437 A progenitor cell committed to the megakaryocyte and erythroid lineages. CFU-EM CFU-MegE MEP Meg/E progenitor colony forming unit erythroid megakaryocyte megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell true A progenitor cell committed to the megakaryocyte and erythroid lineages. GOC:add GOC:dsd GOC:tfm MESH:D055015 PMID:16647566 http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell A oligopotent progenitor cell committed to the lymphoid lineage. common lymphocyte precursor common lymphocyte progenitor common lymphoid precursor CLP ELP committed lymphopoietic stem cell early lymphocyte progenitor lymphoid stem cell lymphopoietic stem cell CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative. common lymphoid progenitor true A oligopotent progenitor cell committed to the lymphoid lineage. GOC:add GOC:dsd GOC:tfm PMID:10407577 PMID:16551251 CLP ELP A stem cell from which all cells of the body can form. FMA:84790 MESH:D039901 totipotential stem cell totipotent stem cell A stem cell from which all cells of the body can form. GOC:add GOC:tfm A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell define using PATO mulit-potent or oligopotent? non-terminally differentiated cell A precursor cell with a limited number of potential fates. SANBI:mhl A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 CALOHA:TS-0650 FBbt:00005083 FMA:70335 VHOG:0001529 myoblast A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. GOC:tfm MESH:D032446 PMID:21849021 A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 CALOHA:TS-0362 FMA:63877 NCIT:C12482 VHOG:0001482 These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. ISBN:0517223651 MESH:D005347 http://en.wikipedia.org/wiki/Fibroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. BTO:0003607 FMA:66783 chrondoplast chondroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. GOC:tfm GO_REF:0000034 ISBN:0618947256 Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell. BTO:0001663 FMA:70576 amelocyte enamel secreting cell non-encoded relationship from VSAO produces VSAO:0000066 ameloblast Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell. GOC:tfm GO_REF:0000034 MESH:D000565 Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell. BTO:0001769 CALOHA:TS-0696 FMA:62999 MESH:D009804 legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin. odontoblast Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell. GO_REF:0000034 ISBN:0618947256 A cell that has a filiform extrusion of the cell surface. VHOG:0001532 XAO:0000031 ciliated cell A cell that has a filiform extrusion of the cell surface. GOC:tfm A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte epithelial cell https://www.swissbiopics.org/api/image/Epithelial_cells.svg A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. FB:ma GOC:tfm MESH:D004847 An epithelial cell that has a cilia. FMA:70605 ciliated epithelial cell An epithelial cell that has a cilia. GOC:tfm An epithelial cell that is part of a duct. duct epithelial cell An epithelial cell that is part of a duct. https://orcid.org/0000-0001-5208-3432 branched duct epithelial cell An endothelial cell that lines the vasculature. cuboidal endothelial cell of vascular tree blood vessel endothelial cell true An endothelial cell that lines the vasculature. GOC:tfm non-branched duct epithelial cell A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. columnar/cuboidal epithelial cell A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. GO:0002065 https://orcid.org/0000-0001-5208-3432 CALOHA:TS-1249 squamous epithelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. FMA:66773 mesotheliocyte mesothelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. GOC:tfm ISBN:0721662544 A cell which moves among different tissues of the body, via blood, lymph, or other medium. circulating cell A cell which moves among different tissues of the body, via blood, lymph, or other medium. GOC:add A cell found predominately in the blood. FMA:62844 MESH:D001773 blood cell true A cell found predominately in the blood. GOC:add GOC:tfm An epithelial cell of the lung. BTO:0004299 lung epithelial cell epithelial cell of lung An epithelial cell of the lung. https://orcid.org/0000-0001-5208-3432 An epithelial cell of the pancreas. BTO:0000028 pancreas epithelial cell pancreatic epithelial cell epithelial cell of pancreas An epithelial cell of the pancreas. GOC:tfm A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. BTO:0000782 CALOHA:TS-1001 FMA:62870 MESH:D013601 VHOG:0001479 T lymphocyte T-cell T-lymphocyte immature T cell mature T cell T cell true A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. GOC:add GOC:tfm ISBN:0781735149 A leukocyte with abundant granules in the cytoplasm. BTO:0000539 BTO:0001026 CALOHA:TS-0422 FMA:62854 granular leucocyte granular leukocyte polymorphonuclear leukocyte granulocyte true A leukocyte with abundant granules in the cytoplasm. GOC:amm GOC:tfm MESH:D006098 http://en.wikipedia.org/wiki/Granulocyte neuron associated cell A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. BTO:0000830 CALOHA:TS-0603 FMA:66784 histaminocyte labrocyte mastocyte tissue basophil Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5. mast cell true A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. GOC:add GOC:dsd GOC:tfm ISBN:068340007X MESH:D008407 PMCID:PMC1312421 PMCID:PMC2855166 PMID:15153310 PMID:16455980 PMID:19671378 PMID:212366338 PMID:9354811 labrocyte ISBN:0721601464 mastocyte ISBN:0721601464 tissue basophil ISBN:068340007X A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell BTO:0004301 The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). sensory epithelial cell A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. GOC:tfm ISBN:0517223651 ISBN:0721662544 Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 FBbt:00005125 FMA:67313 WBbt:0005113 interneuron Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. GOC:tfm MESH:D007395 An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 FBbt:00005123 FMA:83617 WBbt:0005409 motoneuron motor neuron An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. MESH:D009046 PMID:16875686 Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 MESH:D011984 WBbt:0005759 sensory neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. ISBN:0721662544 A neuron whose cell body is within an autonomic ganglion. FMA:80121 autonomic neuron A neuron whose cell body is within an autonomic ganglion. GOC:tfm A neuron that uses acetylcholine as a vesicular neurotransmitter. BTO:0004902 FBbt:00007173 FMA:84796 MESH:D059329 WBbt:0006840 cholinergic neuron A neuron that uses acetylcholine as a vesicular neurotransmitter. GOC:tfm A vertebrate phagocyte with a single nucleus. BTO:0001433 mononuclear phagocyte true A vertebrate phagocyte with a single nucleus. GOC:add GOC:tfm ISBN:0781735149 An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 endotheliocyte From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. GOC:tfm MESH:D042783 PMID:21275341 http://en.wikipedia.org/wiki/Endothelial_cell https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855 CNS neuron (sensu Vertebrata) A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 neuroglial cell neuroglia Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571 glial cell A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 Ectoderm destined to be nervous tissue. neurectoderm cell neurectodermal cell Ectoderm destined to be nervous tissue. GOC:tfm ISBN:068340007X A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. BTO:0002625 BTO:0003298 FMA:70546 bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells BMSC CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 true A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. FB:ma GOC:dsd PMCID:PMC2613570 PMID:10102814 PMID:16923606 PMID:17986482 PMID:19960544 http://en.wikipedia.org/wiki/Mesenchymal_stem_cell http://www.copewithcytokines.de/cope.cgi?key=mesenchymal%20stem%20cells marrow stromal cells PMID:11378515 BMSC CFU-F MSC PMID:11378515 mesenchymal progenitor cells MESH:D044982 mesenchymal stromal cells stem cells, mesenchymal MESH:D044982 A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. BTO:0000443 CALOHA:TS-0012 FMA:63880 adipose cell fat cell adipocyte A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. MESH:D017667 Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. BTO:0000249 CALOHA:TS-0138 FMA:66782 cartilage cell chondrocyte Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. GO_REF:0000034 MESH:D019902 A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response. APC Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells. professional antigen presenting cell A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response. GOC:add ISBN:0781735149 APC simple columnar epithelial cell A pigment cell is a cell that contains pigment granules. VHOG:0001678 chromatocyte chromatophore pigment cell A pigment cell is a cell that contains pigment granules. GOC:tfm pigment cell visual pigment cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 glandular epithelial cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. GOC:tfm A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 secretory cell A cell that specializes in controlled release of one or more substances. GOC:tfm ISBN:0721662544 A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 exocrine cell A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. ISBN:0198547684 A cell that secretes glycosaminoglycans. GAG secreting cell hyaluronic acid secreting cell glycosaminoglycan secreting cell A cell that secretes glycosaminoglycans. GOC:tfm protein secreting cell seromucus secreting cell A cell of the epithelial lining that produce and secrete mucins. BTO:0001540 FMA:13148 http://en.wikipedia.org/wiki/Goblet_cell chalice cell goblet cell A cell of the epithelial lining that produce and secrete mucins. MESH:D020397 A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 endocrinocyte endocrine cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. MESH:D055098 An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. BTO:0003865 FMA:62930 MESH:D019858 enteroendocrine cell An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. GOC:tfm SANBI:mhl A neuron that is capable of some hormone secretion in response to neuronal signals. BTO:0002691 FBbt:00005130 FMA:83810 neurosecretory cell neurosecretory neuron The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron. neuroendocrine cell A neuron that is capable of some hormone secretion in response to neuronal signals. MESH:D055099 The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron. PMID:5342440 https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073 A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. BTO:0000259 FMA:69263 phaeochromocyte chromaffin cell A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. MESH:D019439 peptide hormone secreting cell BTO:0000783 insulin secreting cell A cell that secretes insulin and is located towards the center of the islets of Langerhans. beta cell BTO:0000783 EV:0200009 FMA:70586 MA:0002419 ncithesaurus:Beta_Cell B-cell of pancreatic islet beta cell of pancreatic islet insulin-secreting cell pancreatic B cell pancreatic B-cell pancreatic beta cell pancreatic islet core type B enteroendocrine cell beta cell islet Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. type B pancreatic cell true A cell that secretes insulin and is located towards the center of the islets of Langerhans. GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Pancreatic_b_cell beta cell ZFA:0009102 B-cell of pancreatic islet FMA:70586 beta cell of pancreatic islet FMA:70586 insulin-secreting cell FMA:70586 pancreatic B-cell FMA:70586 pancreatic beta cell FMA:70586 pancreatic islet core MA:0002419 type B enteroendocrine cell FMA:70586 beta cell islet MA:0002419 A cell that secretes glucagon. FMA:84045 glucagon-secreting cell glucagon secreting cell A cell that secretes glucagon. GOC:tfm A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. BTO:0000990 FMA:70585 MESH:D050416 alpha cell of islet of Langerhans pancreatic alpha cell pancreatic A cell A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. GOC:tfm ISBN:0721662544 somatostatin secreting cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. BTO:0000803 FMA:70587 D-cell of pancreatic islet delta cell of islet delta cell of pancreatic islet pancreatic D-cell pancreatic delta cell somatostatin-secreting pancreatic cell pancreatic D cell A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin. FMA:0517223651 GOC:tfm steroid hormone secreting cell The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. BTO:0000575 CALOHA:TS-0454 FMA:14515 Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. GOC:tfm ISBN:0412046911 MESH:D022781 PMID:19717280 http://en.wikipedia.org/wiki/Hepatocyte A cell whose primary function is to shorten. contractile cell A cell whose primary function is to shorten. FB:ma A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. BTO:0000888 BTO:0000902 CALOHA:TS-2032 FBbt:00005074 FMA:67328 WBbt:0003675 muscle fiber myocyte muscle cell https://www.swissbiopics.org/api/image/Muscle_cells.svg A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. MESH:D032342 A somatic cell located in skeletal muscle. BTO:0004392 CALOHA:TS-2158 FMA:9727 skeletal muscle cell cell of skeletal muscle A somatic cell located in skeletal muscle. GOC:tfm A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). non-striated muscle cell BTO:0004576 CALOHA:TS-2159 FMA:14072 SMCs myocytes, smooth muscle smooth muscle fiber smooth muscle cell A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). MESH:D032389 PMID:9315361 http://en.wikipedia.org/wiki/Smooth_muscle_cell SMCs PMID:9315361 myocytes, smooth muscle MESH:D032389 A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell sensory receptor cell A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. mechanoreceptor mechanoreceptor cell A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. MESH:D008465 mechanoreceptor MP:0000972 touch receptor cell A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. chemoreceptor cell A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. MESH:D002628 BTO:0004185 FMA:67860 MESH:D018034 Wikipedia:Olfactory_receptor_neuron Schultze's cell odorant receptor cell olfactory receptor neuron olfactory sensory neuron olfactory receptor cell A specialized cell involved in gustatory sensory perception. FMA:67910 taste bud cell taste receptor cell A specialized cell involved in gustatory sensory perception. GOC:tfm ISBN:0618947256 A cell specialized to detect and transduce light. BTO:0001060 CALOHA:TS-0868 FMA:86740 photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg true A cell specialized to detect and transduce light. MESH:D010786 A cell whose function is determined by the generation or the reception of an electric signal. electrically active cell A cell whose function is determined by the generation or the reception of an electric signal. FB:ma A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. boundary cell lining cell A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. JB:jb A cell located in the synovial joint. CALOHA:TS-0995 synoviocyte synovial cell true A cell whose primary function is to prevent the transport of stuff across compartments. barrier cell A cell whose primary function is to prevent the transport of stuff across compartments. JB:jb A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. BTO:0001238 CALOHA:TS-0922 FMA:72298 VHOG:0001348 Sertoli cell true A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. MESH:D012708 A cell that moves by its own activities. motile cell A cell that moves by its own activities. FB:ma A cell of the outer of the three germ layers of the embryo. FMA:72549 ectoderm cell ectodermal cell A cell of the outer of the three germ layers of the embryo. MESH:D004475 A cell of the middle germ layer of the embryo. FMA:72554 mesoblast mesoderm cell mesodermal cell A cell of the middle germ layer of the embryo. MESH:D008648 A cell of the inner of the three germ layers of the embryo. FMA:72555 endoderm cell endodermal cell A cell of the inner of the three germ layers of the embryo. MESH:D004707 A cell that lacks a nucleus. FMA:68647 non-nucleated cell anucleate cell A cell that lacks a nucleus. FB:ma A cell with a single nucleus. single nucleate cell A cell with a single nucleus. FB:ma GOC:tfm binucleate cell A cell with more than one nucleus. AEO:0000203 WBbt:0008074 syncitium syncytial cell syncytium multinucleate cell A cell with more than one nucleus. FB:ma A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC red blood cell erythrocyte true A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. GOC:tfm MESH:D004912 A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. BTO:0000132 CALOHA:TS-0803 FMA:62851 anucleate thrombocyte blood platelet enucleate thrombocyte Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF. platelet true A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. GOC:add GOC:dsd GOC:tfm MESH:D001792 PMID:11110672 PMID:16987572 PMID:17204662 PMID:17479180 PMID:20414831 http://en.wikipedia.org/wiki/Platelet Any cell capable of ingesting particulate matter via phagocytosis. BTO:0001044 FMA:83806 MESH:D010586 phagocyte Any cell capable of ingesting particulate matter via phagocytosis. GOC:add ISBN:0721601464 A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. BTO:0000801 CALOHA:TS-0587 FMA:63261 FMA:83585 MESH:D008264 histiocyte Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid. macrophage true A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. GOC:add GOC:tfm GO_REF:0000031 PMID:16213494 PMID:1919437 A lymphocyte of B lineage that is capable of B cell mediated immunity. BTO:0000776 CALOHA:TS-0068 FMA:62869 MESH:D001402 VHOG:0001480 B lymphocyte B-cell B-lymphocyte B cell true A lymphocyte of B lineage that is capable of B cell mediated immunity. GOC:add GOC:tfm GO_REF:0000031 ISBN:0781735149 MESH:D005057 eukaryotic cell eye photoreceptor cell A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. structural cell A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. TAIR:sr A peptide hormone secreting cell that produces growth hormone, somatotropin. growth hormone secreting cell somatotrophin secreting cell somatotropin secreting cell A peptide hormone secreting cell that produces growth hormone, somatotropin. GOC:tfm SANBI:mhl A mature sexual reproductive cell having a single set of unpaired chromosomes. CALOHA:TS-0395 FBbt:00005412 FMA:18649 haploid nucleated cell haploid germ cell gamete true A mature sexual reproductive cell having a single set of unpaired chromosomes. GOC:tfm ISBN:0721662544 lens cell crystallin accumulating cell An epithelial cell found in the trachea. FMA:74793 tracheocyte This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell' tracheal epithelial cell true An epithelial cell found in the trachea. GOC:tfm Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. BTO:0003687 FMA:62511 serous cell serous secreting cell Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. GOC:tfm ISBN:0517223651 ISBN:0721662544 A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. sebocyte sebum secreting cell A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. MESH:D012629 BTO:0003689 mucous cell mucus secreting cell A cell that is specialised to accumulate a particular substance(s). stuff accumulating cell A cell that is specialised to accumulate a particular substance(s). FB:ma extracellular matrix secreting cell oxygen accumulating cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 migratory neural crest cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. doi:10.1016/j.stem.2015.02.017 A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. mesenchyme condensation cell A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. GOC:tfm PMID:5025404 A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation. FMA:69262 medullary chromaffin cell of adrenal gland adrenal medulla chromaffin cell A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation. GOC:tfm http://www.britannica.com/EBchecked/topic/6405/adrenal-gland medullary chromaffin cell of adrenal gland FMA:69262 A cell of the sclera of the eye. scleral cell A cell of the sclera of the eye. GOC:add A structural cell that is part of optic choroid. choroidal cell of the eye A structural cell that is part of optic choroid. GOC:add extraembryonic cell A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. FMA:83028 trophoblastic cell trophoblast cell true A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface. GOC:tfm MESH:D014327 A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. epiblast cell A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. GOC:tfm ISBN:0618947256 An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). BTO:0001473 FMA:72551 blastomere blastoderm cell An undifferentiated cell produced by early cleavages of the fertilized egg (zygote). MESH:D001756 ncithesaurus:Blastemal_Cell blastema cell blastemal cell A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell true A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. PMID:18282570 A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. sphincter associated smooth muscle cell true A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. GOC:cjm A smooth muscle cell associated with the vasculature. VSMC vascular smooth muscle cell vascular associated smooth muscle cell true A smooth muscle cell associated with the vasculature. GOC:dsd GOC:tfm An epithelial cell of the integument (the outer layer of an organism). BTO:0001470 CALOHA:TS-0283 FMA:62411 MESH:D000078404 cell of epidermis epithelial cell of skin epidermal cell An epithelial cell of the integument (the outer layer of an organism). Flybase:dsj MA:ma cell of epidermis FMA:62411 epithelial cell of skin FMA:62411 Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 EHDAA2:0004546 FMA:72395 animal zygote Diploid cell produced by the fusion of sperm cell nucleus and egg cell. ISBN:0471245208 tracheoblast A cell whose function is determined by its response to an electric signal. electrically responsive cell A cell whose function is determined by its response to an electric signal. FB:ma ganglion interneuron true An interneuron that has its cell body in a central nervous system. Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. CNS interneuron An interneuron that has its cell body in a central nervous system. doi:10.1016/B978-0-12-817424-1.00001-X A cell that initiates an electrical signal and passes that signal to another cell. electrically signaling cell A cell that initiates an electrical signal and passes that signal to another cell. FB:ma BTO:0001277 CALOHA:TS-0949 male gamete true true A cell that contains more than two haploid sets of chromosomes. polyploid cell A cell that contains more than two haploid sets of chromosomes. FB:ma PMID:32646579 https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy A cell whose nucleus contains a single haploid genome. haploid cell A cell whose nucleus contains a single haploid genome. FB:ma GOC:tfm endopolyploid cell A fibroblast that synthesizes collagen and uses it to produce reticular fibers, thus providing structural support. Reticular cells are found in many organs, including the spleen, lymph nodes and kidneys. Subtypes of reticular cells include epithelial, mesenchymal, and fibroblastic reticular cells. Fibroblastic reticular cells are involved in directing B cells and T cells to specific regions within a tissue, whereas epithelial and mesenchymal reticular cells are associated with certain areas of the brain. FMA:62877 reticulum cell reticular cell https://github.com/obophenotype/cell-ontology/issues/1472 A fibroblast that synthesizes collagen and uses it to produce reticular fibers, thus providing structural support. Reticular cells are found in many organs, including the spleen, lymph nodes and kidneys. Subtypes of reticular cells include epithelial, mesenchymal, and fibroblastic reticular cells. Fibroblastic reticular cells are involved in directing B cells and T cells to specific regions within a tissue, whereas epithelial and mesenchymal reticular cells are associated with certain areas of the brain. GOC:tfm ISBN:0517223651 http://en.wikipedia.org/wiki/Reticular_cell A peptide hormone secreting cell pituitary that produces luteinizing hormone. luteinizing hormone secreting cell A peptide hormone secreting cell pituitary that produces luteinizing hormone. GOC:tfm A peptide hormone cell that secretes prolactin. prolactin secreting cell A peptide hormone cell that secretes prolactin. GOC:tfm SANBI:mhl A cell of the intermediate pituitary that produces melanocyte stimulating hormone. BTO:0002277 melanotrope melanotroph melanocyte stimulating hormone secreting cell A cell of the intermediate pituitary that produces melanocyte stimulating hormone. SANBI:mhl calcitonin secreting cell An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone. BTO:0004712 CALOHA:TS-2140 FMA:69078 parathyroid chief cell parathyroid gland chief cell parathyroid hormone secreting cell principal cell of parathyroid gland chief cell of parathyroid gland An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone. FMA:69078 GOC:tfm ISBN:0517223651 carbohydrate secreting cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). BTO:0002042 CALOHA:TS-0194 FMA:83036 MESH:D003713 interdigitating cell veiled cell dendritic cell A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). GOC:add ISBN:0781735149 Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus. BTO:0000705 CALOHA:TS-2375 FMA:63072 MESH:D007801 LC Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID:19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis. Langerhans cell true Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus. GOC:add GOC:amm GO_REF:0000031 ISBN:0721601464 ISBN:0781735149 PMCID:PMC2346585 PMID:17850486 A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types. adrenaline secreting cell epinephrin secreting cell epinephrine secreting cell A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types. GOC:tfm PMID:12438093 adrenaline secreting cell GO:0048242 mineralocorticoid secreting cell biogenic amine secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). 5-HT secreting cell 5-Hydroxytryptamine secreting cell serotonin secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). GOC:tfm PMID:19630576 A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. noradrenaline secreting cell norepinephrin secreting cell norepinephrine secreting cell noradrenergic cell A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. GOC:tfm ISBN:068340007X A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin. ACTH secreting cell adrenocorticotrophic hormone secreting cell corticotrophin hormone secreting cell corticotropin hormone secreting cell corticotropin secreting cell adrenocorticotropic hormone secreting cell A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin. GOC:tfm SANBI:mhl ACTH secreting cell GO:0051458 corticotropin secreting cell GO:0051458 A cell whose primary function is to protect the organism. defensive cell A cell whose primary function is to protect the organism. JB:jb Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent. MC(TC) MCTC TC mast cells They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype. connective tissue type mast cell true Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent. GOC:add GOC:dsd GOC:tfm PMID:19923473 PMID:9354811 A photoreceptor cell that detects visible light. visible light photoreceptor cell A photoreceptor cell that detects visible light. GOC:tfm A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. BTO:0002064 FMA:83624 stromal cell A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. GOC:tfm MESH:D017154 A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. FMA:62935 D cell type D enteroendocrine cell A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. MESH:D019864 An endorphine cell that secretes enkephalin. enkephalin secreting cell An endorphine cell that secretes enkephalin. GO:tfm A peptide hormone secreting cell that secretes endorphin. endorphin secreting cell A peptide hormone secreting cell that secretes endorphin. GO:tfm An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. BTO:0004108 FMA:67609 G cell type G enteroendocrine cell An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli. GOC:tfm ISBN:0517223651 MESH:D019863 A peptide hormone secreting cell that secretes gastrin. gastrin secreting cell A peptide hormone secreting cell that secretes gastrin. GO:tfm A peptide hormone secreting cell that secretes androgen binding protein. androgen binding protein secreting cell A peptide hormone secreting cell that secretes androgen binding protein. GO:tfm A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. paracrine cell A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it. GOC:tfm ISBN:0198529171 A precursor cell destined to differentiate into cardiac muscle cell. FMA:84797 cardiac muscle progenitor cell cardiomyocyte progenitor cell cardiac muscle myoblast A precursor cell destined to differentiate into cardiac muscle cell. GOC:tfm MESH:D032386 A precursor cell destined to differentiate into smooth muscle myocytes. FMA:84798 myoblast, smooth muscle satellite cell smooth muscle myoblast A precursor cell destined to differentiate into smooth muscle myocytes. GOC:tfm MESH:D032390 myoblast, smooth muscle MESH:D032390 A myoblast that differentiates into skeletal muscle fibers. FMA:84799 skeletal myoblast skeletal muscle myoblast A myoblast that differentiates into skeletal muscle fibers. SANBI:mhl A phagocyte in vertebrates that is able to phagocytosis. phagocyte (sensu Vertebrata) A phagocyte in vertebrates that is able to phagocytosis. GOC:tfm fungal cell A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. FMA:83043 syncytial trophoblast cell syncytiotrophoblastic cell plasmidotrophoblast cell syntrophoblast cell syncytiotrophoblast cell https://github.com/obophenotype/cell-ontology/issues/2100 A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy. GOC:tfm ISBN:0323052908 syncytial trophoblast cell PMID:11787150 syncytiotrophoblastic cell PMID:21733368 A neuron which conveys sensory information centrally from the periphery. FMA:87653 input neuron afferent neuron A neuron which conveys sensory information centrally from the periphery. GOC:tfm MESH:D009475 A neuron which sends impulses peripherally to activate muscles or secretory cells. output neuron efferent neuron A neuron which sends impulses peripherally to activate muscles or secretory cells. MESH:D009476 The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron https://www.swissbiopics.org/api/image/Neuron_cells.svg The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. MESH:D009474 http://en.wikipedia.org/wiki/Neuron A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. BTO:0000775 CALOHA:TS-0583 FMA:62863 MESH:D008214 VHOG:0001535 Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. GOC:add ISBN:0683073696 ISBN:0781735149 An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. FMA:83518 rubriblast pronormoblast proerythroblast true An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. ISBN:0721601464 PMID:1638021 rubriblast ISBN:0721601464 A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast early erythroblast early normoblast prorubricyte basophilic erythroblast true A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. GOC:tfm ISBN:0721601464 basophilic normoblast ISBN:0721601464 early erythroblast ISBN:0721601464 early normoblast ISBN:0721601464 prorubricyte ISBN:0721601464 A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83506 intermediate erythroblast intermediate normoblast polychromatic erythroblast polychromatic normoblast polychromatophilic normoblast rubricyte polychromatophilic erythroblast true A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. ISBN:0721601464 intermediate erythroblast ISBN:0721601464 intermediate normoblast ISBN:0721601464 polychromatic erythroblast ISBN:0721601464 polychromatic normoblast ISBN:0721601464 polychromatophilic normoblast ISBN:0721601464 rubricyte ISBN:0721601464 The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. FMA:84646 acidophilic erythroblast eosinophilic erythroblast late erythoblast orthochromatic normoblast pyknotic eto enrythroblast orthochromatic erythroblast true The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. ISBN:0721601464 acidophilic erythroblast ISBN:0721601464 eosinophilic erythroblast ISBN:0721601464 orthochromatic normoblast ISBN:0721601464 pyknotic eto enrythroblast ISBN:0721601464 The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). BTO:0001164 CALOHA:TS-0610 FMA:84235 MESH:D055016 CFU-Meg Meg-CFC MkP colony-forming unit-megakaryocyte megacaryoblast megacaryocyte progenitor cell megakaryoblast megakaryocytic progenitor cell promegacaryocyte promegakaryocyte Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative. megakaryocyte progenitor cell true The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). GOC:dsd GOC:tfm ISBN:0721601464 CFU-Meg PMID:11722431 PMID:12482498 Meg-CFC PMCID:PMC1794060 MkP PMID:21116988 megakaryocytic progenitor cell PMID:12482498 A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. BTO:0000843 CALOHA:TS-0611 FMA:83555 megacaryocyte megalocaryocyte megalokaryocyte Megakaryocytes are reportedly CD181-positive and CD182-positive. megakaryocyte true A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. ISBN:0721601464 MESH:D008533 PMID:31043076 http://en.wikipedia.org/wiki/Megakaryocyte A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. CFU-C , Colony forming unit in culture colony forming unit granulocyte macrophage granulocyte-macrophage progenitor granulocyte/monocyte precursor granulocyte/monocyte progenitor CFU-GM GMP Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. GOC:amm GOC:dsd GOC:tfm GO_REF:0000031 ISBN:0721601464 MESH:D055014 PMCID:PMC2213186 PMCID:PMC548021 PMID:16551251 PMID:16647566 http://en.wikipedia.org/wiki/CFU-GM http://www.copewithcytokines.de CFU-C , Colony forming unit in culture http://www.copewithcytokines.de colony forming unit granulocyte macrophage ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 granulocyte-macrophage progenitor ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 CFU-GM ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 GMP ISBN:0721601464 PMCID:PMC2213186 PMCID:PMC548021 An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 MESH:D012156 reticulocyte true An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. GOC:add GOC:tfm PMID:15946868 PMID:2037622 A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. BTO:0004657 FMA:83551 Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid. promonocyte true A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules. GOC:tfm ISBN:0721601464 An erythrocyte having a nucleus. RBC red blood cell nucleate erythrocyte true An erythrocyte having a nucleus. GOC:add GOc:tfm A mesenchymal stem cell capable of developing into blood vessel endothelium. angioblast chondroplast These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell true A mesenchymal stem cell capable of developing into blood vessel endothelium. GOC:dsd GOC:tfm PMID:12768659 A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell. BTO:0003866 FMA:83114 MESH:D001078 APUD cell amine precursor uptake and decarboxylation cell A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell. GOC:tfm ISBN:0721662544 A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. cardiac mesenchymal cell A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. PMID:18816864 A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine. FMA:68653 SCTID:176770005 C cell C cell of thyroid gland clear cell of thyroid gland parafollicular cell of thyroid gland thyroid parafollicular cell parafollicular cell true true A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine. GOC:tfm ISBN:0517223651 C cell of thyroid gland FMA:68653 clear cell of thyroid gland FMA:68653 parafollicular cell of thyroid gland FMA:68653 thyroid parafollicular cell FMA:68653 One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. BTO:0001036 CALOHA:TS-0866 FMA:67748 cone retinal cone cell One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. MESH:D017949 cone doi:10.1038/s41598-020-66092-9 An epithelial cell of the cornea. BTO:0004298 CALOHA:TS-0173 FMA:70551 epithelial cell of cornea corneal epithelial cell An epithelial cell of the cornea. GOC:tfm epithelial cell of cornea FMA:70551 Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. BTO:0000876 CALOHA:TS-0638 FMA:62864 Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid. monocyte true Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. GO_REF:0000031 MESH:D009000 The reproductive cell in multicellular organisms. BTO:0000535 NCIT:C12597 VHOG:0001534 WBbt:0006796 germ cell true The reproductive cell in multicellular organisms. MESH:D005854 A steroid hormone secreting cell that secretes androgen. androgen secreting cell A steroid hormone secreting cell that secretes androgen. GOC:tfm An erythrocyte lacking a nucleus. red blood cell RBC enucleate erythrocyte true An erythrocyte lacking a nucleus. GOC:add GOC:tfm RBC One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. BTO:0001024 CALOHA:TS-0870 FMA:67747 rod retinal rod cell One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. MESH:D017948 rod doi:10.1038/s41598-020-66092-9 A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa. BaP CFU-Bas basophilic stem cell colony forming unit basophil BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf). basophil progenitor cell true A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa. GOC:add GOC:dsd PMCID:PMC1312421 http://www.copewithcytokines.de A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). FMA:83625 MESH:D061354 acinic cell acinous cell acinar cell A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). GOC:tfm http://www.copewithcytokines.de A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. large granular lymphocyte null cell BTO:0000914 BTO:0004716 CALOHA:TS-0664 FMA:63147 FMA:83601 MESH:D007694 VHOG:0001697 NK cell natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. GOC:add ISBN:0781735149 PMID:15771571 A cell whose primary function is to support other cell types. BTO:0002315 supportive cell supporting cell A cell whose primary function is to support other cell types. FB:ma GOC:tfm A cell that stains readily in the anterior pituitary gland. FMA:83089 chromophil cell of anterior pituitary gland A cell that stains readily in the anterior pituitary gland. GOC:tfm ISBN:0618947256 An acidophilic chromophil cell that of the anterior pituitary gland. FMA:83093 acidophil cell of pars anterior of adenohypophysis acidophil of pars anterior of adenohypophysis acidophil of pars distalis of adenohypophysis pituitary alpha cell acidophil cell of pars distalis of adenohypophysis An acidophilic chromophil cell that of the anterior pituitary gland. GOC:tfm An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions. folliculo-stellate cell pituitary folliculostellate cell FS cell FSC Sox2-positive stem cell Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets. folliculostellate cell An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions. JB:jb PMID:10495875 PMID:15961560 doi:10.23937/2572-407X.1510006 folliculo-stellate cell doi:10.23937/2572-407X.1510006 pituitary folliculostellate cell PMID:34734454 FS cell PMID:34734454 FSC doi:10.23937/2572-407X.1510006 Sox2-positive stem cell PMID:34734454 Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets. PMID:18287078 PMID:31620083 PMID:34734454 doi:10.23937/2572-407X.1510006 This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation. BTO:0001068 FMA:83417 pinealocyte This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation. GOC:tfm ISBN:0517223651 PMID:16687276 http://en.wikipedia.org/wiki/Pinealocyte A primary oocyte is an oocyte that has not completed female meosis I. BTO:0000512 FMA:18645 primary oogonium primary oocyte true A primary oocyte is an oocyte that has not completed female meosis I. GOC:tfm ISBN:0721662544 A secondary oocyte is an oocyte that has not completed meiosis II. BTO:0003094 FMA:18646 primary oogonium secondary oocyte true A secondary oocyte is an oocyte that has not completed meiosis II. GOC:tfm ISBN:0721662544 A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes. BTO:0001115 CALOHA:TS-2194 FMA:72292 primary spermatocyte A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes. GOC:tfm ISBN:0721662544 One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids. BTO:0000709 CALOHA:TS-2195 FBbt:00004941 FMA:72293 secondary spermatocyte One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids. GOC:tfm ISBN:0721662544 window cell fenestrated cell An extracellular matrix secreting cell that secretes collagen. collagen secreting cell An extracellular matrix secreting cell that secretes collagen. GOC:tfm A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. FMA:70567 gonocyte primitive germ cell primordial germ cell true true A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. GOC:tfm PMID:1381289 A non-terminally differentiated cell that is capable of developing into a muscle cell. muscle precursor cell A non-terminally differentiated cell that is capable of developing into a muscle cell. GOC:add A cell that stores and secretes pancreatic polypeptide hormone. FMA:62938 FMA:83409 type F enteroendocrine cell PP cell A cell that stores and secretes pancreatic polypeptide hormone. GOC:tfm JB:jb PMID:15153415 Epithelial cells derived from neural plate and neural crest. neuroepithelial cell BTO:0004301 FMA:70557 The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell Epithelial cells derived from neural plate and neural crest. GOC:tfm A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 MESH:D053687 somatic stem cell A stem cell that can give rise to cell types of the body other than those of the germ-line. GO:0048103 Muscle cell which has as its direct parts myofilaments organized into sarcomeres. BTO:0002916 CALOHA:TS-2157 FMA:86936 striated muscle cell Muscle cell which has as its direct parts myofilaments organized into sarcomeres. GOC:tfm ISBN:0721662544 An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 MESH:D007962 NCIT:C12529 leucocyte white blood cell immune cell leukocyte true An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. GOC:add GOC:tfm ISBN:978-0-323-05290-0 The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. BTO:0001800 FMA:67765 MESH:D012165 gangliocyte ganglion cell of retina RGC RGCs retinal ganglion cell The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. GOC:dph RGC doi:10.1038/s41598-020-66092-9 RGCs doi:10.1038/s41598-020-66092-9 Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. FMA:83808 cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 MESH:D032383 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. GOC:mtg_cardiacconduct_nov11 GOC:tfm ISBN:0323052908 PMID:22426062 PMID:4711263 cardiac muscle fiber GO:0048739 A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. nucleated thrombocyte true A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. GOC:add GOC:tfm PMID:16360205 A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 MESH:D022423 myeloid cell true A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. GOC:add A immature or mature cell in the lineage leading to and including erythrocytes. CALOHA:TS-0290 FMA:62845 FMA:83516 erythropoietic cell Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell A immature or mature cell in the lineage leading to and including erythrocytes. GOC:add GOC:tfm A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 FMA:83504 MESH:D004900 normoblast erythroblast true A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. GOC:add ISBN:0721601464 PMID:18174176 A cell of the monocyte, granulocyte, or mast cell lineage. myeloid leukocyte true A cell of the monocyte, granulocyte, or mast cell lineage. GOC:add Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0000129 CALOHA:TS-0073 FMA:62862 basophilic leucocyte basophilic leukocyte Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive. basophil true Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. GOC:add GOC:amm GOC:dsd GOC:tfm ISBN:0721601464 MESH:D001491 PMCID:PMC2626675 PMID:11927641 PMID:19741522 PMID:21236338 PMID:9933081 Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. polymorphonuclear leucocyte polymorphonuclear leukocyte BTO:0000399 CALOHA:TS-0279 FMA:62861 MESH:D004804 eosinocyte eosinophilic granulocyte eosinophilic leucocyte eosinophilic leukocyte Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte. eosinophil true Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. GOC:add GOC:amm GOC:dsd GOC:tfm ISBN:0721601464 PMCID:PMC2626675 PMID:10914487 PMID:1662676 Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. PMN poly polymorphonuclear leucocyte polymorphonuclear leukocyte polymorphonuclear neutrophil polynuclear neutrophilic leucocyte polynuclear neutrophilic leukocyte BTO:0000130 CALOHA:TS-0688 FMA:62860 MESH:D009504 neutrocyte neutrophil leucocyte neutrophil leukocyte neutrophilic leucocyte neutrophilic leukocyte neutrophil true Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. GOC:add GOC:amm GOC:tfm ISBN:0721601464 A dendritic cell of the myeloid lineage. interdigitating cell veiled cell BTO:0004721 CD11c+CD123- DC mDC These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8). myeloid dendritic cell true A dendritic cell of the myeloid lineage. GOC:add PMID:10449155 PMID:17332250 PMID:9521319 A phagocyte formed by the fusion of mononuclear phagocytes. multinucleated phagocyte true A phagocyte formed by the fusion of mononuclear phagocytes. GOC:add GOC:tfm A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. mature B lymphocyte mature B-cell mature B-lymphocyte Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive. mature B cell true A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. GOC:add GOC:dsd ISBN:0781735149 A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. BTO:0000392 FMA:70574 MESH:D010950 plasma B cell plasma B-cell plasmacyte plasmocyte effector B cell effector B-cell Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive. plasma cell true A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. GOC:add GOC:dsd GO_REF:0000031 ISBN:0721601464 ISBN:0781735149 PMID:19447676 PMID:20081059 PMID:20839338 PMID:20951740 http://en.wikipedia.org/wiki/Plasma_cell A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. suppressor T cell suppressor T lymphocyte suppressor T-cell suppressor T-lymphocyte BTO:0004520 FMA:84070 MESH:D050378 Treg regulatory T lymphocyte regulatory T-cell regulatory T-lymphocyte This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta. regulatory T cell true A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. GOC:add GO_REF:0000031 An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation. immature B lymphocyte immature B-cell immature B-lymphocyte newly formed B cell Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive. immature B cell An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation. GOC:add GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 ISBN:0781735149 PMID:20081059 PMID:20839338 newly formed B cell ISBN:781735149 A precursor B cell is a B cell with the phenotype CD10-positive. BTO:0001133 CALOHA:TS-0819 pre-B cell precursor B cell true A precursor B cell is a B cell with the phenotype CD10-positive. GOC:rhs GOC:tfm GO_REF:0000031 An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen. transitional B cell transitional stage B lymphocyte transitional stage B-cell transitional stage B-lymphocyte T1 B cell T2 B cell T3 B cell This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'. transitional stage B cell true An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12810111 PMID:22343568 transitional B cell PMID:22343568 A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive. B-1 B lymphocyte B-1 B-cell B-1 B-lymphocyte B-1 cell B1 B cell B1 B lymphocyte B1 B-cell B1 B-lymphocyte B1 cell There are small numbers of B-1 cells found in the lymph nodes and spleen, while larger numbers can be found in the peritoneal and pleural cavities. B-1 B cells are reportedly CD11b-positive, CD20-positive, CD21-positive, CD27-positive, CD44-positive, CD45RB-positive, CD48-positive, CD70-negative, CD150-positive, CD244-negative, CD352-positive, sIgM-positive, and sIgD-low. B-1 B cell true A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive. GOC:add GOC:dsd GO_REF:0000031 PMID:11861604 PMID:20933013 PMID:21220451 http://en.wikipedia.org/wiki/B-1_cell A B-1 B cell that has the phenotype CD5-positive. B-1a B lymphocyte B-1a B-cell B-1a B-lymphocyte B1a B cell B1a B lymphocyte B1a B-cell B1a B-lymphocyte B1a cell CD5(+) B1 cell CD5+ B1 cell CD5-positive B1 cell B-1a B cell true A B-1 B cell that has the phenotype CD5-positive. GOC:add PMID:11861604 A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell. B-1b B lymphocyte B-1b B-cell B-1b B-lymphocyte B1b B cell B1b B lymphocyte B1b B-cell B1b B-lymphocyte B1b cell B-1b B cell true A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell. GOC:add PMID:11861604 A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. B-2 B lymphocyte B-2 B-cell B-2 B-lymphocyte B2 B cell B2 B lymphocyte B2 B-cell B2 B-lymphocyte B2 cell B-0 B cell B-2 B cells are reportedly CD48-positive, CD244-negative, and CD352-positive. B-2 B cell true A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. GOC:add GOC:dsd GOC:tfm ISBN:0781735149 PMID:11861604 PMID:20933013 A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR). immature NK cell p-NK In mouse the NKR are Ly49 molecules and in human these cells express KIR molecules. immature natural killer cell A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR). GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12457618 p-NK PMID:12457618 A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. NKP natural killer cell progenitor pro-natural killer cell null cell preNK cell Most markers only described for human pro NK cells. pro-NK cell true A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative. GOC:add GOC:pam GO_REF:0000031 PMID:11532393 PMID:12457618 PMID:15032583 PMID:15766674 NKP PMID:12457618 PMID:15032583 PMID:15766674 null cell PMID:11532393 preNK cell PMID:11532393 A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. pre-pro B cell BTO:0003104 pro-B lymphocyte pro-B-cell pro-B-lymphocyte progenitor B cell progenitor B lymphocyte progenitor B-cell progenitor B-lymphocyte pre-B cell (Philadelphia nomenclature) Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative. pro-B cell true A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs. GOC:add GOC:dsd ISBN:0781735149 PMID:12633665 PMID:16551251 PMID:18432934 pre-pro B cell PMID:17582343 pre-B cell (Philadelphia nomenclature) PMID:11244048 A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. pro-T lymphocyte progenitor T cell DN1 cell DN1 thymocyte TN1 cell pro-T cell true A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. GOC:add ISBN:0781735149 A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. Note that this is a non-mammalian cell type. thromboblast true A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. GOC:add GOC:tfm PMID:7758949 A myeloblast committed to the basophil lineage. basophilic myeloblast true A myeloblast committed to the basophil lineage. GOC:add ISBN:0721601464 A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative. MCP CFU-MC CFU-Mast colony forming unit mast cell MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa. mast cell progenitor true A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative. GOC:add GOC:dsd PMCID:PMC1183570 PMCID:PMC1312421 PMID:8629001 PMID:9354811 http://www.copewithcytokines.de The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. BTO:0000187 FMA:83524 myeloblast true The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow. GOC:add ISBN:0721601464 http://en.wikipedia.org/wiki/Myeloblast http://www.cap.org A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP hemopoietic progenitor cell Markers differ between mouse and human. hematopoietic multipotent progenitor cell A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. GOC:add GOC:tfm PMID:19022770 A progenitor cell restricted to the lymphoid lineage. lymphoid progenitor cell BTO:0004731 CALOHA:TS-2025 FMA:70338 Note that this is a class of cell types, not an identified single cell type. lymphoid lineage restricted progenitor cell true A progenitor cell restricted to the lymphoid lineage. GOC:add GOC:tfm A progenitor cell restricted to the myeloid lineage. myeloid progenitor cell BTO:0004730 CALOHA:TS-2099 FMA:70339 Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell true A progenitor cell restricted to the myeloid lineage. GOC:add GOC:tfm PMID:19022770 A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 CALOHA:TS-0768 FMA:86713 mononuclear leukocyte peripheral blood mononuclear cell mononuclear cell true A leukocyte with a single non-segmented nucleus in the mature form. GOC:add An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob. ciliated olfactory sensory neuron ciliated sensory neuron ciliated olfactory receptor neuron An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob. PMID:16841163 A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. FMA:84642 FMA:84644 fixed macrophage resting histiocyte tissue-resident macrophage true A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. GOC:ana GO_REF:0000031 PMID:19770654 A tissue-resident macrophage found in the central nervous system. CNS macrophage central nervous system macrophage true A tissue-resident macrophage found in the central nervous system. GO_REF:0000031 PMID:16322748 A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+. Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+. perivascular macrophage true A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+. GOC:tfm GO_REF:0000031 PMID:16507898 An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. myeloid suppressor cell true An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. GOC:add GOC:ana GO_REF:0000031 PMID:16168663 PMID:17016554 PMID:17016559 An immature T cell located in the thymus. immature T cell immature T lymphocyte immature T-cell immature T-lymphocyte BTO:0001372 CALOHA:TS-1042 FMA:72202 MESH:D060168 XAO:0003159 thymic lymphocyte thymocyte true An immature T cell located in the thymus. GOC:add GOC:tfm GO_REF:0000031 PMID:12415312 A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative. DN1 thymic pro-T lymphocyte DN1 thymic pro-T-cell DN1 thymic pro-T-lymphocyte DN1 thymic progenitor T cell DN1 thymocyte double negative 1 preT.DN1.Th DN1 thymic pro-T cell true A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative. GOC:add GOC:tfm GO_REF:0000031 A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. effector T lymphocyte effector T-cell effector T-lymphocyte effector T cell true A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. GOC:PAM-ADD GOC:tfm ISBN:0877799148 PMID:18395547 A effector T cell that provides help in the form of secreted cytokines to other immune cells. BTO:0002417 MESH:D006377 T-helper cell helper T lymphocyte helper T-cell helper T-lymphocyte helper T cell true A effector T cell that provides help in the form of secreted cytokines to other immune cells. GOC:add GOC:pam GOC:tfm GO_REF:0000031 PMID:18395547 Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins. pre-NK cell These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive, alpha-4-beta-7 integrin-high. pre-natural killer cell Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins. GOC:add GOC:dsd GOC:pam GOC:tfm GO_REF:0000031 PMID:16551251 PMID:17100874 A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative. In the mouse this cell expresses CD8-alpha-alpha. thymic conventional dendritic cell true A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative. GOC:add GOC:pam GO_REF:0000031 PMID:19273629 A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage true A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. GOC:add GOC:rhs GOC:tfm GO_REF:0000031 ISBN:0781735149 A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. antibody secreting cell true A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. GOC:add GOC:tfm GO_REF:0000031 ISBN:0721601464 ISBN:0781735149 A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. small pre-BII cell Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. small pre-B-II cell true A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 PMID:16551251 PMID:18432934 PMID:9785673 A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain. BTO:0001133 CALOHA:TS-0819 pre-B-lymphocyte pre-BII cell pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive. pre-B-II cell true A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain. GOC:dsd GOC:rhs GOC:tfm GO_REF:0000031 PMID:9785673 A fully differentiated plasma cell that lives for months. short lived plasma cell true A fully differentiated plasma cell that lives for months. GOC:msz GO_REF:0000031 PMID:16014527 An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative. CD20-negative B cell FMA:84371 CD27-positive, CD38-positive, CD20-negative B cell This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative. plasmablast true An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative. GOC:dsd GOC:msz GOC:tfm GO_REF:0000031 PMCID:PMC2673126 A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell hematopoietic cell A cell of a hematopoietic lineage. GOC:add GO_REF:0000031 Conventional dendritic cell is a dendritic cell that is CD11c-high. interdigitating cell veiled cell FMA:84191 DC1 cDC dendritic reticular cell type 1 DC Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive. conventional dendritic cell true Conventional dendritic cell is a dendritic cell that is CD11c-high. GOC:amm GO_REF:0000031 PMID:17850486 CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative. LSK stem cell Sca1-positive hematopoietic stem cell Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID:19243617). Kit and Sca1-positive hematopoietic stem cell true A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMID:17952047 PMID:19022770 Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617). CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. CD10-positive common lymphocyte precursor CD10-positive common lymphocyte progenitor CD10-positive common lymphoid precursor These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617). CD34-positive, CD38-positive common lymphoid progenitor true A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMCID:PMC2346585 PMID:19022770 CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. CALOHA:TS-0448 CD133-positive hematopoietic stem cell Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617). CD34-positive, CD38-negative hematopoietic stem cell true CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. GOC:add GOC:amm GOC:tfm GO_REF:0000031 PMID:10430905 PMID:11750107 PMID:16551251 PMID:20024907 PMID:9389721 CD133-positive hematopoietic stem cell PMID:16140871 A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. CD71-positive common myeloid precursor Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). CD34-positive, CD38-positive common myeloid progenitor A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. GOC:add GOC:amm GO_REF:0000031 PMCID:PMC2626675 PMID:16551251 CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. CD7-negative lymphoid precursor These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617). CD7-negative lymphoid progenitor cell true CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative. GOC:amm GO_REF:0000031 PMID:16551251 CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative. CD7-positive lymphoid precursor These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID:19243617). CD7-positive lymphoid progenitor cell true CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative. GOC:amm GOC:tfm GO_REF:0000031 PMID:16551251 PMID:19491395 A connective tissue cell found in bone. 2011-11-16T04:28:16Z bone cell A connective tissue cell found in bone. GOC:add GO_REF:0000034 A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20. monocyte This cell type is compatible with the HIPC Lyoplate markers for 'monocyte'. Note that while CD14 is considered a reliable marker for human monocytes, it is only expressed on approximately 85% of mouse monocytes. CD14-positive monocyte A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20. GOC:add PMID:22343568 monocyte PMID:22343568 A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. common myeloid precursor, CD34-positive CFU-GEMM CFU-S CMP colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. common myeloid progenitor, CD34-positive A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. GOC:add GOC:dsd GOC:tfm ISBN:0878932437 PMCID:PMC2212039 PMID:10724173 PMID:16551251 PMID:16647566 CFU-GEMM ISBN:0878932437 CFU-S ISBN:0878932437 CMP ISBN:0878932437 colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte ISBN:0878932437 multipotential myeloid stem cell ISBN:0878932437 myeloid stem cell ISBN:0878932437 pluripotent stem cell (bone marrow) ISBN:0878932437 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. GOC:tfm PMID:19022770 A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. 2017-01-30T18:53:32Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 https://github.com/obophenotype/cell-ontology/issues/448 abnormal cell A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. GOC:add GOC:cg GOC:wdd A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. 2017-01-30T20:20:48Z innate lymphoid cell A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. GOC:add GOC:dsd PMID:23292121 PMID:23348417 A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). BTO:0004911 BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell erythroid progenitor cell, mammalian A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). GOC:add ISBN:0721601464 BFU-E CFU-E An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. 2017-01-30T20:42:44Z group 1 innate lymphoid cell An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. GOC:add GOC:dsd PMID:23348417 An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells. CD34-negative, CD117-positive ILC CD34-negative, CD117-positive ILCP CD34-negative, CD117-positive innate lymphoid cell precusor CD34-negative, CD117-positive innate lymphoid cell, human An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells. GOC:add PMID:30193847 PMID:31201208 An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. CD34-negative, CD56-positive, CD117-positive ILC CD34-negative, CD56-positive, CD117-positive ILCP CD34-negative, CD56-positive, CD117-positive innate lymphoid cell precursor CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. GOC:add PMID:30193847 PMID:31201208 An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. CD34-positive, CD56-positive, CD117-positive CILP CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. GOC:add PMID:30193847 An innate lyphoid cell with an immature phenotype. immature ILC immature innate lymphoid cell An innate lyphoid cell with an immature phenotype. GOC:add A lymphocyte of B lineage that is CD19-positive. Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). lymphocyte of B lineage, CD19-positive A lymphocyte of B lineage that is CD19-positive. GOC:add A B cell that is CD19-positive. B lymphocyte, CD19-positive B-cell, CD19-positive B-lymphocyte, CD19-positive CD19+ B cell CD19-positive B cell B cell, CD19-positive A B cell that is CD19-positive. GOC:add An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative. 2010-04-26T10:14:16Z c- Kit-positive erythroid progenitor cell Markers found on mouse cells. Kit-positive erythroid progenitor cell true An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative. GOC:ak GOC:tfm PMID:19805084 http://www.immgen.org/index_content.html A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative. 2010-01-13T03:19:22Z Markers are for human cells. According to different research groups, CD45RA is present or absent on this cell population. CD34-positive, CD38-positive granulocyte monocyte progenitor true A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative. GOC:tfm PMID:12615892 PMID:19022770 A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative. 2010-01-13T03:43:10Z Markers are associated with human cell type. CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell true A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative. GOC:tfm PMID:12615892 PMID:190227700 A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low. 2010-01-13T03:43:12Z Markers are associated with mouse cells. Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell true A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low. GOC:tfm PMID:12615892 PMID:19022770 http://www.immgen.org/index_content.html A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. 2010-01-19T02:51:58Z MDP macrophage dendritic cell progenitor true A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. GOC:tfm PMID:19273628 A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive. 2010-04-26T10:31:56Z Markers are associated with mouse cells. Kit-low proerythroblast true A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive. GOC:ak GOC:tfm PMID:19805084 A basophilic erythroblast that is Lyg 76-high and is Kit-negative. 2010-04-26T10:41:22Z Cell surface markers are associated with mouse cells. Kit-negative, Ly-76 high basophilic erythroblast true A basophilic erythroblast that is Lyg 76-high and is Kit-negative. GOC:ak GOC:tfm PMID:19805084 A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative. 2010-04-26T10:53:11Z late basophilic and polychromatophilic erythroblast Kit-negative, Ly-76 high polychromatophilic erythroblast true A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative. GOC:ak GOC:tfm PMID:19805084 An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative. 2010-04-26T11:04:15Z Cell surface markers associated with mouse cells. Kit-negative, Ly-76 high orthochromatophilic erythroblasts true An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative. GOC:ak GOC:tfm PMID:19805084 A reticulocyte that is Ly76-high and is Kit-negative. 2010-04-26T11:37:00Z Marker associated with mouse cells. Ly-76 high reticulocyte true A reticulocyte that is Ly76-high and is Kit-negative. GOC:ak GOC:tfm PMID:18539294 An enucleate erythrocyte that is Lyg-76-high. 2010-04-26T11:51:27Z Marker is associated with mouse cell types. Ly-76 high positive erythrocyte true An enucleate erythrocyte that is Lyg-76-high. GOC:ak GOC:tfm PMID:19805084 A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low. 2010-04-26T02:39:15Z Markers are associated with mouse cells. Kit-positive megakaryocyte progenitor cell true A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low. GOC:ak GOC:tfm PMID:16951553 A megakaryocyte cell with is CD9-positive and CD41-positive. 2010-04-27T10:39:07Z Markers are commonly associated with mouse cells. CD9-positive, CD41-positive megakaryocyte cell true A megakaryocyte cell with is CD9-positive and CD41-positive. GOC:tfm A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa 2010-04-27T12:46:33Z BMCP There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. basophil mast progenitor cell A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa GOC:ak GOC:dsd GOC:tfm PMCID:PMC1312421 A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low. 2010-04-27T01:22:19Z Fc-epsilon RIalpha-low mast cell progenitor true A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low. GOC:tfm PMCID:PMC1312421 A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high. 2010-04-27T01:22:32Z Markers are associated with mouse cells. Fc-epsilon RIalpha-high basophil progenitor cell true A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high. GOC:tfm PMCID:PMC1312421 A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. GOC:tfm PMID:19022770 A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. GOC:tfm PMID:19022770 https://orcid.org/0000-0001-5208-3432 A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative. 2010-01-08T09:19:25Z ST stem cell ST-HSC Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low. short term hematopoietic stem cell true A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative. GOC:tfm PMID:15572596 PMID:19022770 A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. 2010-01-08T09:19:28Z LT stem cell LT-HSC Markers are associated with mouse cells. long term hematopoietic stem cell true A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. GOC:tfm PMID:15572596 PMID:17582345 A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative. 2010-01-08T11:16:33Z Markers are associated with mouse cells. Slamf1-negative multipotent progenitor cell true A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative. GOC:tfm PMID:19022770 A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive. 2010-01-08T11:16:35Z KSL cell Markers are associated with mouse cells. Slamf1-positive multipotent progenitor cell true A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive. GOC:tfm PMID:19022770 A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. 2010-01-12T11:14:15Z Cell markers are associated with human hematopoietic multipotent progenitor cells. CD34-positive, CD38-negative multipotent progenitor cell true A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. GOC:tfm PMID:18371405 PMID:19022770 A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative. 2010-04-27T01:22:38Z Markers are associated with mouse cells. Kit-positive, integrin beta7-high basophil mast progenitor cell true A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative. GOC:ak GOC:tfm A conventional thymic dendritic cell that is CD8alpha-positive. 2010-06-07T02:48:36Z CD8alpha-alpha-positive thymic conventional dendritic cell DC.8+.Th CD8alpha-positive thymic conventional dendritic cell true A conventional thymic dendritic cell that is CD8alpha-positive. GOC:tfm PMID:19273629 http://www.immgen.org/index_content.html A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. 2010-06-24T03:16:29Z BTO:0000028 CALOHA:TS-0737 FMA:63032 acinar cell of pancreas pancreatic acinar cell true A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. GOC:tfm ISBN:0517223651 PMID:20395539 http://www.copewithcytokines.de/cope.cgi?key=pancreatic%20acinar%20cells An enteroendocrine cell that produces glucagon. 2010-09-10T10:48:54Z FMA:62939 type A enteroendocrine cell An enteroendocrine cell that produces glucagon. GOC:tfm ISBN:0412046911 Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. 2010-06-28T08:36:15Z BTO:0001032 FMA:14146 Purkinje cell fiber Purkinje muscle cell myocytus conducens cardiacus Purkinje myocyte Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. FMA:0412046911 GOC:tfm PMID:19939742 A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. 2010-06-29T11:41:37Z pacemaker cell BTO:0004190 FMA:67101 P cell cardiac pacemaker cell myocytus nodalis nodal myocyte A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. FMA:67101 GOC:tfm cardiac pacemaker cell GOC:pr Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. 2010-06-29T02:39:32Z FMA:67142 transitional myocyte Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. FMA:67142 GOC:tfm The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). 2010-06-29T11:50:47Z FMA:67111 myocardial endocrine cell The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). FMA:67111 GOC:tfm An epithelial cell derived from endoderm. 2010-06-29T03:38:14Z FMA:69075 endo-epithelial cell An epithelial cell derived from endoderm. FMA:69075 GOC:tfm An epithelial cell derived from ectoderm. 2010-06-29T03:38:22Z FMA:69074 ecto-epithelial cell An epithelial cell derived from ectoderm. FMA:69074 GOC:tfm Epithelial cell derived from mesoderm or mesenchyme. 2010-06-29T03:49:14Z FMA:69076 epithelial mesenchymal cell meso-epithelial cell Epithelial cell derived from mesoderm or mesenchyme. FMA:69076 GOC:tfm Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. 2010-06-30T08:49:43Z FMA:63099 pancreatic ductal cell Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. FMA:63099 GOC:tfm PMID:14740223 A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. 2010-06-30T08:49:52Z FMA:62455 centroacinar cell of Langerhans pancreatic centroacinar cell pancreatic centro-acinar cell A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. GOC:tfm PMID:12142741 PMID:20018761 PMID:8185160 A chromaffin cell of the adrenal medulla that produces epinephrine. 2010-07-14T09:41:42Z FMA:69322 adremergic chromaffin cell adrenal secreting cell of the adrenal medulla epiniphrine secreting cell of the adrenal medulla type II cell of adrenal medulla true A chromaffin cell of the adrenal medulla that produces epinephrine. GOC:tfm A chromaffin cell of the adrenal medulla that produces norepinephrine. 2010-07-14T10:12:24Z FMA:69321 noradrenergic chromaffin cell type I cell of adrenal medulla true A chromaffin cell of the adrenal medulla that produces norepinephrine. GOC:tfm ISBN:068340007X A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. 2010-07-21T01:33:38Z FMA:67968 specialized cardiac myocyte A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. FMA:67968 GOC:tfm A leukocyte that lacks granules. 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte nongranular leukocyte true A leukocyte that lacks granules. GOC:tfm A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell true A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. GOC:tfm ISBN:0618947256 A cell in the hilum of the ovary that produces androgens. 2010-08-23T11:18:18Z FMA:18710 hilar cell of ovary hilus cell of ovary A cell in the hilum of the ovary that produces androgens. GOC:tfm ISBN:068340007X A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol. 2010-08-24T01:37:44Z FMA:69545 adrenal cortex cell adrenocortical cell cortical cell of adrenal gland true A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol. GOC:tfm A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation. 2010-08-20T02:14:25Z innate effector T cell true A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation. GOC:tfm PMID:20581831 A stomal cell of the ovary 2010-08-23T12:10:31Z FMA:72299 ovarian stromal cell stromal cell of ovary A stomal cell of the ovary GOC:tfm ovarian stromal cell GOC:cjm A stromal cell of the ovarian medulla. 2010-08-23T12:12:17Z FMA:256171 stromal cell of ovarian medulla true A stromal cell of the ovarian medulla. GOC:tfm A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. 2010-08-24T02:05:28Z BTO:0004167 FMA:68458 LEC lymphatic endothelial cell endothelial cell of lymphatic vessel true A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. GOC:tfm PMID:17846148 An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 vascular endothelial cell cubodial endothelial cell of vascular tree These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. GOC:dsd GOC:tfm PMID:12768659 A sebum secreting cell of the skin that secretes sebum into the hair follicles. 2010-08-24T09:27:52Z sebocyte BTO:0004613 FMA:70953 acinar cell of sebaceous gland true A sebum secreting cell of the skin that secretes sebum into the hair follicles. GOC:tfm An endothelial cell found in capillaries. 2010-08-24T10:15:00Z BTO:0004956 CALOHA:TS-0112 FMA:67756 capillary endothelial cell An endothelial cell found in capillaries. GOC:tfm A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. 2010-08-24T03:38:29Z FMA:70542 ciliated columnar cell of tracheobronchial tree A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. GOC:tfm ISBN:0517223651 A cell found within the dental pulp. 2010-08-24T02:52:09Z CALOHA:TS-0195 FMA:87170 dental pulp cell A cell found within the dental pulp. GOC:tfm PMID:36267574 An epithelial cell of the uterus. 2010-08-24T10:45:54Z FMA:256161 epithelial cell of uterus true An epithelial cell of the uterus. GOC:tfm A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease. 2010-08-24T03:15:21Z FMA:81099 burr cell echinocyte A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease. GOC:tfm Epithelial cells derived from general body ectoderm and ectoderm placodes. 2010-08-26T08:31:08Z FMA:70556 general ecto-epithelial cell Epithelial cells derived from general body ectoderm and ectoderm placodes. GOC:tfm An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth. 2010-08-26T08:51:27Z FMA:62987 epithelial cell rests of Malassez epithelial debris of Malassez epithelial cell of Malassez true An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth. GOC:tfm ISBN:0517223651 ISBN:0815129521 A specialized cell involved in sensory perception of smell. 2010-08-26T01:47:13Z FMA:67870 olfactory epithelial cell A specialized cell involved in sensory perception of smell. GOC:tfm PMID:7143026 A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature. 2010-08-25T03:10:10Z FMA:83102 folliculostellate cell of pars anterior of adenohypophysis folliculostellate cell of pars distalis of adenohypophysis true A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature. GOC:tfm An epithelial cell found in the lining of the stomach. 2010-08-25T03:22:08Z FMA:62948 epithelial cell of stomach true An epithelial cell found in the lining of the stomach. GOC:tfm A mucous cell in the epithelium of the stomach. 2010-08-25T03:38:51Z FMA:63464 mucous cell of stomach A mucous cell in the epithelium of the stomach. GOC:tfm A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. 2010-08-25T03:57:08Z FMA:62953 stem cell of gastric gland true A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. GOC:tfm ISBN:0517223651 An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 glomerular endothelial cell true An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. GOC:tfm PMID:15840009 A cell involved in the formation of a granulocyte. 2010-08-30T12:54:27Z FMA:83519 granulocytopoietic cell true A cell involved in the formation of a granulocyte. GOC:tfm A cell involved in the formation of a monocyte (monopoiesis). 2010-08-30T01:27:48Z FMA:83552 monopoietic cell true A cell involved in the formation of a monocyte (monopoiesis). GOC:tfm A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes). 2010-08-30T02:00:42Z FMA:86577 HpSC hepatic stem cell https://github.com/obophenotype/cell-ontology/issues/800 true A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes). GOC:tfm PMID:26798363 HpSC PMID:18442648 A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands. 2010-09-02T11:26:49Z FMA:67606 MESH:D024862 oxyphil oncocyte A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands. GOC:tfm ISBN:0721662544 PMID:20013317 An oncocyte located in the parathyroid gland. 2010-09-02T11:33:23Z FMA:69084 oxyphil cell of parathyroid gland An oncocyte located in the parathyroid gland. PMID:20013317 An oncocyte located in the thyroid. 2010-09-02T11:33:26Z FMA:87169 Askanazy cells Hurthle cells oxyphil cell of thyroid An oncocyte located in the thyroid. GOC:tfm PMID:20013317 An epithelial cell of the tracheobronchial tree. 2010-09-02T02:09:14Z FMA:66816 epithelial cell of tracheobronchial tree An epithelial cell of the tracheobronchial tree. GOC:tfm An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells. 2010-09-02T02:53:59Z FMA:69060 undifferentiated columnar cell of tracheobronchial tree intermediate epitheliocyte An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells. GOC:tfm ISBN:0517223651 A cell located between the pinealocytes. 2010-09-02T04:28:41Z FMA:86575 interstitial cell of pineal gland A cell located between the pinealocytes. GOC:tfm ISBN:0517223651 A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. 2010-09-07T10:38:03Z FMA:70950 vertebrate lens cell A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. GOC:tfm ISBN:0721662544 A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. 2010-09-07T10:45:47Z FMA:67559 lens epithelial cell true A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. GOC:tfm ISBN:0721662544 http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Lens_epithelium An epithelial cell of the prostate. 2010-09-07T01:49:29Z FMA:256163 FMA:66817 prostate epithelial cell epithelial cell of prostate true An epithelial cell of the prostate. GOC:tfm An epithelial cell of prostatic duct. 2010-09-07T01:55:51Z FMA:74224 ductal epithelial cell of prostate epithelial cell of prostatic duct true An epithelial cell of prostatic duct. GOC:tfm ductal epithelial cell of prostate FMA:74224 A cell that constitutes the basal layer of epithelium in the prostatic duct. 2010-09-07T01:59:12Z FMA:74226 basal epithelial cell of prostatic duct A cell that constitutes the basal layer of epithelium in the prostatic duct. GOC:tfm PMID:15226377 A fibroblast in the bone marrow. 2010-09-07T02:25:18Z FMA:84377 marrow fibroblast A fibroblast in the bone marrow. GOC:tfm A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. 2010-09-07T02:29:38Z FMA:84467 pulmonary myofibroblast pulmonary septal cell pulmonary interstitial fibroblast true A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. GOC:tfm A cell containing at least one nucleus. 2010-09-07T03:32:33Z FMA:67513 nucleate cell A cell containing at least one nucleus. GOC:tfm A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. 2010-09-08T08:53:42Z FMA:70611 smooth muscle fiber of sphincter of pupil smooth muscle fibre of sphincter of pupil smooth muscle cell of sphincter of pupil true A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. GOC:tfm ISBN:0721662544 ISBN:0721694128 A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). 2010-09-07T03:57:09Z BTO:0002669 FMA:86711 MESH:D000072916 PBSC peripheral blood stem cell true A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). GOC:tfm An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. 2010-09-08T09:26:53Z epithelial cell of alimentary canal An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. GOC:tfm ISBN:0721662544 An epithelial cell of the esophagus. 2010-09-08T09:28:20Z FMA:63071 epithelial cell of esophagus true An epithelial cell of the esophagus. GOC:tfm An epithelial cell of the large intestine. 2010-09-08T09:28:22Z BTO:0004297 FMA:256157 epithelial cell of colon epithelial cell of large intestine true An epithelial cell of the large intestine. GOC:tfm An epithelial cell of the small intestine. 2010-09-08T09:41:46Z FMA:256159 epithelial cell of small intestine true An epithelial cell of the small intestine. GOC:tfm A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell. 2010-09-08T09:50:04Z CALOHA:TS-1266 FMA:86490 endometrial stromal cell endometrial stromal fibroblast stromal cell of endometrium true A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell. PMID:11331626 PMID:30013421 PMID:30309298 Wiki:Decidualization&oldid=908981933#Endometrial_stromal_cells_(ESCs) https://doi.org/10.1038/s41591-020-1040-z endometrial stromal fibroblast PMID:30309298 An epithelial cell of thyroid gland. 2010-09-08T01:46:51Z FMA:256167 MESH:D000072637 epithelial cell of thyroid gland true An epithelial cell of thyroid gland. GOC:tfm A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones. 2010-09-08T01:50:08Z BTO:0003736 CALOHA:TS-1285 FMA:68782 follicular cell of thyroid gland principal cell of thyroid gland thyroid gland follicular cell thyroid follicular cell A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones. GOC:tfm ISBN:0517223651 An epithelial cell of the parathyroid gland. 2010-09-08T02:29:38Z FMA:70547 epithelial cell of parathyroid gland true An epithelial cell of the parathyroid gland. GOC:tfm An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. 2010-09-14T10:57:26Z FMA:63134 endothelial cell of sinusoid An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. GOC:tfm ISBN:0618947256 A type of enteroendocrine cell found in the stomach that secretes glucagon. 2010-09-10T10:54:42Z FMA:83411 type A cell of stomach A type of enteroendocrine cell found in the stomach that secretes glucagon. GOC:tfm A D cell located in the colon. 2010-09-10T11:37:35Z FMA:268744 colon D-cell colonic delta cell delta cell of colon type D cell of colon A D cell located in the colon. GOC:tfm A type D cell of the small intestine. 2010-09-10T01:34:22Z FMA:268736 delta cell of small intestine small intestine D-cell small intestine delta cell type D cell of small intestine A type D cell of the small intestine. GOC:tfm A type D cell found in the stomach. 2010-09-10T01:36:03Z FMA:83410 delta cell of stomach stomach D-cell stomach delta cell type D cell of stomach A type D cell found in the stomach. GOC:tfm A cell type that secretes histamine. 2010-09-10T03:04:42Z histamine secreting cell A cell type that secretes histamine. GOC:tfm A PP cell located in the islets of the pancreas. 2010-09-10T03:30:31Z BTO:0000805 FMA:70588 MESH:D050418 PP cell of pancreatic islet PP-cell of pancreatic islet pancreatic polypeptide-secreting cell The term PP cell of pancreatic acinus was obsoleted due to a lack of evidence, making PP cell of pancreatic islets synonymous with pancreatic PP cell. pancreatic PP cell A PP cell located in the islets of the pancreas. GOC:tfm An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. 2010-09-13T02:34:22Z CALOHA:TS-1040 FMA:72208 epithelial cell of thymus gland epithelial reticular cell epithelial reticular cell of thymus thymic epithelial cell epithelial cell of thymus true An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. FMA:72208 GOC:tfm An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule. 2010-09-13T02:37:23Z FMA:72209 subcapsular thymic epithelial cell type-1 epithelial cell of thymus An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule. GOC:tfm PMID:9264335 subcapsular thymic epithelial cell PMID:18194204 PMID:2694455 A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles. 2010-09-13T03:39:14Z BTO:0003652 FMA:66788 fibroblast-like synoviocyte synovial fibroblast Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. type B synovial cell A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles. GOC:tfm ISBN:0517223651 PMID:34433485 PMID:34772990 synovial fibroblast PMID:23147896 Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. PMID:34433485 https://en.wikipedia.org/wiki/Fibroblast-like_synoviocyte An epithelial cell of a skin gland. 2010-09-14T12:00:07Z FMA:70657 epithelial cell of gland of skin epithelial cell of skin gland An epithelial cell of a skin gland. GOC:tfm An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin. 2010-09-14T02:33:09Z FMA:83095 MESH:D052683 somatotrope somatotropic cell somatrophic cell somatotroph An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin. SANBI:mhl An ecto-epithelial cell of the prostate gland that secretes hormones. 2010-09-14T03:01:58Z CALOHA:TS-1280 FMA:74390 FMA:86774 glandular cell of prostate neuro-epithelial cell of prostate gland endocrine-paracrine cell of prostate gland An ecto-epithelial cell of the prostate gland that secretes hormones. GOC:tfm A cell that is part of the nervous system. 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 neural cell A cell that is part of the nervous system. GOC:tfm ISBN:0618947256 A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 connective tissue cell A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. GOC:tfm ISBN:0618947256 A cell of the embryo. 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 embryonic cell (metazoa) A cell of the embryo. FMA:0618947256 A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. 2010-09-20T10:13:37Z BTO:0000066 amniocyte true A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. BFO:0000066 GOC:tfm PMID:3211847 An epithelial cell of the mammary gland. 2010-09-20T01:49:37Z BTO:0004300 breast epithelial cell mammary epithelial cell mammary gland epithelial cell An epithelial cell of the mammary gland. GOC:tfm PMID:19022771 An epithelial cell of the bronchus. 2010-09-20T02:00:00Z BTO:0002922 bronchial epithelial cell An epithelial cell of the bronchus. GOC:tfm A ciliated cell of the bronchus. 2010-09-20T02:21:12Z ciliated cell of the bronchus A ciliated cell of the bronchus. GOC:tfm PMID:18757316 An adipocyte derived from a neural crest cell. 2010-09-20T02:25:25Z neural crest derived adipocyte An adipocyte derived from a neural crest cell. GOC:tfm PMID:17507398 A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive. 2010-09-21T10:06:53Z p-NK Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). CD56-positive, CD161-positive immature natural killer cell, human A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12457618 p-NK PMID:12457618 A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium. 2010-09-20T03:21:06Z CD133-positive prostate epithelial cell prostate stem cell A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium. GOC:tfm PMID:15226377 An undifferentiated cell of the prostate epithelium that lacks secretory activity. 2010-09-20T03:34:10Z basal cell of prostate epithelium An undifferentiated cell of the prostate epithelium that lacks secretory activity. GOC:tfm PMCID:PMC2673349 A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive. 2010-09-20T04:33:11Z p-NK Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). CD56-negative, CD161-positive immature natural killer cell, human A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive. GOC:add GO_REF:0000031 ISBN:0781735149 PMID:12457618 p-NK PMID:12457618 An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. 2010-09-21T04:33:05Z FMA:75621 endocardial endothelial cell endothelial cell of endocardium endocardial cell An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. GOC:tfm ISSN:0452-3458 endothelial cell of endocardium FMA:75621 A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. 2010-09-21T04:41:06Z pancreatic endocrine progenitor pancreatic islet progenitor cell progenitor cell of endocrine pancreas A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. GOC:tfm PMID:20025937 PMID:20217494 PMID:22728667 A hematopoietic stem cell that exists during embryogenesis. 2010-09-22T09:05:13Z gestational hematopoietic stem cell A hematopoietic stem cell that exists during embryogenesis. GOC:tfm ISBN:978-60327-246-6 A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. 2010-09-22T10:30:02Z placental hematopoietic stem cell A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. GOC:tfm ISBN:978-1-60327-346-6 A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte keratocyte A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. GOC:tfm ISBN:9780702029585 An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. 2010-09-23T03:17:12Z BTO:0004562 cTEC cortical thymic epithelial cell An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. GOC:tfm PMID:18403190 An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. 2010-09-23T03:17:14Z BTO:0004563 mTEC medullary thymic epithelial cell An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. GOC:tfm PMID:18180458 A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure. 2010-09-23T04:18:50Z trabeculocyte trabecular meshwork cell true A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure. GOC:tfm PMID:14500801 An endo-epithelial cell of the respiratory tract. 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell respiratory epithelial cell true An endo-epithelial cell of the respiratory tract. GOC:tfm A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. 2010-09-23T04:42:27Z respiratory mucosa goblet cells respiratory goblet cell A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. GOC:tfm ISBN:0721662544 respiratory mucosa goblet cells MP:0010863 A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. 2010-09-24T01:13:01Z FBbt:00005812 myotubule single cell sarcomere myotube A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. GOC:dos GOC:tfm ISBN:0323052908 PMID:22274696 A T cell that expresses a T cell receptor complex and has completed T cell selection. 2010-10-12T01:56:15Z CD3e-positive T cell mature T-cell CD3epsilon T cell mature T cell true A T cell that expresses a T cell receptor complex and has completed T cell selection. GOC:tfm A T cell that has not completed T cell selection. 2010-10-12T01:56:17Z BTO:0001372 CALOHA:TS-1042 immature T-cell immature T cell true A T cell that has not completed T cell selection. GOC:tfm A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. 2010-10-15T09:24:05Z nucleated reticulocyte true A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. GOC:tfm PMID:18182572 PMID:9011180 PMID:9046052 A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. 2010-10-15T09:24:08Z CALOHA:TS-0864 FMA:66785 enucleated reticulocyte true A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. GOC:tfm ISBN:0-12203-052-4 ISBN:0721601464 A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive. 2010-10-21T01:16:24Z ETP preT.ETP.Th ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative. early T lineage precursor true A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive. GOC:dsd GOC:tfm PMID:16551251 http://www.immgen.org/index_content.html Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. 2010-11-22T01:10:28Z DC.8-4-11b+ spleen double-negative dendritic cell Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell true Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. GOC:tfm http://www.immgen.org/index_content.html A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive. 2010-11-22T03:57:57Z epidermal Langerhans cell true A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive. GOC:tfm http://www.immgen.org/index_content.html A conventional thymic dendritic cell that is CD8alpha-negative. 2010-11-23T10:58:53Z DC.8-.Th CD8alpha-negative thymic conventional dendritic cell true A conventional thymic dendritic cell that is CD8alpha-negative. GOC:tfm PMID:19273629 http://www.immgen.org/index_content.html A conventional dendritic cell that expresses CD11b (ITGAM). 2010-11-23T01:50:05Z CD11b-positive dendritic cell true A conventional dendritic cell that expresses CD11b (ITGAM). GOC:tfm http://www.immgen.org/index_content.html A myeloid suppressor cell that is Gr1-high and CD11c-negative. 2010-11-23T02:15:12Z MDS.Gr1hi Gr1-high myeloid suppressor cell true A myeloid suppressor cell that is Gr1-high and CD11c-negative. GOC:tfm http://www.immgen.org/index_content.html A myeloid suppressor cell that is Gr1-low and CD11c-positive. 2010-11-23T02:19:43Z MDS.Gr1lo Gr1-low myeloid suppressor cell true A myeloid suppressor cell that is Gr1-low and CD11c-positive. GOC:tfm http://www.immgen.org/index_content.html A goblet cell located in the nasal epithelium. 2010-12-03T03:03:02Z MP:0002262 nasal mucosa goblet cell A goblet cell located in the nasal epithelium. GOC:cjm GOC:tfm A specialized cell involved in auditory sensory perception. 2010-12-06T03:18:43Z auditory epithelial cell A specialized cell involved in auditory sensory perception. GOC:tfm A cell located in the heart, including both muscle and non muscle cells. 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 heart cell From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte A cell located in the heart, including both muscle and non muscle cells. GOC:tfm A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc 2010-12-07T04:03:56Z BTO:0002441 FMA:84639 adventitial cell A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc GOC:tfm A smooth muscle cell of the intestine. 2011-01-17T03:39:38Z intestinal smooth muscle cell enteric smooth muscle cell true A smooth muscle cell of the intestine. GOC:tfm A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative. 2011-01-21T01:57:00Z langerin-positive lymph node dendritic cell true A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative. GOC:tfm http://www.immgen.org/index_content.html An epithelial cell of the kidney. 2011-02-08T10:46:34Z KUPO:0001019 kidney epithelial cell true An epithelial cell of the kidney. GOC:tfm KUPO:SJ An adipocyte that is part of subcutaneous adipose tissue. 2011-02-21T02:51:22Z subcutaneous fat cell subcutaneous adipocyte true An adipocyte that is part of subcutaneous adipose tissue. GOC:tfm An epithelial cell of the cervix. 2011-02-24T08:20:08Z cervical canal epithelial cell cervical canal of uterus epithelial cell cervix epithelial cell cervix of uterus epithelial cell epithelial cell of cervical canal epithelial cell of cervical canal of uterus epithelial cell of cervix of uterus epithelial cell of neck of uterus epithelial cell of uterine cervix neck of uterus epithelial cell uterine cervix epithelial cell epithelial cell of cervix An epithelial cell of the cervix. GOC:tfm cervical canal epithelial cell GOC:tfm cervical canal of uterus epithelial cell GOC:tfm cervix epithelial cell GOC:tfm cervix of uterus epithelial cell GOC:tfm epithelial cell of cervical canal GOC:tfm epithelial cell of cervical canal of uterus GOC:tfm epithelial cell of cervix of uterus GOC:tfm epithelial cell of neck of uterus GOC:tfm epithelial cell of uterine cervix GOC:tfm neck of uterus epithelial cell GOC:tfm uterine cervix epithelial cell GOC:tfm An epithelial cell that is part of the amnion. 2011-02-28T12:38:01Z amniotic epithelial cell epithelial cell of amnion An epithelial cell that is part of the amnion. GOC:tfm A mesenchymal stem cell of the amnion membrane. 2011-02-28T12:44:24Z amniotic membrane stem cell amnion mesenchymal stem cell A mesenchymal stem cell of the amnion membrane. GOC:tfm PMID:20446274 PMID:21339039 An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. 2011-02-28T01:20:20Z small bile duct cholangiocyte intrahepatic cholangiocyte true An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. GOC:tfm PMID:23720296 small bile duct cholangiocyte PMID:23720296 A smooth muscle cell of the aorta. 2011-02-28T01:42:12Z BTO:0004577 aortic smooth muscle cell A smooth muscle cell of the aorta. GOC:tfm A mesenchymal stem cell that is part of the bone marrow. 2011-02-28T01:47:47Z mesenchymal stem cell of the bone marrow A mesenchymal stem cell that is part of the bone marrow. GOC:tfm A mesenchymal stem cell of the chorionic membrane. 2011-02-28T03:04:35Z chorionic membrane mesenchymal stem cell A mesenchymal stem cell of the chorionic membrane. GOC:tfm An endothelial cell that is part of the vein. 2011-02-28T03:48:11Z FMA:62104 KUPO:0001099 endothelial cell of vein venous endothelial cell vein endothelial cell true An endothelial cell that is part of the vein. GOC:tfm An endothelial progenitor cell that participates in angiogenesis during development. 2011-02-28T04:20:39Z See CL:0002619. embryonic blood vessel endothelial progenitor cell An endothelial progenitor cell that participates in angiogenesis during development. GOC:tfm A fibroblast of the aortic adventitia. 2011-02-28T04:43:41Z fibroblast of the aortic adventitia true A fibroblast of the aortic adventitia. GOC:tfm A fibroblast that is part of the heart. 2011-02-28T04:57:44Z cardiac fibroblast fibroblast of cardiac tissue true true A fibroblast that is part of the heart. GOC:tfm A fibroblast that is part of the choroid plexus. 2011-02-28T05:01:39Z fibroblast of choroid plexus true A fibroblast that is part of the choroid plexus. GOC:tfm 2011-02-28T05:05:33Z fibroblast of dermis true 2011-02-28T05:09:12Z fibroblast of gingiva true A fibroblast that is part of lung. 2011-02-28T05:11:03Z BTO:0000764 CALOHA:TS-0575 fibroblast of lung true A fibroblast that is part of lung. GOC:tfm A fibroblast of the lymphatic system. 2011-02-28T05:16:18Z fibroblast of lymphatic vessel true A fibroblast of the lymphatic system. GOC:tfm A fibroblast that is part of the mammary gland. 2011-02-28T05:18:38Z fibroblast of mammary gland true A fibroblast that is part of the mammary gland. GOC:tfm A fibroblast of the periodontium. 2011-02-28T05:19:48Z fibroblast of periodontium true A fibroblast of the periodontium. GOC:tfm A fibroblast of pulmonary artery. 2011-02-28T05:22:27Z fibroblast of pulmonary artery true A fibroblast of pulmonary artery. GOC:tfm An animal cell that is part of a hair follicle. 2011-03-01T04:11:01Z hair follicle cell An animal cell that is part of a hair follicle. GOC:tfm An epithelial cell of the intestine. 2011-03-01T05:18:31Z intestinal epithelial cell An epithelial cell of the intestine. GOC:tfm A connective tissue cell of the nucleus pulposus cell of intervertebral disc. 2011-03-02T02:12:23Z nucleus pulposus cell of intervertebral disc A connective tissue cell of the nucleus pulposus cell of intervertebral disc. GOC:tfm A mesenchymal stem cell of the umbilical cord. 2011-03-01T09:55:12Z mesenchymal stem cell of umbilical cord A mesenchymal stem cell of the umbilical cord. GOC:tfm A mesenchymal stem cell of adipose tissue. 2011-03-01T09:57:17Z mesenchymal stem cell of adipose mesenchymal stem cell of adipose tissue A mesenchymal stem cell of adipose tissue. GOC:tfm A mesenchymal stem cell of liver. 2011-03-01T09:58:51Z hepatic mesenchymal stem cell true A mesenchymal stem cell of liver. GOC:tfm A mesenchymal stem cell of the vertebrae. 2011-03-01T10:40:27Z vertebral mesenchymal stem cell true A mesenchymal stem cell of the vertebrae. GOC:tfm A glial cell that myelinates or ensheathes axons in the peripheral nervous system. 2011-03-02T01:19:27Z BTO:0001220 CALOHA:TS-0898 MESH:D012583 A myelinating Schwann cell wraps around a single axon. Myelination occurs in larger diameter axons, while a process called ensheathment occurs on smaller diameter axons in which a single cell wraps around multiple small, unmyelinated axons separating them with a thin layer of cytoplasm. The structure formed is called a Remak bundle. Schwann cell A glial cell that myelinates or ensheathes axons in the peripheral nervous system. GOC:tfm PMID:16807057 A myelinating Schwann cell wraps around a single axon. Myelination occurs in larger diameter axons, while a process called ensheathment occurs on smaller diameter axons in which a single cell wraps around multiple small, unmyelinated axons separating them with a thin layer of cytoplasm. The structure formed is called a Remak bundle. PMID:16807057 A stromal cell of the pancreas. 2011-03-02T02:40:41Z stromal cell of pancreas true A stromal cell of the pancreas. GOC:tfm An epithelial cell of the placenta. 2011-03-02T03:21:30Z placental epithelial cell true An epithelial cell of the placenta. GOC:tfm An epithelial cell of the kidney cortex. KUPO:0001016 renal cortical epithelial cell true true An epithelial cell of the kidney cortex. GOC:tfm A blood vessel endothelial cell that is part of the retina. 2011-03-06T03:28:27Z retinal blood vessel endothelial cell true A blood vessel endothelial cell that is part of the retina. GOC:tfm A smooth muscle cell of the bachiocephalic vasculature. 2011-03-06T05:00:58Z smooth muscle cell of the brachiocephalic vasculature A smooth muscle cell of the bachiocephalic vasculature. GOC:tfm A vascular associated smooth muscle cell of the brain vasculature. 2011-03-06T05:01:20Z smooth muscle cell of the brain vasculature true A vascular associated smooth muscle cell of the brain vasculature. GOC:tfm A smooth muscle of the pulmonary artery. 2011-03-06T05:01:28Z BTO:0003336 smooth muscle cell of the pulmonary artery A smooth muscle of the pulmonary artery. GOC:tfm A smooth muscle cell of the coronary artery. 2011-03-06T05:01:34Z smooth muscle cell of the coronary artery A smooth muscle cell of the coronary artery. GOC:tfm A smooth muscle of the internal thoracic artery. 2011-03-06T05:01:41Z smooth muscle cell of the internal thoracic artery A smooth muscle of the internal thoracic artery. GOC:tfm A smooth muscle cell of the umbilical artery. 2011-03-06T05:01:48Z smooth muscle cell of the umbilical artery A smooth muscle cell of the umbilical artery. GOC:tfm A smooth muscle cell of the subclavian artery. 2011-03-06T05:01:52Z smooth muscle cell of the subclavian artery A smooth muscle cell of the subclavian artery. GOC:tfm Smooth muscle cell of the carotid artery. 2011-03-06T05:01:56Z smooth muscle cell of the carotid artery Smooth muscle cell of the carotid artery. GOC:tfm A smooth muscle cell of the bladder. 2011-03-06T05:43:24Z KUPO:0001122 smooth muscle cell of bladder true A smooth muscle cell of the bladder. GC:tfm 2011-03-06T05:46:39Z BTO:0004402 bronchial smooth muscle cell A smooth muscle cell of the esophagus. 2011-03-06T05:48:17Z smooth muscle cell of the esophagus true A smooth muscle cell of the esophagus. GOC:tfm A smooth muscle cell of the trachea. 2011-03-06T05:50:28Z smooth muscle cell of trachea A smooth muscle cell of the trachea. GOC:tfm A smooth muscle cell of the uterus. 2011-03-06T05:53:28Z uterine smooth muscle cell true A smooth muscle cell of the uterus. GOC:tfm 2011-03-06T06:50:53Z anulus pulposus cell annulus pulposus cell true A neuron of the raphe nuclei. 2011-03-06T07:42:06Z raphe nuclei neuron true A neuron of the raphe nuclei. GOC:tfm An adipocyte that is part of the breast. 2011-03-14T10:17:07Z CALOHA:TS-2377 breast adipocyte fat cell of breast Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma.[CALOHA] adipocyte of breast true An adipocyte that is part of the breast. GOC:tfm A fibroblast of skin. 2011-03-14T12:31:49Z BTO:0001255 CALOHA:TS-0935 skin fibroblast true A fibroblast of skin. GOC:tfm 2011-03-14T12:46:28Z gingival epithelial cell A stromal cell of the prostate. 2011-03-14T02:11:10Z BTO:0003972 prostate stromal cell true A stromal cell of the prostate. GOC:tfm An acinar cell of salivary gland. 2011-03-14T02:22:22Z acinar cell of salivary gland true An acinar cell of salivary gland. GOC:tfm A cell of the seminiferous tubule epithelium. 2011-03-15T11:59:23Z seminiferous tubule epithelial cell true A cell of the seminiferous tubule epithelium. GOC:tfm 2011-06-21T12:28:55Z epithelial cell of upper respiratory tract true 2011-06-21T12:29:31Z epithelial cell of lower respiratory tract true A glandular epithelial cell of the endometrium. 2011-07-08T03:54:08Z FMA:86489 glandular cell of endometrium A glandular epithelial cell of the endometrium. GOC:tfm A glandular epithelial cell of the esophagus. 2011-07-08T03:55:57Z FMA:86548 glandular cell of esophagus true true A glandular epithelial cell of the esophagus. GOC:tfm A glandular epithelial cell of the large intestine. 2011-07-08T04:03:01Z FMA:87194 glandular cell of the large intestine true A glandular epithelial cell of the large intestine. GOC:tfm A glandular epithelial cell that is part of the stomach. 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 glandular cell of stomach true A glandular epithelial cell that is part of the stomach. GOC:tfm A myocardial endocrine cell that is part of the atrium. 2011-07-11T02:45:39Z FMA:83389 myocardial endocrine cell of atrium true A myocardial endocrine cell that is part of the atrium. GOC:tfm A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. 2011-08-16T02:38:01Z retinal progenitor cell A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. GOC:tfm PMID:20959166 PMID:21148186 A skeletal muscle cell that is part of the tongue. 2011-08-16T03:10:02Z tongue muscle cell A skeletal muscle cell that is part of the tongue. GOC:tfm PMID:18816858 A neuroblast derived from a neural crest cell. 2011-08-22T09:24:15Z neural crest derived neuroblast A neuroblast derived from a neural crest cell. GOC:tfm PMID:17407019 A PP cell found in intestine. 2011-09-27T11:59:01Z PP cell of intestine true A PP cell found in intestine. GOC:tfm PMID:2420136 PMID:728970 A cell that is part of a cortex of kidney. 2011-10-25T03:49:41Z kidney cortical cell A CNS interneuron located in the spinal cord. Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron true A CNS interneuron located in the spinal cord. CL:CVS A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. renal principal cell A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. CL:CVS A ciliated epithelial cell with many cilia. multi-ciliated cell multiciliated cell multiciliated epithelial cell MCC multi-ciliated epithelial cell A ciliated epithelial cell with many cilia. CL:CVS MCC Lymphatic progenitor cells. 2012-01-12T04:44:34Z Usually express Prox1, or prox1b. lymphangioblast true Lymphatic progenitor cells. CL:CVS Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. 2012-01-12T05:21:09Z parachordal lymphangioblast vascular lymphangioblast true Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. CL:CVS A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. somatic motor neuron somatomotor neuron A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. ZFIN:CVS Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. hepatoblast https://github.com/obophenotype/cell-ontology/issues/800 Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. GOC:CVS PMID:18356246 PMID:20483998 PMID:26798363 https://orcid.org/0000-0003-1940-6740 Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins. 2012-06-15T01:27:01Z unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 preameloblast Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins. GO_REF:0000034 PMCID:PMC2737325 Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). GO_REF:0000034 scleroblast GO_REF:0000034 Skeletogenic cell that has the potential to develop into a cementoblast. 2012-06-15T04:37:13Z precementoblast Skeletogenic cell that has the potential to develop into a cementoblast. GO_REF:0000034 Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell. 2012-06-15T05:15:11Z preodontoblast Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell. GO_REF:0000034 Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. 2012-06-27T08:27:35Z premigratory neural crest cell Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. UBERONREF:0000002 Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. 2012-06-27T10:44:01Z prechondroblast Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. GO_REF:0000034 Any muscle cell in which the fibers are not organised into sarcomeres. non-striated muscle cell Any muscle cell in which the fibers are not organised into sarcomeres. GOC:DOS Any hematopoietic cell that is a precursor of some other hematopoietic cell type. hematopoietic precursor cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. GOC:dos A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. MESH:D018485 skeletal muscle fiber A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. GOC:tfm ISBN:0323052908 A muscle cell that is part of some visceral muscle. FBbt:00005070 visceral muscle cell A muscle cell that is part of some visceral muscle. GOC:dos A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. striated visceral muscle cell A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. GOC:dos A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. transversely striated visceral muscle cell A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. GOC:dos A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. myogenic precursor cell The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins. adult skeletal muscle myoblast A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. PMID:23303905 myogenic precursor cell PMID:23303905 A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration. mesenchyme cell mesenchymal cell A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. endocardial cushion cell A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. PMID:18816864 An endocrine cell that is part of the pancreas. pancreatic endocrine cell An endocrine cell that is part of the pancreas. GOC:dos 2017-07-09T19:12:36Z visual system neuron An interneuron that has its soma located in the cerebral cortex. cerebral cortex interneuron cortical interneuron Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. 2020-02-29T17:33:55Z mural cell Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. Wiki:Mural_cell&oldid=930603194 2020-02-29T17:37:00Z microcirculation associated smooth muscle cell A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. spinal sensory neuron sensory neuron of spinal nerve A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. GOC:nv GOC:pr Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 retinal cell Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. GOC:pr An enteroendocrine cell that is located in the small intestine. small intestine enteroendocrine cell enteroendocrine cell of small intestine An enteroendocrine cell that is located in the small intestine. http://orcid.org/0000-0003-3440-1876 A lymphocyte that resides in the lamina propria of the large intestine. lamina propria lymphocyte of large intestine This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. lymphocyte of large intestine lamina propria A lymphocyte that resides in the lamina propria of the large intestine. https://orcid.org/0000-0003-4183-8865 A kidney cortical cell that is part of the nephrogenic zone. cortical nephrogenic niche cell cortical nephrogenic zone cell nephrogenic zone cell A kidney cortical cell that is part of the nephrogenic zone. PMID:29449449 https://orcid.org/0000-0002-3163-0115 A stromal cell found in the lamina propria of the large intestine. stromal cell of lamina propria of large intestine A stromal cell found in the lamina propria of the large intestine. http://orcid.org/0000-0003-4183-8865 A stromal cell found in the lamina propria of the small intestine. stromal cell of lamina propria of small intestine A stromal cell found in the lamina propria of the small intestine. http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is part of the small intestine. mesothelial cell of small intestine A mesothelial cell that is part of the small intestine. http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is part of the colon. mesothelial cell of large intestine mesothelial cell of colon A mesothelial cell that is part of the colon. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 A mesothelial cell that is located in a vermiform appendix. appendix mesothelial cell mesothelial cell of appendix vermiformis mesothelial cell of vermiform appendix mesothelial cell of appendix A mesothelial cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 An intestinal enteroendocrine cell that is located in a vermiform appendix. appendix enteroendocrine cell enteroendocrine cell of appendix vermiformis enteroendocrine cell of vermiform appendix enteroendocrine cell of appendix An intestinal enteroendocrine cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A T cell that is located in a vermiform appendix. T cell of appendix vermiformis T cell of vermiform appendix appendix T cell This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. T cell of appendix A T cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A B cell that is located in a vermiform appendix. B cell of appendix vermiformis B cell of vermiform appendix appendix B cell This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. B cell of appendix A B cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A plasma cell that is located in a vermiform appendix. appendix plasma cell plasma cell of appendix vermiformis plasma cell of vermiform appendix This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. plasma cell of appendix A plasma cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A dendritic cell that is located in a vermiform appendix. appendix dendritic cell dendritic cell of appendix vermiformis dendritic cell of vermiform appendix This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. dendritic cell of appendix A dendritic cell that is located in a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the vermiform appendix. stromal cell of appendix lamina propria stromal cell of lamina propria of appendix vermiformis stromal cell of lamina propria of vermiform appendix A stromal cell found in the lamina propria of the vermiform appendix. http://orcid.org/0000-0003-3440-1876 A macrophage located in the vermiform appendix. macrophage of appendix macrophage of appendix vermiformis macrophage of vermiform appendix This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. appendix macrophage A macrophage located in the vermiform appendix. http://orcid.org/0000-0003-3440-1876 A macrophage that is located in the colon. macrophage of colon This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. colon macrophage A macrophage that is located in the colon. http://orcid.org/0000-0003-3440-1876 A goblet cell that is located in the colon. goblet cell of colon colon goblet cell A goblet cell that is located in the colon. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the colon. stromal cell of colon lamina propria stromal cell of lamina propria of colon A stromal cell found in the lamina propria of the colon. http://orcid.org/0000-0003-3440-1876 An enteroendocrine cell that is located in the colon. colon enteroendocrine cell enteroendocrine cell of colon An enteroendocrine cell that is located in the colon. http://orcid.org/0000-0003-3440-1876 A lymphocyte that resides in the lamina propria of the small intestine. Lamina propria leukocytes and intraepithelial lymphocytes are the effector compartments of the gut mucosal immune system. Lymphocytes circulate through gut associated lymphoid tissues until recruitment by intestinal antigens. They are involved in the gut immune response. gastrointestinal tract small intestine (lamina propria) leukocyte small intestine lamina propria leukocyte small intestine lamina propria leukocyte (LPL) gastrointestinal tract (lamina propria) lymphocyte of small intestine lamina propria lymphocyte of small intestine small intestine lamina propria lymphocyte This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. lymphocyte of small intestine lamina propria A lymphocyte that resides in the lamina propria of the small intestine. Lamina propria leukocytes and intraepithelial lymphocytes are the effector compartments of the gut mucosal immune system. Lymphocytes circulate through gut associated lymphoid tissues until recruitment by intestinal antigens. They are involved in the gut immune response. PMID:26551552 https://orcid.org/0000-0003-4183-8865 A B cell found in the lymph node medullary sinus. This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. B cell of medullary sinus of lymph node A B cell found in the lymph node medullary sinus. http://orcid.org/0000-0003-4183-8865 A T cell found in the lymph node medullary sinus. This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. T cell of medullary sinus of lymph node A T cell found in the lymph node medullary sinus. http://orcid.org/0000-0003-4183-8865 A macrophage found in the medullary sinus of the lymph node. medullary sinus macrophage lymph node medullary sinus macrophage This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. macrophage of medullary sinus of lymph node A macrophage found in the medullary sinus of the lymph node. http://orcid.org/0000-0003-4183-8865 A macrophage that is located in the anorectum. macrophage of anorectum This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. anorectum macrophage A macrophage that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 A B cell that is located in the anorectum. This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. B cell of anorectum A B cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 A T cell that is located in the anorectum. This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. T cell of anorectum A T cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 A smooth muscle cell that is located in the anorectum. anorectum smooth muscle cell smooth muscle cell of anorectum A smooth muscle cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 A stromal cell found in the lamina propria of the anorectum. stromal cell of anorectum lamina propria A stromal cell found in the lamina propria of the anorectum. http://orcid.org/0000-0003-3440-1876 A goblet cell that is located in the anorectum. goblet cell of anorectum anorectum goblet cell A goblet cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 A plasma cell that is located in the medullary sinus of the lymph node. medullary plasma cell medullary sinus plasma cell plasma cell of medullary sinus This is a general grouping term created for use in the EMBL-EBI Single Cell Expression Atlas anatomograms. Please use a more specific cell type term for annotation if possible, given the information available to you. plasma cell of medullary sinus of lymph node A plasma cell that is located in the medullary sinus of the lymph node. http://orcid.org/0000-0003-4183-8865 An enteroendocrine cell that is located in the anorectum. anorectum enteroendocrine cell enteroendocrine cell of anorectum An enteroendocrine cell that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An epithelial cell that is part of an endometrial gland. 2021-11-30T16:13:30Z EFO:0010710 endometrial glandular epithelial cell epithelial cell of endometrial gland An epithelial cell that is part of an endometrial gland. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 An endothelial cell that is part of a respiratory system lymphatic vessel. 2021-12-03T14:00:44Z EFO:0010667 endothelial cell of respiratory system lymphatic vessel An endothelial cell that is part of a respiratory system lymphatic vessel. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 An endothelial cell that is part of a placenta. 2021-12-13T13:53:01Z EFO:0010708 placental endothelial cell endothelial cell of placenta An endothelial cell that is part of a placenta. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A smooth muscle cell that is part of a placenta. 2021-12-13T13:56:42Z EFO:0010709 placental smooth muscle cell smooth muscle cell of placenta A smooth muscle cell that is part of a placenta. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 An endothelial cell that is part of a hepatic portal vein. 2021-12-13T14:01:05Z portal endothelial cell EFO:0010704 endothelial cell of hepatic portal vein An endothelial cell that is part of a hepatic portal vein. PMID:30348985 https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 An endothelial cell that is part of a uterus. 2021-12-13T14:39:25Z EFO:0010711 uterine endothelial cell endothelial cell of uterus An endothelial cell that is part of a uterus. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development. 2022-02-21T15:39:10Z embryonic skeletal muscle fiber A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development. PMID:32094117 PMID:7196501 http://orcid.org/0000-0003-2034-601X A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen. 2022-03-17T12:00:44Z portal fibroblast hepatic portal fibroblast A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen. PMID:20209607 PMID:24814904 https://orcid.org/0000-0001-7655-4833 An endothelial cell located in a lymph node lymphatic vessel. lymph node lymphatic vessel endothelial cell https://github.com/obophenotype/cell-ontology/issues/1472 An endothelial cell located in a lymph node lymphatic vessel. https://orcid.org/0000-0001-7655-4833 A stromal cell that is part_of a bone marrow. bone marrow stromal cell stromal cell of bone marrow An epithelial cell that is part_of a umbilical artery. umbilical artery epithelial cell epithelial cell of umbilical artery A mononuclear cell that is part_of a bone marrow. bone marrow mononuclear cell mononuclear cell of bone marrow cardiac blood vessel endothelial cell cardiac endothelial cell camera type eye photoreceptor cell camera-type eye photoreceptor cell A CNS neuron of the cerebral cortex. BTO:0004102 FMA:84104 cortical neuron neuron of cerebral cortex cerebral cortex neuron https://github.com/obophenotype/cell-ontology/issues/1359 A CNS neuron of the cerebral cortex. GOC:tfm A zygote in a plant or an animal. MESH:D015053 zygote cardiac glial cell MESH:D032386 cardiac myoblast A neuron that has its soma in the heart. This term is used in 3 GO terms that were created as part of the heart development focus project. cardiac neuron https://github.com/obophenotype/cell-ontology/pull/1488 A neuron that has its soma in the heart. PMID:12486170 PMID:29265764 A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. spinal cord motor neuron true A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. GOC:nv A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. paraxial mesoderm cell somitic mesoderm cell presomitic mesoderm cell paraxial cell A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. GOC:NV PMID:11687492 A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. neural crest cell A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 A sperm cell that is cabaple of motion (motility). motile sperm cell A sperm cell that is cabaple of motion (motility). PMID:30612620 A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion. flagellated sperm cell A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion. PMID:30612620 https://www.lexico.com/en/definition/flagellum A mesothelial cell that is part of the epicardium. mesothelial cell of epicardium A fibroblast that is part of upper back skin. fibroblast of upper back skin A fibroblast that is part of skin of back. fibroblast of skin of back A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. progenitor cell A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. ISBN:978-1-62808-994-3 https://doi.org/10.1016/B978-0-12-409503-8.00002-0 Any fibroblast that is part of skeletal muscle tissue. skeleton muscle fibroblast skeletal muscle fibroblast Any fibroblast that is part of skeletal muscle tissue. PMID:28369879 https://orcid.org/0000-0001-6164-0667 Any microvascular endothelial cell that is part of the dermis. DMEC cell dermal microvascular endothelium cell dermal microvascular endothelial cell Any microvascular endothelial cell that is part of the dermis. BTO:0004574 CL:patterns/cellPartOfAnatomicalEntity Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. chorionic trophoblast cell Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. GOC:NV Epithelial cell that is part of the colon epithelium. colonic epithelial cell colon epithelial cell Epithelial cell that is part of the colon epithelium. GOC:NV A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell A cell that, by division or terminal differentiation, can give rise to other cell types. GOC:dos A CNS neuron of the forebrain. forebrain neuron neuron of the forebrain true A neuroendocrine cell that is part of the prostate epithelium. neuroendocrine cell of prostate epithelium neuroendocrine cell of the prostate prostate neuroendocrine cell A neuroendocrine cell that is part of the prostate epithelium. PMID:33842835 http://orcid.org/0000-0001-7772-9578 Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. 2010-05-25T01:36:34Z neutrophillic cytoplasm Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. GOC:add Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. GOC:add Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. 2009-12-22T04:24:54Z basophilic cytoplasm Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. GOC:tfm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. 2009-12-28T04:25:23Z polychromatophilic cytoplasm Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. GOC:tfm A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. 2009-12-23T10:53:24Z increased nucleus size A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. GOC:tfm Heterochromatin that is arranged in a carthwheel pattern. 2009-12-28T04:28:35Z cartwheel heterochromatin Heterochromatin that is arranged in a carthwheel pattern. GOC:tfm Any serous secreting cell that is part of the tracheobronchial epithelium. 2020-05-07T16:03:27Z serous cell of tracheobronchial tree tracheobronchial serous cell Any chondrocyte that is part of the tracheobronchial tree. 2020-05-07T17:29:51Z chondrocyte of tracheobronchial tree tracheobronchial chondrocyte Any goblet cell that is part of the tracheobronchial epithelium. 2020-05-07T18:14:52Z goblet cell of tracheobronchial tree tracheobronchial goblet cell A smooth muscle cell that is part of any lymphatic vessel. 2020-07-21T12:29:51Z smooth muscle cell of lymphatic vessel lymphatic vessel smooth muscle cell A smooth muscle cell that is part of any lymphatic vessel. PMID:15109561 A smooth muscle cell that is part of any blood vessel. 2020-07-21T12:42:48Z smooth muscle cell of blood vessel blood vessel smooth muscle cell A smooth muscle cell that is part of any blood vessel. PMID:9108778 A smooth muscle cell that is part of the tracheobronchial tree. 2020-07-21T12:50:22Z smooth muscle cell of tracheobronchial tree tracheobronchial smooth muscle cell A smooth muscle cell that is part of the tracheobronchial tree. PMID:10853867 An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. 2020-09-03T12:24:24Z large bile duct cholangiocyte extrahepatic cholangiocyte An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. PMID:23720296 large bile duct cholangiocyte PMID:23720296 An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. 2020-09-09T13:56:47Z EFO:0010705 periportal LSEC periportal hepatic sinusoidal endothelial cell endothelial cell of periportal hepatic sinusoid An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. PMID:27423426 periportal LSEC PMID:28287163 periportal hepatic sinusoidal endothelial cell PMID:30348985 An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. 2020-09-10T12:38:29Z EFO:0010706 central venous hepatic sinusoidal endothelial cell pericentral LSEC endothelial cell of pericentral hepatic sinusoid An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. PMID:27423426 central venous hepatic sinusoidal endothelial cell PMID:30348985 pericentral LSEC PMID:28287163 Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. 2020-10-14T14:59:07Z intestinal goblet cell intestine goblet cell Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. PMID:1996606 PMID:24942678 intestinal goblet cell PMID:1996606 forebrain neuroblast pronephric nephron tubule epithelial cell metanephric nephron tubule epithelial cell lung goblet cell A cell that is part of a cardiac valve. heart valve cell cardiac valve cell A cell that is part of a cardiac valve. PMID:25311230 heart valve cell PMID:30796046 stomach neuroendocrine cell A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. pulmonary neuroendocrine cell PNEC lung neuroendocrine cell A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. PMID:33355253 doi:10.3109/01902148209069653 doi:10.7554/eLife.78216 pulmonary neuroendocrine cell PMID:33355253 PNEC PMID:33355253 lung ciliated cell lung secretory cell trophectoderm cell trophectodermal cell A smooth muscle cell that is part of the small intestine. FMA:15050 non-striated muscle fiber of small intestine smooth muscle cell of small intestine true A smooth muscle cell that is part of the small intestine. GOC:tfm non-striated muscle fiber of small intestine FMA:15050 A smooth muscle cell that is part of the duodenum. FMA:15058 non-striated muscle fiber of duodenum smooth muscle fiber of duodenum true A smooth muscle cell that is part of the duodenum. GOC:tfm non-striated muscle fiber of duodenum FMA:15058 A smooth muscle cell that is part of the jejunum. FMA:15062 non-striated muscle fiber of jejunum smooth muscle fiber of jejunum true A smooth muscle cell that is part of the jejunum. GOC:tfm non-striated muscle fiber of jejunum FMA:15062 A smooth muscle cell that is part of the ileum. FMA:15066 non-striated muscle fiber of ileum smooth muscle fiber of ileum true A smooth muscle cell that is part of the ileum. GOC:tfm non-striated muscle fiber of ileum FMA:15066 A smooth muscle cell that is part of the large intestine. FMA:15653 non-striated muscle fiber of large intestine smooth muscle cell of large intestine true A smooth muscle cell that is part of the large intestine. GOC:tfm non-striated muscle fiber of large intestine FMA:15653 A smooth muscle cell that is part of the colon. FMA:15663 non-striated muscle fiber of colon smooth muscle cell of colon A smooth muscle cell that is part of the colon. GOC:tfm non-striated muscle fiber of colon FMA:15663 A smooth muscle cell that is part of the cecum. FMA:15681 non-striated muscle fiber of cecum smooth muscle fiber of cecum smooth muscle cell of cecum A smooth muscle cell that is part of the cecum. GOC:tfm non-striated muscle fiber of cecum FMA:15681 A smooth muscle cell that is part of the ascending colon. FMA:17518 non-striated muscle fiber of ascending colon smooth muscle fiber of ascending colon true A smooth muscle cell that is part of the ascending colon. GOC:tfm non-striated muscle fiber of ascending colon FMA:17518 A smooth muscle cell that is part of the transverse colon. FMA:17519 non-striated muscle fiber of transverse colon smooth muscle fiber of transverse colon true A smooth muscle cell that is part of the transverse colon. GOC:tfm non-striated muscle fiber of transverse colon FMA:17519 A smooth muscle cell that is part of the descending colon. FMA:17520 non-striated muscle fiber of descending colon smooth muscle fiber of descending colon true A smooth muscle cell that is part of the descending colon. GOC:tfm non-striated muscle fiber of descending colon FMA:17520 A smooth muscle cell that is part of the sigmoid colon. FMA:17521 non-striated muscle fiber of sigmoid colon smooth muscle cell of sigmoid colon true A smooth muscle cell that is part of the sigmoid colon. GOC:tfm non-striated muscle fiber of sigmoid colon FMA:17521 A smooth muscle cell that is part of the rectum. FMA:17522 non-striated muscle fiber of rectum smooth muscle fiber of rectum smooth muscle cell of rectum A smooth muscle cell that is part of the rectum. GOC:tfm non-striated muscle fiber of rectum FMA:17522 An epithelial cell that is part of the urethra. FMA:256165 epithelial cell of urethra An epithelial cell that is part of the urethra. GOC:tfm A mesothelial cell that is part of the dura mater. FMA:256516 squamous mesothelial cell of dura mater mesothelial cell of dura mater A mesothelial cell that is part of the dura mater. GOC:tfm squamous mesothelial cell of dura mater FMA:256516 A fibroblast that is part of the areolar connective tissue. FMA:261279 fibroblast of areolar connective tissue true A fibroblast that is part of the areolar connective tissue. GOC:tfm A fibroblast that is part of the tunica adventitia of artery. FMA:261285 fibroblast of tunica adventitia of artery true A fibroblast that is part of the tunica adventitia of artery. GOC:tfm A fibroblast that is part of the dense regular elastic tissue. FMA:261287 fibroblast of dense regular elastic tissue A fibroblast that is part of the dense regular elastic tissue. GOC:tfm An adipocyte that is part of the epicardial fat. FMA:261293 adipocyte of epicardial fat epicardial fat cell epicardial adipocyte An adipocyte that is part of the epicardial fat. GOC:tfm adipocyte of epicardial fat FMA:261293 epicardial fat cell FMA:261293 An adipocyte that is part of the epicardial fat of right ventricle. FMA:261297 epicardial adipocyte of right ventricle epicardial fat cell of right ventricle adipocyte of epicardial fat of right ventricle An adipocyte that is part of the epicardial fat of right ventricle. GOC:tfm epicardial adipocyte of right ventricle FMA:261297 epicardial fat cell of right ventricle FMA:261297 An adipocyte that is part of the epicardial fat of left ventricle. FMA:261300 epicardial adipocyte of left ventricle epicardial fat cell of left ventricle adipocyte of epicardial fat of left ventricle An adipocyte that is part of the epicardial fat of left ventricle. GOC:tfm epicardial adipocyte of left ventricle FMA:261300 epicardial fat cell of left ventricle FMA:261300 A goblet cell that is part of the epithelium of bronchus. FMA:263032 goblet cell of epithelium of bronchus bronchial goblet cell A goblet cell that is part of the epithelium of bronchus. GOC:tfm goblet cell of epithelium of bronchus FMA:263032 A goblet cell that is part of the epithelium of stomach. FMA:263035 goblet cell of epithelium of stomach gastric goblet cell A goblet cell that is part of the epithelium of stomach. GOC:tfm goblet cell of epithelium of stomach FMA:263035 A goblet cell that is part of the epithelium of gastric cardiac gland. FMA:263038 goblet cell of epithelium of gastric cardiac gland gastric cardiac gland goblet cell A goblet cell that is part of the epithelium of gastric cardiac gland. GOC:tfm A goblet cell that is part of the epithelium of intestinal villus. FMA:263046 goblet cell of epithelium of intestinal villus intestinal villus goblet cell A goblet cell that is part of the epithelium of intestinal villus. GOC:tfm A goblet cell that is part of the epithelium of large intestine. FMA:263054 goblet cell of epithelium of large intestine large intestine goblet cell A goblet cell that is part of the epithelium of large intestine. GOC:tfm A goblet cell that is part of the epithelium of pancreatic duct. FMA:263058 goblet cell of epithelium of pancreatic duct pancreatic goblet cell A goblet cell that is part of the epithelium of pancreatic duct. GOC:tfm goblet cell of epithelium of pancreatic duct FMA:263058 A goblet cell that is part of the epithelium of pyloric gland. FMA:263061 goblet cell of epithelium of pyloric gland pyloric gastric gland goblet cell A goblet cell that is part of the epithelium of pyloric gland. GOC:tfm A goblet cell that is part of the epithelium proper of duodenum. FMA:263063 goblet cell of epithelium proper of duodenum duodenal goblet cell A goblet cell that is part of the epithelium proper of duodenum. GOC:tfm A goblet cell that is part of the epithelium proper of jejunum. FMA:263065 goblet cell of epithelium proper of jejunum jejunal goblet cell A goblet cell that is part of the epithelium proper of jejunum. GOC:tfm A goblet cell that is part of the epithelium proper of ileum. FMA:263067 goblet cell of epithelium proper of ileum ileal goblet cell A goblet cell that is part of the epithelium proper of ileum. GOC:tfm A goblet cell that is part of the epithelium proper of appendix. FMA:263069 goblet cell of epithelium proper of appendix appendix goblet cell A goblet cell that is part of the epithelium proper of appendix. GOC:tfm A goblet cell that is part of the epithelium of trachea. FMA:263075 goblet cell of epithelium of trachea tracheal goblet cell A goblet cell that is part of the epithelium of trachea. GOC:tfm goblet cell of epithelium of trachea FMA:263075 A serous secreting cell that is part of the epithelium of trachea. FMA:263078 serous cell of epithelium of trachea A serous secreting cell that is part of the epithelium of trachea. GOC:tfm A serous secreting cell that is part of the epithelium of bronchus. FMA:263080 serous cell of epithelium of bronchus A serous secreting cell that is part of the epithelium of bronchus. GOC:tfm A transitional myocyte that is part of the interatrial septum. FMA:263152 transitional myocyte of interatrial septum true A transitional myocyte that is part of the interatrial septum. GOC:tfm A transitional myocyte that is part of the interventricular septum. FMA:263154 transitional myocyte of interventricular septum true A transitional myocyte that is part of the interventricular septum. GOC:tfm A Purkinje myocyte that is part of the interventricular septum. FMA:263182 Purkinje myocyte of interventricular septum true A Purkinje myocyte that is part of the interventricular septum. GOC:tfm An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. BTO:000125 FMA:62911 LSEC endotheliocyte of hepatic sinusoid liver sinusoidal endothelial cell endothelial cell of hepatic sinusoid An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. GOC:tfm PMID:3926620 LSEC PMID:30348985 endotheliocyte of hepatic sinusoid FMA:62911 liver sinusoidal endothelial cell PMID:30348985 An epithelial cell that is part of the appendix. FMA:63602 columnar epitheliocyte of appendix epithelial cell of vermiform appendix epithelial cell of appendix An epithelial cell that is part of the appendix. GOC:tfm columnar epitheliocyte of appendix FMA:63602 epithelial cell of vermiform appendix FMA:63602 A muscle cell that is part of the sinoatrial node. FMA:67102 SA nodal myocyte SA node cardiac muscle cell sinoatrial node cell sinoatrial node myocyte sinuatrial node myocyte myocyte of sinoatrial node A muscle cell that is part of the sinoatrial node. FMA:67102 GOC:tfm SA nodal myocyte FMA:67102 SA node cardiac muscle cell GOC:pr sinoatrial node cell GOC:pr sinuatrial node myocyte FMA:67102 A muscle cell that is part of the atrioventricular node. FMA:67106 AV nodal myocyte AV node cardiac muscle cell AV node cell atrioventricular node cell atrioventricular node myocyte myocyte of atrioventricular node A muscle cell that is part of the atrioventricular node. FMA:67106 GOC:tfm AV nodal myocyte FMA:67106 AV node cardiac muscle cell GOC:pr AV node cell GOC:pr atrioventricular node cell GOC:pr atrioventricular node myocyte FMA:67106 An endothelial cell that is part of the arteriole. FMA:67760 KUPO:0001097 endothelial cell of arteriole true An endothelial cell that is part of the arteriole. GOC:tfm A blood vessel endothelial cell that is part of an arterial endothelium. BTO:0004758 FMA:67761 KUPO:0001095 arterial endothelial cell endothelial cell of artery A blood vessel endothelial cell that is part of an arterial endothelium. GOC:tfm An endothelial cell that is part of the venule. FMA:67762 endothelial cell of venule true An endothelial cell that is part of the venule. GOC:tfm An epithelial cell that is part of the gallbladder. FMA:67780 epithelial cell of gallbladder An epithelial cell that is part of the gallbladder. GOC:tfm A chromaffin cell that is part of the adrenal gland. FMA:69794 adrenal chromaffin cell chromaffin cell of adrenal gland true A chromaffin cell that is part of the adrenal gland. GOC:tfm adrenal chromaffin cell GO:0061104 A chromaffin cell that is part of the adrenal cortex. FMA:69795 chromaffin cell of adrenal cortex Not clear this cell type exists. Can't call it a cortical adrenal cell because of different germ layer origin. adrenal cortex chromaffin cell A chromaffin cell that is part of the adrenal cortex. GOC:tfm A somatic stem cell that is part of the epidermis. FMA:70541 epidermal stem cell stem cell of epidermis true A somatic stem cell that is part of the epidermis. GOC:tfm epidermal stem cell FMA:70541 An epithelial cell that is part of the external acoustic meatus. FMA:70555 epithelial cell of external acoustic meatus An epithelial cell that is part of the external acoustic meatus. GOC:tfm An epithelial cell that is part of the lacrimal drainage system. FMA:70559 epithelial cell of lacrimal duct epithelial cell of lacrimal drainage system true An epithelial cell that is part of the lacrimal drainage system. GOC:tfm PMID:22594785 An epithelial cell that is part of the lacrimal sac. FMA:70560 epithelial cell of lacrimal sac An epithelial cell that is part of the lacrimal sac. GOC:tfm An epithelial cell that is part of the nasolacrimal duct. FMA:70561 epithelial cell of nasolacrimal duct An epithelial cell that is part of the nasolacrimal duct. GOC:tfm A smooth muscle cell that is part of the ciliary body. FMA:70610 smooth muscle cell of ciliary body ciliary muscle cell true A smooth muscle cell that is part of the ciliary body. GOC:tfm smooth muscle cell of ciliary body FMA:70610 A mesothelial cell that is part of the anterior chamber of eyeball. FMA:70615 mesothelial cell of anterior chamber of eye A mesothelial cell that is part of the anterior chamber of eyeball. GOC:tfm An epithelial cell that is part of the sweat gland. FMA:70952 epithelial cell of sweat gland An epithelial cell that is part of the sweat gland. GOC:tfm An epithelial cell that is part of the nephron. FMA:70965 epithelial cell of nephron An epithelial cell that is part of the nephron. GOC:tfm An epithelial cell that is part of the glomerular capsule. FMA:70966 KUPO:0001034 Bowmans capsule epithelial cell epithelial cell of Bowman's capsule epithelial cell of glomerular capsule An epithelial cell that is part of the glomerular capsule. GOC:tfm epithelial cell of Bowman's capsule FMA:70966 An epithelial cell that is part of the collecting duct of renal tubule. FMA:70982 KUPO:0001059 epithelial cell of renal collecting tubule kidney collecting duct epithelial cell true true An epithelial cell that is part of the collecting duct of renal tubule. GOC:tfm epithelial cell of renal collecting tubule FMA:70982 A mesothelial cell that is part of the parietal peritoneum. FMA:72142 mesothelial cell of parietal peritoneum A mesothelial cell that is part of the parietal peritoneum. GOC:tfm A mesothelial cell that is part of the visceral peritoneum. FMA:72143 mesothelial cell of visceral peritoneum A mesothelial cell that is part of the visceral peritoneum. GOC:tfm A chromaffin cell that is part of the ovary. FMA:74319 chromaffin cell of ovary true A chromaffin cell that is part of the ovary. GOC:tfm A chromaffin cell that is part of the right ovary. FMA:74320 chromaffin cell of right ovary A chromaffin cell that is part of the right ovary. GOC:tfm A chromaffin cell that is part of the left ovary. FMA:74321 chromaffin cell of left ovary A chromaffin cell that is part of the left ovary. GOC:tfm A transitional myocyte that is part of the sinoatrial node. FMA:83384 transitinal myocyte of sinuatrial node transitional myocyte of sinoatrial node true A transitional myocyte that is part of the sinoatrial node. GOC:tfm A Purkinje myocyte that is part of the atrioventricular node. FMA:83386 Purkinje myocyte of atrioventricular node true A Purkinje myocyte that is part of the atrioventricular node. GOC:tfm A myocardial endocrine cell that is part of the interventricular septum. FMA:83390 myocardial endocrine cell of interventricular septum true A myocardial endocrine cell that is part of the interventricular septum. GOC:tfm A smooth muscle cell that is part of the prostate gland. FMA:84583 smooth muscle fiber of prostate smooth muscle cell of prostate true A smooth muscle cell that is part of the prostate gland. GOC:tfm smooth muscle fiber of prostate FMA:84583 An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. FMA:86481 epithelial cell of bile duct cholangiocyte true An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. GOC:tfm PMID:16550043 PMID:18356246 A mesothelial cell that is part of the peritoneum. FMA:86736 peritoneal mesothelial cell mesothelial cell of peritoneum A mesothelial cell that is part of the peritoneum. GOC:tfm peritoneal mesothelial cell FMA:86736 A mesothelial cell that is part of the pleura. FMA:86737 pleural mesothelial cell mesothelial cell of pleura A mesothelial cell that is part of the pleura. GOC:tfm pleural mesothelial cell FMA:86737 A mesothelial cell that is part of the parietal pleura. FMA:86738 mesothelial cell of parietal pleura A mesothelial cell that is part of the parietal pleura. GOC:tfm A mesothelial cell that is part of the visceral pleura. FMA:86739 mesothelial cell of visceral pleura A mesothelial cell that is part of the visceral pleura. GOC:tfm An epithelial cell that is part of a nephron tubule. FMA:86785 KUPO:0001022 kidney tubule epithelial cell This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. nephron tubule epithelial cell An epithelial cell that is part of a nephron tubule. GOC:tfm A goblet cell that is part of the small intestine. FMA:86929 goblet cell of epithelium of small intestine goblet cell of small intestine small intestinal goblet cell small intestine goblet cell A goblet cell that is part of the small intestine. GOC:tfm small intestinal goblet cell FMA:86929 A cell that is part of a kidney. KUPO:0001010 kidney cell A cell that is part of kidney interstitium. KUPO:0001013 kidney interstitial cell A cell that is part of a renal medulla. KUPO:0001017 kidney medulla cell A cell that is part of a renal pelvis. KUPO:0001018 kidney pelvis cell A cell that is part of a nephron tubule. KUPO:0001020 kidney tubule cell KUPO:0001023 kidney glomerular epithelial cell An epithelial cell that is part of a renal medulla collecting duct. KUPO:0001060 kidney medulla collecting duct epithelial cell An epithelial cell that is part of a cortical collecting duct. KUPO:0001063 kidney cortex collecting duct epithelial cell KUPO:0001115 lower urinary tract cell KUPO:0001116 ureteral cell KUPO:0001015 kidney nerve cell KUPO:0001021 kidney corpuscule cell true KUPO:0001091 kidney cortex interstitial cell true KUPO:0001092 kidney medulla interstitial cell true true KUPO:0001102 kidney interstitial fibroblast KUPO:0001113 kidney pelvis smooth muscle cell true true KUPO:0001119 ureter adventitial cell true KUPO:0001130 kidney cortex collecting duct principal cell true KUPO:0001036 glomerular cell true KUPO:0001014 kidney blood vessel cell true KUPO:0001029 kidney arterial blood vessel cell true KUPO:0001030 kidney capillary endothelial cell KUPO:0001031 kidney venous blood vessel cell true KUPO:0001118 ureter smooth muscle cell true true KUPO:0001037 glomerular capillary endothelial cell true KUPO:0001038 kidney afferent arteriole cell true KUPO:0001077 kidney cortex artery cell true KUPO:0001084 kidney cortex vein cell true KUPO:0001096 Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure. kidney artery smooth muscle cell KUPO:0001098 Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure. kidney arteriole smooth muscle cell KUPO:0001039 kidney afferent arteriole endothelial cell true KUPO:0001040 kidney afferent arteriole smooth muscle cell KUPO:0001078 arcuate artery cell true KUPO:0001081 interlobular artery cell true KUPO:0001079 arcuate artery endothelial cell true KUPO:0001080 arcuate artery smooth muscle cell KUPO:0001082 interlobulary artery endothelial cell KUPO:0001083 interlobulary artery smooth muscle cell A cell that is part of a collecting duct of renal tubule. KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell kidney collecting duct cell KUPO:0001120 bladder cell KUPO:0001123 urethra cell KUPO:0001128 kidney collecting duct principal cell true An epithelial cell of the exocrine pancreas. FMA:70986 exocrine pancreas cell epithelial cell of exocrine pancreas An epithelial cell of the exocrine pancreas. GOC:tfm The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. intestinal enteroendocrine cell The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. MP:0010802 endothelial cell of lung pulmonary vessel endothelial cell lung endothelial cell BTO:0001141 PAEC cell pulmonary artery endothelial cell PAEC cell BTO:0001141 A vascular endothelial cell found in colon blood vessels. CALOHA:TS-2397 colon endothelial cells colonic endothelial cell colon endothelial cell A vascular endothelial cell found in colon blood vessels. NPX:PDR https://orcid.org/0000-0001-5208-3432 colon endothelial cells CALOHA:TS-2397 colonic endothelial cell CALOHA:TS-2397 Cell of the nasopharyngeal epithelium. CALOHA:TS-2398 nasopharynx respiratory epithelial cells nasopharyngeal epithelial cell Cell of the nasopharyngeal epithelium. NPX:PDR nasopharynx respiratory epithelial cells CALOHA:TS-2398 Squamous cell of uterine cervix epithelium. CALOHA:TS-1251 cervix squamous cell cervix squamous epithelial cell cervix, uterine squamous epithelial cells uterine cervix squamous epithelial cell uterine cervix squamous epithelial cells uterine cervix squamous cell Squamous cell of uterine cervix epithelium. NPX:PDR cervix squamous cell CALOHA:TS-1251 cervix squamous epithelial cell CALOHA:TS-1251 cervix, uterine squamous epithelial cells CALOHA:TS-1251 uterine cervix squamous epithelial cell CALOHA:TS-1251 uterine cervix squamous epithelial cells CALOHA:TS-1251 Squamous cell of oral epithelium. CALOHA:TS-1252 oral cavity mucosa squamous cell oral cavity mucosa squamous epithelial cell oral mucosa squamous epithelial cell oral mucosa squamous epithelial cells oral mucosa squamous cell Squamous cell of oral epithelium. NPX:PDR oral cavity mucosa squamous cell CALOHA:TS-1252 oral cavity mucosa squamous epithelial cell CALOHA:TS-1252 oral mucosa squamous epithelial cell CALOHA:TS-1252 oral mucosa squamous epithelial cells CALOHA:TS-1252 Squamous cell of tonsil epithelium. CALOHA:TS-1253 tonsil squamous epithelial cell tonsil squamous epithelial cells tonsillar squamous cell tonsillar squamous epithelial cell tonsil squamous cell Squamous cell of tonsil epithelium. NPX:PDR tonsil squamous epithelial cell CALOHA:TS-1253 tonsil squamous epithelial cells CALOHA:TS-1253 tonsillar squamous cell CALOHA:TS-1253 tonsillar squamous epithelial cell CALOHA:TS-1253 Squamous cell of vaginal epithelium. CALOHA:TS-1254 vagina squamous epithelial cell vagina squamous epithelial cells vaginal squamous cell vaginal squamous epithelial cell vagina squamous cell Squamous cell of vaginal epithelium. NPX:PDR vagina squamous epithelial cell CALOHA:TS-1254 vagina squamous epithelial cells CALOHA:TS-1254 vaginal squamous cell CALOHA:TS-1254 vaginal squamous epithelial cell CALOHA:TS-1254 Glial cell of cerebral cortex. CALOHA:TS-1256 brain cortex glial cell cerebral cortex glial cells cerebrum cortex glial cell cerebral cortex glial cell Glial cell of cerebral cortex. NPX:PDR brain cortex glial cell CALOHA:TS-1256 cerebral cortex glial cells CALOHA:TS-1256 cerebrum cortex glial cell CALOHA:TS-1256 Glial cell of lateral ventricle. CALOHA:TS-1258 lateral ventricle glial cells lateral ventricle glial cell Glial cell of lateral ventricle. NPX:PDR lateral ventricle glial cells CALOHA:TS-1258 Neuron of lateral ventricle. CALOHA:TS-1261 lateral ventricle neural cell lateral ventricle neuronal cell lateral ventricle neuronal cells lateral ventricle neuron Neuron of lateral ventricle. NPX:PDR lateral ventricle neural cell CALOHA:TS-1261 lateral ventricle neuronal cell CALOHA:TS-1261 lateral ventricle neuronal cells CALOHA:TS-1261 Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1271 appendix glandular cells caecal appendix glandular cell cecal appendix glandular cell vermiform appendix glandular cell appendix glandular cell Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR appendix glandular cells CALOHA:TS-1271 caecal appendix glandular cell CALOHA:TS-1271 cecal appendix glandular cell CALOHA:TS-1271 vermiform appendix glandular cell CALOHA:TS-1271 Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts. CALOHA:TS-1272 breast glandular cell breast glandular cells mammary glandular cell mammary gland glandular cell Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts. HPA:HPA NPX:PDR breast glandular cell CALOHA:TS-1272 breast glandular cells CALOHA:TS-1272 mammary glandular cell CALOHA:TS-1272 Glandular cell of uterine cervix epithelium. CALOHA:TS-1273 cervix glandular cell cervix, uterine glandular cell cervix, uterine glandular cells uterine cervix glandular cell Glandular cell of uterine cervix epithelium. NPX:PDR cervix glandular cell CALOHA:TS-1273 cervix, uterine glandular cell CALOHA:TS-1273 cervix, uterine glandular cells CALOHA:TS-1273 Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1274 colon glandular cells colon glandular cell Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR colon glandular cells CALOHA:TS-1274 Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. CALOHA:TS-1275 duodenum glandular cells duodenum glandular cell Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. NPX:PDR duodenum glandular cells CALOHA:TS-1275 Glandular cell of epididymal epithelium. CALOHA:TS-1276 epididymal glandular cell epididymis glandular cells epididymis glandular cell Glandular cell of epididymal epithelium. NPX:PDR epididymal glandular cell CALOHA:TS-1276 epididymis glandular cells CALOHA:TS-1276 Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells. CALOHA:TS-1277 fallopian tube glandular cell fallopian tube glandular cells uterine tube glandular cell oviduct glandular cell Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells. HPA:HPA NPX:PDR fallopian tube glandular cell CALOHA:TS-1277 fallopian tube glandular cells CALOHA:TS-1277 uterine tube glandular cell CALOHA:TS-1277 Glandular cell of gallbladder epithelium. CALOHA:TS-1278 gall bladder glandular cell gall bladder glandular cells gallbladder glandular cells gallbladder glandular cell Glandular cell of gallbladder epithelium. NPX:PDR gall bladder glandular cell FMA:7202 gall bladder glandular cells CALOHA:TS-1278 gallbladder glandular cells CALOHA:TS-1278 Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells. CALOHA:TS-1279 parathyroid gland glandular cell parathyroid gland glandular cells parathyroid glandular cell Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells. HPA:HPA NPX:PDR parathyroid gland glandular cell CALOHA:TS-1279 parathyroid gland glandular cells CALOHA:TS-1279 Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1281 rectal glandular cell rectum glandular cells rectum glandular cell Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR rectal glandular cell CALOHA:TS-1281 rectum glandular cells CALOHA:TS-1281 Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts. CALOHA:TS-1282 salivary gland glandular cells salivary gland glandular cell Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts. HPA:HPA NPX:PDR salivary gland glandular cells CALOHA:TS-1282 Glandular cell of seminal vesicle epithelium. CALOHA:TS-1283 seminal vesicle glandular cells seminal vesicle glandular cell Glandular cell of seminal vesicle epithelium. NPX:PDR seminal vesicle glandular cells CALOHA:TS-1283 A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . CALOHA:TS-1286 FMA:86928 small bowel glandular cell small intestinal glandular cell small intestine glandular cells small intestine glandular cell A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . NCI_Thesaurus:Small_Intestinal_Glandular_Cell NPX:PDR small bowel glandular cell CALOHA:TS-1286 small intestinal glandular cell CALOHA:TS-1286 small intestine glandular cells CALOHA:TS-1286 Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. BTO:0000028 CALOHA:TS-1242 exocrine pancreas glandular cell pancreas exocrine glandular cells pancreas exocrine glandular cell Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. HPA:HPA NPX:PDR exocrine pancreas glandular cell CALOHA:TS-1242 pancreas exocrine glandular cells CALOHA:TS-1242 Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens. CALOHA:TS-2177 adrenal gland glandular cells adrenal glandular cell suprarenal gland glandular cell adrenal gland glandular cell Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens. NPX:PDR adrenal gland glandular cells CALOHA:TS-2177 adrenal glandular cell CALOHA:TS-2177 suprarenal gland glandular cell CALOHA:TS-2177 Endothelial cells forming the walls of the capillaries within the cerebral cortex. CALOHA:TS-2372 cerebral cortex endothelial cells endothelial cells of cerebral cortex cerebral cortex endothelial cell Endothelial cells forming the walls of the capillaries within the cerebral cortex. NPX:PDR cerebral cortex endothelial cells CALOHA:TS-2372 endothelial cells of cerebral cortex CALOHA:TS-2372 Circulating macrophages and tissue macrophages (alveolar macrophages) of lung. CALOHA:TS-0576 lung macrophages lung macrophage Circulating macrophages and tissue macrophages (alveolar macrophages) of lung. HPA:HPA NPX:PDR lung macrophages CALOHA:TS-0576 Fibroblast from foreskin. CALOHA:TS-0384 BJ fibroblast foreskin fibroblast Fibroblast from foreskin. NPX:PDR Fibroblast from muscle organ. CALOHA:TS-0643 muscle fibroblast Fibroblast from muscle organ. NPX:PDR Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells bone marrow hematopoietic cell Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. NPX:PDR bone marrow hematopoietic cells CALOHA:TS-2109 bone marrow poietic cells CALOHA:TS-2109 Neuron of the cerebellum. CALOHA:TS-2359 FMA:84665 cerebellum neuron cerebellar neuron Neuron of the cerebellum. NPX:PDR cerebellum neuron CALOHA:TS-2359 A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. 2014-02-11T17:29:04Z CL:2000001 peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. GOC:TermGenie A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization. 2014-02-20T23:06:41Z BTO:0002770 BTO:0005756 NCIT:C32429 decidua cell decidual stromal cell CL:2000002 decidual cell A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization. BTO:0002770 NCIT:C32429 PMID:30013421 PMID:30429548 Wiki:Decidual_cells&oldid=937509751 Wiki:Decidualization&oldid=908981933 decidua cell BTO:0002770 NCIT:C32429 decidual stromal cell BTO:0005756 PMID:11719592 Any cell that is part of a pituitary gland. 2014-03-26T22:14:56Z CL:2000004 pituitary gland cell Any cell that is part of a pituitary gland. GOC:TermGenie Any blood vessel endothelial cell that is part of a microvascular endothelium. 2014-06-04T15:07:42Z CL:2000008 microvascular endothelial cell Any blood vessel endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any blood vessel endothelial cell that is part of a dermis. 2014-06-04T15:12:06Z CL:2000010 dermis blood vessel endothelial cell Any blood vessel endothelial cell that is part of a dermis. GOC:TermGenie Any endothelial cell of lymphatic vessel that is part of a dermis. 2014-06-04T15:15:08Z CL:2000011 dermis lymphatic vessel endothelial cell Any endothelial cell of lymphatic vessel that is part of a dermis. GOC:TermGenie Any skin fibroblast that is part of a pedal digit skin. 2014-06-04T15:16:44Z CL:2000012 fibroblast of pedal digit skin Any skin fibroblast that is part of a pedal digit skin. GOC:TermGenie Any skin fibroblast that is part of a skin of abdomen. 2014-06-04T15:18:16Z CL:2000013 fibroblast of skin of abdomen Any skin fibroblast that is part of a skin of abdomen. GOC:TermGenie Any skin fibroblast that is part of a upper leg skin. 2014-06-04T15:19:44Z CL:2000014 fibroblast of upper leg skin Any skin fibroblast that is part of a upper leg skin. GOC:TermGenie Any skin fibroblast that is part of a arm. 2014-06-04T15:29:06Z CL:2000015 fibroblast of arm Any skin fibroblast that is part of a arm. GOC:TermGenie Any lung endothelial cell that is part of a microvascular endothelium. 2014-06-04T16:00:56Z CL:2000016 lung microvascular endothelial cell Any lung endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any fibroblast that is part of a periodontal ligament. 2014-06-04T16:50:33Z CL:2000017 fibroblast of peridontal ligament Any fibroblast that is part of a periodontal ligament. GOC:TermGenie Any endothelial cell of artery that is part of a coronary artery. 2014-06-04T17:08:47Z CL:2000018 endothelial cell of coronary artery Any endothelial cell of artery that is part of a coronary artery. GOC:TermGenie Any native cell that is part of a inner cell mass. 2014-06-24T23:16:53Z CL:2000020 inner cell mass cell Any native cell that is part of a inner cell mass. GOC:TermGenie Any native cell that is part of a sebaceous gland. 2014-06-24T23:17:00Z CL:2000021 sebaceous gland cell Any native cell that is part of a sebaceous gland. GOC:TermGenie Any native cell that is part of a cardiac septum. 2014-06-24T23:17:07Z CL:2000022 cardiac septum cell Any native cell that is part of a cardiac septum. GOC:TermGenie Any neuron that is part of a central nervous system. 2014-06-25T01:17:43Z CL:2000029 central nervous system neuron Any neuron that is part of a central nervous system. GOC:TermGenie Any native cell that is part of a hypothalamus. 2014-06-25T01:17:50Z CL:2000030 hypothalamus cell Any native cell that is part of a hypothalamus. GOC:TermGenie A neuron that is part of a peripheral nervous system. 2014-06-25T02:28:17Z FMA:84664 PNS neuron peripheral neuron CL:2000032 peripheral nervous system neuron A neuron that is part of a peripheral nervous system. GOC:TermGenie ISBN:0721662544 Any microvascular endothelial cell that is part of a urinary bladder. 2014-07-09T00:04:47Z CL:2000040 bladder microvascular endothelial cell Any microvascular endothelial cell that is part of a urinary bladder. GOC:TermGenie Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium. 2014-07-09T00:09:54Z CL:2000041 dermis microvascular lymphatic vessel endothelial cell Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium. GOC:TermGenie Any fibroblast that is part of a embryo. 2014-07-09T00:12:00Z CL:2000042 embryonic fibroblast Any fibroblast that is part of a embryo. GOC:TermGenie Any microvascular endothelial cell that is part of a brain. 2014-07-09T00:24:53Z CL:2000044 brain microvascular endothelial cell Any microvascular endothelial cell that is part of a brain. GOC:TermGenie Any cardiac muscle cell that is part of a cardiac ventricle. 2014-08-12T20:50:28Z CL:2000046 ventricular cardiac muscle cell Any cardiac muscle cell that is part of a cardiac ventricle. GOC:TermGenie Any motor neuron that is part of a brainstem. 2014-10-02T23:52:53Z CL:2000047 brainstem motor neuron Any motor neuron that is part of a brainstem. GOC:TermGenie Any fibroblast that is part of a spleen. 2014-10-06T18:58:47Z CL:2000051 splenic fibroblast Any fibroblast that is part of a spleen. GOC:TermGenie Any endothelial cell of artery that is part of a umbilical cord. 2014-10-06T19:01:48Z CL:2000052 http://www.sciencellonline.com/site/productInformation.php?keyword=8010 umbilical artery endothelial cell Any endothelial cell of artery that is part of a umbilical cord. GOC:TermGenie Any endothelial cell that is part of a spleen. 2014-10-06T19:06:04Z CL:2000053 http://www.sciencellonline.com/site/productInformation.php?keyword=5500 splenic endothelial cell Any endothelial cell that is part of a spleen. GOC:TermGenie Any dendritic cell that is part of a liver. 2014-10-06T19:16:11Z hepatic dendritic cell CL:2000055 http://www.jleukbio.org/content/66/2/322.abstract liver dendritic cell Any dendritic cell that is part of a liver. GOC:TermGenie Any microvascular endothelial cell that is part of a prostate gland. 2014-10-07T17:46:27Z CL:2000059 http://www.sciencellonline.com/site/productInformation.php?keyword=4400 prostate gland microvascular endothelial cell Any microvascular endothelial cell that is part of a prostate gland. GOC:TermGenie Any mesenchymal stem cell that is part of a placenta. 2014-10-07T17:51:11Z CL:2000061 http://www.sciencellonline.com/site/productInformation.php?keyword=7140 placental amniotic mesenchymal stromal cell Any mesenchymal stem cell that is part of a placenta. GOC:TermGenie Any fibroblast that is part of a female gonad. 2014-10-07T17:57:42Z CL:2000063 http://www.sciencellonline.com/site/productInformation.php?keyword=7330 ovarian fibroblast Any fibroblast that is part of a female gonad. GOC:TermGenie Any epithelial cell that is part of a female gonad. 2014-10-07T17:59:13Z CL:2000064 http://www.sciencellonline.com/site/productInformation.php?keyword=7310 ovarian surface epithelial cell Any epithelial cell that is part of a female gonad. GOC:TermGenie Any microvascular endothelial cell that is part of a female urethra. 2014-10-07T18:18:01Z CL:2000065 http://www.sciencellonline.com/site/productInformation.php?keyword=7300 ovarian microvascular endothelial cell Any microvascular endothelial cell that is part of a female urethra. GOC:TermGenie Any fibroblast that is part of a cardiac ventricle. 2014-10-07T18:35:38Z CL:2000066 http://www.sciencellonline.com/site/productInformation.php?keyword=6310 cardiac ventricle fibroblast Any fibroblast that is part of a cardiac ventricle. GOC:TermGenie Any fibroblast that is part of a cardiac atrium. 2014-10-07T18:36:54Z CL:2000067 http://www.sciencellonline.com/site/productInformation.php?keyword=6320 cardiac atrium fibroblast Any fibroblast that is part of a cardiac atrium. GOC:TermGenie Any fibroblast that is part of a pericardium. 2014-10-07T18:38:06Z CL:2000068 http://www.sciencellonline.com/site/productInformation.php?keyword=6430 pericardium fibroblast Any fibroblast that is part of a pericardium. GOC:TermGenie Any fibroblast that is part of a gallbladder. 2014-10-07T18:41:43Z CL:2000069 http://www.sciencellonline.com/site/productInformation.php?keyword=5430 gallbladder fibroblast Any fibroblast that is part of a gallbladder. GOC:TermGenie Any fibroblast that is part of a optic choroid. 2014-10-07T18:50:43Z CL:2000070 http://www.sciencellonline.com/site/productInformation.php?keyword=6620 optic choroid fibroblast Any fibroblast that is part of a optic choroid. GOC:TermGenie Any microvascular endothelial cell that is part of a breast. 2014-10-07T19:55:30Z CL:2000071 http://www.sciencellonline.com/site/productInformation.php?keyword=7600 mammary microvascular endothelial cell Any microvascular endothelial cell that is part of a breast. GOC:TermGenie Any microvascular endothelial cell that is part of a adipose tissue. 2014-10-07T22:13:45Z CL:2000072 http://www.sciencellonline.com/site/productInformation.php?keyword=7200 adipose microvascular endothelial cell Any microvascular endothelial cell that is part of a adipose tissue. GOC:TermGenie Any migratory neural crest cell that is part of a cardiac neural crest. 2014-11-05T01:18:43Z cardiac neural crest cell CL:2000073 migratory cardiac neural crest cell Any migratory neural crest cell that is part of a cardiac neural crest. GOC:TermGenie cardiac neural crest cell PMID:33060096 Any leukocyte that is part of a spleen. 2014-11-05T01:26:50Z CL:2000074 Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology. splenocyte Any leukocyte that is part of a spleen. GOC:TermGenie Any vein endothelial cell that is part of a hindlimb stylopod. 2014-12-02T18:40:47Z CL:2000076 hindlimb stylopod vein endothelial cell Any vein endothelial cell that is part of a hindlimb stylopod. GOC:TermGenie Any mesenchymal stem cell of the bone marrow that is part of a femur. 2014-12-02T19:07:31Z CL:2000079 mesenchymal stem cell of femoral bone marrow Any mesenchymal stem cell of the bone marrow that is part of a femur. GOC:TermGenie Any mesenchymal stem cell of adipose tissue that is part of an abdomen. 2014-12-02T19:10:34Z mesenchymal stem cell of abdominal adipose CL:2000080 mesenchymal stem cell of abdominal adipose tissue Any mesenchymal stem cell of adipose tissue that is part of an abdomen. GOC:TermGenie Any mononuclear cell that is part of a umbilical cord. 2014-12-02T20:14:16Z CL:2000085 mononuclear cell of umbilical cord Any mononuclear cell that is part of a umbilical cord. GOC:TermGenie Any microvascular endothelial cell that is part of a endometrial blood vessel. 2015-03-31T21:02:36Z CL:2000091 endometrial microvascular endothelial cell Any microvascular endothelial cell that is part of a endometrial blood vessel. GOC:TermGenie Any fibroblast of lung that is part of a bronchus. 2015-03-31T21:16:22Z CL:2000093 bronchus fibroblast of lung Any fibroblast of lung that is part of a bronchus. GOC:TermGenie Any hematopoietic stem cell that is part of a umbilical cord blood. 2015-05-26T18:58:34Z CL:2000095 cord blood hematopoietic stem cell Any hematopoietic stem cell that is part of a umbilical cord blood. GOC:TermGenie A ciliated epithelial cell of the esophagus. 2019-02-09T16:40:30Z CL:3000000 ciliated epithelial cell of esophagus A ciliated epithelial cell of the esophagus. GOC:CellBLAST PMID:29802404 Peripheral sensory neuron. 2019-02-25T19:34:33Z CL:3000004 peripheral sensory neuron Peripheral sensory neuron. GOC:CellBLAST PMID:30096314 A fibroblast that is part of the breast. breast fibroblast fibroblast of breast A cell that is part of the brain vasculature. brain vascular cell A cell that is part of the brain vasculature. DOI:10.1101/2022.10.12.511898 A GABAergic inhibitory neuron that is derived from the midbrain. midbrain-derived inhibitory neuron A GABAergic inhibitory neuron that is derived from the midbrain. DOI:10.1101/2022.10.12.511898 A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli. somatosensory neuron A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli. PMID:22865660 Any capillary endothelial cell that is part of a lung. 2021-11-23T02:31:40Z lung capillary endothelial cell pulmonary capillary endothelial cell A stromal cell that is part of the thymus. 2022-07-08T11:39:38Z thymic stromal cell stromal cell of thymus A stromal cell that is part of the thymus. doi:10.1038/s41467-020-20082-7 A fibroblast that is located in the renal medulla interstitium. 2022-07-05T12:13:40Z kidney medullary fibroblast It has been noted that inner medullary fibroblasts are involved in the regulation of water and electrolyte homeostasis. renal medullary fibroblast A fibroblast that is located in the renal medulla interstitium. PMID:10559635 It has been noted that inner medullary fibroblasts are involved in the regulation of water and electrolyte homeostasis. PMID:10559635 A fibroblast that is located in the renal cortical interstitium. 2022-07-05T15:50:17Z kidney cortical fibroblast Renal cortical fibroblasts have key roles in mediating intercellular communication with neighboring/infiltrating cells and extracellular matrix and maintenance of renal tissue architecture. They additionally have an endocrine function in the production of epoetin. renal cortical fibroblast A fibroblast that is located in the renal cortical interstitium. PMID:10559635 Renal cortical fibroblasts have key roles in mediating intercellular communication with neighboring/infiltrating cells and extracellular matrix and maintenance of renal tissue architecture. They additionally have an endocrine function in the production of epoetin. PMID:16230044 A lymphocyte located in blood. 2022-11-04T14:40:00Z blood lymphocyte A lymphocyte located in blood. Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. "Interstitial cell" is a morphological term and refers to a variety of cells with differing origins and phenotypes. 2022-11-30T14:35:08Z interstitial cell Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. "Interstitial cell" is a morphological term and refers to a variety of cells with differing origins and phenotypes. PMID:24987007 An interstitial cell that is part of a cardiac valve leaflet. Along with valve endothelial cells, a valve interstitial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes. 2022-12-06T14:18:45Z VIC cardiac valve interstitial cell valvular interstitial cell Activated valve interstitial cells undergo continual turn over into deactivated fibroblasts and other cell fates (such as apoptosis). valve interstitial cell An interstitial cell that is part of a cardiac valve leaflet. Along with valve endothelial cells, a valve interstitial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes. PMID:25311230 https://doi.org/10.1098/rsif.2017.0580 https://doi.org/10.1161/ATVBAHA.120.314789 https://doi.org/10.1161/JAHA.117.006339 https://doi.org/10.2353/ajpath.2007.070251 VIC PMID:25311230 PMID:30796046 valvular interstitial cell PMID:25311230 Activated valve interstitial cells undergo continual turn over into deactivated fibroblasts and other cell fates (such as apoptosis). PMID:25311230 An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes. 2022-12-09T11:58:49Z VEC valvular endothelial cell At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration. valve endothelial cell An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes. PMID:25311230 VEC PMID:25311230 PMID:30796046 valvular endothelial cell PMID:25311230 At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration. PMID:25311230 A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. 2023-01-25T11:06:01Z ciliated cell of the respiratory tract respiratory ciliated cell A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. PMID:18757316 PMID:21364219 A dental pulp cell that possesses stem-cell-like qualities, including self-renewal capability and multi-lineage differentiation. 2023-01-10T14:02:02Z DPSC dental pulp stem cell A dental pulp cell that possesses stem-cell-like qualities, including self-renewal capability and multi-lineage differentiation. DOI:10.1177/154405910208100806 DPSC A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium. 2023-02-09T11:25:14Z ciliated cell of the uterus uterine ciliated cell ciliated cell of the endometrium endometrium ciliated epithelial cell In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted. endometrial ciliated epithelial cell A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium. doi:10.1038/s41591-020-1040-z https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells In human samples, the expression of FOXJ1 protein, a regulator for motile cilia with epithelial lineage identity, has been noted. ttps://www.nature.com/articles/s41591-020-1040-z A macrophage that expresses the T cell receptor complex at the cell surface. 2023-09-26T12:27:14Z T cell receptor positive macrophage TCR+ macrophage TCR.macs TCR-positive macrophage A macrophage that expresses the T cell receptor complex at the cell surface. PMID:26074923 T cell receptor positive macrophage PMID:26074923 TCR+ macrophage PMID:26074923 TCR.macs PMID:37500727 An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. https://orcid.org/0000-0002-1425-877X 2023-10-13T11:22:42Z UB cell ureteric bud cell PMID:9374839 An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. PMID:17133361 PMID:24183650 PMID:9374839 UB cell PMID:24183650 A(n) endothelial cell that is part of a(n) venule of lymph node. endothelial cell of venule of lymph node A(n) endothelial cell that is part of a(n) venule of lymph node. PMID:28217126 A(n) endothelial cell that is part of a(n) arteriole of lymph node. endothelial cell of arteriole of lymph node A(n) endothelial cell that is part of a(n) arteriole of lymph node. PMID:28217126 A(n) serous secreting cell that is part of a(n) bronchus submucosal gland. serous secreting cell of bronchus submucosal gland A(n) serous secreting cell that is part of a(n) bronchus submucosal gland. PMID:5487122 PMID:9651178 A(n) vein endothelial cell that is part of a(n) respiratory system. vein endothelial cell of respiratory system A(n) vein endothelial cell that is part of a(n) respiratory system. PMID:34030460 A megakaryocyte that is resident in the lung connective tissue. 2023-03-16T11:31:23Z lung resident megakaryocyte lung-resident megakaryocyte MKL lung MKs lung megakaryocyte A megakaryocyte that is resident in the lung connective tissue. PMID:33351116 lung resident megakaryocyte PMID:36524131 lung-resident megakaryocyte PMID:36524131 MKL PMID:36524131 lung MKs PMID:33351116 A mucus secreting cell that is part of a submucosal gland of the trachea. 2023-03-16T13:03:13Z tracheal submucosal gland mucous cell mucus secreting cell of trachea gland A mucus secreting cell that is part of a submucosal gland of the trachea. PMID:18931053 PMID:29656943 tracheal submucosal gland mucous cell PMID:18931053 A mucus secreting cell of a submucosal gland of the bronchus. 2023-03-16T15:12:52Z bronchial gland mucous cell mucus secreting cell of bronchus submucosal gland A mucus secreting cell of a submucosal gland of the bronchus. PMID:19965983 bronchial gland mucous cell PMID:5487122 A mucus secreting cell of a submucosal gland of the tracheobronchial tree. 2023-04-20T10:55:50Z mucus secreting cell of tracheobronchial tree submucosal gland A mucus secreting cell of a submucosal gland of the tracheobronchial tree. PMID:30864819 A taste receptor cell that is part of a taste bud of a tongue. 2023-05-03T07:59:58Z gustatory cell of tongue taste receptor cell of tongue A taste receptor cell that is part of a taste bud of a tongue. DOI:10.1111/j.1096-3642.1981.tb01137.x PMID:10052456 PMID:28655883 http://www.nejohnston.org/Birds/documents/AvianTongues_Johnston.pdf gustatory cell of tongue DOI:10.1016/s0022-5320(69)80043-2 A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. 2023-08-22T13:40:28Z perivascular cell A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. PMID:24928499 PMID:27889329 An endothelial cell that is part of a central vein of liver. endothelial cell of central vein endothelial cell of central vein of liver An endothelial cell that is part of a central vein of liver. PMID:28287163 endothelial cell of central vein PMID:28287163 Any mesenchymal stem cell of adipose tissue that is part of an orbital region. 2023-09-18T10:43:00Z OAMSC Orbital ASCs orbital adipose-derived mesenchymal stem cell mesenchymal stem cell of orbital adipose tissue Any mesenchymal stem cell of adipose tissue that is part of an orbital region. OAMSC PMID:31377878 Orbital ASCs PMID:30210548 orbital adipose-derived mesenchymal stem cell PMID:31377878 Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. Damion Dooley Foodon product type https://en.wikipedia.org/wiki/Food The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations. food product A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. mammalian meat food product This class includes food products which are derived from or produced by a plant. plant food product Cabbage or headed cabbage (comprising several cultivars of Brassica oleracea) is a leafy green or purple biennial plant, grown as an annual vegetable crop for its dense-leaved heads. https://en.wikipedia.org/wiki/Cabbage cabbage food product A seafood product is a vertebrate or invertibrate organism from an aquatic environment. Some of the subclasses are currently freshwater organisms. Damion Dooley animal seafood product fermented dairy food product fermented fish or seafood food product sea water fish food product A food product derived from plant fruit. plant fruit food product sugar condiment A lipid material derived from plants. Physically, oils are liquid at room temperature. Damion Dooley vegetable oil food product A food product which is derived from or produced by an animal that has a vertibrae. Damion Dooley vertebrate animal food product cereal grain food product Damion Dooley 2019-06-11T07:25:19Z alcoholic beverage SIREN DB annotation: * liquid FOODON:03430130 * microbial/enzymatic modification process FOODON:03460119 * curing or aging process FOODON:03460253 fermented beverage fermented grain beverage A food product made from an avian egg. avian egg food product bovine dairy food product cattle dairy food product A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. Damion Dooley https://en.wikipedia.org/wiki/Condiment condiment condiment food product fruit juice food product A food product deriving primarily from corn (maize). Damion Dooley maize food product maize (corn) food product plant inflorescence food product cruciferous food product cruciferous inflorescence food product The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling. Damion Dooley nut food product plant seed food product plant lipid food product plant stem food product invertebrate animal food product A product of the dry seeds of plants of the genus Pisum. Damion Dooley http://en.wikipedia.org/wiki/Legume dry pea food product PULSES are annual leguminous crops yielding from one to 12 grains or seeds of variable size, shape and colour within a pod. They are used for both food and feed. The term "pulses" is limited to crops harvested solely for dry grain, thereby excludingcrops harvested green for food (green peas, green beans, etc.) which are classified as vegetable crops. Also excluded are those crops used mainly for oil extraction (e.g.soybeand and groundnuts) and leguminous crops (e.g. seeds of clover and alfalfa) that are used exclusively for sowing purposes. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef04e.htm#4.02 pulse pulses pulse food product https://en.wikipedia.org/wiki/Legume#Classification_of_pulses A food product that has some spice or herb as a defining ingredient. A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 https://orcid.org/0000-0001-5275-8866 2023-08-16T10:14:35Z herb or spice spice or herb animal lipid food product A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). Damion Dooley fish food product avian food product A beverage derived from plants. plant derived beverage plant derived fermented beverage nonfermented plant derived beverage product A dairy food product has mammilian milk or a milk component as an ingredient. Damion Dooley dairy product milk product dairy food product milk or milk based food product Are all fermented foods considered preserved to some extent? Damion Dooley food (fermented) Beer is a fermented cereal beverage resulting from the fermentation most commonly of malted barley (though wheat, corn, or rice may included), by a yeast, most commonly Saccharomyces cerevisiae, and flavored by dried flowers of hops, Humulus lupulus. https://en.wikipedia.org/wiki/Beer beer beverage A plant food product which derives from one or more vegetables. FAO definition for vegetable: "Vegetables are plants cultivated both as field crops and garden crops, both in the open and under glass." and also: "Vegetables are grouped according to botanic characteristics as follows: leafy or stem vegetables (e.g., cabbage); fruit-bearing vegetables (e.g., melons); flower vegetables (e.g., cauliflowers); root, bulb and tuberous vegetables (e.g., onion); leguminous vegetables (e.g., green peas); other vegetables (e.g., green maize and mushrooms)." vegetable food product Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. botanical fruit food product Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. http://eurovoc.europa.eu/drupal/?q=request&amp;uri=http://eurovoc.europa.eu/1115 http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119 http://www.fao.org/pollination/resources/glossary/en/ https://en.wikipedia.org/wiki/Fruit A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995) http://www.fao.org/pollination/resources/glossary/en/ legume legume food product A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. Regarding American regulatory aspects of egg products, see this summary: https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077 egg food product A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. Wikipedia:Egg_%28food%29 A hen egg food product is any food product consisting mainly of hen eggs or derivatives. https://en.wikipedia.org/wiki/Egg_as_food hen egg food product shellfish food product A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process. https://orcid.org/0000-0002-8844-9165 food fermentation Hoi-dong is fermented sea mussel http://orcid.org/0000-0002-1816-4260 hoi-dong Fermented meat product is any product made primarily of meat subjected to a fermentation process. Damion Dooley fermented meat product An alcoholic drink (or alcoholic beverage) is a drink that contains ethanol, a type of alcohol produced by fermentation of grains, fruits, or other sources of sugar. Damion Dooley https://en.m.wikipedia.org/wiki/Alcoholic_drink alcoholic beverage animal based refined or partially-refined food product A bean vegetable food product is a human or animal food product - such as a snap, shell or dry bean product - derived from the fruit pod, seed, or leaf of one of several genera of the flowering plant family Fabaceae. Note, this was previously labelled "Bean (vegetable) food product". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope. Damion Dooley bean food product A broad bean food product is a product derived from the broad bean plant. Damion Dooley broad bean food product broccoli food product brussels sprout food product cabbage juice food product A cabbage vegetable food product is a food product derived from the head or leaf portion of a cabbage plant. Damion Dooley 2019-06-27T13:30:10Z https://upload.wikimedia.org/wikipedia/commons/thumb/6/6f/Cabbage_and_cross_section_on_white.jpg/640px-Cabbage_and_cross_section_on_white.jpg cabbage head food product A food product that derives from a cauliflower plant. cauliflower food product cephalopod food product A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. food product component cloves clove food product vegetable corn food product cow milk based food product crustacean food product Damion Dooley Damion Dooley's note: This category was created to organize SIREN inspired food products. It will probably get merged with the upper level 'dietary supplement' food product type items. dietary or therapeutic formulation food product fermented cereal beverage A product made from the North American term for maize (Zea mays) grown for livestock fodder (silage), ethanol, cereal and processed food products. The principal field corn varieties are dent corn, flint corn, flour corn (also known as soft corn) which includes blue corn (Zea mays amylacea), and waxy corn. Damion Dooley dry corn food product dry corn field corn food product field corn sweetener product fish refined food product food flavoring or seasoning product food supplement food product fruit based alcoholic beverage gluten refined food product grain based alcoholic beverage human milk based food product barley malt beverage mollusk food product mollusc food product mussel food product nonalcoholic beverage A food product having peanuts as an ingredient. Damion Dooley 2019-06-19T22:56:38Z SIREN DB annotation: * seed (anatomical part) FOODON:03420155 peanut food product plant based refined or partially-refined food product An edible plant fat or oil product with characteristics that consumers desire such as bland flavour and odour, clear appearance, light colour, stability to oxidation and suitability for frying, and which is the result of a refining process that removes free fatty acids. Damion Dooley plant fat or oil refined food product plant floret vegetable food product A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product. plant fruit as vegetable food product plant head vegetable food product food product by consumer group plant seed vegetable food product A food product deriving from a plant stem or spear part. plant stem or spear food product plant sweetener organ meat product A food product deriving from one or more pumpkins. pumpkin food product rape fat or oil refined food product rapeseed food product refined or partially-refined food product sesame food product soybean refined food product soybean seed (field) food product http://purl.obolibrary.org/obo/FOODON_00002266 A soybean food product is a product derived from the soybean plant. Damion Dooley soy product soybean food product http://purl.obolibrary.org/obo/FOODON_00002265 A food product deriving from one or more squashes. squash food product sugar based cacao food product sugar cane refined or partially-refined food product sunflower food product sweetener food product vitamin and mineral food supplement food product vitamin as food supplement food product A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition) Damion Dooley food product by meal type A food product consisting of food material derived primarily from a single organism. Damion Dooley food product by organism Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience food foodstuff nourishment sustenance This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/ food material requires discussion A process involving the physical transformation of a food source or food product into some derived organic material or food product https://orcid.org/0000-0002-8844-9165 food transformation process Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Damion Dooley https://en.wikipedia.org/wiki/Invertebrate animal invertebrate animal Food material which has been categorized by a characteristic such as granularity or temperature. Damion Dooley This term was renamed from "food product by quality" to align better with COB "characteristic" label, and as well to disambiguate from other use of "quality" as a food grading. This term is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. food material by characteristic A physical object quality which describes a characteristic of some food material. http://orcid.org/0000-0001-8008-8249 food material characteristic A food product consisting of food material derived from ingredients sourced from multiple organisms. Damion Dooley 2019-01-23T22:40:32Z multi-ingredient The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? multi-component food product Dairy cattle are a type of cattle bred for the ability to produce large quantities of milk, from which dairy products are made. This class covers both male and female members of a dairy breed. Damion Dooley https://en.wikipedia.org/wiki/Dairy_cattle 2019-01-26T22:49:27Z dairy cattle https://en.wikipedia.org/wiki/List_of_dairy_cattle_breeds Taurine cattle (Bos taurus taurus), also called European cattle, are a subspecies of domesticated cattle originating in the Near East. Both taurine cattle and indicine cattle (zebus) are descended from the aurochs. Taurine cattle were originally considered a distinct species, but are now typically grouped with zebus and aurochs into one species, Bos taurus. Most modern breeds of cattle are taurine cattle. Damion Dooley 2019-01-28T02:41:04Z taurine cattle An aquatic invertebrate may live entirely beneath the water, or may live upon its surface or on the plants surrounding it. Some breathe air, others breathe water. To move, they may walk, swim, float, skate, fly or glide on their bellies—or they may not move much at all. Because snails are members of gastropod, a subclass of molluscs, ... leading to aquatic invertebrates, we can't make aquatic invertebrates disjoint with terrestrial invertebrates. Damion Dooley https://nature.mdc.mo.gov/discover-nature/general-species-information/aquatic-invertebrate-facts 2019-04-29T19:23:38Z aquatic invertebrate A food product organized by the process which it results from. Damion Dooley 2019-05-23T23:02:07Z food product by process A lipid food product is a food product made primarily of plant or animal fat or oil Damion Dooley 2019-06-11T09:18:41Z fats and oils oils and fats lipid food product A seed of a bean plant from one of several genera of the flowering plant family (Fabaceae). Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet. Damion Dooley https://orcid.org/0000-0001-5275-8866 2020-10-14T07:28:59 bean bean Damion Dooley 2019-07-10T00:16:38Z vetch food product A seed of a vetch plant. Damion Dooley https://en.wikipedia.org/wiki/Vicia 2019-07-10T01:33:15Z vetch seed vetch seed Damion Dooley 2019-07-12T17:18:31Z pea food product Damion Dooley 2019-07-16T15:15:04Z broad bean (raw) A liver food product is a food product that derives from one or more liver organs. Damion Dooley 2019-08-02T18:22:37Z liver food product A kidney food product is a food product that derives from one or more kidney organs Damion Dooley 2019-08-02T18:27:53Z kidney food product A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless. 2019-08-12T23:41:29Z fish cutlet fish steak A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. A whole animal. 2019-08-14T18:02:36Z 2023-08-01T21:25:29Z A whole animal can be dead or alive, but its body must be relatively intact. animal A leaf of a plant that is used for flavoring. The leaves, flowers, or stems of plants, typically excluding vegetables, used for flavoring or as a garnish. https://orcid.org/0000-0001-5275-8866 2019-08-24T15:26:51Z 2023-08-16T10:14:35Z herb food product 2019-08-24T15:43:48Z saffron saffron food product A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). https://en.wikipedia.org/wiki/Vegetarian_cuisine 2019-09-11T21:12:43Z vegetarian food vegetarian food product A seed of a peanut plant (Arachis hypogaea). http://orcid.org/0000-0002-8844-9165 peanut peanut 2020-01-08T00:20:27Z echinoderm food product A genus of plants in the mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants. bok choy vegetable food product bomdong vegetable food product broccolini vegetable food product choy sum vegetable food product collard greens vegetable food product gai lan vegetable food product komatsuna vegetable food product mizuna vegetable food product rutabaga vegetable food product savoy cabbage vegetable food product tatsoi vegetable food product cole crop vegetable food product cruciferous vegetable food product brassica food product 2020-09-09T19:28:43Z Maize plant An orange-yellow pepo fruit of a pumpkin plant. https://orcid.org/0000-0001-5275-8866 2020-10-14T01:29:01 pumpkin pumpkin A pepo fruit varietal of a squash plant (Cucurbita). https://en.wikipedia.org/wiki/Cucurbita https://orcid.org/0000-0001-5275-8866 2020-10-20T12:01:59 squash squash A seed of a sunflower plant (Helianthus annuus) https://en.wikipedia.org/wiki/Sunflower_seed 2020-11-30T04:49:32 sunflower seed sunflower seed (whole kernel) An anatomical part of a plant that is consumed by humans or other animals as food. https://en.wikipedia.org/wiki/Vegetable 2021-02-12T18:49:32 vegetable A pepo fruit of a winter squash plant harvested in the fall. https://en.wikipedia.org/wiki/Winter_squash https://orcid.org/0000-0002-7463-6306 2021-07-22T17:39:12 winter squash winter squash A food product that is derived from some animal 2023-08-01T21:25:29Z animal food product A piece or pieces or amount of substance derived from one or more organisms. 2023-03-02T22:30:19Z organism piece A severed part of an animal that is not a body product. 2023-08-01T21:25:29Z animal piece A characteristic of an animal, plant, fungi or algae, or a substantial piece thereof, which has not had material processing done to it that affects its biochemical composition. 2023-06-18T09:30:05Z raw An animal organ that derives from an animal. 2023-07-13T04:53:21Z 2023-08-01T21:25:29Z animal organ A whole raw fish. 2023-10-05T21:38:04Z fish (raw) Material which is produced by an animal. 2023-08-01T21:25:29Z This includes things like eggs and milk. animal organism substance An egg which is produced by an oviperous animal. 2023-08-01T21:25:29Z animal egg https://ucmp.berkeley.edu/vertebrates/tetrapods/amniota.html 2023-08-01T21:25:29Z animal shelled egg Milk which is produced by animal lactation. 2023-08-01T21:25:29Z animal milk 2023-08-01T21:25:29Z animal blood A muscle tissue cut that is derived from some animal. 2023-08-01T21:25:29Z animal muscle tissue cut Fat derived from some animal. 2023-08-01T21:25:29Z animal fat A whole animal heart that derives from an animal. 2023-08-01T21:25:29Z animal heart A whole animal brain that derives from an animal. 2023-08-01T21:25:29Z animal brain A whole animal kidney that derives from an animal. 2023-08-01T21:25:29Z animal kidney A whole animal liver that derives from an animal. 2023-08-01T21:25:29Z animal liver A whole animal spleen that derives from an animal. 2023-08-01T21:25:29Z animal spleen A whole animal lung that derives from an animal. 2023-08-01T21:25:29Z animal lung A whole animal tongue that derives from an animal. 2023-08-01T21:25:29Z animal tongue A whole animal rectum that derives from an animal. 2023-08-01T21:25:29Z animal rectum A whole animal thymus that derives from an animal. 2023-08-01T21:25:29Z animal thymus A whole animal pancreas that derives from an animal. 2023-08-01T21:25:29Z animal pancreas A whole animal ovary that derives from an animal. 2023-08-01T21:25:29Z animal ovary A whole animal testicle that derives from an animal. 2023-08-01T21:25:29Z animal testis animal testicle A whole animal stomach that derives from an animal. 2023-08-01T21:25:29Z animal stomach A whole animal ear that derives from an animal. 2023-08-01T21:25:29Z animal ear A whole animal small intestine that derives from an animal. 2023-08-01T21:25:29Z animal small intestine A piece of animal meat that is derived from animal. 2023-08-01T21:25:29Z animal meat Damion Dooley Feb 6, 2017: Good meat cut resources to incorporate for Canada: The CFIA Meat Cuts Manual http://www.inspection.gc.ca/food/labelling/meat-cuts/eng/1300126276015/1300126372856 piece of animal meat A whole thigh that derives from an animal. 2023-08-01T21:25:29Z animal thigh A whole drumstick that derives from an animal. 2023-08-01T21:25:29Z animal drumstick A whole wing that derives from an animal. 2023-08-01T21:25:29Z animal wing A whole foot that derives from an animal. 2023-08-01T21:25:29Z animal foot A whole neck that derives from an animal. 2023-08-01T21:25:29Z animal neck A whole back that derives from an animal. 2023-08-01T21:25:29Z animal back A whole leg that derives from an animal. 2023-08-01T21:25:29Z animal leg A whole oviduct that derives from an animal. 2023-08-01T21:25:29Z animal oviduct A whole trachea that derives from an animal. 2023-08-01T21:25:29Z animal trachea A piece of wing that derives from an animal wing. 2023-08-01T21:25:29Z piece of animal wing A piece of neck that derives from an animal neck. 2023-08-01T21:25:29Z piece of animal neck A piece of back that derives from an animal back. 2023-08-01T21:25:29Z piece of animal back A piece of leg that derives from an animal leg. 2023-08-01T21:25:29Z piece of animal leg A whole raw shell-off hen egg is the egg yolk and egg white obtained from a cracked egg. Damion Dooley SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * whole egg FOODON:03420274 hen egg (shell off, raw) SIREN DB annotation: * part of animal FOODON:03420164 fish (whole or pieces) A seed of a broad bean plant (Vicia faba). http://orcid.org/0000-0002-8844-9165 Windsor bean broad bean broadbean faba bean fava bean Horse bean field bean tic bean tick bean broad bean fructose food product A pod of a peanut plant. Damion Dooley SIREN DB annotation: * whole, natural shape FOODON:03430150 * seed in shell or hull FOODON:03420227 peanut pod fresh bean SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * seed, skin present, germ present FOODON:03420133 bean (raw) A seed of a soyabean plant (Glycine max). http://orcid.org/0000-0002-8844-9165 soy bean soya bean soybean soybean SIREN DB annotation: * liquid FOODON:03430130 * part of plant FOODON:03420174 vegetable juice food product A bean substance is a substance made by processing seed from a bean plant. Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc. Damion Dooley https://en.wikipedia.org/wiki/Bean SIREN DB annotation: * seed (anatomical part) FOODON:03420155 bean (whole or pieces) SIREN DB annotation: * liquid, low viscosity, with no visible particles FOODON:03430123 * germinated or sprouted seed FOODON:03420102 * flavoring, spice or herb added, natural FOODON:03460229 * alcohol fermentation process FOODON:03460232 * carbonated by fermentation FOODON:03460246 * preservation by filtration FOODON:03470121 barley malt beer beverage A liquid prepared for consumption, or a product that can be combined with water or milk to make one. Damion Dooley 2019-09-12T00:00:00 beverage food product SIREN DB annotation: * part of animal FOODON:03420164 animal-derived food SIREN DB annotation: * solid FOODON:03430151 * not heat-treated FOODON:03440003 * part of plant FOODON:03420174 vegetable (raw) milk cow milk SIREN DB annotation: * liquid, low viscosity, with no visible particles FOODON:03430123 * milk (mammary secretion) UBERON:0001913 cow milk (liquid) soy beverage SIREN DB annotation: * liquid FOODON:03430130 * seed, skin present, germ present FOODON:03420133 soybean beverage A food product derived from a spice. https://en.wikipedia.org/wiki/Spice SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * part of plant FOODON:03420174 spice food product SIREN DB annotation: * whole, shape achieved by forming FOODON:03430147 * fully heat-treated FOODON:03440014 * ingredient: sucrose CHEBI:17992 * microbial/enzymatic modification process FOODON:03460119 * curing or aging process FOODON:03460253 * ingredient: flavoring or spice extract or concentrate added FOODON:03460100 * ingredient: chocolate or cocoa added FOODON:03460231 * ingredient: vegetable fat or oil added FOODON:03460263 dark chocolate Breast milk is the milk produced by the breasts (or mammary glands) of a human female to feed a child. https://en.wikipedia.org/wiki/Breast_milk SIREN DB annotation: * liquid, low viscosity, with no visible particles FOODON:03430123 * milk (mammary secretion) UBERON:0001913 human milk (raw) SIREN DB annotation: * whole, natural shape FOODON:03430150 * seed (anatomical part) FOODON:03420155 edible seed food product SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * shelled egg UBERON:0007379 hen egg (shell on, raw) Note that this allows for several kinds of fruit in one sample, e.g. "some fruit (raw)" allows "apple (raw)" and "orange (raw)". Damion Dooley fruit SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * fruit part FOODON:03420167 fruit (raw) sunflower seed SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * seed (anatomical part) FOODON:03420155 sunflower seed (whole kernel, raw) SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * seed, skin present, germ present FOODON:03420133 pumpkin seed (shell off) SIREN DB annotation: * seed (anatomical part) FOODON:03420155 soybean (whole or pieces) SIREN DB annotation: * liquid, high viscosity, with small particles FOODON:03430121 * not heat-treated FOODON:03440003 * extract, concentrate or isolate of plant or animal FOODON:03420228 sugar cane juice (pure) SIREN DB annotation: * liquid, high viscosity, with no visible particles FOODON:03430139 * fat or oil FOODON:03420190 fish oil SIREN DB annotation: * solid FOODON:03430151 * not heat-treated FOODON:03440003 * skeletal meat part FOODON:03420175 meat (raw) SIREN DB annotation: * surrounded by 'can, bottle or jar' FOODON:03490194 * whole, natural shape FOODON:03430150 * fully heat-treated FOODON:03440014 * seed, skin present, germ present FOODON:03420133 * rehydration process FOODON:03460259 * sterilization by heating FOODON:03470123 peas (rehydrated, canned) raw milk milk SIREN DB annotation: * liquid, low viscosity, with no visible particles FOODON:03430123 * not heat-treated FOODON:03440003 * milk (mammary secretion) UBERON:0001913 * not pasteurized claim or use FOODON:03510121 cow milk (raw) SIREN DB annotation: * sliced FOODON:03430137 * skeletal meat part FOODON:03420175 fish (portion cut) fish cutlet (raw) raw fish cutlet raw fish steak SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * skeletal meat part FOODON:03420175 fish steak (raw) A whole raw liver is a whole liver organ obtained from an animal during a butchery process. Damion Dooley liver SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * liver UBERON:0002107 liver (raw) SIREN DB annotation: * seed (anatomical part) FOODON:03420155 * microbial/enzymatic modification process FOODON:03460119 * curing or aging process FOODON:03460253 fermented bean product canola meal SIREN DB annotation: * medium ground FOODON:03430117 * seed, skin present, germ present FOODON:03420133 * water removal process FOODON:03460138 * fat removal process FOODON:03460161 * food animal as consumer FOODON:03510015 rapeseed meal A seed of a sesame plant (Sesamum indicum). sesame SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * seed, skin present, germ present FOODON:03420133 sesame seed SIREN DB annotation: * liquid, high viscosity, with no visible particles FOODON:03430139 * fat or oil FOODON:03420190 oil SIREN DB annotation: * liquid, high viscosity, with no visible particles FOODON:03430139 * fat or oil FOODON:03420190 * food bleaching process FOODON:03460197 rapeseed oil A seed of a legume plant in the family Fabaceae. https://orcid.org/0000-0001-5275-8866 2020-10-21T09:28:28 SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * seed (anatomical part) FOODON:03420155 legume SIREN DB annotation: * whole, shape achieved by forming FOODON:03430147 * ingredient: nutrient or dietary substance added FOODON:03460194 * dietary claim or use FOODON:03510023 vitamin supplement, prenatal A whole raw kidney is a kidney obtained from an animal during a butchery process. kidney SIREN DB annotation: * whole, natural shape FOODON:03430150 * not heat-treated FOODON:03440003 * kidney UBERON:0002113 kidney (raw) A food product that has not been cooked. SIREN DB annotation: * not heat-treated FOODON:03440003 food (raw) processed food product SIREN DB annotation: * liquid, high viscosity, with no visible particles FOODON:03430139 * high fructose syrup FOODON:03420272 corn syrup (high fructose) SIREN DB annotation: * ingredient: nutrient or dietary substance added FOODON:03460194 multivitamin preparation A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish. Damion Dooley SIREN DB annotation: * skeletal meat part FOODON:03420175 fish product (unspecified species) https://en.wikipedia.org/wiki/Fish_products A whole vegetable or some substance made from a processed vegetable. https://en.wikipedia.org/wiki/Vegetable https://orcid.org/0000-0001-5275-8866 2022-04-13T09:20:12Z vegetable vegetable (whole or pieces) juice juice beverage An egg produced by a chicken hen. egg chicken egg hen egg This term is ambiguous about whether shell remains on egg or not, i.e. this encompasses both an uncooked egg in shell, or a boiled peeled egg, or a fried egg. SIREN DB annotation: * whole egg FOODON:03420274 hen egg SIREN DB annotation: * fat or oil FOODON:03420190 vegetable fat food product A commercial product which is monosaccharide fructose, dried, ground, and of high purity. crystaline fructose SIREN DB annotation: * crystal FOODON:03430143 * fructose CHEBI:28757 * water removal process FOODON:03460138 * preservation by dehydration or drying FOODON:03470116 crystaline fructose A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). SIREN DB annotation: * animal body or body part FOODON:03420127 meat (whole or pieces) Liquid food prepared from fruit (21 CFR 146). Products prepared from fruit juice by thickening with pectin are indexed under *FRUIT JELLY*; those thickened with gelatin are under *FRUIT BUTTER, JELLY, PRESERVE OR RELATED PRODUCT*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0104 fruit juice or related product (us cfr) Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0105 condiment, dressing, gravy or sauce gravy, condiment, dressing or sauce sauce, condiment, dressing or gravy dressing, condiment, gravy or sauce (us cfr) Beverage containing no more than 0.5% alcohol; it may be flavored, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices, diluted fruit juices and vegetable juices. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0112 malt beverage, nonalcoholic nonalcoholic beverage (us cfr) Aromatic or pungent plant product used whole or ground as a seasoning in food products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0113 herb or spice spice or herb (us cfr) A substance having greater than 2% of the caloric value of sucrose per equivalent unit of sweetening capacity. For example, the amount of such subtance having the sweetening capacity of 1 teaspoon of sucrose would have more than 0.4 calories (21 CFR 170.3(o)(21)). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0118 nutritive carbohydrate sweetener sweetener, nutritive nutritive sweetener (us cfr) Any form of whole or milled grain, prepared grain product or starch containing product derived from non-grain sources. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0125 grain or starch product (us cfr) The liquid extracted or expressed from mature fruit with or without the application of heat. Includes concentrated juice and single-strength juice. If the single-strength juice is prepared from concentrate, then *WATER ADDED* should be used. Carbonated fruit juices are indexed by *FRUIT JUICE* or *FRUIT JUICE, DILUTED* and *CARBONATED* or the appropriate narrower term. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0127 juice, fruit fruit juice (us cfr) Extract, concentrate or isolate derived from a food source through one or more refining steps (see *EXTRACT, CONCENTRATE OR ISOLATE OF PLANT OR ANIMAL*) and marketed as such. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0129 refined or partially-refined food product (us cfr) Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0133 seasoning or flavoring flavoring or seasoning (us cfr) A multiple-component food product typically containing a protein source, a vegetable, and a potato, rice or cereal-based component packaged to be served after heating, either as separate items or courses or mixed as recipe components; see 21 CFR 102.26, 102.28 and 104.47 for nutritional quality guidelines. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0139 compartmentalized dinner dinner with components separated in serving containers dinner, compartmentalized food packs with separate components heat and serve dinner multiple-course dinner tv dinner multicomponent meal (us cfr) Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0143 pie filling, fruit fruit or fruit product (us cfr) Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0148 milk or milk product (us cfr) Food product prepared by milling a grain or by producing flour, meal or grits from a non-grain source such as beans, starchy roots or tubers. Refined starch is indexed under *REFINED OR PARTIALLY REFINED FOOD PRODUCT*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0149 milled grain or starch product (us cfr) Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0150 meat or meat product (from mammal) (us cfr) Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0152 vegetable or vegetable product (us cfr) Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0164 dairy product (us cfr) Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0172 prepared dish prepared food product (us cfr) Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0179 relish or condiment condiment or relish (us cfr) Alcoholic beverage prepared from water, malted grain and hops (humulus) by brewing. Examples are beer, ale and malt liquor (27 CFR 7.10). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0195 malt beverage (us cfr) Products of the flesh of animals. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0217 meat, poultry, seafood or related product (us cfr) Alcoholic or nonalcoholic beverage; excludes milk and milk-based beverages, fruit juices and fruit juice drinks, and vegetable juices. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0229 beverage (us cfr) A product added to a food item to achieve some degree of sweet taste; it may be nutritive or nonnutritive. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0237 sweetener (us cfr) Fruits and vegetables in all forms. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0257 fruit or vegetable product (us cfr) Nuts in all forms, including nut butters and pastes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0260 nut or nut product (us cfr) Fresh egg in shell, liquid, frozen, dried egg or egg component, or egg product analog. Includes boiled, poached, scrambled, and fried eggs. Excludes prepared egg dishes, such as omelettes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0261 egg or egg product (us cfr) The liquid extracted or expressed from mature vegetables with or without optional ingredients such as seasoning or salt. Products prepared from vegetable juice by thickening with gelatin or pectin are indexed under the broader term *VEGETABLE OR VEGETABLE PRODUCT*. For part or portion, index the part or the plant from which the juice was extracted, rather than *PLANT EXTRACT, CONCENTRATE, OR ISOLATE*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0264 juice, vegetable vegetable juice (us cfr) Flesh from fish or shellfish. Includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0267 seafood or seafood product (us cfr) Any form of cacao, cacao product, chocolate, chocolate product or chocolate product analog except chocolate candy; includes such products as cacao beans, cacao nibs, chocolate liquor, sweet or milk chocolate, and chocolate syrup; excludes flavors and extracts derived from cacao beans and chocolate- or cacao-flavored foods (21 CFR 163). [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0272 chocolate or cacao product cacao or chocolate product (us cfr) Beverage containing more than 0.5% alcohol; includes distilled spirits, malt beverage, and wine. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0278 alcoholic beverage (us cfr) Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0289 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. USA agency food product type http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0305 seed or seed product (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0306 nut or seed product (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0308 supplemental formulation (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0309 therapeutic formulation dietary or therapeutic formulation (us cfr) Renamed from *PRODUCT TYPE, CODEX ALIMENTARIUS* in LanguaL 2008. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0352 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. international agency food product type An agency food product type is a class of food product defined by an agency or consortium. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0361 This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. agency food product type Codex Alimentarius, Volume 2 - 1993, Section 2: Pesticide Residues in Food. The Codex Classification of food and animal feed commodities moving in trade and the description of the various items and groups of food and animal feedstuffs included in the present document have been developed by the Codex Committee on Pesticide Residues. It was first adopted by the 18th Session of the Codex Alimentarius Commission, (1989). The Codex Classification includes food commodities and animal feedstuffs for which Codex maximum residue limits will not necessarily be established. The Classification is intended to be as complete a listing of food commodities in trade as possible, classified into groups on the basis of the commodity's similar potential for pesticide residues. The Classification may also be appropriate for other purposes such as setting maximum levels for other types of residues or for other contaminants in food. The Codex Classification should be consulted in order to obtain a precise description of the food or animal feed commodities and, especially, in cases where Codex maximum residue limits have been set for groups of food and groups of animal feedstuffs. The Codex Classification is intended to promote harmonization of the terms used to describe commodities which are subject to maximum residue limits and of the approach to grouping commodities with similar potential for residue for which a common group maximum residue limit can be set. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0643 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. Codex Alimentarius classification of food and feed commodities http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0644 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. a. primary food commodities of plant origin (ccpr) Vegetables are foods derived from many different kinds of plants mostly annual and usually cultivated, commonly known by custom and tradition as "vegetables". In several countries, some of these commodities grown on large areas are distinguished as "field crops" or arable crops e.g. sugar beet. For the sake of convenience in this guide such crops are classified under Type 2 Vegetables. Exposure to pesticides is dependent on the particular part of the plant used for food and the growing practices. Vegetables may be consumed in whole or in part and in the form of fresh, dried or processed foods. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0650 02 vegetables (ccpr) Brassica (cole or cabbage) vegetables and flowerhead brassicas are foods derived from the leafy heads, stems and immature inflorescences of plants belonging to the genus Brassica or the family Cruciferae. Although Kohlrabi does not comply fully with the description above, for convenience and because of the similarity in residue behaviour the commodity is classified in this group. Koblrabi is a tuber-like enlargement of the stem. The edible part of the crop is partly protected from pesticides applied during the growing season by outer leaves, or skin (Kohlrabi). The entire vegetable after discarding obviously decomposed or withered leaves may be consumed. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0675 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. http://langual.org langual:A1270 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. U.S. code of federal regulations, title 21 food product type https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl Index dietary/food supplements according to legal and market definitions. http://langual.org SUBSET_SIREN:F15918 http://www.langual.org/langual_thesaurus.asp?termid=A1298 food supplement nutritional supplement subset_siren LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. The United States defines dietary supplements in the Dietary Supplement Health and Education Act of 1994 (DSHEA). Pub L 103-417, 108 STAT. 4235, (Oct. 25, 1994): A dietary supplement is a product taken by mouth that contains a "dietary ingredient" intended to supplement the diet. The "dietary ingredients" in these products may include: vitamins, minerals, herbs or other botanicals, amino acids, and substances such as enzymes, organ tissues, glandulars, and metabolites. Dietary supplements can also be extracts or concentrates, and may be found in many forms such as tablets, capsules, softgels, gelcaps, liquids, or powders. In the European Union, food supplements are framed by two kinds of regulations: - the EU vertical regulation relating to food supplements, composed with the directive 2002/46/CE (essentially for the definition of food supplements) and the regulation 1170/2009 (which lists the vitamins and minerals, and the chemical forms of the substances allowed in food supplements); - the EU transversal regulation relating to foodstuffs and especially the 2006/1924 regulation concerning nutrition and health claims, and the EU labeling transversal regulations, 90/496/EC and 2008/100/EC. The EU regulation 2002/46/CE defines food supplements as "foodstuffs the purpose of which is to supplement the normal diet and which are concentrated sources of nutrients or other substances with a nutritional or physiological effect, alone or in combination, marketed in dose form, namely forms such as capsules, pastilles, tablets, pills and other similar forms, sachets of powder, ampoules of liquids, drop dispensing bottles, and other similar forms of liquids and powders designed to be taken in measured small unit quantities". [Directive 2002/46/EC] Codex Alimentarius also includes supplements containing vitamins or dietary minerals [http://www.codexalimentarius.net/download/standards/10206/cxg_055e.pdf] dietary supplement Fibre supplements (or fiber supplements) are considered to be a form of a subgroup of functional dietary fibre, and in the United States are defined by the Institute of Medicine (IOM). According to the IOM, functional fibre "consists of isolated, non-digestible carbohydrates that have beneficial physiological effects in humans". Fibre supplements are widely available, and can be found in forms such as powders, tablets and capsules. Consumption of fibre supplements may be for: improving dietary intake, lowering blood cholesterol, alleviating irritable bowel syndrome, reducing the risk of colon cancer, and increasing feelings of satiety. [http://en.wikipedia.org/wiki/Fibre_supplements] WIKIPEDIA:Fibre_supplements http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A1328 fiber fiber supplement fibre fibre supplement dietary supplement, fibre pea plant edible seed cultivars Examples of stem vegetables are kohlrabi, celery, fennel and rhubarb. Examples of shoot vegetables are asparagus, hop, bamboo shoots and taugé. A vegetable having shoot or stem which can be cooked and eaten. shoot vegetable spear vegetable stem or spear vegetable plant fruit plant used as vegetable polysaccharide-producing plant sugar-producing plant plant used for producing extract or concentrate starch-producing plant oil-producing plant An aquatic animal is an animal, either vertebrate or invertebrate, which lives in the water for most or all of its lifetime. This is equivalent to: 'fish (food source)' or 'shellfish (food source)' or 'crustacean (food source)' or 'echinoderm (food source)' or 'coelenterate (food source)' However, this disjunction appears to be a burden on reasoners, and so this is currently not implemented. fish or lower water animal floret plant used as vegetable Any chemical or chemical mixture that exists in a food material or was added to a food material. LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds). Note however that the LanguaL category includes additives which may be naturally derived, such as agar. chemical food component grain or seed-producing plant carbohydrate-producing plant vegetable-producing plant, above-ground parts Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. Damion Dooley https://en.wikipedia.org/wiki/Mammal mammal fruit-producing plant Aquatic animals other than fish and shellfish aquatic invertebrate animal (excluding shellfish) A legume is a plant or its fruit or seed in the family *Fabaceae* (or *Leguminosae*). Legumes are grown agriculturally, primarily for their grain seed called pulse, for livestock forage and silage, and as soil-enhancing green manure. Well-known legumes include alfalfa, clover, peas, beans, chickpeas, lentils, lupin bean, mesquite, carob, soybeans, peanuts and tamarind. [https://en.wikipedia.org/wiki/Legume] fabaceae pod or seed vegetable plant edible seed producing plant flavor-producing plant herb-producing plant spice or flavor-producing plant Winter squash is an annual fruit representing several squash species within the genus Cucurbita. It differs from summer squash in that it is harvested and eaten in the mature fruit stage when the seeds within have matured fully and the skin has hardened into a tough rind. At this stage, most varieties of this fruit can be stored for use during the winter. curcurbita winter squash Cucurbita moschata Cucurbita pepo cucurbita maxima winter squash plant Californiacondor head vegetable plant A dairy cow is an adult female member of a dairy cattle breed cow domesticated cattle dairy cow squash plant nut producing plant A gill-bearing aquatic craniate animal that lacks limbs with digits. Damion Dooley "Most fish are ectothermic ('cold-blooded'), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature." - https://en.wikipedia.org/wiki/Fish fish Mussel is the common name used for members of several families of bivalve molluscs, from saltwater and freshwater habitats. These groups have in common a shell whose outline is elongated and asymmetrical compared with other edible clams, which are often more or less rounded or oval. Damion Dooley https://en.wikipedia.org/wiki/Mussel https://upload.wikimedia.org/wikipedia/commons/thumb/4/45/CornishMussels.JPG/640px-CornishMussels.JPG palaeoheterodonta pteriomorphia eolife:2235 langual:B1223 mytilidae mussel MANSFELD:10138 PLANTS:SEOR4 simsim Sesamum indicum L. Sesamum orientale L. sesamum indicum sesamum orientale sesame plant MANSFELD:36372 PLANTS:ZEMA Zea mays L. maize zea mays LanguaL curation note: Use 'field corn' for any breakfast cereals or snack foods having 'corn' as the main ingredient. Zia mays plant Rapeseed (*Brassica napus*), also known as rape, oilseed rape, charlock (and, in the case of one particular group of cultivars, canola), is a bright-yellow flowering member of the family *Brassicaceae* (mustard or cabbage family), cultivated mainly for its oil-rich seed. It is the third-largest source of vegetable oil in the world. [https://en.wikipedia.org/wiki/Rapeseed] MANSFELD:24078 brassica napus rape plant Brassica napus L. emend. Metzg. var. napus canola canola plant oilseed rape plant rapeseed plant MANSFELD:12338 Syzygium aromaticum (L.) Merr. & L.M. Perry caryophyllus eugenia aromatica syzygium aromaticum clove plant A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. Damion Dooley animal LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. vertebrate animal Any grass cultivated (grown) for the edible components of its grain. Damion Dooley grain plant MANSFELD:30744 Pisum sativum L. green pea plant lathyrus l. pisum l. pea plant Yeasts are eukaryotic micro-organisms classified in the kingdom *Fungi*, with 1,500 species currently described estimated to be only 1% of all fungal species. WIKIPEDIA:Yeast yeast *Vicia faba*, the Broad Bean, is a species of bean (*Fabaceae*) native to north Africa and southwest Asia, and extensively cultivated elsewhere. A variety is provisionally recognized: Vicia faba var. equina Pers. - Horse Bean. Although usually classified in the same genus Vicia as the vetches, some botanists treat it in a separate monotypic genus *Faba*. The term fava bean (from the Italian fava, meaning "broad bean") is usually used in English speaking countries such as the US, however the term broad bean is the most common name in the UK. WIKIPEDIA:Vicia_faba vicia faba MANSFELD:30416 PLANTS:VIFA faba bean plant fava bean plant horse bean plant horsebean plant Vicia faba L. Vicia faba L. (varieties for human consumption) broad bean plant Crustaceans form a large, diverse arthropod taxon which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill, woodlice, and barnacles. [https://en.wikipedia.org/wiki/Crustacean] crustacea crustacean MANSFELD:35616 Saccharum officinarum L. saccharum officinarum sugar cane plant Field corn is maize of varieties that (in contrast with sweet corn and popcorn) are not, in the United States, grown primarily for consumption as human food in the form of fresh kernels. More than 98% of corn-growing land in the U.S. is in use for field-corn production. Principal field corn varieties are Dent corn, Flint corn, Flour corn (including blue corn (*Zea mays amylacea*), and Waxy corn. WIKIPEDIA:Field_corn PLANTS:ZEMAM2 Zea mays L. ssp. mays Zea mays L. subsp. mays Zea mays ssp. mays L. corn, field dent corn flint corn maize podcorn zea mays var. indentata (not acc.) zea mays var. indurata (not acc.) Field corn is a general term used in North America for corn varieties other than sweet corn, popcorn, yellow food grade corn used for yellow corn meal or flour and corn starch, and white food-grade corn used for white meal or flour and corn starch. Source: https://en.wikipedia.org/wiki/Field_corn LanguaL curation note: Searching note--use 'field corn' for any breakfast cereal or snack food having 'corn' as the first ingredient. field corn plant The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. Covers both freshwater and saltwater organisms shellfish Broccoli is a plant in the cabbage family, whose large flower head is used as a vegetable. The word broccoli, from the Italian plural of broccolo, refers to "the flowering top of a cabbage". Broccoli is usually boiled or steamed, but may be eaten raw and has become popular as a raw vegetable in hors d'oeuvre trays. Broccoli is classified in the *Italica* cultivar group of the species *Brassica oleracea*. Broccoli has large flower heads, usually green in color, arranged in a tree-like fashion on branches sprouting from a thick, edible stalk. The mass of flower heads is surrounded by leaves. Broccoli most closely resembles cauliflower, which is a different cultivar group of the same species. WIKIPEDIA:Broccoli MANSFELD:37506 PLANTS:BROLB Brassica oleracea L. var. botrytis L. Brassica oleracea L. var. italica Plenck Brassica oleracea var. botrytis L. brassica oleracea l. convar. botrytis var. italica brassica oleracea var. botrytis brassica oleracea var. italica broccoli plant field pumpkin pumpkin plant This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. organism by alternate grouping A bean plant is one of several genera of the flowering plant family Fabaceae, which has seed pods, seeds, and/or leaf material used for human or animal food. https://en.wikipedia.org/wiki/Bean bean plant vegetable-producing plant nut or edible seed producing plant MANSFELD:23884 PLANTS:BROLG Brassica oleracea L. var. gemmifera DC. Brassica oleracea L. var. gemmifera Zenker Brassica oleracea var. gemmifera (DC.) Zenker Brassica oleracea var. gemmifera DC. brassica oleracea var. gemmifera brussels sprout plant MANSFELD:30514 Lathyrus sativus L. tare vicia vetch plant Cucurbita (Latin for gourd) is a genus of herbaceous vines in the gourd family, Cucurbitaceae, also known as cucurbits, native to the Andes and Mesoamerica. Five species are grown worldwide for their edible fruit, variously known as squash, pumpkin, or gourd depending on species, variety, and local parlance, and for their seeds. MANSFELD:4048 Cucurbita maxima L. (Duch.) pumpkin plant cucurbita spp. pumpkin, squash or gourd squash, gourd or pumpkin plant *Mollusca* is a large phylum of invertebrate animals whose members are known as molluscs or mollusks. Molluscs are the largest marine phylum, comprising about 23% of all the named marine organisms. Numerous molluscs also live in freshwater and terrestrial habitats. [https://en.wikipedia.org/wiki/Mollusca] EC:No 216/2009 MOL Mollusca mollusk mollusc *Bivalvia*, in previous centuries referred to as the *Lamellibranchiata* and *Pelecypoda*, is a class of marine and freshwater molluscs that have laterally compressed bodies enclosed by a shell consisting of two hinged parts. Bivalves as a group have no head and they lack some usual molluscan organs like the radula and the odontophore. They include the clams, oysters, cockles, mussels, scallops, and numerous other families that live in saltwater, as well as a number of families that live in freshwater.[https://en.wikipedia.org/wiki/Bivalvia] bivalvia lamellibranchiata pelecypod pelecypoda bivalve Echinoderm is the common name given to any member of the phylum *Echinodermata* of marine animals. The adults are recognizable by their (usually five-point) radial symmetry, and include such well-known animals as sea stars, sea urchins, sand dollars, and sea cucumbers, as well as the sea lilies or "stone lilies". [https://en.wikipedia.org/wiki/Echinoderm] EC:No 1637/2001 ECH Echinodermata Echinodermata Klein, 1734 echinodermata echinoderm A cephalopod is any member of the molluscan class *Cephalopoda* such as a squid, octopus or nautilus. These exclusively marine animals are characterized by bilateral body symmetry, a prominent head, and a set of arms or tentacles modified from the primitive molluscan foot. Fishermen sometimes call them inkfish, referring to their common ability to squirt ink. [https://en.wikipedia.org/wiki/Cephalopod] cephalopoda cephalopod *Coelenterata* is an obsolete term encompassing the animal phyla *Cnidaria* (coral animals, true jellies, sea anemones, sea pens, and their allies) and *Ctenophora* (comb jellies). [https://en.wikipedia.org/wiki/Coelenterata] coelenterata coelenterate This section and its narrover terms refer to the European Commission food additive regulation according to COMMISSION REGULATION (EU) No 1129/2011 of 11 November 2011 amending Annex II to Regulation (EC) No 1333/2008 of the European Parliament and of the Council by establishing a Union list of food additives [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2011:295:0001:0177:EN:PDF] and its basis, the four Food Additive Directives: the EEC Framework Directive on Food Additives (89/107/EEC), the Directive on colours (94/36/EC), the Directive on sweeteners (94/35/EC) and the 'miscellaneous' Directive (95/2/EC) plus amendments [http://ec.europa.eu/food/fs/sfp/flav_index_en.html] and/or Codex Alimentarius Commission General Standard for Food Additives (CODEX STAN 192, revised 2011) [http://www.codexalimentarius.net/download/standards/4/CXS_192e.pdf]. If used for food supplement substances, thissection and its narrover terms refer to the European Commission regulation in general [http://ec.europa.eu/food/food/labellingnutrition/supplements/index_en.htm] and specifically to the EC Directive on the approximation of the laws of the Members States relating to food supplements (2002/46/EC) [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. Damion Dooley's note: manysubclasses here are currently originating from LanguaL additives that have not yet been matched to CHEBI ontology terms. If matches are possible they will be implemented over time, at which point the corresponding FoodOn id's will be deprecated. food additive A chemical food component in liquid form. Liquid as food source liquid chemical food component Food additive; technological purpose(s): bulking agent, humectant, sequestrant, stabilizer, sweetener. Codex::420(ii) Europe::420 LanguaL curation note: See "food additive" comments. sorbitol syrup LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. plant by general taxa CCPR: PLANTS:BRASS2 Brassica Brassica L. Brassica sp. Brassica spp. brassica spp. brassica species The *Cucurbitaceae*, also called cucurbits and the gourd family, are a plant family consisting of about 965 species in around 95 genera, the most important of which are: *Cucurbita* - squash, pumpkin, zucchini, some gourds; *Lagenaria* - calabash, and others that are inedible; *Citrullus* - watermelon (*C. lanatus, C. colocynthis*) and others; *Cucumis* - cucumber (*C. sativus*), various melons; *Luffa* - luffa, loofah cucurbitaceae gourd/squash family Tunicates, previously known as *Urochordata* or urochordates, are members of the *Tunicata*, a subphylum of the phylum *Chordata*. They are marine filter feeders with a saclike morphology. In their respiration and feeding they take in water through an incurrent (or inhalant) siphon and expel the filtered water through an excurrent (or exhalant) siphon. Most adult tunicates are sessile and attached to rocks or similarly suitable surfaces on the ocean floor; others such as salps, doliolids and pyrosomes swim in the pelagic zone as adults. Various species are commonly known as sea squirts or sea pork. WIKIPEDIA:Tunicate oopah sea squirt tunicata tunicate A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary. sugar Anatomical or other part(s) or substances derived from plant or animal or fungal organisms. This was renamed from "part of organism" (and from LanguaL's original "part of plant or animal") to encompass organism material that is produced by an animal or plant rather than "part of" it, such as an egg, and might not be countable per se, such as milk. Additionally the existing definition's "from which a food product or its major ingredient is derived." was removed as an unnecessary constraint. [2023/03/02] LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." organism material Bone, feathers, shell, skin or trim fat. LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. nonmeat part of animal A whole animal or some material processed from a animal. 2023-08-01T21:25:29Z This class and its subclasses can be used if it is ambiguous whether the reference is being made to a whole animal or some part of it, including parts of organs rather than whole organs. LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. animal (whole or pieces) LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED* in LanguaL 2008. fruit, peel removed Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide. carbohydrate extract, concentrate, or isolate A material that derives from some animal. 2023-08-01T21:25:29Z Langual note: Includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. animal material The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. berry berry or fruit (anatomical part) fruit or berry, peel undetermined hip (fruit) infructescence LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. Renamed from *FRUIT OR BERRY* in LanguaL 2008. fruit part Bone (endoskeleton) or shell (exoskeleton) of animals, or any part thereof. shell (animal) bone or shell Extract, concentrate or isolate high in gluten, the predominant protein of wheat or corn. langual:C0177 gluten seed part Food substance or component consisting predominantly of mixed glycerol esters of fatty acids and, in far lesser amounts, of fatty acids, sterols and pigments. A fat is a solid at room temperature, an oil is a liquid at room temperature (20 degrees C.). Excludes essential oils. Damion Dooley 2019-06-20T05:09:36Z langual:C0190 oil or fat SIREN DB annotation: * liquid, high viscosity, with no visible particles FOODON:03430139 * solid FOODON:03430151 * fat or oil FOODON:03420190 fat or oil Poultry, game bird or turtle eggs. LanguaL curation note: Fish roe are indexed under *OVARY, ROE*. egg or egg component Edible organ meat, including blood and bone marrow. variety meat organ meat LanguaL curation note: Used for seeds in hard shells rather than pods. Examples include brazil nuts, walnuts, almonds and peanuts. seed(s) in shell or hull A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. langual:C0228 Damion Dooley's note: Items in this branch will be merged into foodon food product branch. extract, concentrate or isolate of plant or animal flesh of fruit LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED, CORE, PIT OR SEED REMOVED* in LanguaL 2008. fruit, peel removed, core, pit or seed removed Extract, concentrate or isolate high in protein; may contain amino acids, polypeptides and enzymes. protein extract, concentrate or isolate LanguaL curation note: Used when a sugar syrup or sugar syrup solids is the major ingredient. Sugar syrup is a liquid or semiliquid high in sugar content derived from a plant source through extraction possibly followed by conversion and/or concentration. A sugar syrup usually contains several sugars in varying proportions. Sugar syrup solids are derived by removing water from sugar syrup. sugar syrup or syrup solids langual:C0272 high fructose syrup The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM seed oil A liquid that flows slowly at room temperature. Examples are: some heavy liqueurs, evaporated milk, vegetable oil, molasses and honey. The range of high viscosity liquids spans sucrose solutions between 45 and 70% solids (viscosity range from 10 to 500 centipoise). Prefer 'solid pieces' factor term to 'small particles' if both appear in the food. liquid, thick food (liquid, high viscosity) A liquid that flows very easily at room temperature. Examples are: water, apple juice, sherry, acidophilus milk, whipping cream and some heavy liqueurs. The range of low viscosity liquid spans sucrose solutions between 0 and 45% solids (viscosity range from 1 to 10 centipoise). Prefer 'solid pieces' factor term to 'small particles' if both appear in the food. liquid, thin food (liquid, low viscosity) The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995] Damion Dooley's note: these categories need to be mapped over to PATO phenotypic categories, with a suitable treatment of mixtures of solids that are divided into parts. food physical quality A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. fluid SIREN DB annotation: * liquid FOODON:03430130 food (liquid) Refers to natural or formed shape as appropriate, regardless of size, which may vary from very large (e.g., beef carcass) to very small (e.g., poppy seed, yeast cell). whole LanguaL curation note: Whole refers not only to a whole plant or animal but also to a whole part as indexed in C. PART OF PLANT OR ANIMAL; examples of whole natural products are: an apple, rice in grain form, an asparagus spear, a spinach leaf, a beef carcass, a dressed chicken, a chicken drumstick, a calf liver. Products may have been slightly modified during processing and preservation (e.g., raisins or a pear that has been peeled and cored). whole, natural shape A solid product is a hard or soft product capable of retaining its own shape at room temperature (20 degrees C.). A soft product that is spreadable or formable is considered semisolid. solid food (solid) Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. http://www.langual.org/langual_thesaurus.asp?termid=H0111 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food treatment process A food modification process by microbial or enzymatic action which results in molecular changes in any food component. http://www.langual.org/langual_thesaurus.asp?termid=H0119 fermented, unspecified LanguaL curation note: If salt, sugar or other food additive is used to aid in the modification process, index it by the appropriate term under *INGREDIENT ADDED*. microbial/enzymatic modification process http://www.langual.org/langual_thesaurus.asp?termid=H0141 LanguaL curation note: Used when the food product underwent mechanical, chemical or enzymatic modification that has affected the texture, flavor or other characteristic of the product. food modification process This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred. nut or seed added langual:H0177 LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. plant seed or nut food product http://www.langual.org/langual_thesaurus.asp?termid=H0230 LanguaL curation note: Used for products in which either carbohydrates, proteins or fats were modified through microbial processes. Enzymatic or other biological processes may also be involved. If two or more of these components are modified in significant amounts, index under *FERMENTED/MODIFIED, MULTIPLE COMPONENT*. single component food fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0232 alcohol fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0256 yeast leavened carbohydrate fermentation A fat or oil derived from vegetable material Damion Dooley vegetable fat or oil added langual:H0263 This is a convenience class inherited from LanguaL vegetable fat or oil The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. http://www.langual.org/langual_thesaurus.asp?termid=J0107 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food preservation process A animal cut of meat that is primal, sub-primal or a retail cut. https://en.wikipedia.org/wiki/Primal_cut 2023-08-01T21:25:29Z A cut of meat may have an arbitrary boundary that does not conform to an anatomical part. For example, a steak can be taken from a variety of locations. animal cut of meat The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. biological_process GO:0000002 mitochondrial genome maintenance The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome. GOC:ai GOC:vw The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GO:0019952 GO:0050876 Wikipedia:Reproduction reproductive physiological process biological_process GO:0000003 reproduction The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. GOC:go_curators GOC:isa_complete GOC:jl ISBN:0198506732 Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. biological_process GO:0000018 regulation of DNA recombination Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins. citrulline metabolism biological_process GO:0000052 citrulline metabolic process The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins. ISBN:0198506732 The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GO:0016359 mitotic chromosome segregation mitotic sister-chromatid adhesion release biological_process GO:0000070 mitotic sister chromatid segregation The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. GOC:ai GOC:jl The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine. sulfur amino acid metabolism sulphur amino acid metabolic process sulphur amino acid metabolism biological_process GO:0000096 sulfur amino acid metabolic process The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine. GOC:ai A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. https://github.com/geneontology/go-ontology/issues/23114 https://github.com/geneontology/go-ontology/issues/23195 microtubule cytoskeleton organisation biological_process microtubule cytoskeleton organization and biogenesis GO:0000226 microtubule cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah microtubule cytoskeleton organisation GOC:mah microtubule cytoskeleton organization and biogenesis GOC:mah A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. nuclear interphase chromosome cellular_component GO:0000228 nuclear chromosome A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. GOC:dph GOC:mah A chromosome found in the mitochondrion of a eukaryotic cell. NIF_Subcellular:sao1186327184 mitochondrial DNA mtDNA cellular_component mitochondrial genome GO:0000262 mitochondrial chromosome A chromosome found in the mitochondrion of a eukaryotic cell. GOC:mah The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. glycan biosynthesis glycan biosynthetic process polysaccharide anabolism polysaccharide biosynthesis polysaccharide formation polysaccharide synthesis biological_process GO:0000271 polysaccharide biosynthetic process The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0044244 polysaccharide breakdown polysaccharide catabolism polysaccharide degradation multicellular organismal polysaccharide catabolic process biological_process GO:0000272 polysaccharide catabolic process The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. PMID:33139480 Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GO:0007067 Wikipedia:Mitosis biological_process mitosis GO:0000278 Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. mitotic cell cycle Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 Reactome:69278 The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. biological_process karyokinesis GO:0000280 nuclear division The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei. GOC:mah A ribosome contained within a subcellular membrane-bounded organelle. cellular_component GO:0000313 organellar ribosome A ribosome contained within a subcellular membrane-bounded organelle. GOC:mah GOC:mcc A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. cellular_component GO:0000323 lytic vacuole A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. GOC:krc The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GO:0000789 GO:0000790 GO:0005717 NIF_Subcellular:sao1615953555 cytoplasmic chromatin nuclear chromatin cellular_component chromosome scaffold GO:0000785 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. GOC:elh PMID:20404130 A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. https://github.com/geneontology/go-ontology/issues/22355 GO:0005719 GO:0035327 NIF_Subcellular:sao445485807 Wikipedia:Euchromatin transcriptionally active chromatin cellular_component nuclear euchromatin GO:0000791 euchromatin A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation. PMID:32017156 A compact and highly condensed form of chromatin that is refractory to transcription. https://github.com/geneontology/go-ontology/issues/22355 GO:0005720 GO:0035328 NIF_Subcellular:sao581845896 Wikipedia:Heterochromatin transcriptionally inactive chromatin transcriptionally silent chromatin nuclear heterochromatin cellular_component GO:0000792 heterochromatin A compact and highly condensed form of chromatin that is refractory to transcription. PMID:32017156 The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. biological_process GO:0000819 sister chromatid segregation The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets. GOC:ai GOC:elh Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. regulation of glutamine family amino acid metabolism biological_process GO:0000820 regulation of glutamine family amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. regulation of arginine metabolism biological_process GO:0000821 regulation of arginine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GOC:go_curators The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). skeletal development biological_process GO:0001501 skeletal system development The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). GOC:dph GOC:jid GOC:tb The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. Wikipedia:Ossification bone biosynthesis bone formation osteogenesis biological_process GO:0001503 Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. ossification The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:mtg_mpo PMID:17572649 A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. biological_process GO:0001508 Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. action potential A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity. retinoid metabolism biological_process GO:0001523 retinoid metabolic process The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity. ISBN:0198506732 Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. ciliary/flagellar motility biological_process ciliary or bacterial-type flagellar motility GO:0001539 Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC. cilium or flagellum-dependent cell motility Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. GOC:cilia GOC:hjd GOC:krc A process that results in a parallel arrangement of microtubules. microtubule bundling biological_process GO:0001578 microtubule bundle formation A process that results in a parallel arrangement of microtubules. GOC:dph A homeostatic process in which an organism modulates its internal body temperature. Wikipedia:Thermoregulation thermoregulation biological_process GO:0001659 temperature homeostasis A homeostatic process in which an organism modulates its internal body temperature. GOC:jl thermoregulation GOC:dph GOC:tb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. response to hypoxic stress response to lowered oxygen tension response to intermittent hypoxia response to sustained hypoxia biological_process GO:0001666 Note that this term should not be confused with 'response to anoxia ; GO:0034059'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%. response to hypoxia Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. GOC:hjd Cell migration that is accomplished by extension and retraction of a pseudopodium. ameboid cell migration amoeboid cell migration amoeboidal cell migration biological_process GO:0001667 Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration Cell migration that is accomplished by extension and retraction of a pseudopodium. GOC:dph The formation of the acrosome from the spermatid Golgi. acrosome formation biological_process GO:0001675 acrosome assembly The formation of the acrosome from the spermatid Golgi. GOC:dph GOC:hjd GOC:tb acrosome formation GOC:dph GOC:tb The chemical reactions and pathways involving a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons. https://github.com/geneontology/go-ontology/issues/26445 long-chain fatty acid metabolism biological_process GO:0001676 While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). long-chain fatty acid metabolic process The chemical reactions and pathways involving a long-chain fatty acid. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons. GOC:ajp The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. hydrochloric acid secretion biological_process GO:0001696 gastric acid secretion The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:hjd The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. biological_process GO:0001701 in utero embryonic development The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus. GOC:go_curators GOC:mtg_sensu The formation of the ectoderm, mesoderm and endoderm during gastrulation. biological_process GO:0001704 formation of primary germ layer The formation of the ectoderm, mesoderm and endoderm during gastrulation. GOC:go_curators The formation of ectoderm during gastrulation. biological_process GO:0001705 ectoderm formation The formation of ectoderm during gastrulation. GOC:go_curators The formation of the endoderm during gastrulation. endoblast formation biological_process GO:0001706 endoderm formation The formation of the endoderm during gastrulation. GOC:go_curators endoblast formation GOC:dph GOC:sdb_2009 GOC:tb The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts. biological_process GO:0001707 mesoderm formation The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts. GOC:go_curators The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes. branching morphogenesis biological_process GO:0001763 morphogenesis of a branching structure The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes. ISBN:0721662544 branching morphogenesis GOC:dph The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. biological_process GO:0001773 myeloid dendritic cell activation The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor. GOC:mgi_curators ISBN:0781735149 A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell. https://github.com/geneontology/go-ontology/issues/24416 biological_process GO:0001775 cell activation A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell. GOC:mgi_curators The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. https://github.com/geneontology/go-ontology/issues/19116 GO:0042032 GO:0042089 GO:0042107 GO:0050663 cytokine biosynthetic process cytokine metabolic process cytokine secretion interferon production interferon secretion interleukin production interleukin secretion biological_process GO:0001816 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 interferon production GOC:add GOC:mah interferon secretion GOC:add GOC:mah interleukin production GOC:add GOC:mah http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F interleukin secretion GOC:add GOC:mah http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F Any process that modulates the frequency, rate, or extent of production of a cytokine. GO:0042035 GO:0050707 regulation of cytokine anabolism regulation of cytokine biosynthesis regulation of cytokine formation regulation of cytokine synthesis regulation of cytokine biosynthetic process regulation of cytokine secretion biological_process GO:0001817 regulation of cytokine production Any process that modulates the frequency, rate, or extent of production of a cytokine. GOC:add ISBN:0781735149 Any process that stops, prevents, or reduces the rate of production of a cytokine. GO:0042036 GO:0050710 down regulation of cytokine biosynthetic process down regulation of cytokine production down-regulation of cytokine biosynthetic process down-regulation of cytokine production downregulation of cytokine biosynthetic process downregulation of cytokine production negative regulation of cytokine anabolism negative regulation of cytokine biosynthesis negative regulation of cytokine formation negative regulation of cytokine synthesis inhibition of cytokine biosynthetic process inhibition of cytokine production negative regulation of cytokine biosynthetic process negative regulation of cytokine secretion biological_process GO:0001818 negative regulation of cytokine production Any process that stops, prevents, or reduces the rate of production of a cytokine. GOC:add ISBN:0781735149 Any process that activates or increases the frequency, rate or extent of production of a cytokine. GO:0042108 GO:0050715 up regulation of cytokine production up-regulation of cytokine production upregulation of cytokine production activation of cytokine production positive regulation of cytokine biosynthetic process positive regulation of cytokine secretion stimulation of cytokine production biological_process GO:0001819 positive regulation of cytokine production Any process that activates or increases the frequency, rate or extent of production of a cytokine. GOC:add ISBN:0781735149 The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. 5-HT secretion 5-hydroxytryptamine secretion biological_process serotonin release GO:0001820 serotonin secretion The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells. GOC:ef ISBN:0198506732 ISBN:0781735149 serotonin release GOC:tb The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems. biological_process GO:0001821 histamine secretion The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems. GOC:mah ISBN:0198506732 ISBN:0781735149 The morphogenesis of an embryonic epithelium into a tube-shaped structure. biological_process GO:0001838 embryonic epithelial tube formation The morphogenesis of an embryonic epithelium into a tube-shaped structure. GOC:dph ISBN:0824072820 The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001679 Wikipedia:Neurulation neural tube morphogenesis neurulation biological_process GO:0001841 neural tube formation The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GOC:dph ISBN:0878932437 neural tube morphogenesis GOC:dph The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline. biological_process GO:0001843 neural tube closure The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline. GOC:dph ISBN:0878932437 Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter. up regulation of neurotransmitter secretion up-regulation of neurotransmitter secretion upregulation of neurotransmitter secretion activation of neurotransmitter secretion stimulation of neurotransmitter secretion biological_process GO:0001956 positive regulation of neurotransmitter secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter. GOC:hjd Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells. Wikipedia:Intramembranous_ossification dermal ossification biological_process intramembranous bone ossification GO:0001957 An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division. intramembranous ossification Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells. ISBN:0878932437 dermal ossification GO_REF:0000034 intramembranous bone ossification GOC:cjm Replacement ossification wherein bone tissue replaces cartilage. Wikipedia:Endochondral_ossification biological_process GO:0001958 endochondral ossification Replacement ossification wherein bone tissue replaces cartilage. GO_REF:0000034 ISBN:0878932437 The regulation of blood pressure mediated by detection of stimuli and a neurological response. blood pressure regulation by neurological process neurological process involved in regulation of systemic arterial blood pressure neurological system process involved in regulation of systemic arterial blood pressure biological_process fast control of arterial pressure GO:0001976 nervous system process involved in regulation of systemic arterial blood pressure The regulation of blood pressure mediated by detection of stimuli and a neurological response. GOC:mtg_cardio ISBN:0721643949 neurological process involved in regulation of systemic arterial blood pressure GOC:dph GOC:tb A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system. biological_process renal blood volume control of blood pressure renal regulation of blood volume GO:0001977 renal system process involved in regulation of blood volume A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system. GOC:dph GOC:tb ISBN:0721643949 renal regulation of blood volume GOC:dph GOC:tb The process in which hormones modulate the force with which blood passes through the circulatory system. A hormone is one of a group of substances formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which they have a specific regulatory action. blood pressure regulation by hormone hormonal regulation of blood pressure biological_process hormonal control of blood pressure GO:0001990 regulation of systemic arterial blood pressure by hormone The process in which hormones modulate the force with which blood passes through the circulatory system. A hormone is one of a group of substances formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which they have a specific regulatory action. GOC:mtg_cardio ISBN:0721643949 The regulation of blood pressure mediated by the signaling molecule vasopressin. Vasopressin is produced in the hypothalamus, and affects vasoconstriction, and renal water transport. blood pressure regulation by vasopressin biological_process vasopressin control of blood pressure GO:0001992 regulation of systemic arterial blood pressure by vasopressin The regulation of blood pressure mediated by the signaling molecule vasopressin. Vasopressin is produced in the hypothalamus, and affects vasoconstriction, and renal water transport. GOC:mtg_cardio ISBN:0721643949 The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. epithelium morphogenesis biological_process GO:0002009 morphogenesis of an epithelium The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube. GOC:dph GOC:jl GOC:tb ISBN:0198506732 Any process that modulates the frequency or rate of heart contraction. cardiac chronotropy regulation of heart contraction rate regulation of rate of heart contraction biological_process GO:0002027 regulation of heart rate Any process that modulates the frequency or rate of heart contraction. GOC:dph GOC:tb PMID:10358008 cardiac chronotropy GOC:dph GOC:tb The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. up regulation of mesenchymal cell proliferation up-regulation of mesenchymal cell proliferation upregulation of mesenchymal cell proliferation activation of mesenchymal cell proliferation stimulation of mesenchymal cell proliferation biological_process GO:0002053 positive regulation of mesenchymal cell proliferation The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells. GOC:dph A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. neurological control of breathing regulation of respiratory gaseous exchange by neurological system process biological_process GO:0002087 regulation of respiratory gaseous exchange by nervous system process A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates. GOC:dph GOC:tb PMID:12458206 neurological control of breathing GOC:dph GOC:tb The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. biological_process GO:0002200 Note that this process covers somatic recombination, gene conversion, hypermutation, N-region addition, and alternate splicing processes of immune receptor diversification. somatic diversification of immune receptors The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences. GOC:add ISBN:0781735149 PMID:16102575 PMID:16166509 The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response. biological_process somatic recombination of antibody genes during immune response somatic recombination of immunoglobulin genes during immune response GO:0002204 somatic recombination of immunoglobulin genes involved in immune response The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response. GOC:add ISBN:0781735149 somatic recombination of immunoglobulin genes during immune response GOC:dph The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response. biological_process somatic diversification of antibodies during immune response somatic diversification of immunoglobulins during immune response GO:0002208 somatic diversification of immunoglobulins involved in immune response The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response. GOC:add ISBN:0781735149 PMID:14991701 somatic diversification of immunoglobulins during immune response GOC:dph The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. NK cell mediated immunity biological_process GO:0002228 natural killer cell mediated immunity The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. GOC:add GO_REF:0000022 ISBN:0781735149 The movement of an immune cell in response to an external stimulus contributing to an inflammatory response. biological_process immune cell chemotaxis during inflammatory response leucocyte chemotaxis during inflammatory response leukocyte chemotaxis during inflammatory response GO:0002232 leukocyte chemotaxis involved in inflammatory response The movement of an immune cell in response to an external stimulus contributing to an inflammatory response. GOC:add ISBN:0781735149 leukocyte chemotaxis during inflammatory response GOC:dph The movement of an immune cell in response to an external stimulus a part of an immune response. immune cell chemotaxis during immune response leucocyte chemotaxis during immune response biological_process GO:0002233 leukocyte chemotaxis involved in immune response The movement of an immune cell in response to an external stimulus a part of an immune response. GOC:add ISBN:0781735149 The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. haematopoietic progenitor cell differentiation haemopoietic progenitor cell differentiation hemopoietic progenitor cell differentiation biological_process GO:0002244 hematopoietic progenitor cell differentiation The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. GOC:add GOC:rl ISBN:0781735149 PMID:16551251 The series of events that restore integrity to damaged tissue that contribute to an inflammatory response. biological_process healing during inflammatory response inflammatory response wound healing GO:0002246 wound healing involved in inflammatory response The series of events that restore integrity to damaged tissue that contribute to an inflammatory response. GOC:jal ISBN:0721601871 healing during inflammatory response GOC:dph inflammatory response wound healing GOC:dph An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). Wikipedia:Adaptive_immune_system acquired immune response immune memory response biological_process GO:0002250 adaptive immune response An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). GOC:add GO_REF:0000022 ISBN:0781735149 acquired immune response ISBN:068340007X immune memory response GOC:add An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues. immune response in organ or tissue biological_process GO:0002251 organ or tissue specific immune response An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues. GOC:jal GO_REF:0000022 Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation. https://github.com/geneontology/go-ontology/issues/18737 biological_process GO:0002252 immune effector process Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation. GOC:add GO_REF:0000022 ISBN:0781735149 The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. biological_process GO:0002262 myeloid cell homeostasis The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. CL:0000763 GOC:add A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. biological_process cell activation during immune response GO:0002263 cell activation involved in immune response A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. GOC:add GO_REF:0000022 ISBN:0781735149 cell activation during immune response GOC:tb A change in the morphology or behavior of a leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an inflammatory response. biological_process immune cell activation during inflammatory response leukocyte activation during inflammatory response GO:0002269 leukocyte activation involved in inflammatory response A change in the morphology or behavior of a leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an inflammatory response. GOC:add ISBN:0781735149 leukocyte activation during inflammatory response GOC:tb A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. myeloid leucocyte activation biological_process GO:0002274 myeloid leukocyte activation A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. GOC:add ISBN:0781735149 A change in the morphology or behavior of a myeloid cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. biological_process myeloid cell activation during immune response GO:0002275 myeloid cell activation involved in immune response A change in the morphology or behavior of a myeloid cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 myeloid cell activation during immune response GOC:tb The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process myeloid dendritic cell activation during immune response GO:0002277 myeloid dendritic cell activation involved in immune response The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 myeloid dendritic cell activation during immune response GOC:tb The process in which an immature myeloid dendritic cell acquires the specialized features of a mature myeloid dendritic cell as part of an immune response. biological_process myeloid dendritic cell differentiation during immune response GO:0002284 myeloid dendritic cell differentiation involved in immune response The process in which an immature myeloid dendritic cell acquires the specialized features of a mature myeloid dendritic cell as part of an immune response. GOC:add ISBN:0781735149 myeloid dendritic cell differentiation during immune response GOC:tb A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process lymphocyte activation during immune response GO:0002285 lymphocyte activation involved in immune response A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 lymphocyte activation during immune response GOC:tb The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. biological_process T cell activation during immune response T lymphocyte activation during immune response T-cell activation during immune response T-lymphocyte activation during immune response GO:0002286 T cell activation involved in immune response The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 T cell activation during immune response GOC:tb The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. biological_process T cell development involved in immune response T cell differentiation during immune response T lymphocyte differentiation during immune response T-cell differentiation during immune response T-lymphocyte differentiation during immune response GO:0002292 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T cell differentiation involved in immune response The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. GOC:add ISBN:0781735149 T cell development involved in immune response GOC:add T cell differentiation during immune response GOC:tb The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. biological_process B cell activation during immune response B lymphocyte activation during immune response B-cell activation during immune response B-lymphocyte activation during immune response GO:0002312 B cell activation involved in immune response The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:jal B cell activation during immune response GOC:tb The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response. biological_process mature B cell development involved in immune response mature B cell differentiation during immune response mature B lymphocyte differentiation during immune response mature B-cell differentiation during immune response mature B-lymphocyte differentiation during immune response GO:0002313 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. mature B cell differentiation involved in immune response The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response. GOC:jal mature B cell development involved in immune response GOC:add mature B cell differentiation during immune response GOC:tb The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen. mature B lymphocyte differentiation mature B-cell differentiation mature B-lymphocyte differentiation biological_process mature cell development GO:0002335 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. mature B cell differentiation The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen. GOC:jal ISBN:0781735149 mature cell development GOC:add The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. histamine production involved in acute inflammatory response biological_process GO:0002349 histamine production involved in inflammatory response The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 PMID:16730260 The synthesis or release of serotonin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. serotonin production involved in acute inflammatory response biological_process GO:0002351 serotonin production involved in inflammatory response The synthesis or release of serotonin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 PMID:16730260 A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. biological_process immune cell activation during immune response leucocyte activation during immune response leukocyte activation during immune response GO:0002366 leukocyte activation involved in immune response A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. GOC:add ISBN:0781735149 leukocyte activation during immune response GOC:tb The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. GO:0002374 GO:0002375 cytokine biosynthetic process involved in immune response biological_process cytokine production during immune response cytokine secretion during immune response cytokine secretion involved in immune response GO:0002367 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. cytokine production involved in immune response The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. GOC:add GO_REF:0000022 ISBN:0781735149 cytokine production during immune response GOC:dph cytokine secretion during immune response GOC:dph Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. Wikipedia:Immune_system biological_process GO:0002376 Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). immune system process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. GOC:add GO_REF:0000022 The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GO:0002378 GO:0048305 antibody production immunoglobulin biosynthetic process immunoglobulin secretion biological_process GO:0002377 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. immunoglobulin production The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. GO:0002379 GO:0002380 immunoglobulin production involved in immunoglobulin mediated immune response immunoglobulin biosynthetic process involved in immune response immunoglobulin secretion involved in immune response biological_process antibody production during immune response antibody secretion during immune response immunoglobulin production during immune response immunoglobulin production involved in immune response GO:0002381 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. immunoglobulin production involved in immunoglobulin-mediated immune response The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 PMID:9185563 immunoglobulin production during immune response GOC:dph immunoglobulin production involved in immune response GOC:dph An immune response taking place in the liver. biological_process GO:0002384 hepatic immune response An immune response taking place in the liver. GOC:jal GO_REF:0000022 ISBN:0781735149 The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels. biological_process production of cellular mediator of immune response GO:0002440 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. production of molecular mediator of immune response The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels. GOC:add GO_REF:0000022 ISBN:0781735149 The regulated release of histamine by a cell as part of an inflammatory response. histamine secretion involved in acute inflammatory response biological_process GO:0002441 histamine secretion involved in inflammatory response The regulated release of histamine by a cell as part of an inflammatory response. GOC:add ISBN:0781735149 The regulated release of serotonin by a cell as part of an inflammatory response. serotonin secretion involved in acute inflammatory response biological_process serotonin release involved in inflammatory response GO:0002442 serotonin secretion involved in inflammatory response The regulated release of serotonin by a cell as part of an inflammatory response. GOC:add ISBN:0781735149 serotonin release involved in inflammatory response GOC:tb Any process involved in the carrying out of an immune response by a leukocyte. GO:0019723 GO:0042087 immune cell effector process immune cell mediated immunity leucocyte immune effector process leucocyte mediated immunity leukocyte immune effector process biological_process cell-mediated immune response cellular immune response GO:0002443 leukocyte mediated immunity Any process involved in the carrying out of an immune response by a leukocyte. GOC:add GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a lymphocyte. cell-mediated immunity cellular immune response biological_process GO:0002449 lymphocyte mediated immunity Any process involved in the carrying out of an immune response by a lymphocyte. GOC:add GO_REF:0000022 ISBN:0781735149 Any process involved in the carrying out of an immune response by a T cell. cell-mediated immunity cellular immune response T lymphocyte mediated immunity T-cell mediated immunity T-lymphocyte mediated immunity biological_process GO:0002456 T cell mediated immunity Any process involved in the carrying out of an immune response by a T cell. GOC:add GO_REF:0000022 ISBN:0781735149 An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. biological_process GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. GOC:add GOC:mtg_sensu ISBN:0781735149 ISBN:1405196831 Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation. immune response-dependent tolerance induction biological_process GO:0002461 tolerance induction dependent upon immune response Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation. GOC:jal GO_REF:0000022 ISBN:0781735149 Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues. biological_process GO:0002465 peripheral tolerance induction Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues. GOC:jal GO_REF:0000022 ISBN:0781735149 The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex. peptide or polysaccharide antigen processing and presentation of via MHC class II biological_process GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex. GOC:add ISBN:0781735149 PMID:15531770 PMID:15771591 PMID:16153240 A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. biological_process GO:0002507 tolerance induction A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. GOC:jal GO_REF:0000022 ISBN:0781735149 The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process GO:0002520 immune system development The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:add GOC:dph The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. immune cell differentiation leucocyte differentiation biological_process GO:0002521 leukocyte differentiation The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. CL:0000738 GOC:add PMID:16551264 The movement of a leukocyte within or between different tissues and organs of the body as part of an immune response. immune cell migration during immune response immune cell trafficking during immune response leucocyte migration during immune response leucocyte trafficking during immune response leukocyte trafficking during immune response biological_process GO:0002522 leukocyte migration involved in immune response The movement of a leukocyte within or between different tissues and organs of the body as part of an immune response. GOC:add ISBN:0781735149 PMID:14680625 PMID:14708592 PMID:7507411 PMID:8600538 The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response. biological_process immune cell migration during inflammatory response immune cell trafficking during inflammatory response leucocyte migration during inflammatory response leucocyte trafficking during inflammatory response leukocyte migration during inflammatory response leukocyte trafficking during inflammatory response GO:0002523 leukocyte migration involved in inflammatory response The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response. GOC:add ISBN:0781735149 PMID:14680625 PMID:14708592 PMID:7507411 PMID:8600538 leukocyte migration during inflammatory response GOC:dph The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels. production of molecular mediator involved in acute inflammatory response biological_process production of cellular mediator of acute inflammation GO:0002532 production of molecular mediator involved in inflammatory response The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add GOC:dph GOC:tb ISBN:0781735149 The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. cytokine production involved in acute inflammatory response biological_process GO:0002534 cytokine production involved in inflammatory response The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels. arachidonic acid metabolite production involved in acute inflammatory response production of arachidonic acid metabolites involved in acute inflammatory response production of arachidonic acid metabolites involved in inflammatory response biological_process GO:0002538 arachidonic acid metabolite production involved in inflammatory response The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels. GOC:add ISBN:0781735149 arachidonic acid metabolite production involved in acute inflammatory response GOC:mah The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. prostaglandin production involved in acute inflammatory response biological_process GO:0002539 prostaglandin production involved in inflammatory response The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. biological_process GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus. GOC:add ISBN:0781735149 PMID:16102575 PMID:16166509 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. myeloid leucocyte differentiation biological_process GO:0002573 myeloid leukocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage. GOC:add PMID:16551251 The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a thrombocyte, a nucleated cell found in all vertebrates but mammals involved in hemostasis. biological_process GO:0002574 Note that platelets are the non-nucleated mammalian functional equivalent of the nucleated thrombocytes of non-mammalian vertebrates and are sometimes also referred to as thrombocytes. Platelet formation in mammals is covered by the biological_process term platelet formation ; GO:0030220. thrombocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a thrombocyte, a nucleated cell found in all vertebrates but mammals involved in hemostasis. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation. biological_process GO:0002577 regulation of antigen processing and presentation Any process that modulates the frequency, rate, or extent of antigen processing and presentation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation. down regulation of antigen processing and presentation down-regulation of antigen processing and presentation downregulation of antigen processing and presentation inhibition of antigen processing and presentation biological_process GO:0002578 negative regulation of antigen processing and presentation Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation. up regulation of antigen processing and presentation up-regulation of antigen processing and presentation upregulation of antigen processing and presentation activation of antigen processing and presentation stimulation of antigen processing and presentation biological_process GO:0002579 positive regulation of antigen processing and presentation Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation. GOC:add Any process that modulates the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. regulation of peptide or polysaccharide antigen processing and presentation via MHC class II biological_process GO:0002580 regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Any process that modulates the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. down regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II down-regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II downregulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II negative regulation of peptide or polysaccharide antigen processing and presentation via MHC class II inhibition of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II biological_process GO:0002581 negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. GOC:add Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. positive regulation of peptide or polysaccharide antigen processing and presentation via MHC class II up regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II up-regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II upregulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II activation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II stimulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II biological_process GO:0002582 positive regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II. GOC:add Any process that modulates the frequency, rate, or extent of immunoglobulin production. GO:0002640 GO:0051023 regulation of antibody production regulation of immunoglobulin biosynthetic process regulation of immunoglobulin secretion biological_process GO:0002637 regulation of immunoglobulin production Any process that modulates the frequency, rate, or extent of immunoglobulin production. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of immunoglobulin production. GO:0002641 GO:0051025 down regulation of immunoglobulin production down-regulation of immunoglobulin production downregulation of immunoglobulin production inhibition of immunoglobulin production negative regulation of immunoglobulin biosynthetic process negative regulation of immunoglobulin secretion biological_process GO:0002638 negative regulation of immunoglobulin production Any process that stops, prevents, or reduces the frequency, rate, or extent of immunoglobulin production. GOC:add Any process that activates or increases the frequency, rate, or extent of immunoglobulin production. GO:0002642 GO:0051024 up regulation of immunoglobulin production up-regulation of immunoglobulin production upregulation of immunoglobulin production activation of immunoglobulin production positive regulation of immunoglobulin biosynthetic process positive regulation of immunoglobulin secretion stimulation of immunoglobulin production biological_process GO:0002639 positive regulation of immunoglobulin production Any process that activates or increases the frequency, rate, or extent of immunoglobulin production. GOC:add Any process that modulates the frequency, rate, or extent of tolerance induction. biological_process GO:0002643 regulation of tolerance induction Any process that modulates the frequency, rate, or extent of tolerance induction. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction. down regulation of tolerance induction down-regulation of tolerance induction downregulation of tolerance induction inhibition of tolerance induction biological_process GO:0002644 negative regulation of tolerance induction Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction. GOC:add Any process that activates or increases the frequency, rate, or extent of tolerance induction. up regulation of tolerance induction up-regulation of tolerance induction upregulation of tolerance induction activation of tolerance induction stimulation of tolerance induction biological_process GO:0002645 positive regulation of tolerance induction Any process that activates or increases the frequency, rate, or extent of tolerance induction. GOC:add Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response. regulation of immune response-dependent tolerance induction biological_process GO:0002652 regulation of tolerance induction dependent upon immune response Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction dependent upon immune response. down regulation of tolerance induction dependent upon immune response down-regulation of tolerance induction dependent upon immune response downregulation of tolerance induction dependent upon immune response negative regulation of immune response-dependent tolerance induction inhibition of tolerance induction dependent upon immune response biological_process GO:0002653 negative regulation of tolerance induction dependent upon immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction dependent upon immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response. positive regulation of immune response-dependent tolerance induction up regulation of tolerance induction dependent upon immune response up-regulation of tolerance induction dependent upon immune response upregulation of tolerance induction dependent upon immune response activation of tolerance induction dependent upon immune response stimulation of tolerance induction dependent upon immune response biological_process GO:0002654 positive regulation of tolerance induction dependent upon immune response Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response. GOC:add Any process that modulates the frequency, rate, or extent of peripheral tolerance induction. biological_process GO:0002658 regulation of peripheral tolerance induction Any process that modulates the frequency, rate, or extent of peripheral tolerance induction. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of peripheral tolerance induction. down regulation of peripheral tolerance induction down-regulation of peripheral tolerance induction downregulation of peripheral tolerance induction inhibition of peripheral tolerance induction biological_process GO:0002659 negative regulation of peripheral tolerance induction Any process that stops, prevents, or reduces the frequency, rate, or extent of peripheral tolerance induction. GOC:add Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction. up regulation of peripheral tolerance induction up-regulation of peripheral tolerance induction upregulation of peripheral tolerance induction activation of peripheral tolerance induction stimulation of peripheral tolerance induction biological_process GO:0002660 positive regulation of peripheral tolerance induction Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction. GOC:add Any process that modulates the frequency, rate, or extent of an immune system process. biological_process GO:0002682 regulation of immune system process Any process that modulates the frequency, rate, or extent of an immune system process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. down regulation of immune system process down-regulation of immune system process downregulation of immune system process inhibition of immune system process biological_process GO:0002683 negative regulation of immune system process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune system process. up regulation of immune system process up-regulation of immune system process upregulation of immune system process activation of immune system process stimulation of immune system process biological_process GO:0002684 positive regulation of immune system process Any process that activates or increases the frequency, rate, or extent of an immune system process. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte migration. regulation of immune cell migration regulation of leucocyte migration biological_process GO:0002685 regulation of leukocyte migration Any process that modulates the frequency, rate, or extent of leukocyte migration. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration. down regulation of leukocyte migration down-regulation of leukocyte migration downregulation of leukocyte migration negative regulation of immune cell migration negative regulation of leucocyte migration inhibition of leukocyte migration biological_process GO:0002686 negative regulation of leukocyte migration Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte migration. positive regulation of immune cell migration positive regulation of leucocyte migration up regulation of leukocyte migration up-regulation of leukocyte migration upregulation of leukocyte migration activation of leukocyte migration stimulation of leukocyte migration biological_process GO:0002687 positive regulation of leukocyte migration Any process that activates or increases the frequency, rate, or extent of leukocyte migration. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis. regulation of immune cell chemotaxis regulation of leucocyte chemotaxis biological_process GO:0002688 regulation of leukocyte chemotaxis Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte chemotaxis. down regulation of leukocyte chemotaxis down-regulation of leukocyte chemotaxis downregulation of leukocyte chemotaxis negative regulation of immune cell chemotaxis negative regulation of leucocyte chemotaxis inhibition of leukocyte chemotaxis biological_process GO:0002689 negative regulation of leukocyte chemotaxis Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte chemotaxis. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis. positive regulation of immune cell chemotaxis positive regulation of leucocyte chemotaxis up regulation of leukocyte chemotaxis up-regulation of leukocyte chemotaxis upregulation of leukocyte chemotaxis activation of leukocyte chemotaxis stimulation of leukocyte chemotaxis biological_process GO:0002690 positive regulation of leukocyte chemotaxis Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte activation. regulation of immune cell activation regulation of leucocyte activation biological_process GO:0002694 regulation of leukocyte activation Any process that modulates the frequency, rate, or extent of leukocyte activation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation. down regulation of leukocyte activation down-regulation of leukocyte activation downregulation of leukocyte activation negative regulation of immune cell activation negative regulation of leucocyte activation inhibition of leukocyte activation biological_process GO:0002695 negative regulation of leukocyte activation Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte activation. positive regulation of immune cell activation positive regulation of leucocyte activation up regulation of leukocyte activation up-regulation of leukocyte activation upregulation of leukocyte activation activation of leukocyte activation stimulation of leukocyte activation biological_process GO:0002696 positive regulation of leukocyte activation Any process that activates or increases the frequency, rate, or extent of leukocyte activation. GOC:add Any process that modulates the frequency, rate, or extent of an immune effector process. biological_process GO:0002697 regulation of immune effector process Any process that modulates the frequency, rate, or extent of an immune effector process. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process. down regulation of immune effector process down-regulation of immune effector process downregulation of immune effector process inhibition of immune effector process biological_process GO:0002698 negative regulation of immune effector process Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process. GOC:add Any process that activates or increases the frequency, rate, or extent of an immune effector process. up regulation of immune effector process up-regulation of immune effector process upregulation of immune effector process activation of immune effector process stimulation of immune effector process biological_process GO:0002699 positive regulation of immune effector process Any process that activates or increases the frequency, rate, or extent of an immune effector process. GOC:add Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response. biological_process GO:0002700 regulation of production of molecular mediator of immune response Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of the production of molecular mediator of immune response. down regulation of production of molecular mediator of immune response down-regulation of production of molecular mediator of immune response downregulation of production of molecular mediator of immune response inhibition of production of molecular mediator of immune response biological_process GO:0002701 negative regulation of production of molecular mediator of immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of the production of molecular mediator of immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of the production of molecular mediator of immune response. up regulation of production of molecular mediator of immune response up-regulation of production of molecular mediator of immune response upregulation of production of molecular mediator of immune response activation of production of molecular mediator of immune response stimulation of production of molecular mediator of immune response biological_process GO:0002702 positive regulation of production of molecular mediator of immune response Any process that activates or increases the frequency, rate, or extent of the production of molecular mediator of immune response. GOC:add Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. regulation of immune cell mediated immunity regulation of leucocyte mediated immunity biological_process GO:0002703 regulation of leukocyte mediated immunity Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity. down regulation of leukocyte mediated immunity down-regulation of leukocyte mediated immunity downregulation of leukocyte mediated immunity negative regulation of immune cell mediated immunity negative regulation of leucocyte mediated immunity inhibition of leukocyte mediated immunity biological_process GO:0002704 negative regulation of leukocyte mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. positive regulation of immune cell mediated immunity positive regulation of leucocyte mediated immunity up regulation of leukocyte mediated immunity up-regulation of leukocyte mediated immunity upregulation of leukocyte mediated immunity activation of leukocyte mediated immunity stimulation of leukocyte mediated immunity biological_process GO:0002705 positive regulation of leukocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity. biological_process GO:0002706 regulation of lymphocyte mediated immunity Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte mediated immunity. down regulation of lymphocyte mediated immunity down-regulation of lymphocyte mediated immunity downregulation of lymphocyte mediated immunity inhibition of lymphocyte mediated immunity biological_process GO:0002707 negative regulation of lymphocyte mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity. up regulation of lymphocyte mediated immunity up-regulation of lymphocyte mediated immunity upregulation of lymphocyte mediated immunity activation of lymphocyte mediated immunity stimulation of lymphocyte mediated immunity biological_process GO:0002708 positive regulation of lymphocyte mediated immunity Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of T cell mediated immunity. regulation of T lymphocyte mediated immunity regulation of T-cell mediated immunity regulation of T-lymphocyte mediated immunity biological_process GO:0002709 regulation of T cell mediated immunity Any process that modulates the frequency, rate, or extent of T cell mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell mediated immunity. down regulation of T cell mediated immunity down-regulation of T cell mediated immunity downregulation of T cell mediated immunity negative regulation of T lymphocyte mediated immunity negative regulation of T-cell mediated immunity negative regulation of T-lymphocyte mediated immunity inhibition of T cell mediated immunity biological_process GO:0002710 negative regulation of T cell mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity. positive regulation of T lymphocyte mediated immunity positive regulation of T-cell mediated immunity positive regulation of T-lymphocyte mediated immunity up regulation of T cell mediated immunity up-regulation of T cell mediated immunity upregulation of T cell mediated immunity activation of T cell mediated immunity stimulation of T cell mediated immunity biological_process GO:0002711 positive regulation of T cell mediated immunity Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of B cell mediated immunity. regulation of B lymphocyte mediated immunity regulation of B-cell mediated immunity regulation of B-lymphocyte mediated immunity biological_process GO:0002712 regulation of B cell mediated immunity Any process that modulates the frequency, rate, or extent of B cell mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell mediated immunity. down regulation of B cell mediated immunity down-regulation of B cell mediated immunity downregulation of B cell mediated immunity negative regulation of B lymphocyte mediated immunity negative regulation of B-cell mediated immunity negative regulation of B-lymphocyte mediated immunity inhibition of B cell mediated immunity biological_process GO:0002713 negative regulation of B cell mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity. positive regulation of B lymphocyte mediated immunity positive regulation of B-cell mediated immunity positive regulation of B-lymphocyte mediated immunity up regulation of B cell mediated immunity up-regulation of B cell mediated immunity upregulation of B cell mediated immunity activation of B cell mediated immunity stimulation of B cell mediated immunity biological_process GO:0002714 positive regulation of B cell mediated immunity Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of natural killer cell mediated immunity. GO:0045845 regulation of NK cell mediated immunity biological_process regulation of natural killer cell activity GO:0002715 regulation of natural killer cell mediated immunity Any process that modulates the frequency, rate, or extent of natural killer cell mediated immunity. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell mediated immunity. GO:0030102 down regulation of natural killer cell mediated immunity down-regulation of natural killer cell mediated immunity downregulation of natural killer cell mediated immunity negative regulation of NK cell mediated immunity inhibition of natural killer cell mediated immunity biological_process negative regulation of NK cell activity negative regulation of natural killer cell activity GO:0002716 negative regulation of natural killer cell mediated immunity Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell mediated immunity. GOC:add Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated immunity. GO:0045846 positive regulation of NK cell mediated immunity up regulation of natural killer cell mediated immunity up-regulation of natural killer cell mediated immunity upregulation of natural killer cell mediated immunity activation of natural killer cell mediated immunity stimulation of natural killer cell mediated immunity biological_process positive regulation of NK cell activity positive regulation of natural killer cell activity GO:0002717 positive regulation of natural killer cell mediated immunity Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated immunity. GOC:add Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response. GO:0002739 GO:0002742 regulation of cytokine biosynthetic process involved in immune response regulation of cytokine secretion involved in immune response biological_process regulation of cytokine production during immune response GO:0002718 regulation of cytokine production involved in immune response Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response. GOC:add regulation of cytokine production during immune response GOC:dph Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production contributing to an immune response. GO:0002740 GO:0002743 down-regulation of cytokine production during immune response negative regulation of cytokine biosynthetic process involved in immune response negative regulation of cytokine secretion involved in immune response biological_process down regulation of cytokine production during immune response downregulation of cytokine production during immune response inhibition of cytokine production during immune response negative regulation of cytokine production during immune response GO:0002719 negative regulation of cytokine production involved in immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production contributing to an immune response. GOC:add negative regulation of cytokine production during immune response GOC:dph Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response. GO:0002741 GO:0002744 activation of cytokine production during immune response positive regulation of cytokine biosynthetic process involved in immune response positive regulation of cytokine secretion involved in immune response stimulation of cytokine production during immune response biological_process positive regulation of cytokine production during immune response up regulation of cytokine production during immune response up-regulation of cytokine production during immune response upregulation of cytokine production during immune response GO:0002720 positive regulation of cytokine production involved in immune response Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response. GOC:add positive regulation of cytokine production during immune response GOC:dph Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation. biological_process GO:0002761 regulation of myeloid leukocyte differentiation Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation. down regulation of myeloid leukocyte differentiation down-regulation of myeloid leukocyte differentiation downregulation of myeloid leukocyte differentiation inhibition of myeloid leukocyte differentiation biological_process GO:0002762 negative regulation of myeloid leukocyte differentiation Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation. up regulation of myeloid leukocyte differentiation up-regulation of myeloid leukocyte differentiation upregulation of myeloid leukocyte differentiation activation of myeloid leukocyte differentiation stimulation of myeloid leukocyte differentiation biological_process GO:0002763 positive regulation of myeloid leukocyte differentiation Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation. GOC:add The controlled release of a peptide from a cell or a tissue. biological_process GO:0002790 peptide secretion The controlled release of a peptide from a cell or a tissue. GOC:add Any process that modulates the frequency, rate, or extent of peptide secretion. biological_process GO:0002791 regulation of peptide secretion Any process that modulates the frequency, rate, or extent of peptide secretion. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. down regulation of peptide secretion down-regulation of peptide secretion downregulation of peptide secretion inhibition of peptide secretion biological_process GO:0002792 negative regulation of peptide secretion Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. GOC:add Any process that activates or increases the frequency, rate, or extent of peptide secretion. up regulation of peptide secretion up-regulation of peptide secretion upregulation of peptide secretion activation of peptide secretion stimulation of peptide secretion biological_process GO:0002793 positive regulation of peptide secretion Any process that activates or increases the frequency, rate, or extent of peptide secretion. GOC:add Any process that modulates the frequency, rate, or extent of an adaptive immune response. biological_process GO:0002819 regulation of adaptive immune response Any process that modulates the frequency, rate, or extent of an adaptive immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response. down regulation of adaptive immune response down-regulation of adaptive immune response downregulation of adaptive immune response inhibition of adaptive immune response biological_process GO:0002820 negative regulation of adaptive immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of an adaptive immune response. up regulation of adaptive immune response up-regulation of adaptive immune response upregulation of adaptive immune response activation of adaptive immune response stimulation of adaptive immune response biological_process GO:0002821 positive regulation of adaptive immune response Any process that activates or increases the frequency, rate, or extent of an adaptive immune response. GOC:add Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. biological_process GO:0002822 regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GOC:add GOC:mtg_sensu Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. biological_process GO:0002823 negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GOC:add GOC:mtg_sensu Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. biological_process GO:0002824 positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata. GOC:add GOC:mtg_sensu Any process that modulates the frequency, rate, or extent of a type 2 immune response. regulation of T-helper 2 type immune response regulation of Th2 immune response biological_process GO:0002828 regulation of type 2 immune response Any process that modulates the frequency, rate, or extent of a type 2 immune response. GOC:add regulation of T-helper 2 type immune response GOC:add regulation of Th2 immune response GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response. down regulation of type 2 immune response down-regulation of type 2 immune response downregulation of type 2 immune response inhibition of type 2 immune response negative regulation of T-helper 2 type immune response negative regulation of Th2 immune response biological_process GO:0002829 negative regulation of type 2 immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response. GOC:add negative regulation of T-helper 2 type immune response GOC:add negative regulation of Th2 immune response GOC:add Any process that activates or increases the frequency, rate, or extent of a type 2 immune response. up regulation of type 2 immune response up-regulation of type 2 immune response upregulation of type 2 immune response activation of type 2 immune response positive regulation of T-helper 2 type immune response positive regulation of Th2 immune response stimulation of type 2 immune response biological_process GO:0002830 positive regulation of type 2 immune response Any process that activates or increases the frequency, rate, or extent of a type 2 immune response. GOC:add positive regulation of T-helper 2 type immune response GOC:add positive regulation of Th2 immune response GOC:add Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. biological_process GO:0002831 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to biotic stimulus Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. down regulation of response to biotic stimulus down-regulation of response to biotic stimulus downregulation of response to biotic stimulus inhibition of response to biotic stimulus biological_process GO:0002832 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to biotic stimulus Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. up regulation of response to biotic stimulus up-regulation of response to biotic stimulus upregulation of response to biotic stimulus activation of response to biotic stimulus stimulation of response to biotic stimulus biological_process GO:0002833 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to biotic stimulus Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. GOC:add Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response. biological_process GO:0002889 regulation of immunoglobulin mediated immune response Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of an immunoglobulin mediated immune response. down regulation of immunoglobulin mediated immune response down-regulation of immunoglobulin mediated immune response downregulation of immunoglobulin mediated immune response inhibition of immunoglobulin mediated immune response biological_process GO:0002890 negative regulation of immunoglobulin mediated immune response Any process that stops, prevents, or reduces the frequency, rate, or extent of an immunoglobulin mediated immune response. GOC:add Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response. up regulation of immunoglobulin mediated immune response up-regulation of immunoglobulin mediated immune response upregulation of immunoglobulin mediated immune response activation of immunoglobulin mediated immune response stimulation of immunoglobulin mediated immune response biological_process GO:0002891 positive regulation of immunoglobulin mediated immune response Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response. GOC:add A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. puberty biological_process reproductive developmental process GO:0003006 developmental process involved in reproduction A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring. GOC:dph GOC:isa_complete puberty GOC:dph reproductive developmental process GOC:dph GOC:tb A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process GO:0003008 system process A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. GOC:mtg_cardio A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. biological_process muscle physiological process GO:0003012 muscle system process A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers. GOC:mtg_cardio A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. Wikipedia:Circulatory_system biological_process GO:0003013 circulatory system process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. GOC:mtg_cardio A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). excretory system process biological_process kidney system process GO:0003014 renal system process A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). GOC:cjm GOC:mtg_cardio GOC:mtg_kidney_jan10 A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. biological_process cardiac process GO:0003015 heart process A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. GOC:mtg_cardio A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GO:0010802 respiratory gaseous exchange biological_process GO:0003016 respiratory system process A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange. GOC:dph GOC:mtg_cardio GOC:tb The series of events in which an oxygen stimulus is received by a cell and converted into a molecular signal. biological_process GO:0003032 detection of oxygen The series of events in which an oxygen stimulus is received by a cell and converted into a molecular signal. GOC:mtg_cardio The regulation of blood pressure mediated by biochemical signaling: hormonal, autocrine or paracrine. blood pressure regulation mediated by a chemical signal biological_process GO:0003044 regulation of systemic arterial blood pressure mediated by a chemical signal The regulation of blood pressure mediated by biochemical signaling: hormonal, autocrine or paracrine. GOC:mtg_cardio Renal process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. renal control of blood pressure renal regulation of systemic arterial blood pressure biological_process GO:0003071 renal system process involved in regulation of systemic arterial blood pressure Renal process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. GOC:dph GOC:mtg_cardio GOC:tb renal regulation of systemic arterial blood pressure GOC:dph GOC:tb The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. biological_process GO:0003073 regulation of systemic arterial blood pressure The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. GOC:mtg_cardio Renal process involved in the maintenance of an internal steady state of water in the body. water homeostasis by the renal system biological_process GO:0003091 renal water homeostasis Renal process involved in the maintenance of an internal steady state of water in the body. GOC:mtg_cardio Any process that modulates the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process in which blood is filtered by the glomerulus into the renal tubule. biological_process GO:0003093 regulation of glomerular filtration Any process that modulates the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process in which blood is filtered by the glomerulus into the renal tubule. GOC:mtg_cardio The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. biological_process GO:0003094 glomerular filtration The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. GOC:mtg_cardio GOC:sart ISBN:0721643949 The directed movement of water (H2O) by the renal system. biological_process GO:0003097 renal water transport The directed movement of water (H2O) by the renal system. GOC:mtg_cardio Any process that activates or increases the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule. biological_process GO:0003104 positive regulation of glomerular filtration Any process that activates or increases the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule. GOC:mtg_cardio Any process that stops, prevents, or reduces the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule. biological_process GO:0003105 negative regulation of glomerular filtration Any process that stops, prevents, or reduces the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule. GOC:mtg_cardio Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. dph 2009-11-02T02:07:40Z biological_process GO:0003330 regulation of extracellular matrix constituent secretion Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. dph 2009-11-02T02:11:22Z biological_process GO:0003331 positive regulation of extracellular matrix constituent secretion Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. GOC:dph GOC:tb Any process that decreases the rate, frequency, or extent the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. dph 2009-11-02T02:13:49Z biological_process GO:0003332 negative regulation of extracellular matrix constituent secretion Any process that decreases the rate, frequency, or extent the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. GOC:dph GOC:tb The directed, self-propelled movement of a cilium. https://github.com/geneontology/go-ontology/issues/19809 dph 2009-11-24T09:56:26Z GO:0036142 microtubule-based flagellum movement flagellar movement flagellum movement biological_process ciliary motility cilium beating flagellar motility GO:0003341 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium movement The directed, self-propelled movement of a cilium. GOC:dph GOC:jl flagellar movement GOC:bf cilium beating GOC:ascb_2009 GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. dph 2009-12-03T10:12:00Z GO:1900172 regulation of microtubule-based flagellum movement biological_process regulation of flagellar movement regulation of flagellum movement GO:0003352 Note that we deem cilium and microtubule-based flagellum to be equivalent. regulation of cilium movement Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. GOC:dph regulation of flagellar movement GOC:TermGenie Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. dph 2009-12-03T10:16:10Z GO:1900174 positive regulation of microtubule-based flagellum movement biological_process positive regulation of flagellar movement positive regulation of flagellum movement GO:0003353 Note that we deem cilium and microtubule-based flagellum to be equivalent. positive regulation of cilium movement Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. GOC:dph positive regulation of flagellar movement GOC:TermGenie Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. dph 2009-12-03T10:17:47Z GO:1900173 negative regulation of microtubule-based flagellum movement biological_process negative regulation of flagellum movement GO:0003354 Note that we deem cilium and microtubule-based flagellum to be equivalent. negative regulation of cilium movement Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium. GOC:dph A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+. EC:2.7.2.3 KEGG_REACTION:R01512 MetaCyc:PHOSGLYPHOS-RXN RHEA:14801 Reactome:R-HSA-70486 Reactome:R-HSA-71850 molecular_function 3-PGK 3-phosphoglycerate kinase activity 3-phosphoglycerate phosphokinase activity 3-phosphoglyceric acid kinase activity 3-phosphoglyceric acid phosphokinase activity 3-phosphoglyceric kinase activity ATP-3-phospho-D-glycerate-1-phosphotransferase activity ATP:3-phospho-D-glycerate 1-phosphotransferase activity ATP:D-3-phosphoglycerate 1-phosphotransferase activity PGK glycerate 3-phosphate kinase activity glycerophosphate kinase activity phosphoglyceric acid kinase activity phosphoglyceric kinase activity phosphoglycerokinase activity GO:0004618 phosphoglycerate kinase activity Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+. EC:2.7.2.3 RHEA:14801 Reactome:R-HSA-70486 PGK complexes (PGK1,2) phosphorylate 3PG to form 1,3BPG Reactome:R-HSA-71850 1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ATP 3-PGK EC:2.7.2.3 3-phosphoglycerate kinase activity EC:2.7.2.3 3-phosphoglycerate phosphokinase activity EC:2.7.2.3 3-phosphoglyceric acid kinase activity EC:2.7.2.3 3-phosphoglyceric acid phosphokinase activity EC:2.7.2.3 3-phosphoglyceric kinase activity EC:2.7.2.3 ATP-3-phospho-D-glycerate-1-phosphotransferase activity EC:2.7.2.3 ATP:3-phospho-D-glycerate 1-phosphotransferase activity EC:2.7.2.3 ATP:D-3-phosphoglycerate 1-phosphotransferase activity EC:2.7.2.3 PGK EC:2.7.2.3 glycerate 3-phosphate kinase activity EC:2.7.2.3 glycerophosphate kinase activity EC:2.7.2.3 phosphoglyceric acid kinase activity EC:2.7.2.3 phosphoglyceric kinase activity EC:2.7.2.3 phosphoglycerokinase activity EC:2.7.2.3 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate. https://github.com/geneontology/go-ontology/issues/24905 https://github.com/geneontology/go-ontology/issues/25780 RHEA:15901 Reactome:R-HSA-71445 Reactome:R-HSA-71654 PGM molecular_function D-phosphoglycerate 2,3-phosphomutase activity PGA mutase activity PGAM activity phosphoglycerate phosphomutase activity phosphoglyceromutase activity GO:0004619 phosphoglycerate mutase activity Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate. RHEA:15901 Reactome:R-HSA-71445 PGAM dimers (PGAM1,2) isomerise 2PG to 3PG Reactome:R-HSA-71654 3-Phospho-D-glycerate <=> 2-Phospho-D-glycerate Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O. EC:4.2.1.11 MetaCyc:2PGADEHYDRAT-RXN RHEA:10164 Reactome:R-HSA-70494 Reactome:R-HSA-71660 2-phospho-D-glycerate-hydrolase activity nervous-system specific enolase molecular_function 14-3-2-protein 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming) 2-phospho-D-glycerate hydro-lyase activity 2-phosphoglycerate dehydratase activity 2-phosphoglycerate enolase activity 2-phosphoglyceric dehydratase activity enolase activity gamma-enolase activity phosphoenolpyruvate hydratase activity GO:0004634 phosphopyruvate hydratase activity Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O. EC:4.2.1.11 ISBN:0198506732 Reactome:R-HSA-70494 Enolase dimers (ENO1,2,3) convert PEP to 2PG Reactome:R-HSA-71660 2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O nervous-system specific enolase EC:4.2.1.11 14-3-2-protein EC:4.2.1.11 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming) EC:4.2.1.11 2-phospho-D-glycerate hydro-lyase activity EC:4.2.1.11 2-phosphoglycerate dehydratase activity EC:4.2.1.11 2-phosphoglycerate enolase activity EC:4.2.1.11 2-phosphoglyceric dehydratase activity EC:4.2.1.11 enolase activity EC:4.2.1.11 gamma-enolase activity EC:4.2.1.11 phosphoenolpyruvate hydratase activity EC:4.2.1.11 Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. GO:0004926 GO:0099600 transmembrane receptor activity Reactome:R-HSA-193672 transmembrane signalling receptor activity molecular_function GO:0004888 This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores. transmembrane signaling receptor activity Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction. GOC:go_curators Wikipedia:Transmembrane_receptor transmembrane receptor activity GOC:bf GOC:signaling Reactome:R-HSA-193672 Sphingomyelinase is activated by the NGF:p75NTR complex transmembrane signalling receptor activity GOC:mah Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. GO:0001622 GO:0001623 GO:0001624 GO:0001625 GO:0016526 Reactome:R-HSA-114552 Reactome:R-HSA-114558 Reactome:R-HSA-167408 Wikipedia:GPCR G protein coupled receptor activity G protein linked receptor activity G-protein coupled receptor activity G-protein linked receptor activity GPCR activity ligand-dependent GPCR activity receptor activity, G-protein coupled EBV-induced receptor Epstein-Barr Virus-induced receptor activity G-protein coupled receptor activity, unknown ligand Mas proto-oncogene receptor activity RDC1 receptor activity SREB receptor orphan G protein coupled receptor activity orphan G-protein coupled receptor activity orphan GPCR activity super conserved receptor expressed in brain receptor activity molecular_function GO:0004930 G protein-coupled receptor activity Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. GOC:bf Wikipedia:GPCR http://www.iuphar-db.org Reactome:R-HSA-114552 Thrombin-activated PARs activate G12/13 Reactome:R-HSA-114558 Thrombin-activated PARs activate Gq Reactome:R-HSA-167408 The high affinity receptor complex binds to G-protein receptor activity, G-protein coupled GOC:bf Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GO:0005478 Reactome:R-HSA-168313 Reactome:R-HSA-178215 molecular_function carrier GO:0005215 Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GOC:ai GOC:dgf Reactome:R-HSA-168313 Virion-associated M2 protein mediated ion infusion Reactome:R-HSA-178215 SMAD7:SMURF1 complex is exported to the cytosol A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). https://github.com/geneontology/go-ontology/issues/17729 GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). GOC:pdt subcellular entity NIF_Subcellular:nlx_subcell_100315 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. Wikipedia:Extracellular extracellular cellular_component GO:0005576 Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'. extracellular region The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. GOC:go_curators A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. fibrinogen fibrinogen alpha chain fibrinogen beta chain fibrinogen gamma chain cellular_component GO:0005577 fibrinogen complex A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. ISBN:0198547684 A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. GOC:dos GOC:mah ISBN:0721639976 PMID:19693541 PMID:21421911 Any triple helical collagen trimer that forms fibrils. cellular_component GO:0005583 fibrillar collagen trimer Any triple helical collagen trimer that forms fibrils. GOC:mah ISBN:0721639976 PMID:21421911 A collagen trimer containing alpha(I) chains. The most common form of type I collagen is a heterotrimer containing two alpha1(I) chains and one alpha2(I) chain; homotrimers containing three alpha1(I) chains are also found. Type I collagen triple helices associate to form banded fibrils. Wikipedia:Collagen_type_I cellular_component GO:0005584 collagen type I trimer A collagen trimer containing alpha(I) chains. The most common form of type I collagen is a heterotrimer containing two alpha1(I) chains and one alpha2(I) chain; homotrimers containing three alpha1(I) chains are also found. Type I collagen triple helices associate to form banded fibrils. GOC:mah GOC:sl ISBN:0721639976 A collagen homotrimer of alpha1(II) chains; type II collagen triple helices associate to form fibrils. Wikipedia:Collagen_type_II cellular_component GO:0005585 collagen type II trimer A collagen homotrimer of alpha1(II) chains; type II collagen triple helices associate to form fibrils. ISBN:0721639976 A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes. Wikipedia:Collagen_type_IV cellular_component GO:0005587 collagen type IV trimer A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes. ISBN:0721639976 PMID:19693541 PMID:21421911 A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. GO:0005605 GO:0008003 Wikipedia:Basement_membrane cellular_component basal lamina basement lamina lamina densa GO:0005604 Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. basement membrane A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers. ISBN:0198547684 PMID:22505934 That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. NIF_Subcellular:sao1425028079 cellular_component intercellular space GO:0005615 Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term. extracellular space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. ISBN:0198547684 A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. https://github.com/geneontology/go-ontology/issues/17776 Wikipedia:Intracellular internal to cell intracellular protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular anatomical structure A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. https://github.com/geneontology/go-ontology/issues/19036 cell and encapsulating structures NIF_Subcellular:sao1813327414 Wikipedia:Cell_(biology) cellular_component GO:0005623 This term was obsoleted because it was redundant with the root class of the cell ontology, CL:0000000. obsolete cell true OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:go_curators A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component GO:0005635 nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. ISBN:0198547684 A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. NIF_Subcellular:sao1820400233 Wikipedia:Nucleolus cellular_component GO:0005730 nucleolus A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. ISBN:0198506732 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. https://github.com/geneontology/go-ontology/issues/23023 Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component GO:0005739 Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. GOC:giardia ISBN:0198506732 The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space. cellular_component GO:0005740 mitochondrial envelope The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space. GOC:ai GOC:pz The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. GO:0031980 NIF_Subcellular:sao1804523077 Wikipedia:Mitochondrial_matrix mitochondrial lumen mitochondrial stroma cellular_component GO:0005759 mitochondrial matrix The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. GOC:as ISBN:0198506732 A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes. 55S ribosome, mitochondrial cellular_component GO:0005761 mitochondrial ribosome A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes. GOC:mah ISBN:0198506732 A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. NIF_Subcellular:sao585356902 Wikipedia:Lysosome cellular_component GO:0005764 lysosome A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. GOC:mah ISBN:0198506732 A lysosome before it has fused with a vesicle or vacuole. NIF_Subcellular:sao1140587416 cellular_component GO:0005766 primary lysosome A lysosome before it has fused with a vesicle or vacuole. GOC:jl ISBN:0815316194 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 The volume enclosed within the vacuolar membrane. cellular_component GO:0005775 vacuolar lumen The volume enclosed within the vacuolar membrane. ISBN:0198506732 A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. Golgi NIF_Subcellular:sao451912436 Wikipedia:Golgi_apparatus Golgi complex Golgi ribbon cellular_component GO:0005794 Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. Golgi apparatus A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. ISBN:0198506732 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0033279 NIF_Subcellular:sao1429207766 Wikipedia:Ribosome free ribosome membrane bound ribosome cellular_component ribosomal RNA GO:0005840 ribosome An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. ISBN:0198506732 free ribosome NIF_Subcellular:sao1139385046 membrane bound ribosome NIF_Subcellular:sao1291545653 A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. Wikipedia:Cytoskeleton cellular_component GO:0005856 cytoskeleton A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. GOC:mah PMID:16959967 PMID:27419875 A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. FMA:63851 NIF_Subcellular:sao952483289 Wikipedia:Intermediate_filament cellular_component intermediate filament associated protein type I intermediate filament associated protein type II intermediate filament associated protein GO:0005882 intermediate filament A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. ISBN:0198506732 http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. FMA:63850 NIF_Subcellular:sao1588493326 Wikipedia:Actin microfilament cellular_component GO:0005884 actin filament A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane. GOC:mah ISBN:0198506732 PMID:10666339 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005887 GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane integral component of plasma membrane integral to plasma membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. NIF_Subcellular:sao671419673 Wikipedia:Microvillus cellular_component microvilli GO:0005902 Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta. microvillus Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells. ISBN:0815316194 microvilli NIF_Subcellular:sao671419673 A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects. https://github.com/geneontology/go-ontology/issues/22122 cell-cell contact region cell-cell contact zone NIF_Subcellular:sao1922892319 intercellular junction cellular_component GO:0005911 cell-cell junction A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects. GOC:aruk GOC:bc GOC:dgh GOC:hb GOC:mah PMID:21422226 PMID:28096264 intercellular junction NIF_Subcellular:sao1395777368 A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GOC:cilia GOC:curators GOC:kmv GOC:vw ISBN:0198547684 PMID:16824949 PMID:17009929 PMID:20144998 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. https://github.com/geneontology/go-ontology/issues/26298 Wikipedia:Cell_cortex ectoplasm cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. https://github.com/geneontology/go-ontology/issues/22880 jl 2012-10-23T15:40:34Z GO:0044261 GO:0044723 Wikipedia:Carbohydrate_metabolism carbohydrate metabolism biological_process GO:0005975 carbohydrate metabolic process The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. GO:0044263 polysaccharide metabolism glycan metabolic process glycan metabolism multicellular organismal polysaccharide metabolic process biological_process GO:0005976 polysaccharide metabolic process The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. ISBN:0198547684 The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. glycogen metabolism biological_process GO:0005977 glycogen metabolic process The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. MetaCyc:GLYCOGENSYNTH-PWY glycogen anabolism glycogen biosynthesis glycogen formation glycogen synthesis biological_process GO:0005978 glycogen biosynthetic process The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. regulation of glycogen anabolism regulation of glycogen biosynthesis regulation of glycogen formation regulation of glycogen synthesis biological_process GO:0005979 regulation of glycogen biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. MetaCyc:GLYCOCAT-PWY glycogen breakdown glycogen catabolism glycogen degradation glycogenolysis biological_process GO:0005980 glycogen catabolic process The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues. ISBN:0198506732 glycogenolysis GOC:sl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. regulation of glycogen breakdown regulation of glycogen catabolism regulation of glycogen degradation regulation of glycogenolysis biological_process GO:0005981 regulation of glycogen catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. GOC:go_curators regulation of glycogenolysis GOC:sl The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. monosaccharide metabolism biological_process GO:0005996 monosaccharide metabolic process The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. ISBN:0198506732 The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. cellular glucose metabolic process glucose metabolism biological_process GO:0006006 glucose metabolic process The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. ISBN:0198506732 cellular glucose metabolic process GOC:vw The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan metabolism biological_process GO:0006022 aminoglycan metabolic process The chemical reactions and pathways involving aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. aminoglycan anabolism aminoglycan biosynthesis aminoglycan formation aminoglycan synthesis biological_process GO:0006023 aminoglycan biosynthetic process The chemical reactions and pathways resulting in the formation of aminoglycans, any polymer containing amino groups that consists of more than about 10 monosaccharide residues joined to each other by glycosidic linkages. GOC:ai ISBN:0198506732 The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. glycosaminoglycan anabolism glycosaminoglycan biosynthesis glycosaminoglycan formation glycosaminoglycan synthesis biological_process GO:0006024 glycosaminoglycan biosynthetic process The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. ISBN:0192800981 The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom. alcohol metabolism biological_process GO:0006066 alcohol metabolic process The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom. ISBN:0198506732 The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. organic acid metabolism biological_process GO:0006082 organic acid metabolic process The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 The chemical reactions and pathways involving pyruvate, 2-oxopropanoate. GO:0006087 MetaCyc:P41-PWY Wikipedia:Pyruvic_acid pyruvate metabolism biological_process pyruvate dehydrogenase bypass GO:0006090 pyruvate metabolic process The chemical reactions and pathways involving pyruvate, 2-oxopropanoate. GOC:go_curators The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. energy pathways biological_process intermediary metabolism metabolic energy generation GO:0006091 generation of precursor metabolites and energy The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. GOC:jl intermediary metabolism GOC:mah The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. https://github.com/geneontology/go-ontology/issues/21176 GO:0019641 GO:0019642 MetaCyc:GLYCOLYSIS-VARIANTS biological_process Embden-Meyerhof pathway Embden-Meyerhof-Parnas pathway anaerobic glycolysis glycolysis modifed Embden-Meyerhof pathway GO:0006096 glycolytic process The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. GOC:bf GOC:dph ISBN:0201090910 ISBN:0716720094 ISBN:0879010479 Wikipedia:Glycolysis glycolysis GOC:dph Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. regulation of carbohydrate metabolism biological_process GO:0006109 regulation of carbohydrate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. GOC:go_curators Any process that modulates the frequency, rate or extent of glycolysis. GO:0090525 regulation of glycolysis involved in cellular glucose homeostasis biological_process GO:0006110 regulation of glycolytic process Any process that modulates the frequency, rate or extent of glycolysis. GOC:go_curators The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. energy reserve metabolism biological_process GO:0006112 energy reserve metabolic process The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen. GOC:mah Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides. regulation of nucleotide metabolism biological_process GO:0006140 regulation of nucleotide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines. regulation of purine base metabolic process regulation of purine base metabolism biological_process GO:0006141 regulation of purine nucleobase metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines. GOC:go_curators regulation of purine base metabolic process GOC:go_curators The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine. purine base metabolic process purine base metabolism purine metabolic process purine metabolism biological_process GO:0006144 purine nucleobase metabolic process The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine. GOC:go_curators purine base metabolic process GOC:go_curators The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine nucleotide metabolism purine metabolic process purine metabolism biological_process GO:0006163 purine nucleotide metabolic process The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine nucleotide breakdown purine nucleotide catabolism purine nucleotide degradation biological_process GO:0006195 purine nucleotide catabolic process The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GOC:go_curators ISBN:0198506732 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. biological_process GO:0006310 DNA recombination Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. ISBN:0198506732 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0006416 GO:0006453 GO:0043037 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation biological_process GO:0006412 translation The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GOC:go_curators The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GO:0006442 GO:0006455 protein synthesis elongation translation elongation biological_process GO:0006414 translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GOC:ems Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0006445 regulation of protein anabolism regulation of protein biosynthesis regulation of protein formation regulation of protein synthesis biological_process GO:0006417 regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete Any process that modulates the frequency, rate, extent or accuracy of translational elongation. biological_process GO:0006448 regulation of translational elongation Any process that modulates the frequency, rate, extent or accuracy of translational elongation. GOC:go_curators The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. Wikipedia:Proteolysis peptidolysis ATP-dependent proteolysis biological_process GO:0006508 This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing. proteolysis The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GOC:bf GOC:mah ATP-dependent proteolysis GOC:mah The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. peptide metabolism biological_process GO:0006518 peptide metabolic process The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. GOC:go_curators The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. https://github.com/geneontology/go-ontology/issues/17904 GO:0006519 cellular amino acid metabolic process cellular amino acid metabolism biological_process amino acid and derivative metabolism cellular amino acid and derivative metabolic process GO:0006520 amino acid metabolic process The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. regulation of amino acid metabolism biological_process GO:0006521 regulation of cellular amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. GOC:go_curators The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. Wikipedia:Arginine arginine metabolism biological_process GO:0006525 arginine metabolic process The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GOC:go_curators The chemical reactions and pathways involving glycine, aminoethanoic acid. glycine metabolism biological_process GO:0006544 glycine metabolic process The chemical reactions and pathways involving glycine, aminoethanoic acid. GOC:go_curators The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid. isoleucine metabolism biological_process GO:0006549 isoleucine metabolic process The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid. GOC:ai The chemical reactions and pathways involving leucine, 2-amino-4-methylpentanoic acid. leucine metabolism biological_process GO:0006551 leucine metabolic process The chemical reactions and pathways involving leucine, 2-amino-4-methylpentanoic acid. GOC:ai The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid. Wikipedia:Lysine lysine metabolism biological_process GO:0006553 lysine metabolic process The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid. GOC:go_curators The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. methionine and threonine metabolic process methionine and threonine metabolism UM-BBD_pathwayID:met methionine metabolism biological_process GO:0006555 methionine metabolic process The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid. phenylalanine metabolic process phenylalanine metabolism L-phenylalanine metabolism biological_process GO:0006558 L-phenylalanine metabolic process The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid. GOC:jsg GOC:mah The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid. L-serine metabolism biological_process GO:0006563 L-serine metabolic process The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid. GOC:ai GOC:jsg The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid. UM-BBD_pathwayID:tyr Wikipedia:Tyrosine tyrosine metabolism biological_process GO:0006570 tyrosine metabolic process The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid. GOC:go_curators The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid. valine metabolism biological_process GO:0006573 valine metabolic process The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid. GOC:ai The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents. amino acid derivative metabolic process cellular amino acid derivative metabolic process cellular amino acid derivative metabolism cellular modified amino acid metabolism modified amino acid metabolic process modified amino acid metabolism biological_process GO:0006575 cellular modified amino acid metabolic process The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents. GOC:ai cellular modified amino acid metabolism GOC:mah modified amino acid metabolic process GOC:mah modified amino acid metabolism GOC:mah The chemical reactions and pathways involving any betaine, the N-trimethyl derivative of an amino acid. betaine metabolic process betaine metabolism biological_process GO:0006577 amino-acid betaine metabolic process The chemical reactions and pathways involving any betaine, the N-trimethyl derivative of an amino acid. GOC:mah ISBN:0198506732 The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones. biological_process GO:0006590 Note that this term does not fall under the general GO definition for biosynthetic processes, which is 'The chemical reactions and pathways resulting in the formation of... ', because thyroid hormones can only be formed by the proteolysis of a larger molecule (see term definition). The word 'generation' is therefore used in place of biosynthesis. thyroid hormone generation The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones. GOC:jl ISBN:0716720094 The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. ornithine metabolism biological_process GO:0006591 ornithine metabolic process The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. GOC:jl ISBN:0192801023 Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes. biological_process vacuolar protein maturation vacuolar proteolysis GO:0006624 vacuolar protein processing Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes. GOC:mah The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. Wikipedia:Lipid_metabolism lipid metabolism biological_process GO:0006629 lipid metabolic process The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. GOC:ma The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. Wikipedia:Fatty_acid_metabolism fatty acid metabolism biological_process GO:0006631 fatty acid metabolic process The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. ISBN:0198547684 The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. Wikipedia:Steroid_metabolisms#Steroid_biosynthesis steroid anabolism steroid biosynthesis steroid formation steroid synthesis steroidogenesis biological_process GO:0006694 steroid biosynthetic process The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification. GOC:go_curators The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. bile acid anabolism bile acid biosynthesis bile acid formation bile acid synthesis biological_process GO:0006699 bile acid biosynthetic process The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile. GOC:go_curators The chemical reactions and pathways resulting in the formation of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. glucocorticoid anabolism glucocorticoid biosynthesis glucocorticoid formation glucocorticoid synthesis biological_process GO:0006704 glucocorticoid biosynthetic process The chemical reactions and pathways resulting in the formation of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. mineralocorticoid anabolism mineralocorticoid biosynthesis mineralocorticoid formation mineralocorticoid synthesis biological_process GO:0006705 mineralocorticoid biosynthetic process The chemical reactions and pathways resulting in the formation of mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. ISBN:0198506732 The chemical reactions and pathways involving isoprenoid compounds, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. GO:0016096 isoprenoid metabolism polyisoprenoid metabolic process polyisoprenoid metabolism polyterpene metabolic process polyterpene metabolism biological_process GO:0006720 isoprenoid metabolic process The chemical reactions and pathways involving isoprenoid compounds, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. ISBN:0198547684 The chemical reactions and pathways involving terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure and including derivatives with various functional groups. terpenoid metabolism biological_process GO:0006721 terpenoid metabolic process The chemical reactions and pathways involving terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure and including derivatives with various functional groups. ISBN:0198506732 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving any phosphorylated nucleoside. nucleoside phosphate metabolism biological_process GO:0006753 nucleoside phosphate metabolic process The chemical reactions and pathways involving any phosphorylated nucleoside. GOC:mah The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems. vitamin metabolism biological_process GO:0006766 vitamin metabolic process The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems. GOC:ai The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water. water-soluble vitamin metabolism biological_process GO:0006767 water-soluble vitamin metabolic process The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water. GOC:jl The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water. fat-soluble vitamin metabolism biological_process GO:0006775 fat-soluble vitamin metabolic process The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene. vitamin A metabolism biological_process GO:0006776 vitamin A metabolic process The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene. GOC:jl http://www.dentistry.leeds.ac.uk/biochem/thcme/vitamins.html#k The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. Wikipedia:Sulfur_metabolism sulfur metabolism sulphur metabolic process sulphur metabolism biological_process GO:0006790 sulfur compound metabolic process The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:ai The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). phosphorus metabolism biological_process GO:0006793 phosphorus metabolic process The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). GOC:ai The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. phosphate metabolism biological_process phosphate metabolic process GO:0006796 phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. GOC:ai The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. https://github.com/geneontology/go-ontology/issues/26424 nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. https://github.com/geneontology/go-ontology/issues/20292 jl 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. GOC:dos GOC:dph GOC:jl GOC:mah The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. ion transport biological_process GO:0006811 monoatomic ion transport The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GOC:ai The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0006833 water transport The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. sodium:neurotransmitter transport biological_process GO:0006836 neurotransmitter transport The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell. GOC:ai The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. biological_process GO:0006837 serotonin transport The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems. GOC:ai The transport of substances that occurs outside cells. biological_process GO:0006858 extracellular transport The transport of substances that occurs outside cells. GOC:go_curators The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. biological_process GO:0006869 lipid transport The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. ISBN:0198506732 A homeostatic process involved in the maintenance of a steady state level of monoatomic ions within a cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. https://github.com/geneontology/go-ontology/issues/24455 cellular ion homeostasis cellular monoatomic ion homeostasis biological_process GO:0006873 intracellular monoatomic ion homeostasis A homeostatic process involved in the maintenance of a steady state level of monoatomic ions within a cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GOC:mah A homeostatic process involved in the maintenance of a steady state level of calcium ions within a cell. regulation of calcium ion concentration cellular calcium ion homeostasis biological_process GO:0006874 intracellular calcium ion homeostasis A homeostatic process involved in the maintenance of a steady state level of calcium ions within a cell. GOC:ceb GOC:mah The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/go-ontology/issues/24907 https://github.com/geneontology/go-ontology/issues/25268 GO:0016193 GO:0016196 GO:0098701 Wikipedia:Endocytosis endocytic import into cell vesicle endocytosis plasma membrane invagination biological_process nonselective vesicle endocytosis GO:0006897 endocytosis A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle. GOC:mah ISBN:0198506732 ISBN:0716731363 Wikipedia:Endocytosis The evagination of a membrane, resulting in formation of a vesicle. jl 2013-12-19T15:26:17Z GO:0006902 GO:1902591 membrane evagination vesicle biosynthesis vesicle formation biological_process nonselective vesicle assembly single organism membrane budding single-organism membrane budding vesicle budding GO:0006900 vesicle budding from membrane The evagination of a membrane, resulting in formation of a vesicle. GOC:jid GOC:tb single organism membrane budding GOC:TermGenie The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. biological_process GO:0006903 vesicle targeting The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. GOC:mah PMID:17335816 A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. https://github.com/geneontology/go-ontology/issues/24907 Wikipedia:Phagocytosis biological_process GO:0006909 phagocytosis A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. ISBN:0198506732 A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GO:0006917 GO:0008632 cell suicide cellular suicide Wikipedia:Apoptosis apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process apoptosis activator activity caspase-dependent programmed cell death commitment to apoptosis induction of apoptosis induction of apoptosis by p53 signaling (initiator) caspase activity GO:0006915 apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:cjm GOC:dhl GOC:ecd GOC:go_curators GOC:mtg_apoptosis GOC:tb ISBN:0198506732 PMID:18846107 PMID:21494263 apoptotic cell death GOC:sl apoptotic program GOC:add The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. cellular component disassembly involved in apoptotic process disassembly of cell structures cellular component disassembly involved in apoptosis biological_process GO:0006921 cellular component disassembly involved in execution phase of apoptosis The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis taxis in response to chemical stimulus biological_process GO:0006935 chemotaxis The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). ISBN:0198506732 A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Wikipedia:Muscle_contraction biological_process GO:0006936 muscle contraction A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. GOC:ef GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of muscle contraction. biological_process GO:0006937 regulation of muscle contraction Any process that modulates the frequency, rate or extent of muscle contraction. GOC:go_curators A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length. visceral muscle contraction biological_process GO:0006939 smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length. GOC:ef GOC:jl GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of smooth muscle contraction. biological_process GO:0006940 regulation of smooth muscle contraction Any process that modulates the frequency, rate or extent of smooth muscle contraction. GOC:go_curators A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope. sarcomeric muscle contraction biological_process GO:0006941 striated muscle contraction A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope. GOC:jl GOC:mtg_muscle ISBN:0198506732 Any process that modulates the frequency, rate or extent of striated muscle contraction. biological_process GO:0006942 regulation of striated muscle contraction Any process that modulates the frequency, rate or extent of striated muscle contraction. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GO:0002217 GO:0042829 defence response physiological defense response biological_process antimicrobial peptide activity defense/immunity protein activity GO:0006952 defense response Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GOC:go_curators The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. inflammation Wikipedia:Inflammation biological_process GO:0006954 inflammatory response The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. GO_REF:0000022 ISBN:0198506732 Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. GOC:add GO_REF:0000022 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis GO:0006997 nucleus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GOC:dph GOC:ems GOC:jl GOC:mah nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. mitochondria organization mitochondrial biogenesis mitochondrial organization mitochondrion biogenesis mitochondrion organisation biological_process mitochondrion organization and biogenesis GO:0007005 mitochondrion organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. GOC:dph GOC:jl GOC:mah GOC:sgd_curators PMID:9786946 mitochondria organization GOC:mah mitochondrion organisation GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. mitochondrial membrane organisation biological_process mitochondrial membrane organization and biogenesis GO:0007006 mitochondrial membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. GOC:ai GOC:dph GOC:jl GOC:mah mitochondrial membrane organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. cytoskeleton organisation biological_process cytoskeletal organization and biogenesis cytoskeletal regulator activity cytoskeleton organization and biogenesis GO:0007010 cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:dph GOC:jl GOC:mah cytoskeletal organization and biogenesis GOC:mah cytoskeleton organization and biogenesis GOC:mah Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. https://github.com/geneontology/go-ontology/issues/19809 biological_process GO:0007017 microtubule-based process Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. GOC:mah A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0007018 microtubule-based movement A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 Any process involved in the maintenance of an internal steady state of calcium ions in the vacuole or between a vacuole and its surroundings. biological_process GO:0007036 vacuolar calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions in the vacuole or between a vacuole and its surroundings. GOC:ai GOC:mah The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. Wikipedia:Cell_cycle cell-division cycle biological_process GO:0007049 cell cycle The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. GOC:go_curators GOC:mtg_cell_cycle The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. Wikipedia:Chromosome_segregation chromosome division biological_process chromosome transmission GO:0007059 chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:jl GOC:mah GOC:mtg_cell_cycle GOC:vw The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. biological_process GO:0007076 mitotic chromosome condensation The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells. GOC:mah ISBN:0815316194 Any process that modulates the frequency, rate or extent of mitosis. regulation of mitosis biological_process GO:0007088 regulation of mitotic nuclear division Any process that modulates the frequency, rate or extent of mitosis. GOC:go_curators A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. Wikipedia:Mitosis#Endomitosis biological_process endomitosis GO:0007113 Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins. endomitotic cell cycle A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell. GOC:curators GOC:dos GOC:expert_vm The second nuclear division of meiosis, in which the two chromatids in each chromosome are separated, resulting in four daughter nuclei from the two nuclei produced in meiosis II. Wikipedia:Meiosis#Meiosis_II meiosis II nuclear division biological_process GO:0007135 meiosis II The second nuclear division of meiosis, in which the two chromatids in each chromosome are separated, resulting in four daughter nuclei from the two nuclei produced in meiosis II. GOC:dph GOC:mah ISBN:0198547684 A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. male nuclear division biological_process male meiosis GO:0007140 male meiotic nuclear division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline. GOC:dph GOC:mah GOC:vw A cell cycle process comprising the steps by which a cell progresses through male meiosis II, the second meiotic division in the male germline. male meiosis II nuclear division biological_process GO:0007142 male meiosis II A cell cycle process comprising the steps by which a cell progresses through male meiosis II, the second meiotic division in the male germline. GOC:dph GOC:mah A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. female meiosis female meiotic division biological_process GO:0007143 Note that female germ lines can be found in female or hermaphroditic organisms, so this term can be used to annotate gene products from hermaphrodites such as those of C. elegans. See also the biological process term 'meiotic nuclear division; GO:0140013'. female meiotic nuclear division A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline. GOC:dph GOC:ems GOC:mah GOC:vw The cell cycle process in which the second meiotic division occurs in the female germline. female meiosis II nuclear division biological_process GO:0007147 female meiosis II The cell cycle process in which the second meiotic division occurs in the female germline. GOC:mah Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. dos 2014-04-15T15:59:10Z GO:0098602 Wikipedia:Cell_adhesion biological_process cell adhesion molecule activity single organism cell adhesion GO:0007155 cell adhesion The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules. GOC:hb GOC:pf The attachment of a leukocyte to another cell via adhesion molecules. leukocyte adhesion leukocyte cell adhesion biological_process GO:0007159 leukocyte cell-cell adhesion The attachment of a leukocyte to another cell via adhesion molecules. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. down regulation of cell adhesion down-regulation of cell adhesion downregulation of cell adhesion inhibition of cell adhesion biological_process cell adhesion receptor inhibitor activity GO:0007162 negative regulation of cell adhesion Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion. GOC:go_curators The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023014 GO:0023015 GO:0023016 GO:0023033 GO:0023045 Wikipedia:Signal_transduction signal transduction by cis-phosphorylation signal transduction by conformational transition signal transduction by protein phosphorylation signal transduction by trans-phosphorylation signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane. GO:0038042 G protein coupled receptor protein signaling pathway G protein coupled receptor protein signalling pathway G-protein coupled receptor protein signal transduction G-protein coupled receptor protein signaling pathway G-protein coupled receptor signalling pathway G-protein-coupled receptor protein signalling pathway GPCR signaling pathway GPCR signalling pathway G-protein coupled receptor signaling pathway via GPCR dimer dimeric G-protein coupled receptor signaling pathway dimeric G-protein coupled receptor signalling pathway biological_process GO:0007186 G protein-coupled receptor signaling pathway The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane. GOC:bf GOC:mah PMID:16902576 PMID:24568158 Wikipedia:G_protein-coupled_receptor G-protein coupled receptor protein signaling pathway GOC:bf G-protein coupled receptor signaling pathway via GPCR dimer GOC:bf dimeric G-protein coupled receptor signalling pathway GOC:mah Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. cell-cell signalling biological_process GO:0007267 cell-cell signaling Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. GOC:dos GOC:mah The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. signal transmission across a synapse synaptic transmission Wikipedia:Neurotransmission biological_process neurotransmission GO:0007268 chemical synaptic transmission The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:jl MeSH:D009435 neurotransmission GOC:dph The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. GO:0010554 neurotransmitter release neurotransmitter secretory pathway biological_process GO:0007269 A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin. neurotransmitter secretion The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission. GOC:dph The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. cholinergic synaptic transmission biological_process GO:0007271 synaptic transmission, cholinergic The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse. GOC:dos Wikipedia:Cholinergic The process of synaptic transmission from a neuron to a muscle, across a synapse. biological_process GO:0007274 neuromuscular synaptic transmission The process of synaptic transmission from a neuron to a muscle, across a synapse. GOC:dos GOC:jl MeSH:D009435 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). https://github.com/geneontology/go-ontology/issues/21234 biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GO:0009552 biological_process gametogenesis GO:0007276 gamete generation The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. GOC:ems GOC:mtg_sensu The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. germ-cell development gametogenesis primordial germ cell development biological_process GO:0007281 germ cell development The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism. GOC:go_curators The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa. Wikipedia:Spermatogenesis generation of spermatozoa biological_process GO:0007283 spermatogenesis The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa. GOC:jid ISBN:9780878933846 PMID:28073824 PMID:30990821 generation of spermatozoa The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. Wikipedia:Spermiogenesis spermatid cell development spermiogenesis biological_process GO:0007286 spermatid development The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure. GOC:dph GOC:go_curators The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement. biological_process GO:0007288 sperm axoneme assembly The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement. GOC:bf GOC:cilia ISBN:0198547684 The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. spermatid nuclear differentiation biological_process GO:0007289 See also the Cell Ontology term 'spermatid ; CL:0000018'. spermatid nucleus differentiation The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization. GOC:bf GOC:dph GOC:jl GOC:mah Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. biological_process GO:0007292 female gamete generation Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction. GOC:dph ISBN:0198506732 The introduction of semen or sperm into the genital tract of a female. Wikipedia:Insemination biological_process GO:0007320 insemination The introduction of semen or sperm into the genital tract of a female. ISBN:0582227089 Any process that modulates the rate or extent of progress through the mitotic cell cycle. mitotic cell cycle modulation mitotic cell cycle regulation modulation of mitotic cell cycle progression regulation of mitotic cell cycle progression regulation of progression through mitotic cell cycle biological_process mitotic cell cycle regulator GO:0007346 regulation of mitotic cell cycle Any process that modulates the rate or extent of progress through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb regulation of progression through mitotic cell cycle GOC:dph GOC:tb A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. Wikipedia:Gastrulation biological_process GO:0007369 gastrulation A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GOC:curators ISBN:9780878933846 The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation. biological_process GO:0007398 ectoderm development The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation. GOC:dph GOC:tb The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. biological_process pan-neural process GO:0007399 nervous system development The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state. GOC:dgh The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. biological_process GO:0007492 endoderm development The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues. GOC:dph GOC:tb The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. biological_process GO:0007498 mesoderm development The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue. GOC:dph GOC:tb The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. Wikipedia:Gestation gestation biological_process carrying of young GO:0007565 female pregnancy The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. ISBN:0192800825 The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. breathing respiration biological_process GO:0007585 respiratory gaseous exchange by respiratory system The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. ISBN:0198506732 The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. Wikipedia:Digestion biological_process GO:0007586 digestion The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:isa_complete ISBN:0198506732 The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds. https://github.com/geneontology/go-ontology/issues/22368 Wikipedia:Excretion biological_process GO:0007588 excretion The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds. ISBN:0192801023 The controlled release of a fluid by a cell or tissue in an animal. biological_process GO:0007589 body fluid secretion The controlled release of a fluid by a cell or tissue in an animal. GOC:ai GOC:dph GOC:mah GOC:tb The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young. Wikipedia:Lactation milk secretion biological_process GO:0007595 lactation The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young. ISBN:0198506732 milk secretion GOC:pr The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. Wikipedia:Coagulation blood clotting biological_process GO:0007596 blood coagulation The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. PMID:30700128 The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. Wikipedia:Hemostasis biological_process GO:0007599 hemostasis The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part. ISBN:0198506732 The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. Wikipedia:Perception biological_process GO:0007600 sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai GOC:dph The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. Wikipedia:Visual_perception sense of sight sensory visual perception vision biological_process GO:0007601 visual perception The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. GOC:ai The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. Wikipedia:Hearing_(sense) hearing perception of sound biological_process GO:0007605 sensory perception of sound The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound. GOC:ai The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. chemosensory perception biological_process GO:0007606 sensory perception of chemical stimulus The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. Wikipedia:Olfaction olfaction scent perception sense of smell smell perception biological_process GO:0007608 sensory perception of smell The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process. GOC:ai The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 The acquisition and processing of information and/or the storage and retrieval of this information over time. biological_process GO:0007611 learning or memory The acquisition and processing of information and/or the storage and retrieval of this information over time. GOC:jid PMID:8938125 The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task). Wikipedia:Memory biological_process GO:0007613 memory The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task). GOC:curators ISBN:0582227089 The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. Wikipedia:Mating_behaviour mating behaviour biological_process GO:0007617 mating behavior The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. GOC:ai GOC:dph The act of sexual union between male and female, involving the transfer of sperm. biological_process GO:0007620 copulation The act of sexual union between male and female, involving the transfer of sperm. ISBN:0721662544 The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. behavior via locomotion locomotion in response to stimulus locomotory behavioral response to stimulus locomotory behaviour locomotory behavioural response to stimulus biological_process GO:0007626 locomotory behavior The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. GOC:dph The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GO:0070261 biological_process hemolymph circulation GO:0008015 blood circulation The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GOC:mtg_heart ISBN:0192800825 Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. regulation of cardiac contraction biological_process GO:0008016 regulation of heart contraction Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph GOC:go_curators GOC:tb Any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/23112 GO:0008105 GO:0016249 GO:0034613 cellular protein localisation cellular protein localization protein localisation channel localizer activity biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization GO:0008104 protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai cellular protein localisation GOC:mah protein localisation GOC:mah channel localizer activity GOC:mah asymmetric protein localisation GOC:mah A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. Wikipedia:Steroid_metabolism steroid metabolism biological_process GO:0008202 steroid metabolic process The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. ISBN:0198547684 The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. cholesterol metabolism biological_process GO:0008203 cholesterol metabolic process The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. ISBN:0198506732 The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. bile acid metabolism biological_process GO:0008206 bile acid metabolic process The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. GOC:go_curators The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects. glucocorticoid metabolism glucocorticosteroid metabolic process glucocorticosteroid metabolism biological_process GO:0008211 glucocorticoid metabolic process The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects. ISBN:0198506732 The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance. mineralocorticoid metabolism biological_process GO:0008212 mineralocorticoid metabolic process The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance. ISBN:0198506732 Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. Wikipedia:Blood_pressure#Regulation blood pressure regulation biological_process blood pressure homeostasis control of blood pressure GO:0008217 regulation of blood pressure Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure. GOC:dph GOC:mtg_cardio ISBN:0721643949 Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). https://github.com/geneontology/go-ontology/issues/24680 biological_process accidental cell death necrosis GO:0008219 This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). GOC:mah GOC:mtg_apoptosis PMID:25236395 Any process that modulates the frequency, rate or extent of G protein-coupled receptor signaling pathway. regulation of G protein coupled receptor protein signaling pathway regulation of G protein coupled receptor protein signalling pathway regulation of G-protein coupled receptor protein signaling pathway regulation of G-protein coupled receptor protein signalling pathway regulation of G-protein-coupled receptor protein signalling pathway regulation of GPCR protein signaling pathway regulation of GPCR protein signalling pathway biological_process GO:0008277 regulation of G protein-coupled receptor signaling pathway Any process that modulates the frequency, rate or extent of G protein-coupled receptor signaling pathway. GOC:go_curators The multiplication or reproduction of cells, resulting in the expansion of a cell population. biological_process cell proliferation GO:0008283 This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. cell population proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. GOC:mah GOC:mb Any process that activates or increases the rate or extent of cell proliferation. up regulation of cell proliferation up-regulation of cell proliferation upregulation of cell proliferation activation of cell proliferation stimulation of cell proliferation biological_process positive regulation of cell proliferation GO:0008284 positive regulation of cell population proliferation Any process that activates or increases the rate or extent of cell proliferation. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of cell proliferation. down regulation of cell proliferation down-regulation of cell proliferation downregulation of cell proliferation inhibition of cell proliferation biological_process negative regulation of cell proliferation GO:0008285 negative regulation of cell population proliferation Any process that stops, prevents or reduces the rate or extent of cell proliferation. GOC:go_curators Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. Reactome:R-HSA-2142859 Reactome:R-HSA-561041 Reactome:R-HSA-9794830 molecular_function GO:0008514 organic anion transmembrane transporter activity Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai Reactome:R-HSA-2142859 Growing HA is extruded from the cell by ABCC5 Reactome:R-HSA-561041 OAT1-3 transport organic anions with antiport of dicarboxylic acids Reactome:R-HSA-9794830 SLC22A8 transports Cipro into renal cell The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. lipid anabolism lipid biosynthesis lipid formation lipid synthesis lipogenesis biological_process GO:0008610 lipid biosynthetic process The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GOC:go_curators lipogenesis GOC:sl The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y. GO:0006861 GO:0008644 sugar transport biological_process GO:0008643 carbohydrate transport The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y. GOC:ai The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule. bf 2010-04-08T10:27:23Z GO:0008646 GO:0008647 GO:0035428 high-affinity hexose transport low-affinity hexose transport biological_process hexose membrane transport hexose transport GO:0008645 Note that this term is not intended for use in annotating lateral movement within membranes. hexose transmembrane transport The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule. GOC:vw The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. jl 2012-10-17T15:52:35Z GO:0044243 GO:0044712 Wikipedia:Catabolism breakdown catabolism degradation multicellular organismal catabolic process biological_process single-organism catabolic process GO:0009056 catabolic process The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. ISBN:0198547684 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043285 GO:0044266 biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation multicellular organismal macromolecule catabolic process biological_process cellular macromolecule catabolic process cellular macromolecule catabolism cellular macromolecule degradation GO:0009057 macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. jl 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process GO:0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. glutamine family amino acid metabolism biological_process GO:0009064 glutamine family amino acid metabolic process The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. GOC:ai The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine. aspartate family amino acid metabolism biological_process GO:0009066 aspartate family amino acid metabolic process The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine. GOC:ai The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine. serine family amino acid metabolism biological_process GO:0009069 serine family amino acid metabolic process The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine. GOC:ai The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). aromatic amino acid family metabolic process aromatic amino acid family metabolism biological_process GO:0009072 aromatic amino acid metabolic process The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). GOC:go_curators The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine. branched chain family amino acid metabolism biological_process GO:0009081 branched-chain amino acid metabolic process The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine. GOC:ai branched chain family amino acid metabolism GOC:ai The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. nucleobase metabolism biological_process GO:0009112 nucleobase metabolic process The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. GOC:ma The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates). nucleotide metabolism biological_process GO:0009117 nucleotide metabolic process The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates). GOC:ma The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar. nucleoside diphosphate metabolism biological_process GO:0009132 nucleoside diphosphate metabolic process The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar. nucleoside diphosphate breakdown nucleoside diphosphate catabolism nucleoside diphosphate degradation biological_process GO:0009134 nucleoside diphosphate catabolic process The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar. purine nucleoside diphosphate metabolism biological_process GO:0009135 purine nucleoside diphosphate metabolic process The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar. purine nucleoside diphosphate breakdown purine nucleoside diphosphate catabolism purine nucleoside diphosphate degradation biological_process GO:0009137 purine nucleoside diphosphate catabolic process The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar. nucleoside triphosphate metabolism biological_process GO:0009141 nucleoside triphosphate metabolic process The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar. purine nucleoside triphosphate metabolism biological_process GO:0009144 purine nucleoside triphosphate metabolic process The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine ribonucleotide metabolism biological_process GO:0009150 purine ribonucleotide metabolic process The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. purine ribonucleotide breakdown purine ribonucleotide catabolism purine ribonucleotide degradation biological_process GO:0009154 purine ribonucleotide catabolic process The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates). nucleotide breakdown nucleotide catabolism nucleotide degradation biological_process GO:0009166 nucleotide catabolic process The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates). GOC:go_curators The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar. purine ribonucleoside diphosphate metabolism biological_process GO:0009179 purine ribonucleoside diphosphate metabolic process The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar. purine ribonucleoside diphosphate breakdown purine ribonucleoside diphosphate catabolism purine ribonucleoside diphosphate degradation biological_process GO:0009181 purine ribonucleoside diphosphate catabolic process The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar. ribonucleoside diphosphate metabolism biological_process GO:0009185 ribonucleoside diphosphate metabolic process The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar. ribonucleoside diphosphate breakdown ribonucleoside diphosphate catabolism ribonucleoside diphosphate degradation biological_process GO:0009191 ribonucleoside diphosphate catabolic process The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar. ribonucleoside triphosphate metabolism biological_process GO:0009199 ribonucleoside triphosphate metabolic process The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar. purine ribonucleoside triphosphate metabolism biological_process GO:0009205 purine ribonucleoside triphosphate metabolic process The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. cobalamin metabolism vitamin B12 metabolic process vitamin B12 metabolism vitamin B12 reduction biological_process GO:0009235 cobalamin metabolic process The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. GOC:go_curators The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. glucan anabolism glucan biosynthesis glucan formation glucan synthesis biological_process GO:0009250 glucan biosynthetic process The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues. glucan breakdown glucan catabolism glucan degradation biological_process GO:0009251 glucan catabolic process The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues. GOC:go_curators The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GO:0009121 ribonucleotide metabolism biological_process GO:0009259 ribonucleotide metabolic process The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GOC:go_curators ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. ribonucleotide breakdown ribonucleotide catabolism ribonucleotide degradation biological_process GO:0009261 ribonucleotide catabolic process The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GOC:go_curators ISBN:0198506732 The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined. Wikipedia:Nucleoid cellular_component GO:0009295 nucleoid The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined. GOC:bm GOC:ma ISBN:3540076689 The controlled release of proteins from a cell. GO:0045166 GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment biological_process GO:0009306 protein secretion The controlled release of proteins from a cell. GOC:ai The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. jl 2009-07-15T11:55:44Z GO:0044106 amine metabolism cellular amine metabolic process biological_process GO:0009308 amine metabolic process The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. response to electromagnetic radiation stimulus response to radiation stimulus biological_process GO:0009314 Note that 'radiation' refers to electromagnetic radiation of any wavelength. response to radiation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation. GOC:jl Wikipedia:Electromagnetic_radiation Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. biological_process GO:0009416 response to light stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. GOC:go_curators ISBN:0582227089 The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. carnitine metabolism vitamin Bt metabolic process vitamin Bt metabolism biological_process GO:0009437 carnitine metabolic process The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. GOC:jl ISBN:0198506732 The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). https://github.com/geneontology/go-ontology/issues/20176 Wikipedia:Fertilisation syngamy biological_process GO:0009566 fertilization The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:tb ISBN:0198506732 The series of events in which an external stimulus is received by a cell and converted into a molecular signal. biological_process perception of external stimulus GO:0009581 detection of external stimulus The series of events in which an external stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. biological_process perception of abiotic stimulus GO:0009582 detection of abiotic stimulus The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal. GOC:hb The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal. detection of light biological_process perception of light GO:0009583 detection of light stimulus The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal. GOC:go_curators The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm. biological_process perception of visible light GO:0009584 detection of visible light The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm. GOC:go_curators ISBN:0198506732 The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. chemoperception detection of chemical substance biological_process chemoreception perception of chemical stimulus perception of chemical substance GO:0009593 detection of chemical stimulus The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal. GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to external stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. response to biotic stress biological_process GO:0009607 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to biotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. GO:0002245 physiological response to wounding biological_process GO:0009611 response to wounding Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. mechanical stimulus response biological_process chemi-mechanical coupling GO:0009612 response to mechanical stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus. https://github.com/geneontology/go-ontology/issues/16572 response to abiotic stress biological_process GO:0009628 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to abiotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. detoxification response biological_process toxin resistance toxin susceptibility/resistance GO:0009636 response to toxic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. GOC:lr The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GO:0009795 embryogenesis and morphogenesis Wikipedia:Embryogenesis embryogenesis embryonal development biological_process GO:0009790 embryo development The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. GOC:go_curators GOC:isa_complete GOC:mtg_sensu The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. biological_process GO:0009791 post-embryonic development The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development. GOC:go_curators The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. embryogenesis biological_process GO:0009792 embryo development ending in birth or egg hatching The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell. GOC:go_curators GOC:isa_complete GOC:mtg_sensu Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. histogenesis and organogenesis biological_process GO:0009887 animal organ morphogenesis Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dgh GOC:go_curators ISBN:0471245208 ISBN:0721662544 The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. histogenesis and organogenesis Wikipedia:Histogenesis histogenesis biological_process GO:0009888 tissue development The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure. ISBN:0471245208 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. regulation of breakdown regulation of catabolism regulation of degradation biological_process GO:0009894 regulation of catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. down regulation of catabolic process down-regulation of catabolic process downregulation of catabolic process negative regulation of breakdown negative regulation of catabolism negative regulation of degradation inhibition of catabolic process biological_process GO:0009895 negative regulation of catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. positive regulation of breakdown positive regulation of catabolism positive regulation of degradation up regulation of catabolic process up-regulation of catabolic process upregulation of catabolic process activation of catabolic process stimulation of catabolic process biological_process GO:0009896 positive regulation of catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0009914 hormone transport The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:tb Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm negative regulation of signalling pathway GOC:mah Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete Compaction of chromatin structure prior to meiosis in eukaryotic cells. chromosome condensation involved in meiotic cell cycle biological_process GO:0010032 meiotic chromosome condensation Compaction of chromatin structure prior to meiosis in eukaryotic cells. PMID:10072401 chromosome condensation involved in meiotic cell cycle GOC:dph GOC:tb A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. endomembrane organization endomembrane system organisation biological_process GO:0010256 endomembrane system organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. GOC:mah GOC:sm endomembrane system organisation GOC:mah The infolding of a membrane. jl 2013-12-02T13:58:34Z GO:1902534 biological_process single-organism membrane invagination GO:0010324 membrane invagination The infolding of a membrane. GOC:tb The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. biological_process GO:0010463 mesenchymal cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. biological_process GO:0010464 regulation of mesenchymal cell proliferation Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:dph GOC:tb The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. https://github.com/geneontology/go-ontology/issues/22557 https://github.com/geneontology/go-ontology/issues/25419 Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes. GOC:txnOH-2018 PMID:25934543 PMID:31580950 Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process gene regulation regulation of gene product expression GO:0010468 This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 gene regulation GOC:cjm Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. regulation of receptor activity regulation of signalling receptor activity biological_process GO:0010469 regulation of signaling receptor activity Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity. GOC:dph GOC:tb Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. biological_process GO:0010470 regulation of gastrulation Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010556 regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010562 positive regulation of phosphorus metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010563 negative regulation of phosphorus metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. biological_process GO:0010564 regulation of cell cycle process Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. biological_process GO:0010565 regulation of cellular ketone metabolic process Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010604 positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0010605 negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. posttranscriptional regulation of gene expression biological_process GO:0010608 post-transcriptional regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. GOC:dph GOC:tb The activation of endogenous cellular processes that result in the death of a cell as part of its development. developmental programmed cell death programmed cell death involved in development biological_process GO:0010623 This process is part of the natural developmental program of some cell types, but it does not always happen as part of the development or shaping of a gross anatomical structure. programmed cell death involved in cell development The activation of endogenous cellular processes that result in the death of a cell as part of its development. GOC:dph GOC:mtg_apoptosis GOC:tb Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process GO:0010628 positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). https://github.com/geneontology/go-ontology/issues/22557 biological_process gene silencing GO:0010629 This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). GOC:txnOH-2018 Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. positive regulation of organelle organisation biological_process positive regulation of organelle organization and biogenesis GO:0010638 positive regulation of organelle organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. negative regulation of organelle organisation biological_process negative regulation of organelle organization and biogenesis GO:0010639 negative regulation of organelle organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010647 positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010648 negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine. biological_process GO:0010700 negative regulation of norepinephrine secretion Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the regulated release of norepinephrine. biological_process GO:0010701 positive regulation of norepinephrine secretion Any process that increases the frequency, rate or extent of the regulated release of norepinephrine. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010720 positive regulation of cell development Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0010721 negative regulation of cell development Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:BHF GOC:dph GOC:tb Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. biological_process GO:0010817 regulation of hormone levels Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. GOC:BHF GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. regulation of mitochondrion organisation biological_process GO:0010821 regulation of mitochondrion organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb regulation of mitochondrion organisation GOC:mah Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. positive regulation of mitochondrion organisation biological_process GO:0010822 positive regulation of mitochondrion organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb positive regulation of mitochondrion organisation GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. negative regulation of mitochondrion organisation biological_process GO:0010823 negative regulation of mitochondrion organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb negative regulation of mitochondrion organisation GOC:mah Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of glucose transport GO:0010827 regulation of glucose transmembrane transport Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process positive regulation of glucose transport GO:0010828 positive regulation of glucose transmembrane transport Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process negative regulation of glucose transport GO:0010829 negative regulation of glucose transmembrane transport Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:dph GOC:tb Any process in which a lipid is transported to, or maintained in, a specific location. lipid localisation biological_process GO:0010876 lipid localization Any process in which a lipid is transported to, or maintained in, a specific location. GOC:BHF GOC:dph GOC:tb lipid localisation GOC:mah Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. biological_process GO:0010893 positive regulation of steroid biosynthetic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. biological_process GO:0010894 negative regulation of steroid biosynthetic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:BHF GOC:tb Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. regulation of glucose metabolism biological_process GO:0010906 regulation of glucose metabolic process Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. GOC:BHF GOC:tb regulation of glucose metabolism GOC:tb Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. positive regulation of glucose metabolism biological_process GO:0010907 positive regulation of glucose metabolic process Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. GOC:BHF GOC:tb positive regulation of glucose metabolism GOC:tb Any process that modulates the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. biological_process GO:0010911 regulation of isomerase activity Any process that modulates the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. GOC:dph GOC:tb Any process that increases the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. biological_process GO:0010912 positive regulation of isomerase activity Any process that increases the activity of an isomerase. An isomerase catalyzes the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. GOC:dph GOC:tb The cellular component assembly that is part of the initial shaping of the component during its developmental progression. biological_process GO:0010927 cellular component assembly involved in morphogenesis The cellular component assembly that is part of the initial shaping of the component during its developmental progression. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-04-27T09:53:22Z biological_process GO:0010948 negative regulation of cell cycle process Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage. tb 2009-04-27T12:09:13Z positive regulation of protein maturation by peptide bond cleavage biological_process GO:0010954 positive regulation of protein processing Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage. GOC:dph GOC:mah GOC:tb positive regulation of protein maturation by peptide bond cleavage GOC:bf Any process that decreases the rate, frequency or extent of protein maturation by peptide bond cleavage. tb 2009-04-27T12:10:19Z negative regulation of protein maturation by peptide bond cleavage biological_process GO:0010955 negative regulation of protein processing Any process that decreases the rate, frequency or extent of protein maturation by peptide bond cleavage. GOC:dph GOC:mah GOC:tb negative regulation of protein maturation by peptide bond cleavage GOC:bf Any process involved in the maintenance of an internal steady state of magnesium ions within an organism or cell. tb 2009-05-06T11:47:17Z biological_process GO:0010960 magnesium ion homeostasis Any process involved in the maintenance of an internal steady state of magnesium ions within an organism or cell. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. tb 2009-05-11T12:17:53Z biological_process GO:0010962 regulation of glucan biosynthetic process Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues. GOC:dph GOC:tb The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. tb 2009-05-27T10:56:08Z microtubule-based transport establishment of localization by movement along microtubule movement along microtubule biological_process GO:0010970 transport along microtubule The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. GOC:dph GOC:mah GOC:tb establishment of localization by movement along microtubule GOC:dph A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. https://github.com/geneontology/go-ontology/issues/24835 GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process PCD RCD caspase-independent apoptosis GO:0012501 Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children. programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GOC:lr GOC:mtg_apoptosis A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component GO:0012505 endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh The lipid bilayer surrounding any membrane-bounded vesicle in the cell. NIF_Subcellular:sao1153182838 cellular_component GO:0012506 vesicle membrane The lipid bilayer surrounding any membrane-bounded vesicle in the cell. GOC:mah GOC:vesicle The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube. GO:0014024 primary neural tube morphogenesis primary neurulation biological_process neural rod cavitation GO:0014020 primary neural tube formation The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube. GOC:ef ISBN:0878932585 PMID:15327780 primary neural tube morphogenesis GOC:dph The regulated release of dopamine by a cell. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone. biological_process GO:0014046 dopamine secretion The regulated release of dopamine by a cell. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone. GOC:ef The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS). biological_process GO:0014055 acetylcholine secretion, neurotransmission The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS). GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine. biological_process GO:0014056 regulation of acetylcholine secretion, neurotransmission Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine. up regulation of acetylcholine secretion up-regulation of acetylcholine secretion upregulation of acetylcholine secretion activation of acetylcholine secretion stimulation of acetylcholine secretion biological_process GO:0014057 positive regulation of acetylcholine secretion, neurotransmission Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine. down regulation of acetylcholine secretion down-regulation of acetylcholine secretion downregulation of acetylcholine secretion inhibition of acetylcholine secretion biological_process GO:0014058 negative regulation of acetylcholine secretion, neurotransmission Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of dopamine. biological_process GO:0014059 regulation of dopamine secretion Any process that modulates the frequency, rate or extent of the regulated release of dopamine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of epinephrine. regulation of adrenaline secretion biological_process GO:0014060 regulation of epinephrine secretion Any process that modulates the frequency, rate or extent of the regulated release of epinephrine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine. regulation of noradrenaline secretion biological_process GO:0014061 regulation of norepinephrine secretion Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine. GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of serotonin. biological_process regulation of serotonin release GO:0014062 regulation of serotonin secretion Any process that modulates the frequency, rate or extent of the regulated release of serotonin. GOC:ef regulation of serotonin release GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin. down regulation of serotonin secretion down-regulation of serotonin secretion downregulation of serotonin secretion inhibition of serotonin secretion biological_process positive regulation of serotonin release GO:0014063 negative regulation of serotonin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin. GOC:ef positive regulation of serotonin release GOC:tb Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin. up regulation of serotonin secretion up-regulation of serotonin secretion upregulation of serotonin secretion activation of serotonin secretion stimulation of serotonin secretion biological_process positive regulation of serotonin release GO:0014064 positive regulation of serotonin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin. GOC:ef positive regulation of serotonin release GOC:tb A process in which force is generated within phasic smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the phasic smooth muscle, the muscle contraction occurs without an ordered sarcomeric structure. Phasic smooth muscle contraction occurs in a series of discrete contractions and relaxations. biological_process GO:0014821 phasic smooth muscle contraction A process in which force is generated within phasic smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the phasic smooth muscle, the muscle contraction occurs without an ordered sarcomeric structure. Phasic smooth muscle contraction occurs in a series of discrete contractions and relaxations. GOC:mtg_muscle A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the gastro-intestinal system. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The gastro-intestinal system generally refers to the digestive structures stretching from the mouth to anus, but does not include the accessory glandular organs (liver, pancreas and biliary tract). biological_process GO:0014831 gastro-intestinal system smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the gastro-intestinal system. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The gastro-intestinal system generally refers to the digestive structures stretching from the mouth to anus, but does not include the accessory glandular organs (liver, pancreas and biliary tract). GOC:mtg_muscle MA:0001523 MSH:D041981 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary bladder. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary bladder is a musculomembranous sac along the urinary tract. biological_process GO:0014832 urinary bladder smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary bladder. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary bladder is a musculomembranous sac along the urinary tract. GOC:mr GOC:mtg_muscle PMID:11768524 PMID:18276178 PMID:538956 A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary tract. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary tract consists of organs of the body that produce and discharge urine. These include the kidneys, ureters, bladder, and urethra. biological_process GO:0014848 urinary tract smooth muscle contraction A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary tract. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary tract consists of organs of the body that produce and discharge urine. These include the kidneys, ureters, bladder, and urethra. GOC:ef GOC:mtg_muscle MA:0000325 MSH:D014551 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport biological_process GO:0015031 protein transport The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. RHEA:28695 Reactome:R-HSA-2752067 molecular_function GO:0015106 bicarbonate transmembrane transporter activity Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-. GOC:ai Reactome:R-HSA-2752067 BESTs transport cytosolic HCO3- to extracellular region The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. cellular_component GO:0015629 actin cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes. GOC:jl ISBN:0395825172 ISBN:0815316194 The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015669 gas transport The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015671 oxygen transport The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage. biological_process GO:0015695 organic cation transport The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage. GOC:ai The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015701 bicarbonate transport The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. biological_process GO:0015711 organic anion transport The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai GOC:krc The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015718 monocarboxylic acid transport The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bile acid transport bile salt transport biological_process GO:0015721 bile acid and bile salt transport The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:krc PMID:12663868 PMID:14699511 The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. vw 2017-02-19T10:41:27Z GO:1905950 biological_process monosaccharide transport GO:0015749 monosaccharide transmembrane transport The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. GOC:TermGenie GOC:vw GO_REF:0000069 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015833 peptide transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process amine/polyamine transport GO:0015837 amine transport The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai ISBN:0198506732 The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015873 biological_process GO:0015844 monoamine transport The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015849 organic acid transport The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ISBN:0198506732 The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. organic alcohol transport biological_process GO:0015850 organic hydroxy compound transport The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom. GOC:ai The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. biological_process GO:0015870 acetylcholine transport The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions. GOC:ai The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline. biological_process GO:0015872 dopamine transport The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline. GOC:ai The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. levarterenol transport noradrenaline transport biological_process GO:0015874 norepinephrine transport The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine. GOC:ai ISBN:0198506732 The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. chemoorganotrophy biological_process GO:0015980 energy derivation by oxidation of organic compounds The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released. GOC:mah A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane Wikipedia:Transmembrane_protein integral component of membrane integral to membrane membrane region region of membrane whole membrane cellular_component transmembrane GO:0016020 membrane A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GOC:dos GOC:mah ISBN:0815316194 transmembrane GOC:mah A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. vesicle organisation biological_process vesicle organization and biogenesis GO:0016050 vesicle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle. GOC:mah vesicle organization and biogenesis GOC:mah The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0006093 anabolic carbohydrate metabolic process anabolic carbohydrate metabolism carbohydrate anabolism carbohydrate biosynthesis carbohydrate formation carbohydrate synthesis biological_process GO:0016051 carbohydrate biosynthetic process The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. jl 2012-10-23T16:34:39Z GO:0006095 GO:0044276 GO:0044724 carbohydrate breakdown carbohydrate catabolism carbohydrate degradation catabolic carbohydrate metabolic process catabolic carbohydrate metabolism multicellular organismal carbohydrate catabolic process biological_process single-organism carbohydrate catabolic process GO:0016052 carbohydrate catabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. organic acid anabolism organic acid biosynthesis organic acid formation organic acid synthesis biological_process GO:0016053 organic acid biosynthetic process The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 An immune response mediated by immunoglobulins, whether cell-bound or in solution. antibody-mediated immune response biological_process GO:0016064 immunoglobulin mediated immune response An immune response mediated by immunoglobulins, whether cell-bound or in solution. GOC:add GO_REF:0000022 ISBN:0781735149 The chemical reactions and pathways involving diterpenoid compounds, terpenoids with four isoprene units. diterpenoid metabolism diterpene metabolic process diterpene metabolism biological_process GO:0016101 diterpenoid metabolic process The chemical reactions and pathways involving diterpenoid compounds, terpenoids with four isoprene units. ISBN:0198547684 The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. sterol metabolism biological_process GO:0016125 sterol metabolic process The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. ISBN:0198547684 A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. https://github.com/geneontology/go-ontology/issues/25421 GO:0006899 vesicle transport vesicular transport nonselective vesicle transport biological_process protein sorting along secretory pathway vesicle trafficking GO:0016192 vesicle-mediated transport A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. GOC:ai GOC:mah ISBN:08789310662000 vesicular transport GOC:mah true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Wikipedia:Phosphorylation biological_process GO:0016310 phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. ISBN:0198506732 The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female. biological_process GO:0016321 female meiosis chromosome segregation The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female. GOC:ai The process in which the anatomical structures of embryonic epithelia are generated and organized. biological_process GO:0016331 morphogenesis of embryonic epithelium The process in which the anatomical structures of embryonic epithelia are generated and organized. GOC:jl Recombination occurring within or between DNA molecules in somatic cells. biological_process GO:0016444 somatic cell DNA recombination Recombination occurring within or between DNA molecules in somatic cells. GOC:ma The somatic process that results in the generation of sequence diversity of immunoglobulins. somatic diversification of antibodies biological_process GO:0016445 somatic diversification of immunoglobulins The somatic process that results in the generation of sequence diversity of immunoglobulins. GOC:add GOC:ma ISBN:0781735149 The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. somatic recombination of antibody gene segments biological_process GO:0016447 somatic recombination of immunoglobulin gene segments The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus. GOC:add ISBN:0781735149 The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. https://github.com/geneontology/go-ontology/issues/24787 Wikipedia:Cell_migration biological_process GO:0016477 cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. GOC:cjm GOC:dph GOC:ems GOC:pf Wikipedia:Cell_migration Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein. GO:0051605 protein maturation by peptide bond cleavage protein maturation by peptide bond hydrolysis biological_process peptidolysis during protein maturation protein maturation by proteolysis GO:0016485 protein processing Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein. GOC:curators GOC:jl GOC:jsg protein maturation by peptide bond cleavage GOC:bf protein maturation by peptide bond hydrolysis GOC:mah peptidolysis during protein maturation GOC:mah protein maturation by proteolysis GOC:mah Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. EC:1.-.-.- Reactome:R-HSA-1614362 Reactome:R-HSA-209921 Reactome:R-HSA-209960 Reactome:R-HSA-3095889 Reactome:R-HSA-390425 Reactome:R-HSA-390438 Reactome:R-HSA-5662660 Reactome:R-HSA-8878581 Reactome:R-HSA-8936442 Reactome:R-HSA-9020249 Reactome:R-HSA-9020260 Reactome:R-HSA-9024624 Reactome:R-HSA-9024630 Reactome:R-HSA-9025007 Reactome:R-HSA-9026001 Reactome:R-HSA-9026917 Reactome:R-HSA-9027033 Reactome:R-HSA-9693722 redox activity oxidoreductase activity, acting on other substrates molecular_function GO:0016491 oxidoreductase activity Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GOC:go_curators Reactome:R-HSA-1614362 SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases Reactome:R-HSA-209921 Monoiodinated tyrosine can be deiodinated Reactome:R-HSA-209960 Diiodinated tyrosine can be deiodinated Reactome:R-HSA-3095889 MMACHC dealkylates RCbl Reactome:R-HSA-390425 FAR1 reduces PalmCoA to HXOL Reactome:R-HSA-390438 FAR2 reduces PalmCoA to HXOL Reactome:R-HSA-5662660 Dopachrome is transformed to DHICA by DCT Reactome:R-HSA-8878581 TYRP1 oxidises DHICA to IQCA Reactome:R-HSA-8936442 MARC1,MARC2 reduce N-hydroxylated compounds Reactome:R-HSA-9020249 Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6 Reactome:R-HSA-9020260 Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5 Reactome:R-HSA-9024624 Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6 Reactome:R-HSA-9024630 Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5 Reactome:R-HSA-9025007 Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1 Reactome:R-HSA-9026001 Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA Reactome:R-HSA-9026917 Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA Reactome:R-HSA-9027033 Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA Reactome:R-HSA-9693722 Unknown sepiapterin synthase transforms PTHP to sepiapterin Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. EC:1.2.1.- Reactome:R-HSA-1222583 molecular_function GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. GOC:jl Reactome:R-HSA-1222583 MscR reduces nitrosomycothiol to ammonia Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2.-.-.- Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-8868783 molecular_function GO:0016740 transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7.-.- molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor). EC:2.7.2.- molecular_function GO:0016774 phosphotransferase activity, carboxyl group as acceptor Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor). GOC:jl Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. EC:4.-.-.- Reactome:R-HSA-5696408 Reactome:R-HSA-6782895 molecular_function GO:0016829 lyase activity Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. ISBN:0198547684 Reactome:R-HSA-5696408 PXLP-K278-PHYKPL tetramer hydrolyses 5PHL Reactome:R-HSA-6782895 TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe) Catalysis of the breakage of a carbon-oxygen bond. EC:4.2.-.- other carbon-oxygen lyase activity molecular_function GO:0016835 carbon-oxygen lyase activity Catalysis of the breakage of a carbon-oxygen bond. EC:4.2.-.- Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. EC:4.2.1.- Reactome:R-HSA-9014627 molecular_function GO:0016836 hydro-lyase activity Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. EC:4.2.1.- Reactome:R-HSA-9014627 SDS dimers:PXLP dehydrate L-Thr to 2AA Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. EC:5.-.-.- Reactome:R-HSA-6787623 other isomerase activity molecular_function GO:0016853 isomerase activity Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5. ISBN:0198506732 Reactome:R-HSA-6787623 TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal Catalysis of the transfer of a functional group from one position to another within a single molecule. EC:5.4.-.- mutase activity intramolecular transferase activity, transferring other groups molecular_function GO:0016866 intramolecular transferase activity Catalysis of the transfer of a functional group from one position to another within a single molecule. GOC:mah Catalysis of the transfer of a phosphate group from one position to another within a single molecule. https://github.com/geneontology/go-ontology/issues/26155 GO:0016777 EC:5.4.2.- intramolecular transferase activity, phosphotransferases phosphomutase activity phosphotransferase activity, with regeneration of donors, apparently catalyzing intramolecular transfers molecular_function GO:0016868 intramolecular phosphotransferase activity Catalysis of the transfer of a phosphate group from one position to another within a single molecule. GOC:mah Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. EC:1.2.-.- oxidoreductase activity, acting on the aldehyde or oxo group of donors, other acceptors molecular_function GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. GOC:ai The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. stem cell renewal biological_process GO:0017145 stem cell division The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. GOC:jid ISBN:0582227089 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0016478 down regulation of protein biosynthetic process down-regulation of protein biosynthetic process downregulation of protein biosynthetic process negative regulation of protein anabolism negative regulation of protein biosynthesis negative regulation of protein biosynthetic process negative regulation of protein formation negative regulation of protein synthesis inhibition of protein biosynthetic process biological_process protein biosynthesis inhibitor activity protein biosynthetic process inhibitor activity GO:0017148 negative regulation of translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis biological_process GO:0018130 heterocycle biosynthetic process The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198547684 The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. UM-BBD_pathwayID:phe carbolic acid metabolic process carbolic acid metabolism hydroxybenzene metabolic process hydroxybenzene metabolism phenol-containing compound metabolism biological_process GO:0018958 Note that phenol metabolism is not included as a child of 'xenobiotic metabolism' because although it is synthesized industrially, phenol is also found naturally in animal wastes and other organic materials. It is often formed by the activity of microorganisms, which can chemically modify a variety of xenobiotic and naturally occurring phenolic compounds. phenol-containing compound metabolic process The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring. ISBN:0198506732 The specific behavior of an organism that is associated with reproduction. https://github.com/geneontology/go-ontology/issues/23491 jl 2012-09-19T16:01:37Z GO:0033057 GO:0044704 GO:0044705 reproductive behavior in a multicellular organism reproductive behaviour multi-organism reproductive behavior multicellular organism reproductive behavior biological_process single-organism reproductive behavior GO:0019098 reproductive behavior The specific behavior of an organism that is associated with reproduction. GOC:jl GOC:pr Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. regulation of lipid metabolism biological_process GO:0019216 regulation of lipid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GO:0006632 regulation of fatty acid metabolism biological_process GO:0019217 regulation of fatty acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. regulation of steroid metabolism biological_process GO:0019218 regulation of steroid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0019219 regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. regulation of phosphate metabolism biological_process GO:0019220 regulation of phosphate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. conduction of nerve impulse signal transmission along a neuron biological_process GO:0019226 transmission of nerve impulse The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission. GOC:curators ISBN:0815316194 conduction of nerve impulse GOC:dph The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process. Wikipedia:Nociception perception of physiological pain biological_process nociception GO:0019233 sensory perception of pain The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process. GOC:curators The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule. hexose metabolism biological_process GO:0019318 hexose metabolic process The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule. ISBN:0198506732 The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. pyridine nucleotide metabolism biological_process GO:0019362 pyridine nucleotide metabolic process The chemical reactions and pathways involving a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. GOC:jl The chemical reactions and pathways resulting in the breakdown of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. pyridine nucleotide breakdown pyridine nucleotide catabolism pyridine nucleotide degradation biological_process GO:0019364 pyridine nucleotide catabolic process The chemical reactions and pathways resulting in the breakdown of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base. GOC:jl GOC:pde GOC:vw The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic hydrocarbon biosynthesis aromatic hydrocarbon biosynthetic process biological_process GO:0019438 aromatic compound biosynthetic process The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound breakdown aromatic compound catabolism aromatic compound degradation aromatic hydrocarbon catabolic process aromatic hydrocarbon catabolism biological_process GO:0019439 aromatic compound catabolic process The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways involving a protein. Includes protein modification. https://github.com/geneontology/go-ontology/issues/23112 GO:0006411 GO:0044267 GO:0044268 Wikipedia:Protein_metabolism cellular protein metabolic process cellular protein metabolism protein metabolic process and modification protein metabolism protein metabolism and modification multicellular organismal protein metabolic process biological_process GO:0019538 protein metabolic process The chemical reactions and pathways involving a protein. Includes protein modification. GOC:ma The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound. organophosphate metabolism biological_process GO:0019637 organophosphate metabolic process The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound. ISBN:0198506732 The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar. ribose phosphate metabolism biological_process GO:0019693 ribose phosphate metabolic process The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar. GOC:ai Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. B lymphocyte mediated immune effector process B lymphocyte mediated immunity B-cell mediated immune effector process B-cell mediated immunity B-lymphocyte mediated immune effector process B-lymphocyte mediated immunity biological_process GO:0019724 B cell mediated immunity Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. GOC:add GO_REF:0000022 ISBN:0781735149 Any process involved in the maintenance of an internal steady state at the level of the cell. biological_process GO:0019725 cellular homeostasis Any process involved in the maintenance of an internal steady state at the level of the cell. GOC:isa_complete GOC:jl ISBN:0395825172 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving isoprenoids. regulation of isoprenoid metabolism biological_process GO:0019747 regulation of isoprenoid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving isoprenoids. GOC:go_curators The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). carboxylic acid metabolism biological_process GO:0019752 carboxylic acid metabolic process The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. antibody cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add GOC:jl ISBN:0781765196 An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. GO:0042570 B lymphocyte receptor complex B-cell receptor complex B-lymphocyte receptor complex BCR complex immunoglobulin complex, membrane bound cellular_component B cell receptor accessory molecule complex antibody GO:0019815 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. GOC:add ISBN:0781735149 antibody GOC:mah The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. GO:0030333 Wikipedia:Antigen_presentation antigen presentation antigen processing biological_process GO:0019882 antigen processing and presentation The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. GOC:add GO_REF:0000022 ISBN:0781735149 PMID:15771591 PMID:15928678 A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). https://github.com/geneontology/go-ontology/issues/22929 Wikipedia:Sexual_reproduction biological_process GO:0019953 Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times. sexual reproduction A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid). Wikipedia:Sexual_reproduction A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state. biological_process GO:0021700 developmental maturation A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium. biological_process GO:0021915 neural tube development The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium. GOC:cls GOC:dgh GOC:dph GOC:jid GO_REF:0000021 The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. biological_process GO:0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. GOC:isa_complete GOC:mtg_cell_cycle Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. biological_process GO:0022407 regulation of cell-cell adhesion Any process that modulates the frequency, rate or extent of attachment of a cell to another cell. GOC:isa_complete Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell. down regulation of cell-cell adhesion down-regulation of cell-cell adhesion downregulation of cell-cell adhesion inhibition of cell-cell adhesion biological_process GO:0022408 negative regulation of cell-cell adhesion Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell. GOC:isa_complete Any process that activates or increases the rate or extent of cell adhesion to another cell. up regulation of cell-cell adhesion up-regulation of cell-cell adhesion upregulation of cell-cell adhesion activation of cell-cell adhesion stimulation of cell-cell adhesion biological_process GO:0022409 positive regulation of cell-cell adhesion Any process that activates or increases the rate or extent of cell adhesion to another cell. GOC:isa_complete A cellular process that results in the breakdown of a cellular component. GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process GO:0022411 cellular component disassembly A cellular process that results in the breakdown of a cellular component. GOC:isa_complete A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. reproductive cellular process in multicellular organism biological_process GO:0022412 cellular process involved in reproduction in multicellular organism A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism. GOC:isa_complete A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. jl 2012-09-19T15:56:06Z GO:0044702 biological_process single organism reproductive process GO:0022414 reproductive process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:dph GOC:isa_complete A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0022600 digestive system process A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:isa_complete GOC:jid GOC:mtg_cardio Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. regulation of morphogenesis biological_process GO:0022603 regulation of anatomical structure morphogenesis Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. GOC:mah The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GO:0005386 GO:0015563 GO:0015646 GO:0022891 GO:0022892 Reactome:R-HSA-1236947 Reactome:R-HSA-429036 Reactome:R-HSA-5638209 Reactome:R-HSA-5671707 Reactome:R-HSA-6784434 Reactome:R-HSA-6784436 molecular_function substrate-specific transmembrane transporter activity substrate-specific transporter activity uptake permease activity uptake transmembrane transporter activity GO:0022857 transmembrane transporter activity Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GOC:jid GOC:mtg_transport ISBN:0815340729 Reactome:R-HSA-1236947 Egress of internalized antigen to the cytosol via sec61 Reactome:R-HSA-429036 SLC2A9 transports Fru, Glc, urate Reactome:R-HSA-5638209 Defective SLC2A9 does not transport Fru, Glc, urate Reactome:R-HSA-5671707 Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA Reactome:R-HSA-6784434 An unknown carrier transports cytosolic glyoxylate to the peroxisome Reactome:R-HSA-6784436 An unknown carrier transports mitochondrial glyoxylate to the cytosol Any process that modulates the frequency, rate or extent of transmembrane transporter activity. biological_process GO:0022898 regulation of transmembrane transporter activity Any process that modulates the frequency, rate or extent of transmembrane transporter activity. GOC:dph GOC:mtg_cardio GOC:mtg_transport Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. 2010-02-16T09:30:50Z biological_process regulation of gene expression as a consequence of signal transmission GO:0023019 signal transduction involved in regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another. GOC:mtg_signal regulation of gene expression as a consequence of signal transmission GOC:bf Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. jl 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling GO:0023052 Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. 2010-02-16T09:30:50Z signal secretion biological_process GO:0023061 signal release The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. GOC:mtg_signal signal secretion GOC:bf A homeostatic process involved in the maintenance of a steady state level of monoatomic cations within a cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom. https://github.com/geneontology/go-ontology/issues/24455 cellular cation homeostasis cellular monoatomic cation homeostasis biological_process GO:0030003 intracellular monoatomic cation homeostasis A homeostatic process involved in the maintenance of a steady state level of monoatomic cations within a cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom. GOC:ceb GOC:mah The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. Wikipedia:Myofibril cellular_component GO:0030016 myofibril The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism. ISBN:0815316194 The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. Wikipedia:Sarcomere cellular_component GO:0030017 sarcomere The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs. ISBN:0815316194 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. https://github.com/geneontology/go-ontology/issues/26279 cell projection organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis GO:0030030 cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. formation of a cell surface projection biological_process cell projection biogenesis GO:0030031 cell projection assembly Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection biogenesis GOC:mah A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. Wikipedia:Cell_junction cellular_component GO:0030054 cell junction A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. GOC:aruk GOC:bc GOC:mah ISBN:0198506732 PMID:26820516 PMID:28096264 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html The regulated release of a peptide hormone from a cell. biological_process GO:0030072 peptide hormone secretion The regulated release of a peptide hormone from a cell. GOC:mah The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects. https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045 biological_process GO:0030073 insulin secretion The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects. GOC:mah ISBN:0198506732 The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. https://github.com/geneontology/go-ontology/issues/22178 Wikipedia:Haematopoiesis blood cell biosynthesis blood cell formation haemopoiesis hematopoiesis biological_process GO:0030097 hemopoiesis The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. GOC:dgh ISBN:0198506732 The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. GO:0046650 lymphocyte cell differentiation lymphocytic blood cell differentiation biological_process lymphocyte development GO:0030098 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. lymphocyte differentiation The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. CL:0000542 GOC:go_curators lymphocyte development GOC:add The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. biological_process GO:0030099 myeloid cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages. GOC:add ISBN:0781735149 Any process that modulates the frequency, rate or extent of endocytosis. biological_process GO:0030100 regulation of endocytosis Any process that modulates the frequency, rate or extent of endocytosis. GOC:go_curators The regulated release of vasopressin from secretory granules into the blood. biological_process GO:0030103 vasopressin secretion The regulated release of vasopressin from secretory granules into the blood. GOC:mah A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. secretory vesicle cellular_component GO:0030141 Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. secretory granule A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. GOC:mah ISBN:0198506732 The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. https://github.com/geneontology/go-ontology/issues/24390 Wikipedia:Cellular_differentiation biological_process GO:0030154 cell differentiation The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state. ISBN:0198506732 Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. biological_process cell adhesion receptor regulator activity GO:0030155 regulation of cell adhesion Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix. GOC:mah Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. regulation of peptidolysis biological_process GO:0030162 regulation of proteolysis Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. GOC:mah The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. GO:0042115 B lymphocyte differentiation B-cell differentiation B-lymphocyte differentiation biological_process B cell development GO:0030183 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. B cell differentiation The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. GOC:mah GO_REF:0000022 B cell development GOC:add The chemical reactions and pathways involving melatonin (N-acetyl-5-methoxytryptamine). melatonin metabolism biological_process GO:0030186 melatonin metabolic process The chemical reactions and pathways involving melatonin (N-acetyl-5-methoxytryptamine). GOC:mah ISBN:0198506732 The chemical reactions and pathways resulting in the formation of melatonin (N-acetyl-5-methoxytryptamine). melatonin anabolism melatonin biosynthesis melatonin formation melatonin synthesis biological_process GO:0030187 melatonin biosynthetic process The chemical reactions and pathways resulting in the formation of melatonin (N-acetyl-5-methoxytryptamine). GOC:mah ISBN:0198506732 Any process that modulates the frequency, rate or extent of blood coagulation. biological_process GO:0030193 regulation of blood coagulation Any process that modulates the frequency, rate or extent of blood coagulation. GOC:mah Any process that activates or increases the frequency, rate or extent of blood coagulation. up regulation of blood coagulation up-regulation of blood coagulation upregulation of blood coagulation activation of blood coagulation stimulation of blood coagulation biological_process GO:0030194 positive regulation of blood coagulation Any process that activates or increases the frequency, rate or extent of blood coagulation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation. down regulation of blood coagulation down-regulation of blood coagulation downregulation of blood coagulation inhibition of blood coagulation biological_process GO:0030195 negative regulation of blood coagulation Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. extracellular matrix organisation biological_process extracellular matrix organization and biogenesis GO:0030198 extracellular matrix organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. GOC:mah extracellular matrix organization and biogenesis GOC:mah The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. heparin metabolism biological_process heparan sulfate metabolic process GO:0030202 heparin metabolic process The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. glycosaminoglycan metabolism biological_process GO:0030203 glycosaminoglycan metabolic process The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars. ISBN:0192800981 The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. heparin anabolism heparin biosynthesis heparin formation heparin synthesis biological_process heparan sulfate biosynthetic process GO:0030210 heparin biosynthetic process The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. hyaluronan metabolism biological_process GO:0030212 hyaluronan metabolic process The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. GOC:mah ISBN:0198506732 The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. hyaluronan anabolism hyaluronan biosynthesis hyaluronan formation hyaluronan synthesis biological_process GO:0030213 hyaluronan biosynthetic process The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine. GOC:mah ISBN:0198506732 The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. GO:0042112 GO:0046652 T lymphocyte differentiation T-cell differentiation T-lymphocyte differentiation biological_process T cell development GO:0030217 Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. T cell differentiation The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. GOC:jid GOC:mah GO_REF:0000022 T cell development GOC:add The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. Wikipedia:Erythropoiesis RBC differentiation erythrocyte cell differentiation erythropoiesis red blood cell differentiation biological_process GO:0030218 erythrocyte differentiation The process in which a myeloid precursor cell acquires specializes features of an erythrocyte. GOC:mah RBC differentiation CL:0000232 erythropoiesis GOC:add GOC:dph red blood cell differentiation CL:0000232 The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. megakaryocyte cell differentiation biological_process GO:0030219 megakaryocyte differentiation The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte. GOC:mah The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell. basophil cell differentiation biological_process GO:0030221 basophil differentiation The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell. GOC:jid GOC:mah The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. monocyte cell differentiation biological_process GO:0030224 monocyte differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte. GOC:mah The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. macrophage cell differentiation biological_process GO:0030225 macrophage differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage. GOC:add ISBN:0781735149 The regulated release of growth hormone from secretory granules into the blood. somatotropin secretion biological_process GO:0030252 growth hormone secretion The regulated release of growth hormone from secretory granules into the blood. GOC:mah somatotropin secretion GOC:mah The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GO:0000068 DNA condensation eukaryotic chromosome condensation nuclear chromosome condensation biological_process GO:0030261 chromosome condensation The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:mah ISBN:0815316194 DNA condensation Wikipedia:DNA_condensation eukaryotic chromosome condensation GOC:bf nuclear chromosome condensation GOC:bf Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. apoptotic nuclear change biological_process GO:0030262 apoptotic nuclear changes Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. GOC:mah GOC:mtg_apoptosis The compaction of chromatin during apoptosis. Wikipedia:Pyknosis pyknosis biological_process GO:0030263 apoptotic chromosome condensation The compaction of chromatin during apoptosis. GOC:mah Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. regulation of bone biosynthesis regulation of bone formation biological_process GO:0030278 regulation of ossification Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. down regulation of ossification down-regulation of ossification downregulation of ossification negative regulation of bone biosynthesis negative regulation of bone formation inhibition of ossification biological_process GO:0030279 negative regulation of ossification Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. cellular_component GO:0030312 The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'. external encapsulating structure A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. GOC:go_curators The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. osteoclast cell differentiation biological_process GO:0030316 osteoclast differentiation The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue. CL:0000092 GOC:add ISBN:0781735149 PMID:12161749 The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm. GO:0097724 GO:1905419 sperm motility sperm movement Wikipedia:Sperm_motility flagellated sperm movement sperm flagellum movement sperm flagellum movement involved in flagellated sperm motility sperm flagellum movement involved in flagellated sperm movement biological_process GO:0030317 flagellated sperm motility The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000060 PMID:26680031 sperm flagellum movement GOC:cilia GOC:krc sperm flagellum movement involved in flagellated sperm movement GOC:TermGenie Any process that modulates the frequency, rate or extent of cell migration. biological_process GO:0030334 regulation of cell migration Any process that modulates the frequency, rate or extent of cell migration. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell migration. up regulation of cell migration up-regulation of cell migration upregulation of cell migration activation of cell migration stimulation of cell migration biological_process GO:0030335 positive regulation of cell migration Any process that activates or increases the frequency, rate or extent of cell migration. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. down regulation of cell migration down-regulation of cell migration downregulation of cell migration inhibition of cell migration biological_process GO:0030336 negative regulation of cell migration Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. GOC:go_curators The expulsion of feces from the rectum. Wikipedia:Defecation biological_process GO:0030421 defecation The expulsion of feces from the rectum. GOC:mah A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards. Wikipedia:Peristalsis biological_process GO:0030432 peristalsis A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards. ISBN:0198506732 The movement of a leukocyte in response to an external stimulus. immune cell chemotaxis leucocyte chemotaxis biological_process GO:0030595 leukocyte chemotaxis The movement of a leukocyte in response to an external stimulus. GOC:add GOC:jl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. regulation of vitamin metabolism biological_process GO:0030656 regulation of vitamin metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. GOC:mah The lipid bilayer surrounding a cytoplasmic vesicle. cellular_component GO:0030659 cytoplasmic vesicle membrane The lipid bilayer surrounding a cytoplasmic vesicle. GOC:mah The lipid bilayer surrounding a secretory granule. secretory vesicle membrane cellular_component GO:0030667 secretory granule membrane The lipid bilayer surrounding a secretory granule. GOC:mah The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. biological_process GO:0030705 cytoskeleton-dependent intracellular transport The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides. regulation of nucleotide breakdown regulation of nucleotide catabolism regulation of nucleotide degradation biological_process GO:0030811 regulation of nucleotide catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides. down regulation of nucleotide catabolic process down-regulation of nucleotide catabolic process downregulation of nucleotide catabolic process negative regulation of nucleotide breakdown negative regulation of nucleotide catabolism negative regulation of nucleotide degradation inhibition of nucleotide catabolic process biological_process GO:0030812 negative regulation of nucleotide catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides. positive regulation of nucleotide breakdown positive regulation of nucleotide catabolism positive regulation of nucleotide degradation up regulation of nucleotide catabolic process up-regulation of nucleotide catabolic process upregulation of nucleotide catabolic process activation of nucleotide catabolic process stimulation of nucleotide catabolic process biological_process GO:0030813 positive regulation of nucleotide catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of nucleotides. GOC:mah The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. granulocyte cell differentiation biological_process GO:0030851 granulocyte differentiation The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils. GOC:ecd http://life.nthu.edu.tw/~g864204/dict-search1.htm Any process that modulates the frequency, rate or extent of granulocyte differentiation. biological_process GO:0030852 regulation of granulocyte differentiation Any process that modulates the frequency, rate or extent of granulocyte differentiation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation. down regulation of granulocyte differentiation down-regulation of granulocyte differentiation downregulation of granulocyte differentiation inhibition of granulocyte differentiation biological_process GO:0030853 negative regulation of granulocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation. GOC:mah Any process that activates or increases the frequency, rate or extent of granulocyte differentiation. up regulation of granulocyte differentiation up-regulation of granulocyte differentiation upregulation of granulocyte differentiation activation of granulocyte differentiation stimulation of granulocyte differentiation biological_process GO:0030854 positive regulation of granulocyte differentiation Any process that activates or increases the frequency, rate or extent of granulocyte differentiation. GOC:mah The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages. mammogenesis biological_process GO:0030879 mammary gland development The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages. PMID:9576833 mammogenesis GOC:dph Any process that modulates the frequency or rate of myeloid dendritic cell activation. biological_process GO:0030885 regulation of myeloid dendritic cell activation Any process that modulates the frequency or rate of myeloid dendritic cell activation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid dendritic cell activation. down regulation of myeloid dendritic cell activation down-regulation of myeloid dendritic cell activation downregulation of myeloid dendritic cell activation inhibition of myeloid dendritic cell activation biological_process GO:0030886 negative regulation of myeloid dendritic cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid dendritic cell activation. GOC:mah Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation. up regulation of myeloid dendritic cell activation up-regulation of myeloid dendritic cell activation upregulation of myeloid dendritic cell activation activation of myeloid dendritic cell activation stimulation of myeloid dendritic cell activation biological_process GO:0030887 positive regulation of myeloid dendritic cell activation Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation. GOC:mah Any collagen trimer that passes through a lipid bilayer membrane. MACIT cellular_component GO:0030936 transmembrane collagen trimer Any collagen trimer that passes through a lipid bilayer membrane. ISBN:0721639976 MACIT ISBN:0198599587 A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. intraflagellar transport complex intraflagellar transport particle cellular_component IFT complex GO:0030990 Note that we deem cilia and microtubule-based flagella to be equivalent. intraciliary transport particle A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. GOC:cilia GOC:kmv PMID:14570576 PMID:22118932 PMID:23945166 A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. GO:0005578 NIF_Subcellular:nlx_subcell_20090513 Wikipedia:Extracellular_matrix proteinaceous extracellular matrix matrisome cellular_component GO:0031012 extracellular matrix A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. GOC:BHF GOC:mah GOC:rph NIF_Subcellular:nlx_subcell_20090513 PMID:21123617 PMID:28089324 Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. NIF_Subcellular:sao772007592 dense core vesicle cellular_component GO:0031045 dense core granule Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted. NIF_Subcellular:sao772007592 PMID:14690495 dense core vesicle GOC:kmv A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). Wikipedia:Regeneration_(biology) biological_process GO:0031099 regeneration The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass). GOC:mah GOC:pr A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement. pseudopodium organisation biological_process pseudopodium organization and biogenesis GO:0031268 pseudopodium organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement. GOC:pg pseudopodium organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process GO:0031326 regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis inhibition of cellular biosynthetic process biological_process GO:0031327 negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process activation of cellular biosynthetic process stimulation of cellular biosynthetic process biological_process GO:0031328 positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. regulation of cellular breakdown regulation of cellular catabolism regulation of cellular degradation biological_process GO:0031329 regulation of cellular catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. down regulation of cellular catabolic process down-regulation of cellular catabolic process downregulation of cellular catabolic process negative regulation of cellular breakdown negative regulation of cellular catabolism negative regulation of cellular degradation inhibition of cellular catabolic process biological_process GO:0031330 negative regulation of cellular catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. positive regulation of cellular breakdown positive regulation of cellular catabolism positive regulation of cellular degradation up regulation of cellular catabolic process up-regulation of cellular catabolic process upregulation of cellular catabolic process activation of cellular catabolic process stimulation of cellular catabolic process biological_process GO:0031331 positive regulation of cellular catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. regulation of sulfur amino acid metabolism biological_process GO:0031335 regulation of sulfur amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. down regulation of sulfur amino acid metabolic process down-regulation of sulfur amino acid metabolic process downregulation of sulfur amino acid metabolic process negative regulation of sulfur amino acid metabolism inhibition of sulfur amino acid metabolic process biological_process GO:0031336 negative regulation of sulfur amino acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. positive regulation of sulfur amino acid metabolism up regulation of sulfur amino acid metabolic process up-regulation of sulfur amino acid metabolic process upregulation of sulfur amino acid metabolic process activation of sulfur amino acid metabolic process stimulation of sulfur amino acid metabolic process biological_process GO:0031337 positive regulation of sulfur amino acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. regulation of cell projection organisation biological_process regulation of cell projection organization and biogenesis GO:0031344 regulation of cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah regulation of cell projection organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. down regulation of cell projection organization down-regulation of cell projection organization downregulation of cell projection organization negative regulation of cell projection organisation inhibition of cell projection organization biological_process negative regulation of cell projection organization and biogenesis GO:0031345 negative regulation of cell projection organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah down regulation of cell projection organization GOC:mah negative regulation of cell projection organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. positive regulation of cell projection organisation up regulation of cell projection organization up-regulation of cell projection organization upregulation of cell projection organization activation of cell projection organization stimulation of cell projection organization biological_process positive regulation of cell projection organization and biogenesis GO:0031346 positive regulation of cell projection organization Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections. GOC:mah positive regulation of cell projection organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of a defense response. biological_process GO:0031347 regulation of defense response Any process that modulates the frequency, rate or extent of a defense response. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response. down regulation of defense response down-regulation of defense response downregulation of defense response inhibition of defense response biological_process GO:0031348 negative regulation of defense response Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response. GOC:mah Any process that activates or increases the frequency, rate or extent of a defense response. up regulation of defense response up-regulation of defense response upregulation of defense response activation of defense response stimulation of defense response biological_process GO:0031349 positive regulation of defense response Any process that activates or increases the frequency, rate or extent of a defense response. GOC:mah A vesicle found in the cytoplasm of a cell. GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle cytoplasmic membrane-enclosed vesicle cytoplasmic, membrane-bounded vesicle GO:0031410 cytoplasmic vesicle A vesicle found in the cytoplasm of a cell. GOC:ai GOC:mah GOC:vesicles A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/22021 GO:0034629 establishment and maintenance of protein complex localization protein complex localisation biological_process cellular protein complex localisation cellular protein complex localization cellular protein-containing complex localization establishment and maintenance of cellular protein complex localization protein complex localization GO:0031503 protein-containing complex localization A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. GOC:mah protein complex localisation GOC:mah cellular protein complex localisation GOC:mah Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. regulation of neurological process regulation of neurological system process regulation of neurophysiological process biological_process GO:0031644 regulation of nervous system process Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system. GOC:dph GOC:mah GOC:tb regulation of neurological process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. down regulation of neurological process down-regulation of neurological process downregulation of neurological process negative regulation of neurological process negative regulation of neurological system process negative regulation of neurophysiological process inhibition of neurological process biological_process GO:0031645 negative regulation of nervous system process Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb negative regulation of neurological process GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of a neurophysiological process. positive regulation of neurological process positive regulation of neurological system process positive regulation of neurophysiological process up regulation of neurological process up-regulation of neurological process upregulation of neurological process activation of neurological process stimulation of neurological process biological_process GO:0031646 positive regulation of nervous system process Any process that activates or increases the frequency, rate or extent of a neurophysiological process. GOC:dph GOC:mah GOC:tb positive regulation of neurological process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids. regulation of glucocorticoid metabolism biological_process GO:0031943 regulation of glucocorticoid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids. down regulation of glucocorticoid metabolic process down-regulation of glucocorticoid metabolic process downregulation of glucocorticoid metabolic process negative regulation of glucocorticoid metabolism inhibition of glucocorticoid metabolic process biological_process GO:0031944 negative regulation of glucocorticoid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids. positive regulation of glucocorticoid metabolism up regulation of glucocorticoid metabolic process up-regulation of glucocorticoid metabolic process upregulation of glucocorticoid metabolic process activation of glucocorticoid metabolic process stimulation of glucocorticoid metabolic process biological_process GO:0031945 positive regulation of glucocorticoid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids. biological_process GO:0031946 regulation of glucocorticoid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids. down regulation of glucocorticoid biosynthetic process down-regulation of glucocorticoid biosynthetic process downregulation of glucocorticoid biosynthetic process inhibition of glucocorticoid biosynthetic process biological_process GO:0031947 negative regulation of glucocorticoid biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids. up regulation of glucocorticoid biosynthetic process up-regulation of glucocorticoid biosynthetic process upregulation of glucocorticoid biosynthetic process activation of glucocorticoid biosynthetic process stimulation of glucocorticoid biosynthetic process biological_process GO:0031948 positive regulation of glucocorticoid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids. GOC:mah Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. GOC:mah GOC:pz Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. NIF_Subcellular:sao1045389829 cellular_component GO:0031966 mitochondrial membrane Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. GOC:mah NIF_Subcellular:sao1045389829 A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component GO:0031967 organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. cellular_component GO:0031974 membrane-enclosed lumen The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. GOC:add GOC:mah A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component GO:0031975 envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz The volume enclosed by the nuclear inner membrane. cellular_component GO:0031981 nuclear lumen The volume enclosed by the nuclear inner membrane. GOC:mah GOC:pz Any small, fluid-filled, spherical organelle enclosed by membrane. GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component membrane-bounded vesicle membrane-enclosed vesicle GO:0031982 vesicle Any small, fluid-filled, spherical organelle enclosed by membrane. GOC:mah GOC:pz GOC:vesicles Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. locomotion during locomotory behaviour biological_process GO:0031987 locomotion involved in locomotory behavior Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of insulin. up regulation of insulin secretion up-regulation of insulin secretion upregulation of insulin secretion activation of insulin secretion stimulation of insulin secretion biological_process GO:0032024 positive regulation of insulin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of insulin. GOC:mah The chemical reactions and pathways involving mitochondrial DNA. mitochondrial DNA metabolism mtDNA metabolic process mtDNA metabolism biological_process GO:0032042 mitochondrial DNA metabolic process The chemical reactions and pathways involving mitochondrial DNA. GOC:mah The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. blebbing membrane blebbing cell blebbing plasma membrane bleb assembly plasma membrane blebbing biological_process GO:0032060 bleb assembly The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses. GOC:mah GOC:mtg_apoptosis PMID:12083798 PMID:16624291 Wikipedia:Bleb_(cell_biology) blebbing GOC:pr membrane blebbing GOC:pr plasma membrane bleb assembly GOC:pr plasma membrane blebbing GOC:pr Any process that modulates the frequency, rate or extent of a response to an external stimulus. biological_process GO:0032101 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to external stimulus Any process that modulates the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. down regulation of response to external stimulus down-regulation of response to external stimulus downregulation of response to external stimulus inhibition of response to external stimulus biological_process GO:0032102 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to external stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that activates, maintains or increases the rate of a response to an external stimulus. up regulation of response to external stimulus up-regulation of response to external stimulus upregulation of response to external stimulus activation of response to external stimulus stimulation of response to external stimulus biological_process GO:0032103 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to external stimulus Any process that activates, maintains or increases the rate of a response to an external stimulus. GOC:mah Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. biological_process GO:0032222 regulation of synaptic transmission, cholinergic Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. down regulation of synaptic transmission, cholinergic down-regulation of synaptic transmission, cholinergic downregulation of synaptic transmission, cholinergic inhibition of synaptic transmission, cholinergic biological_process GO:0032223 negative regulation of synaptic transmission, cholinergic Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. up regulation of synaptic transmission, cholinergic up-regulation of synaptic transmission, cholinergic upregulation of synaptic transmission, cholinergic activation of synaptic transmission, cholinergic stimulation of synaptic transmission, cholinergic biological_process GO:0032224 positive regulation of synaptic transmission, cholinergic Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine. GOC:mah The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone. gonadotrophin secretion biological_process GO:0032274 gonadotropin secretion The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone. GOC:mah ISBN:0721662544 The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. biological_process GO:0032275 luteinizing hormone secretion The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin. regulation of gonadotrophin secretion biological_process GO:0032276 regulation of gonadotropin secretion Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a gonadotropin. down regulation of gonadotropin secretion down-regulation of gonadotropin secretion downregulation of gonadotropin secretion negative regulation of gonadotrophin secretion inhibition of gonadotropin secretion biological_process GO:0032277 negative regulation of gonadotropin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a gonadotropin. GOC:mah negative regulation of gonadotrophin secretion GOC:dph Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin. positive regulation of gonadotrophin secretion up regulation of gonadotropin secretion up-regulation of gonadotropin secretion upregulation of gonadotropin secretion activation of gonadotropin secretion stimulation of gonadotropin secretion biological_process GO:0032278 positive regulation of gonadotropin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin. GOC:mah positive regulation of gonadotrophin secretion GOC:dph Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone. regulation of hormone metabolism biological_process GO:0032350 regulation of hormone metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any hormone. down regulation of hormone metabolic process down-regulation of hormone metabolic process downregulation of hormone metabolic process negative regulation of hormone metabolism inhibition of hormone metabolic process biological_process GO:0032351 negative regulation of hormone metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any hormone. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any hormone. positive regulation of hormone metabolism up regulation of hormone metabolic process up-regulation of hormone metabolic process upregulation of hormone metabolic process activation of hormone metabolic process stimulation of hormone metabolic process biological_process GO:0032352 positive regulation of hormone metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any hormone. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. down regulation of hormone biosynthetic process down-regulation of hormone biosynthetic process downregulation of hormone biosynthetic process inhibition of hormone biosynthetic process biological_process GO:0032353 negative regulation of hormone biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032368 regulation of lipid transport Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of lipid transport down-regulation of lipid transport downregulation of lipid transport inhibition of lipid transport biological_process GO:0032369 negative regulation of lipid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of lipid transport up-regulation of lipid transport upregulation of lipid transport activation of lipid transport stimulation of lipid transport biological_process GO:0032370 positive regulation of lipid transport Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. biological_process GO:0032386 regulation of intracellular transport Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. down regulation of intracellular transport down-regulation of intracellular transport downregulation of intracellular transport inhibition of intracellular transport biological_process GO:0032387 negative regulation of intracellular transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. up regulation of intracellular transport up-regulation of intracellular transport upregulation of intracellular transport activation of intracellular transport stimulation of intracellular transport biological_process GO:0032388 positive regulation of intracellular transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that modulates the activity of a transporter. biological_process GO:0032409 regulation of transporter activity Any process that modulates the activity of a transporter. GOC:mah Any process that stops or reduces the activity of a transporter. down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process GO:0032410 negative regulation of transporter activity Any process that stops or reduces the activity of a transporter. GOC:mah Any process that activates or increases the activity of a transporter. up regulation of transporter activity up-regulation of transporter activity upregulation of transporter activity activation of transporter activity stimulation of transporter activity biological_process GO:0032411 positive regulation of transporter activity Any process that activates or increases the activity of a transporter. GOC:mah An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GO:0000141 GO:0030482 cellular_component actin cable GO:0032432 actin filament bundle An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GOC:mah actin cable GOC:mah Any process involved in the maintenance of an internal steady state of calcium ions within the Golgi apparatus of a cell or between the Golgi and its surroundings. Golgi calcium ion concentration regulation calcium ion homeostasis in Golgi regulation of Golgi calcium ion concentration regulation of calcium ion concentration in Golgi biological_process GO:0032468 Golgi calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions within the Golgi apparatus of a cell or between the Golgi and its surroundings. GOC:mah Any biological process, occurring at the level of a multicellular organism, pertinent to its function. jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. biological_process GO:0032504 multicellular organism reproduction The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GOC:isa_complete GOC:jid The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code. mitochondrial protein anabolism mitochondrial protein biosynthesis mitochondrial protein formation mitochondrial protein synthesis mitochondrial protein translation biological_process GO:0032543 mitochondrial translation The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code. GOC:go_curators The directed movement of a protein from one location to another within a lipid bilayer. protein translocation within membrane receptor translocation within membrane receptor transport within lipid bilayer biological_process GO:0032594 protein transport within lipid bilayer The directed movement of a protein from one location to another within a lipid bilayer. GOC:mah The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. GO:0042095 GO:0072643 IFNG production interferon-gamma production type II IFN production interferon-gamma biosynthetic process interferon-gamma secretion biological_process GO:0032609 type II interferon production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 IFNG production GOC:mah type II IFN production GOC:mah Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GO:0045072 GO:1902713 regulation of interferon-gamma production regulation of interferon-gamma biosynthetic process regulation of interferon-gamma secretion biological_process GO:0032649 regulation of type II interferon production Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GO:0045077 GO:1902714 down regulation of interferon-gamma production down-regulation of interferon-gamma production downregulation of interferon-gamma production negative regulation of interferon-gamma production inhibition of interferon-gamma production negative regulation of interferon-gamma biosynthetic process negative regulation of interferon-gamma secretion biological_process GO:0032689 negative regulation of type II interferon production Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GO:0045078 GO:1902715 positive regulation of interferon-gamma production up regulation of interferon-gamma production up-regulation of interferon-gamma production upregulation of interferon-gamma production activation of interferon-gamma production positive regulation of interferon-gamma biosynthetic process positive regulation of interferon-gamma secretion stimulation of interferon-gamma production biological_process GO:0032729 positive regulation of type II interferon production Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon. GOC:add GOC:mah PMID:15546383 The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue. biological_process GO:0032782 bile acid secretion The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue. GOC:ecd The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). monocarboxylate metabolic process monocarboxylic acid metabolism biological_process GO:0032787 monocarboxylic acid metabolic process The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). GOC:vk Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of epinephrine. down regulation of epinephrine secretion down-regulation of epinephrine secretion downregulation of epinephrine secretion negative regulation of adrenaline secretion inhibition of epinephrine secretion biological_process GO:0032811 negative regulation of epinephrine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of epinephrine. GOC:vk Any process that activates or increases the frequency, rate or extent of the regulated release of epinephrine. positive regulation of adrenaline secretion up regulation of epinephrine secretion up-regulation of epinephrine secretion upregulation of epinephrine secretion activation of epinephrine secretion stimulation of epinephrine secretion biological_process GO:0032812 positive regulation of epinephrine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of epinephrine. GOC:vk All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. cellular_component GO:0032838 plasma membrane bounded cell projection cytoplasm All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. GOC:krc GOC:mah Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:14Z GO:1903827 regulation of cellular protein localisation regulation of cellular protein localization regulation of protein localisation biological_process GO:0032880 regulation of protein localization Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. GOC:dph GOC:mah GOC:tb regulation of cellular protein localisation GOC:TermGenie regulation of protein localisation GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides. biological_process GO:0032881 regulation of polysaccharide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides. biological_process GO:0032885 regulation of polysaccharide biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides. GOC:mah Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. biological_process GO:0032886 regulation of microtubule-based process Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032890 regulation of organic acid transport Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of organic acid transport down-regulation of organic acid transport downregulation of organic acid transport inhibition of organic acid transport biological_process GO:0032891 negative regulation of organic acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of organic acid transport up-regulation of organic acid transport upregulation of organic acid transport activation of organic acid transport stimulation of organic acid transport biological_process GO:0032892 positive regulation of organic acid transport Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The controlled release of a substance by a cell. Wikipedia:Secretion cellular secretion biological_process GO:0032940 secretion by cell The controlled release of a substance by a cell. GOC:mah The controlled release of a substance by a tissue. tissue secretion biological_process expulsion of gland contents GO:0032941 secretion by tissue The controlled release of a substance by a tissue. GOC:mah expulsion of gland contents GOC:mah The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system. https://github.com/geneontology/go-ontology/issues/25496 https://github.com/geneontology/go-ontology/issues/26249 cellular component morphogenesis cellular structure morphogenesis biological_process GO:0032989 cellular anatomical entity morphogenesis The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GOC:dos GOC:mah A macromolecular complex containing both protein and DNA molecules. DNA-protein complex cellular_component GO:0032993 Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. protein-DNA complex A macromolecular complex containing both protein and DNA molecules. GOC:mah DNA-protein complex GOC:mah A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin. immunoglobulin receptor complex Fc-receptor complex FcR complex cellular_component GO:0032997 Fc receptor complex A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin. GOC:add ISBN:0781735149 A protein complex composed of an Fc-gamma RIII alpha chain and an Fc-epsilon RI gamma chain dimer with or without an Fc-epsilon RI beta chain and additional signaling components. The complex functions primarily as an activating receptor for IgG. IgG receptor complex immunoglobulin G receptor complex FcgRIII complex cellular_component GO:0033001 Fc-gamma receptor III complex A protein complex composed of an Fc-gamma RIII alpha chain and an Fc-epsilon RI gamma chain dimer with or without an Fc-epsilon RI beta chain and additional signaling components. The complex functions primarily as an activating receptor for IgG. GOC:add ISBN:0781735149 PMID:11244038 PMID:12413532 The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole metabolism biological_process GO:0033013 tetrapyrrole metabolic process The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. GOC:mah Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process GO:0033036 macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. regulation of organelle organisation biological_process regulation of organelle organization and biogenesis GO:0033043 regulation of organelle organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. regulation of chromosome organisation biological_process regulation of chromosome organization and biogenesis GO:0033044 regulation of chromosome organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome. GOC:mah regulation of chromosome organisation GOC:mah regulation of chromosome organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of sister chromatid segregation. biological_process GO:0033045 regulation of sister chromatid segregation Any process that modulates the frequency, rate or extent of sister chromatid segregation. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation. biological_process GO:0033046 negative regulation of sister chromatid segregation Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation. GOC:mah Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis. biological_process GO:0033047 regulation of mitotic sister chromatid segregation Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis. biological_process GO:0033048 negative regulation of mitotic sister chromatid segregation Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides. regulation of purine nucleotide breakdown regulation of purine nucleotide catabolism regulation of purine nucleotide degradation biological_process GO:0033121 regulation of purine nucleotide catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides. negative regulation of purine nucleotide breakdown negative regulation of purine nucleotide catabolism negative regulation of purine nucleotide degradation biological_process GO:0033122 negative regulation of purine nucleotide catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides. positive regulation of purine nucleotide breakdown positive regulation of purine nucleotide catabolism positive regulation of purine nucleotide degradation biological_process GO:0033123 positive regulation of purine nucleotide catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of purine nucleotides. GOC:mah The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). Wikipedia:V(D)J_recombination V(D)J joining V-D-J joining V-D-J recombination V-J joining V-J recombination biological_process GO:0033151 V(D)J recombination The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). GOC:add ISBN:0781700221 ISBN:0781735149 The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. immunoglobulin V(D)J joining immunoglobulin V-D-J joining immunoglobulin V-D-J recombination immunoglobulin V-J joining immunoglobulin V-J recombination biological_process GO:0033152 immunoglobulin V(D)J recombination The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined. GOC:add ISBN:0781735149 immunoglobulin V(D)J joining GOC:add immunoglobulin V-D-J joining GOC:add immunoglobulin V-D-J recombination GOC:add immunoglobulin V-J joining GOC:add immunoglobulin V-J recombination GOC:add Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. biological_process GO:0033157 regulation of intracellular protein transport Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. regulation of amine metabolism regulation of cellular amine metabolic process biological_process GO:0033238 regulation of amine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. negative regulation of amine metabolism negative regulation of cellular amine metabolic process biological_process GO:0033239 negative regulation of amine metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. positive regulation of amine metabolism positive regulation of cellular amine metabolic process biological_process GO:0033240 positive regulation of amine metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. secretory granule organisation biological_process secretory granule organization and biogenesis GO:0033363 secretory granule organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. GOC:mah secretory granule organisation GOC:mah secretory granule organization and biogenesis GOC:mah A process in which a protein is transported to, or maintained in, a location within an organelle. protein localisation to organelle protein localization in organelle biological_process GO:0033365 protein localization to organelle A process in which a protein is transported to, or maintained in, a location within an organelle. GOC:mah protein localisation to organelle GOC:mah protein localization in organelle GOC:mah A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell. biological_process GO:0033500 carbohydrate homeostasis A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of dopamine. down regulation of dopamine secretion down-regulation of dopamine secretion downregulation of dopamine secretion inhibition of dopamine secretion biological_process GO:0033602 negative regulation of dopamine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of dopamine. GOC:sl Any process that activates or increases the frequency, rate or extent of the regulated release of dopamine. up regulation of dopamine secretion up-regulation of dopamine secretion upregulation of dopamine secretion activation of dopamine secretion stimulation of dopamine secretion biological_process GO:0033603 positive regulation of dopamine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of dopamine. GOC:sl Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine. down regulation of catecholamine secretion down-regulation of catecholamine secretion downregulation of catecholamine secretion inhibition of catecholamine secretion biological_process GO:0033604 negative regulation of catecholamine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine. up regulation of catecholamine secretion up-regulation of catecholamine secretion upregulation of catecholamine secretion activation of catecholamine secretion stimulation of catecholamine secretion biological_process GO:0033605 positive regulation of catecholamine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. down regulation of kinase activity down-regulation of kinase activity downregulation of kinase activity inhibition of kinase activity kinase inhibitor biological_process GO:0033673 negative regulation of kinase activity Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. up regulation of kinase activity up-regulation of kinase activity upregulation of kinase activity kinase activator stimulation of kinase activity biological_process GO:0033674 positive regulation of kinase activity Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that modulates the frequency, rate or extent of the regulated release of luteinizing hormone. biological_process GO:0033684 regulation of luteinizing hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of luteinizing hormone. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of luteinizing hormone. down regulation of luteinizing hormone secretion down-regulation of luteinizing hormone secretion downregulation of luteinizing hormone secretion inhibition of luteinizing hormone secretion biological_process GO:0033685 negative regulation of luteinizing hormone secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of luteinizing hormone. GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of luteinizing hormone. up regulation of luteinizing hormone secretion up-regulation of luteinizing hormone secretion upregulation of luteinizing hormone secretion activation of luteinizing hormone secretion stimulation of luteinizing hormone secretion biological_process GO:0033686 positive regulation of luteinizing hormone secretion Any process that activates or increases the frequency, rate or extent of the regulated release of luteinizing hormone. GOC:mah Any process of regulating the production and elimination of erythrocytes within an organism. RBC homeostasis red blood cell homeostasis biological_process GO:0034101 erythrocyte homeostasis Any process of regulating the production and elimination of erythrocytes within an organism. GOC:add PMID:10694114 PMID:14754397 RBC homeostasis CL:0000232 red blood cell homeostasis CL:0000232 The process in which a carbohydrate is transported across a membrane. carbohydrate membrane transport transmembrane carbohydrate transport biological_process GO:0034219 Note that this term is not intended for use in annotating lateral movement within membranes. carbohydrate transmembrane transport The process in which a carbohydrate is transported across a membrane. GOC:mah transmembrane carbohydrate transport GOC:dph GOC:tb A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GO:0099131 ion transmembrane transport ion membrane transport transmembrane ion transport ATP hydrolysis coupled ion transmembrane transport biological_process GO:0034220 Note that this term is not intended for use in annotating lateral movement within membranes. monoatomic ion transmembrane transport A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GOC:mah transmembrane ion transport GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. regulation of amide metabolism regulation of cellular amide metabolic process biological_process GO:0034248 regulation of amide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. negative regulation of amide metabolism negative regulation of cellular amide metabolic process biological_process GO:0034249 negative regulation of amide metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. positive regulation of amide metabolism positive regulation of cellular amide metabolic process biological_process GO:0034250 positive regulation of amide metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. https://github.com/geneontology/go-ontology/issues/26424 cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation biological_process nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GO:0034655 nucleobase-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. regulation of membrane transport biological_process GO:0034762 regulation of transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. down regulation of transmembrane transport down-regulation of transmembrane transport downregulation of transmembrane transport negative regulation of membrane transport inhibition of transmembrane transport biological_process GO:0034763 negative regulation of transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. positive regulation of membrane transport up regulation of transmembrane transport up-regulation of transmembrane transport upregulation of transmembrane transport activation of transmembrane transport stimulation of transmembrane transport biological_process GO:0034764 positive regulation of transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. regulation of ion transmembrane transport regulation of ion membrane transport regulation of transmembrane ion transport biological_process GO:0034765 regulation of monoatomic ion transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah regulation of transmembrane ion transport GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. negative regulation of ion transmembrane transport down regulation of transmembrane ion transport down-regulation of transmembrane ion transport downregulation of transmembrane ion transport negative regulation of ion membrane transport negative regulation of transmembrane ion transport inhibition of transmembrane ion transport biological_process GO:0034766 negative regulation of monoatomic ion transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah negative regulation of transmembrane ion transport GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. positive regulation of ion transmembrane transport positive regulation of ion membrane transport positive regulation of transmembrane ion transport up regulation of transmembrane ion transport up-regulation of transmembrane ion transport upregulation of transmembrane ion transport activation of transmembrane ion transport stimulation of transmembrane ion transport biological_process GO:0034767 positive regulation of monoatomic ion transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah The peptide cleavage of mitochondrial proteins, including cleavage contributing to their import. biological_process mitochondrial protein modification GO:0034982 mitochondrial protein processing The peptide cleavage of mitochondrial proteins, including cleavage contributing to their import. GOC:curators The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GO:0035083 GO:0035084 ciliary axoneme assembly cilium axoneme assembly flagellar axoneme assembly flagellum axoneme assembly biological_process axoneme biogenesis cilium axoneme biogenesis GO:0035082 Note that cilia and eukaryotic flagella are deemed to be equivalent. axoneme assembly The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. GOC:bf GOC:cilia GOC:jl ISBN:0815316194 axoneme biogenesis GOC:mah cilium axoneme biogenesis GOC:mah Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow. tube lumen formation biological_process lumen formation in an anatomical structure GO:0035148 tube formation Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow. GOC:bf tube lumen formation GOC:dph GOC:mah lumen formation in an anatomical structure GOC:dph GOC:mah The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. biological_process GO:0035239 tube morphogenesis The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GOC:bf PMID:14624839 The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. biological_process GO:0035265 organ growth The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. GOC:bf ISBN:0471245208 ISBN:0721662544 The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. biological_process GO:0035295 tube development The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. PMID:12526790 An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. bf 2010-03-11T10:46:10Z pre-BCR cellular_component GO:0035369 Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome. pre-B cell receptor complex An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. GOC:add ISBN:0781765196 PMID:16464608 PMID:17306522 The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. bf 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 intracellular signal transduction pathway signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway GO:0035556 intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. GOC:bf GOC:jl GOC:signaling ISBN:3527303782 intracellular signaling cascade GOC:signaling The directed movement of a protein to a specific location within the extracellular region. bf 2010-11-09T10:25:08Z establishment of protein localisation in extracellular region establishment of protein localization in extracellular region biological_process GO:0035592 establishment of protein localization to extracellular region The directed movement of a protein to a specific location within the extracellular region. GOC:BHF GOC:bf establishment of protein localisation in extracellular region GOC:mah The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. bf 2011-03-17T10:55:42Z intraflagellar transport Reactome:R-HSA-5620924.2 biological_process intraciliary transport involved in cilium morphogenesis intraflagellar transport involved in cilium morphogenesis GO:0035735 intraciliary transport involved in cilium assembly The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. GOC:bf GOC:cilia Reactome:R-HSA-5620924.2 Any process that modulates the amount of urine excreted from the body over a unit of time. bf 2011-04-20T01:17:38Z regulation of urinary volume regulation of urine flow biological_process GO:0035809 regulation of urine volume Any process that modulates the amount of urine excreted from the body over a unit of time. GOC:mtg_25march11 GOC:yaf The regulated release of parathyroid hormone into the circulatory system. bf 2011-06-22T09:28:54Z PTH secretion parathormone secretion parathyrin secretion biological_process GO:0035898 parathyroid hormone secretion The regulated release of parathyroid hormone into the circulatory system. GOC:cjm PMID:12171519 PMID:21164021 PTH secretion PMID:12171519 PR:000013429 parathormone secretion PR:000013429 parathyrin secretion PR:000013429 The regulated release of any steroid that acts as a hormone into the circulatory system. bf 2011-07-20T01:01:00Z biological_process GO:0035929 steroid hormone secretion The regulated release of any steroid that acts as a hormone into the circulatory system. GOC:sl The regulated release of any corticosteroid hormone into the circulatory system. bf 2011-07-20T01:03:22Z corticosteroid secretion biological_process GO:0035930 corticosteroid hormone secretion The regulated release of any corticosteroid hormone into the circulatory system. GOC:sl corticosteroid secretion GOC:bf The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism. bf 2011-07-20T01:04:59Z biological_process GO:0035931 mineralocorticoid secretion The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism. GOC:sl The regulated release of aldosterone into the circulatory system. Aldosterone is a pregnane-based steroid hormone produced by the outer-section (zona glomerulosa) of the adrenal cortex in the adrenal gland, and acts on the distal tubules and collecting ducts of the kidney to cause the conservation of sodium, secretion of potassium, increased water retention, and increased blood pressure. The overall effect of aldosterone is to increase reabsorption of ions and water in the kidney. bf 2011-07-20T01:06:24Z biological_process GO:0035932 aldosterone secretion The regulated release of aldosterone into the circulatory system. Aldosterone is a pregnane-based steroid hormone produced by the outer-section (zona glomerulosa) of the adrenal cortex in the adrenal gland, and acts on the distal tubules and collecting ducts of the kidney to cause the conservation of sodium, secretion of potassium, increased water retention, and increased blood pressure. The overall effect of aldosterone is to increase reabsorption of ions and water in the kidney. GOC:sl The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates. bf 2011-07-20T01:11:31Z biological_process GO:0035935 androgen secretion The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates. GOC:sl The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues. bf 2011-12-19T01:47:22Z biological_process GO:0036072 direct ossification The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues. GO_REF:0000034 Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation. bf 2011-12-19T01:53:16Z indirect ossification biological_process GO:0036075 replacement ossification Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation. GO_REF:0000034 indirect ossification GO_REF:0000034 The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation. bf 2012-03-26T01:16:55Z MSH secretion biological_process GO:0036160 melanocyte-stimulating hormone secretion The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation. GOC:cjm Wikipedia:Melanocyte-stimulating_hormone MSH secretion GOC:cjm The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism, from a cell. bf 2012-03-26T01:30:32Z biological_process GO:0036161 calcitonin secretion The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism, from a cell. GOC:cjm A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. bf 2012-04-20T10:20:47Z myocyte projection muscle arm myopodia cellular_component GO:0036194 muscle cell projection A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. CL:0000187 GOC:kmv PMID:15930100 PMID:22464329 myocyte projection CL:0000187 muscle arm GOC:kmv myopodia GOC:kmv Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen. bf 2012-07-20T01:05:46Z response to lowered oxygen levels biological_process GO:0036293 This term should be used when a decrease in oxygen levels is not considered a stress response. For a hypoxic stress response, consider instead 'response to hypoxia ; GO:0001666'. response to decreased oxygen levels Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen. GOC:al response to lowered oxygen levels GOC:bf The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. bf 2014-07-24T10:06:19Z cellular_component GO:0036477 somatodendritic compartment The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. GOC:PARL GOC:pad Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. bf 2011-08-01T02:45:27Z GO:0004872 GO:0019041 receptor activity receptor activity involved in signal transduction signalling receptor activity molecular_function GO:0038023 signaling receptor activity Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. GOC:bf GOC:signaling receptor activity involved in signal transduction GOC:bf The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. biological_process GO:0040008 regulation of growth Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. GOC:ems GOC:mah Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. biological_process GO:0040012 regulation of locomotion Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. GOC:ems Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. down regulation of locomotion down-regulation of locomotion downregulation of locomotion inhibition of locomotion biological_process GO:0040013 negative regulation of locomotion Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators The first few specialized divisions of an activated animal egg. biological_process GO:0040016 embryonic cleavage The first few specialized divisions of an activated animal egg. GOC:clt ISBN:0070524300 Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. up regulation of locomotion up-regulation of locomotion upregulation of locomotion activation of locomotion stimulation of locomotion biological_process GO:0040017 positive regulation of locomotion Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of embryonic development. up regulation of embryonic development up-regulation of embryonic development upregulation of embryonic development activation of embryonic development stimulation of embryonic development biological_process GO:0040019 positive regulation of embryonic development Any process that activates or increases the frequency, rate or extent of embryonic development. GOC:go_curators Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. regulation of meiosis biological_process GO:0040020 regulation of meiotic nuclear division Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes. GOC:ems GOC:ma regulation of meiosis GOC:vw The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0042044 fluid transport The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The series of events that restore integrity to a damaged tissue, following an injury. Wikipedia:Wound_healing biological_process GO:0042060 wound healing The series of events that restore integrity to a damaged tissue, following an injury. GOC:bf PMID:15269788 The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GO:0035734 Wikipedia:Intraflagellar_transport intraflagellar transport intraflagellar transport involved in cilium organization intraflagellar transport involved in microtubule-based flagellum organisation biological_process IFT GO:0042073 Note that we deem cilium and microtubule-based flagellum to be equivalent. intraciliary transport The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. GOC:cilia GOC:kmv PMID:17981739 PMID:18180368 PMID:22869374 Reactome:R-HSA-5620924.2 The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). biological_process GO:0042074 cell migration involved in gastrulation The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression). GOC:jl ISBN:0878932437 http://www.cellmigration.org/ An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects. T-helper 2 type immune response Th2 immune response biological_process GO:0042092 type 2 immune response An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects. GOC:add ISBN:0781735149 PMID:18000958 PMID:18007680 PMID:20065995 PMID:20200518 T-helper 2 type immune response GOC:add Th2 immune response GOC:add A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. Wikipedia:T_cell_receptor T lymphocyte receptor complex T-cell receptor complex T-lymphocyte receptor complex TCR complex cellular_component TCR GO:0042101 T cell receptor complex A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. GOC:mah ISBN:0781735149 TCR complex GOC:bf The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. T lymphocyte activation T-cell activation T-lymphocyte activation biological_process GO:0042110 T cell activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:mgi_curators ISBN:0781735149 The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. B lymphocyte activation B-cell activation B-lymphocyte activation biological_process GO:0042113 B cell activation The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. GOC:mgi_curators ISBN:0781735149 Any process that modulates the frequency, rate or extent of cell proliferation. biological_process regulation of cell proliferation GO:0042127 regulation of cell population proliferation Any process that modulates the frequency, rate or extent of cell proliferation. GOC:jl The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone metabolism biological_process GO:0042180 cellular ketone metabolic process The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:jl ISBN:0787650153 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance biological_process GO:0042221 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:jl response to chemical stimulus GOC:dos The regrowth of lost or destroyed tissues. biological_process GO:0042246 tissue regeneration The regrowth of lost or destroyed tissues. GOC:curators Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. biological_process GO:0042325 regulation of phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. GOC:jl Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. down regulation of phosphorylation down-regulation of phosphorylation downregulation of phosphorylation inhibition of phosphorylation biological_process GO:0042326 negative regulation of phosphorylation Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. up regulation of phosphorylation up-regulation of phosphorylation upregulation of phosphorylation activation of phosphorylation stimulation of phosphorylation biological_process GO:0042327 positive regulation of phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. GOC:jl The directed movement of a motile cell or organism in response to an external stimulus. Wikipedia:Taxis directed movement in response to stimulus biological_process GO:0042330 taxis The directed movement of a motile cell or organism in response to an external stimulus. GOC:jl ISBN:0192801023 The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3). vitamin D metabolism calciferol metabolic process calciferol metabolism cholecalciferol metabolic process cholecalciferol metabolism ergocalciferol metabolic process ergocalciferol metabolism biological_process GO:0042359 vitamin D metabolic process The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3). GOC:mah ISBN:0471331309 The chemical reactions and pathways involving vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant. tocopherol metabolic process tocopherol metabolism vitamin E metabolism alpha-tocopherol metabolic process alpha-tocopherol metabolism biological_process GO:0042360 vitamin E metabolic process The chemical reactions and pathways involving vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule. naphthoquinone metabolic process naphthoquinone metabolism vitamin K metabolism biological_process GO:0042373 vitamin K metabolic process The chemical reactions and pathways involving any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals. Vitamin K substances share a methylated naphthoquinone ring structure and vary in the aliphatic side chains attached to the molecule. GOC:jl http://www.dentistry.leeds.ac.uk/biochem/thcme/vitamins.html#k Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. biological_process GO:0042391 regulation of membrane potential Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane. GOC:jl GOC:mtg_cardio GOC:tb ISBN:0198506732 The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine. thyroid hormone metabolism biological_process GO:0042403 thyroid hormone metabolic process The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton. GO:0042434 indole and derivative metabolic process indole and derivative metabolism indole-containing compound metabolism ketole metabolic process ketole metabolism indole derivative metabolic process indole derivative metabolism biological_process GO:0042430 indole-containing compound metabolic process The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl GOC:mah The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton. indole derivative biosynthesis indole derivative biosynthetic process indole-containing compound anabolism indole-containing compound biosynthesis indole-containing compound formation indole-containing compound synthesis biological_process GO:0042435 indole-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton. GOC:jl The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. https://github.com/geneontology/go-ontology/issues/23965 GO:0034754 hormone metabolism biological_process cellular hormone metabolic process GO:0042445 hormone metabolic process The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. GOC:jl The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. hormone anabolism hormone biosynthesis hormone formation hormone synthesis biological_process GO:0042446 hormone biosynthetic process The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. GOC:jl The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel. odontogeny odontosis tooth development odontogenesis of dentine-containing teeth odontogenesis of dentine-containing tooth biological_process GO:0042475 Note that placoid scales found in the cartilaginous fishes presumably develop through the same processes, but are found on the dermis, rather than in the mouth or pharynx. See Wikipedia:Placoid_scale#Placoid_scales. odontogenesis of dentin-containing tooth The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel. GOC:cjm GOC:mah GOC:mtg_sensu PMID:10333884 PMID:15355794 odontogenesis of dentine-containing tooth GOC:mah The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. GO:0042477 Wikipedia:Odontogenesis odontogeny odontosis tooth morphogenesis odontogenesis of calcareous or chitinous tooth biological_process tooth development GO:0042476 odontogenesis The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth. GO:0042484 regulation of tooth development regulation of odontogenesis of calcareous or chitinous tooth biological_process GO:0042481 regulation of odontogenesis Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth. GOC:jl Any process that activates or increases the frequency, rate or extent of the formation and development of a tooth or teeth. GO:0042485 positive regulation of tooth development up regulation of odontogenesis up-regulation of odontogenesis upregulation of odontogenesis activation of odontogenesis positive regulation of odontogenesis of calcareous or chitinous tooth stimulation of odontogenesis biological_process GO:0042482 positive regulation of odontogenesis Any process that activates or increases the frequency, rate or extent of the formation and development of a tooth or teeth. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth. GO:0042486 down regulation of odontogenesis down-regulation of odontogenesis downregulation of odontogenesis negative regulation of tooth development inhibition of odontogenesis negative regulation of odontogenesis of calcareous or chitinous tooth biological_process GO:0042483 negative regulation of odontogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth. GOC:jl Any process that modulates the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. regulation of odontogenesis of dentine-containing teeth regulation of odontogenesis of dentine-containing tooth biological_process GO:0042487 regulation of odontogenesis of dentin-containing tooth Any process that modulates the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. GOC:jl GOC:mtg_sensu PMID:15355794 regulation of odontogenesis of dentine-containing tooth GOC:mah Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. activation of odontogenesis stimulation of odontogenesis up regulation of odontogenesis up-regulation of odontogenesis upregulation of odontogenesis positive regulation of odontogenesis of dentine-containing teeth biological_process positive regulation of odontogenesis of dentine-containing tooth GO:0042488 positive regulation of odontogenesis of dentin-containing tooth Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates. GOC:jl PMID:15355794 Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx. down regulation of odontogenesis down-regulation of odontogenesis downregulation of odontogenesis inhibition of odontogenesis negative regulation of odontogenesis negative regulation of odontogenesis of dentine-containing teeth biological_process negative regulation of odontogenesis of dentine-containing tooth GO:0042489 negative regulation of odontogenesis of dentin-containing tooth Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx. GOC:jl GOC:mtg_sensu PMID:15355794 An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. Wikipedia:Antibody antibody cellular_component GO:0042571 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex, circulating An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. GOC:add ISBN:0781735149 antibody GOC:add Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. primary granule cellular_component GO:0042582 azurophil granule Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid. GOC:jl PMID:17152095 A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. cellular_component GO:0042588 zymogen granule A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. GOC:jl ISBN:0198506732 The lipid bilayer surrounding a zymogen granule. cellular_component GO:0042589 zymogen granule membrane The lipid bilayer surrounding a zymogen granule. GOC:jl Any biological process involved in the maintenance of an internal steady state. GO:0032844 GO:0032845 GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process biological_process negative regulation of homeostatic process positive regulation of homeostatic process regulation of homeostatic process GO:0042592 homeostatic process Any biological process involved in the maintenance of an internal steady state. GOC:jl ISBN:0395825172 Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. biological_process GO:0042593 glucose homeostasis Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. GOC:go_curators A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. cellular_component GO:0042611 MHC protein complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. GOC:add GOC:jl ISBN:0781735149 PMID:15928678 PMID:16153240 A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. cellular_component GO:0042613 MHC class II protein complex A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. GOC:add GOC:jl ISBN:0120781859 PMID:15928678 The region of a mitochondrion to which the DNA is confined. cellular_component GO:0042645 mitochondrial nucleoid The region of a mitochondrion to which the DNA is confined. GOC:jl The expulsion of seminal fluid, thick white fluid containing spermatozoa, from the male genital tract. biological_process GO:0042713 sperm ejaculation The expulsion of seminal fluid, thick white fluid containing spermatozoa, from the male genital tract. GOC:jl http://www.cogsci.princeton.edu/~wn/ A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin. Wikipedia:Fibrinolysis biological_process GO:0042730 fibrinolysis A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin. GOC:jl PMID:15842654 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. regulation of sulfur metabolism regulation of sulphur metabolic process regulation of sulphur metabolism biological_process GO:0042762 regulation of sulfur metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. GOC:go_curators The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0042886 amide transport The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl ISBN:0198506732 Any process that modulates the occurrence or rate of cell death by apoptotic process. regulation of apoptosis biological_process apoptosis regulator activity GO:0042981 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. regulation of apoptotic process Any process that modulates the occurrence or rate of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis A prolongation or process extending from a cell, e.g. a flagellum or axon. cell process cellular process cellular projection cellular_component GO:0042995 cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. NIF_Subcellular:sao867568886 neuron process neuron protrusion neuronal cell projection neurite cellular_component nerve fiber GO:0043005 neuron projection A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl http://www.cogsci.princeton.edu/~wn/ neuron protrusion NIF_Subcellular:sao250931889 nerve fiber GOC:dph The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching. biological_process GO:0043009 chordate embryonic development The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching. GOC:mtg_sensu The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. Wikipedia:Dendritic_cell biological_process GO:0043011 myeloid dendritic cell differentiation The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin. CL:0000782 GOC:jl The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. NIF_Subcellular:sao1044911821 Wikipedia:Soma_(biology) neuron cell body neuronal cell soma cellular_component GO:0043025 Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. neuronal cell body The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites. GOC:go_curators The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide. peptide anabolism peptide biosynthesis peptide formation peptide synthesis biological_process GO:0043043 peptide biosynthetic process The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide. GOC:dph GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite. extracellular structure organisation extracellular structure organization and biogenesis biological_process GO:0043062 extracellular structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite. GOC:ai GOC:dph GOC:jl GOC:mah extracellular structure organization and biogenesis GOC:dph GOC:jl GOC:mah Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. up regulation of apoptosis up-regulation of apoptosis upregulation of apoptosis activation of apoptosis positive regulation of apoptosis stimulation of apoptosis biological_process pro-apoptosis GO:0043065 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. positive regulation of apoptotic process Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GO:0006916 anti-apoptosis down regulation of apoptosis down-regulation of apoptosis downregulation of apoptosis inhibition of apoptosis negative regulation of apoptosis biological_process apoptosis inhibitor activity pro-survival GO:0043066 This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. negative regulation of apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043070 regulation of non-apoptotic programmed cell death biological_process GO:0043067 regulation of programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043071 up regulation of programmed cell death up-regulation of programmed cell death upregulation of programmed cell death activation of programmed cell death positive regulation of non-apoptotic programmed cell death stimulation of programmed cell death biological_process GO:0043068 positive regulation of programmed cell death Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043072 down regulation of programmed cell death down-regulation of programmed cell death downregulation of programmed cell death inhibition of programmed cell death negative regulation of non-apoptotic programmed cell death biological_process GO:0043069 negative regulation of programmed cell death Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the activity of an enzyme. GO:0048554 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process GO:0043086 negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. establishment and maintenance of translational machinery localization establishment and maintenance of translational protein localization regulation of translation by machinery localisation translational machinery localization translational protein localization biological_process GO:0043143 regulation of translation by machinery localization Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. GOC:jl regulation of translation by machinery localisation GOC:mah translational machinery localization GOC:dph GOC:tb The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/26424 GO:0034960 GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things. biological_process GO:0043207 response to external biotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things. GOC:go_curators Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. cellular_component GO:0043230 extracellular organelle Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi. GOC:jl PMID:9914479 Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. intracellular non-membrane-enclosed organelle cellular_component GO:0043232 intracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. GOC:go_curators The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component GO:0043233 organelle lumen The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. GOC:jl GOC:mah Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. cellular_component GO:0043235 receptor complex Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates. regulation of carbohydrate anabolism regulation of carbohydrate biosynthesis regulation of carbohydrate formation regulation of carbohydrate synthesis biological_process GO:0043255 regulation of carbohydrate biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates. GOC:jl Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell. extracellular non-membrane-enclosed organelle cellular_component GO:0043264 extracellular non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell. GOC:jl Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. regulation of ion transport biological_process GO:0043269 regulation of monoatomic ion transport Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of ion transport up-regulation of ion transport upregulation of ion transport activation of ion transport stimulation of ion transport biological_process GO:0043270 positive regulation of monoatomic ion transport Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. negative regulation of ion transport down regulation of ion transport down-regulation of ion transport downregulation of ion transport inhibition of ion transport biological_process GO:0043271 negative regulation of monoatomic ion transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. contractile fibre cellular_component GO:0043292 contractile fiber Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle. GOC:go_curators ISBN:0815316194 The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). keto acid metabolic process keto acid metabolism ketoacid metabolic process ketoacid metabolism oxo acid metabolic process oxo acid metabolism oxoacid metabolism biological_process GO:0043436 oxoacid metabolic process The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). Wikipedia:Oxyacid Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. biological_process GO:0043467 regulation of generation of precursor metabolites and energy Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. GOC:jl Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates. biological_process GO:0043470 regulation of carbohydrate catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates. GOC:mlg Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 regulation of kinase activity Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:bf Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment. biological_process GO:0043576 regulation of respiratory gaseous exchange Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment. GOC:jl The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells. amide metabolism cellular amide metabolic process biological_process GO:0043603 amide metabolic process The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells. GOC:curators The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. biological_process GO:0043604 amide biosynthetic process The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group. GOC:curators The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-). dicarboxylate metabolic process dicarboxylate metabolism dicarboxylic acid metabolism biological_process GO:0043648 dicarboxylic acid metabolic process The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+. EC:1.2.1.59 MetaCyc:GAPDHSYNEC-RXN D-glyceraldehyde 3-phosphate:NAD(P)+ oxidoreductase (phosphorylating) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) (phosphorylating) triosephosphate dehydrogenase (NAD(P)) molecular_function NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase activity triosephosphate dehydrogenase (NAD(P)+) GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+. EC:1.2.1.59 NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase activity EC:1.2.1.59 triosephosphate dehydrogenase (NAD(P)+) EC:1.2.1.59 The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues. glucan metabolism biological_process GO:0044042 glucan metabolic process The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues. GOC:jl Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. biological_process GO:0044057 regulation of system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. GOC:jl Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0044058 regulation of digestive system process Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:jl Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. regulation of endocrine system process biological_process GO:0044060 regulation of endocrine process Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. GOC:jl Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity. biological_process GO:0044062 regulation of excretion Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity. GOC:jl Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system. biological_process GO:0044065 regulation of respiratory system process Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system. GOC:jl A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 cellular component biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. GOC:jl GOC:mah Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044087 regulation of cellular component biogenesis Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. biological_process GO:0044089 positive regulation of cellular component biogenesis Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. GOC:jl Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jl 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jl 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 primary metabolism biological_process GO:0044238 primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. cellular breakdown cellular catabolism cellular degradation biological_process GO:0044248 cellular catabolic process The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis biological_process GO:0044249 cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways involving lipids, as carried out by individual cells. cellular lipid metabolism biological_process GO:0044255 cellular lipid metabolic process The chemical reactions and pathways involving lipids, as carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. nitrogen compound breakdown nitrogen compound catabolism nitrogen compound degradation biological_process GO:0044270 cellular nitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis biological_process GO:0044271 cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. sulfur compound anabolism sulfur compound biosynthesis sulfur compound formation sulfur compound synthesis sulfur biosynthesis sulfur biosynthetic process biological_process GO:0044272 sulfur compound biosynthetic process The chemical reactions and pathways resulting in the formation of compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:jl The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:05:20Z small molecule metabolism biological_process GO:0044281 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule metabolic process The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:06:49Z small molecule biosynthesis biological_process GO:0044283 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. jl 2010-02-05T10:37:16Z FBbt:00005107 FMA:67301 Wikipedia:Cell_body cell soma cellular_component GO:0044297 Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections. cell body The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections. GOC:go_curators Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 biological process involved in interspecies interaction between organisms Any process evolved to enable an interaction with an organism of a different species. GOC:cc The aggregation, arrangement and bonding together of a set of components to form a motile cilium. krc 2015-02-06T17:23:23Z GO:1903887 biological_process motile primary cilia assembly motile primary cilia formation motile primary cilium assembly motile primary cilium formation nodal cilium assembly nodal cilium formation GO:0044458 motile cilium assembly The aggregation, arrangement and bonding together of a set of components to form a motile cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000079 PMID:19776033 PMID:21129373 ZFIN:dsf motile primary cilia assembly GOC:TermGenie motile primary cilia formation GOC:TermGenie motile primary cilium formation GOC:TermGenie nodal cilium assembly GOC:TermGenie nodal cilium formation GOC:TermGenie A biological process that directly contributes to the process of producing new individuals, involving another organism. jl 2012-09-19T15:56:30Z biological_process GO:0044703 multi-organism reproductive process A biological process that directly contributes to the process of producing new individuals, involving another organism. GOC:jl A multicellular organism process which involves another multicellular organism of the same or different species. https://github.com/geneontology/go-ontology/issues/21459 jl 2012-09-19T16:06:16Z biological_process GO:0044706 multi-multicellular organism process A multicellular organism process which involves another multicellular organism of the same or different species. GOC:jl A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. jl 2013-03-27T15:09:58Z microtubule-based flagellum organization biological_process GO:0044782 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:cilia GOC:jl The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation. Wikipedia:Thymocyte T lymphocyte selection T-cell selection T-lymphocyte selection biological_process GO:0045058 T cell selection The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation. ISBN:0781735149 PMID:12414722 Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. GO:0002226 Wikipedia:Innate_immune_system innate immunity nonspecific immune response biological_process GO:0045087 innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. GOC:add GOC:ebc GOC:mtg_sensu GO_REF:0000022 innate immunity GOC:pg Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. biological_process GO:0045088 regulation of innate immune response Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. GOC:ebc Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. up regulation of innate immune response up-regulation of innate immune response upregulation of innate immune response stimulation of innate immune response biological_process GO:0045089 positive regulation of innate immune response Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection. GOC:ebc A filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells. The keratins are the most diverse classes of IF proteins, with a large number of keratin isoforms being expressed. Each type of epithelium always expresses a characteristic combination of type I and type II keratins. cellular_component acidic keratin basic/neutral keratin GO:0045095 keratin filament A filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells. The keratins are the most diverse classes of IF proteins, with a large number of keratin isoforms being expressed. Each type of epithelium always expresses a characteristic combination of type I and type II keratins. ISBN:0716731363 Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell. cellular_component GO:0045111 intermediate filament cytoskeleton Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell. ISBN:0716731363 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle. biological_process GO:0045132 meiotic chromosome segregation The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle. GOC:ai GOC:mah The cell cycle process in which sister chromatids are organized and then physically separated and randomly apportioned to two sets during the second division of the meiotic cell cycle. meiosis II, chromosome segregation biological_process GO:0045144 meiotic sister chromatid segregation The cell cycle process in which sister chromatids are organized and then physically separated and randomly apportioned to two sets during the second division of the meiotic cell cycle. GOC:ai ISBN:0815316194 The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus. Wikipedia:Immunoglobulin_class_switching class switch recombination class switching isotype switch recombination biological_process GO:0045190 Note that IgM and IgD can be coexpressed by B cells via an alternate splicing mechanism, but true recombinational isotype switching to IgD has been demonstrated as well. Note that this term is best used to annotate gene products which are involved in the mechanism of DNA recombination used in isotype switching, like the B cell specific Swap70 factor in the mouse, rather than gene products which promote isotype switching such as cytokines or co-stimulatory molecules, which should instead be annotated to 'regulation of isotype switching ; GO:0045191'. isotype switching The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus. ISBN:0781735149 Any process that modulates the frequency, rate or extent of isotype switching. regulation of class switch recombination regulation of class switching regulation of isotype switch recombination biological_process GO:0045191 regulation of isotype switching Any process that modulates the frequency, rate or extent of isotype switching. GOC:ai The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. NIF_Subcellular:sao914572699 Wikipedia:Chemical_synapse synaptic junction mixed synapse cellular_component electrotonic synapse GO:0045202 synapse The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. GOC:aruk ISBN:0198506732 PMID:24619342 PMID:29383328 PMID:31998110 mixed synapse NIF_Subcellular:sao1506103497 electrotonic synapse NIF_Subcellular:sao1311109124 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell. external encapsulating structure organisation external encapsulating structure organization and biogenesis biological_process GO:0045229 external encapsulating structure organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell. GOC:ai GOC:dph GOC:jl GOC:mah external encapsulating structure organization and biogenesis GOC:dph GOC:jl GOC:mah A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. Wikipedia:Immunologic_activation immune cell activation leucocyte activation biological_process GO:0045321 leukocyte activation A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor. GOC:add Any process that modulates the frequency, rate or extent of B cell differentiation. regulation of B lymphocyte differentiation regulation of B-cell differentiation regulation of B-lymphocyte differentiation biological_process regulation of B cell development GO:0045577 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of B cell differentiation Any process that modulates the frequency, rate or extent of B cell differentiation. GOC:go_curators regulation of B cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation. down regulation of B cell differentiation down-regulation of B cell differentiation downregulation of B cell differentiation negative regulation of B lymphocyte differentiation negative regulation of B-cell differentiation negative regulation of B-lymphocyte differentiation inhibition of B cell differentiation biological_process negative regulation of B cell development GO:0045578 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of B cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation. GOC:go_curators negative regulation of B cell development GOC:add Any process that activates or increases the frequency, rate or extent of B cell differentiation. positive regulation of B lymphocyte differentiation positive regulation of B-cell differentiation positive regulation of B-lymphocyte differentiation up regulation of B cell differentiation up-regulation of B cell differentiation upregulation of B cell differentiation activation of B cell differentiation stimulation of B cell differentiation biological_process positive regulation of B cell development GO:0045579 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of B cell differentiation Any process that activates or increases the frequency, rate or extent of B cell differentiation. GOC:go_curators positive regulation of B cell development GOC:add Any process that modulates the frequency, rate or extent of T cell differentiation. regulation of T lymphocyte differentiation regulation of T-cell differentiation regulation of T-lymphocyte differentiation biological_process regulation of T cell development GO:0045580 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of T cell differentiation Any process that modulates the frequency, rate or extent of T cell differentiation. GOC:go_curators regulation of T cell development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation. down regulation of T cell differentiation down-regulation of T cell differentiation downregulation of T cell differentiation negative regulation of T lymphocyte differentiation negative regulation of T-cell differentiation negative regulation of T-lymphocyte differentiation inhibition of T cell differentiation biological_process negative regulation of T cell development GO:0045581 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of T cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation. GOC:go_curators negative regulation of T cell development GOC:add Any process that activates or increases the frequency, rate or extent of T cell differentiation. positive regulation of T lymphocyte differentiation positive regulation of T-cell differentiation positive regulation of T-lymphocyte differentiation up regulation of T cell differentiation up-regulation of T cell differentiation upregulation of T cell differentiation activation of T cell differentiation stimulation of T cell differentiation biological_process positive regulation of T cell development GO:0045582 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of T cell differentiation Any process that activates or increases the frequency, rate or extent of T cell differentiation. GOC:go_curators positive regulation of T cell development GOC:add Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. biological_process GO:0045595 regulation of cell differentiation Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. down regulation of cell differentiation down-regulation of cell differentiation downregulation of cell differentiation inhibition of cell differentiation biological_process GO:0045596 negative regulation of cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell differentiation. up regulation of cell differentiation up-regulation of cell differentiation upregulation of cell differentiation activation of cell differentiation stimulation of cell differentiation biological_process GO:0045597 positive regulation of cell differentiation Any process that activates or increases the frequency, rate or extent of cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of lymphocyte differentiation. biological_process regulation of lymphocyte development GO:0045619 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. regulation of lymphocyte differentiation Any process that modulates the frequency, rate or extent of lymphocyte differentiation. GOC:go_curators regulation of lymphocyte development GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation. down regulation of lymphocyte differentiation down-regulation of lymphocyte differentiation downregulation of lymphocyte differentiation inhibition of lymphocyte differentiation biological_process negative regulation of lymphocyte development GO:0045620 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. negative regulation of lymphocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation. GOC:go_curators negative regulation of lymphocyte development GOC:add Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation. up regulation of lymphocyte differentiation up-regulation of lymphocyte differentiation upregulation of lymphocyte differentiation activation of lymphocyte differentiation stimulation of lymphocyte differentiation biological_process positive regulation of lymphocyte development GO:0045621 Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. positive regulation of lymphocyte differentiation Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation. GOC:go_curators positive regulation of lymphocyte development GOC:add Any process that modulates the frequency, rate or extent of myeloid cell differentiation. biological_process GO:0045637 regulation of myeloid cell differentiation Any process that modulates the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. down regulation of myeloid cell differentiation down-regulation of myeloid cell differentiation downregulation of myeloid cell differentiation inhibition of myeloid cell differentiation biological_process GO:0045638 negative regulation of myeloid cell differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. up regulation of myeloid cell differentiation up-regulation of myeloid cell differentiation upregulation of myeloid cell differentiation activation of myeloid cell differentiation stimulation of myeloid cell differentiation biological_process GO:0045639 positive regulation of myeloid cell differentiation Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of basophil differentiation. biological_process GO:0045640 regulation of basophil differentiation Any process that modulates the frequency, rate or extent of basophil differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation. down regulation of basophil differentiation down-regulation of basophil differentiation downregulation of basophil differentiation inhibition of basophil differentiation biological_process GO:0045641 negative regulation of basophil differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of basophil differentiation. up regulation of basophil differentiation up-regulation of basophil differentiation upregulation of basophil differentiation activation of basophil differentiation stimulation of basophil differentiation biological_process GO:0045642 positive regulation of basophil differentiation Any process that activates or increases the frequency, rate or extent of basophil differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of erythrocyte differentiation. regulation of RBC differentiation regulation of red blood cell differentiation biological_process GO:0045646 regulation of erythrocyte differentiation Any process that modulates the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators regulation of RBC differentiation CL:0000232 regulation of red blood cell differentiation CL:0000232 Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation. down regulation of erythrocyte differentiation down-regulation of erythrocyte differentiation downregulation of erythrocyte differentiation negative regulation of RBC differentiation negative regulation of red blood cell differentiation inhibition of erythrocyte differentiation biological_process GO:0045647 negative regulation of erythrocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators negative regulation of RBC differentiation CL:0000232 negative regulation of red blood cell differentiation CL:0000232 Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. positive regulation of RBC differentiation positive regulation of red blood cell differentiation up regulation of erythrocyte differentiation up-regulation of erythrocyte differentiation upregulation of erythrocyte differentiation activation of erythrocyte differentiation stimulation of erythrocyte differentiation biological_process GO:0045648 positive regulation of erythrocyte differentiation Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation. GOC:go_curators positive regulation of RBC differentiation CL:0000232 positive regulation of red blood cell differentiation CL:0000232 Any process that modulates the frequency, rate or extent of macrophage differentiation. biological_process GO:0045649 regulation of macrophage differentiation Any process that modulates the frequency, rate or extent of macrophage differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation. down regulation of macrophage differentiation down-regulation of macrophage differentiation downregulation of macrophage differentiation inhibition of macrophage differentiation biological_process GO:0045650 negative regulation of macrophage differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of macrophage differentiation. up regulation of macrophage differentiation up-regulation of macrophage differentiation upregulation of macrophage differentiation activation of macrophage differentiation stimulation of macrophage differentiation biological_process GO:0045651 positive regulation of macrophage differentiation Any process that activates or increases the frequency, rate or extent of macrophage differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of megakaryocyte differentiation. biological_process GO:0045652 regulation of megakaryocyte differentiation Any process that modulates the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation. down regulation of megakaryocyte differentiation down-regulation of megakaryocyte differentiation downregulation of megakaryocyte differentiation inhibition of megakaryocyte differentiation biological_process GO:0045653 negative regulation of megakaryocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation. up regulation of megakaryocyte differentiation up-regulation of megakaryocyte differentiation upregulation of megakaryocyte differentiation activation of megakaryocyte differentiation stimulation of megakaryocyte differentiation biological_process GO:0045654 positive regulation of megakaryocyte differentiation Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of monocyte differentiation. biological_process GO:0045655 regulation of monocyte differentiation Any process that modulates the frequency, rate or extent of monocyte differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation. down regulation of monocyte differentiation down-regulation of monocyte differentiation downregulation of monocyte differentiation inhibition of monocyte differentiation biological_process GO:0045656 negative regulation of monocyte differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of monocyte differentiation. up regulation of monocyte differentiation up-regulation of monocyte differentiation upregulation of monocyte differentiation activation of monocyte differentiation stimulation of monocyte differentiation biological_process GO:0045657 positive regulation of monocyte differentiation Any process that activates or increases the frequency, rate or extent of monocyte differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of osteoclast differentiation. biological_process GO:0045670 regulation of osteoclast differentiation Any process that modulates the frequency, rate or extent of osteoclast differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation. down regulation of osteoclast differentiation down-regulation of osteoclast differentiation downregulation of osteoclast differentiation inhibition of osteoclast differentiation biological_process GO:0045671 negative regulation of osteoclast differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of osteoclast differentiation. up regulation of osteoclast differentiation up-regulation of osteoclast differentiation upregulation of osteoclast differentiation activation of osteoclast differentiation stimulation of osteoclast differentiation biological_process GO:0045672 positive regulation of osteoclast differentiation Any process that activates or increases the frequency, rate or extent of osteoclast differentiation. GOC:go_curators Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation. biological_process GO:0045700 regulation of spermatid nuclear differentiation Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation. down regulation of spermatid nuclear differentiation down-regulation of spermatid nuclear differentiation downregulation of spermatid nuclear differentiation inhibition of spermatid nuclear differentiation biological_process GO:0045701 negative regulation of spermatid nuclear differentiation Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation. up regulation of spermatid nuclear differentiation up-regulation of spermatid nuclear differentiation upregulation of spermatid nuclear differentiation activation of spermatid nuclear differentiation stimulation of spermatid nuclear differentiation biological_process GO:0045702 positive regulation of spermatid nuclear differentiation Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. down regulation of glycogen biosynthetic process down-regulation of glycogen biosynthetic process downregulation of glycogen biosynthetic process negative regulation of glycogen anabolism negative regulation of glycogen biosynthesis negative regulation of glycogen formation negative regulation of glycogen synthesis inhibition of glycogen biosynthetic process biological_process GO:0045719 negative regulation of glycogen biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the formation of a cilium. positive regulation of flagellum assembly up regulation of cilium assembly up-regulation of cilium assembly upregulation of cilium assembly activation of cilium assembly stimulation of cilium assembly biological_process positive regulation of flagellum biogenesis GO:0045724 positive regulation of cilium assembly Any process that activates or increases the frequency, rate or extent of the formation of a cilium. GOC:cilia GOC:go_curators positive regulation of flagellum biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. positive regulation of glycogen anabolism positive regulation of glycogen biosynthesis positive regulation of glycogen formation positive regulation of glycogen synthesis up regulation of glycogen biosynthetic process up-regulation of glycogen biosynthetic process upregulation of glycogen biosynthetic process activation of glycogen biosynthetic process stimulation of glycogen biosynthetic process biological_process GO:0045725 positive regulation of glycogen biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GO:0045946 positive regulation of protein anabolism positive regulation of protein biosynthesis positive regulation of protein biosynthetic process positive regulation of protein formation positive regulation of protein synthesis up regulation of protein biosynthetic process up-regulation of protein biosynthetic process upregulation of protein biosynthetic process activation of protein biosynthetic process stimulation of protein biosynthetic process biological_process GO:0045727 positive regulation of translation Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:dph GOC:go_curators GOC:tb positive regulation of protein biosynthetic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of G protein-coupled receptor signaling pathway. down regulation of G-protein coupled receptor protein signaling pathway down-regulation of G-protein coupled receptor protein signaling pathway downregulation of G-protein coupled receptor protein signaling pathway negative regulation of G protein coupled receptor protein signaling pathway negative regulation of G protein coupled receptor protein signalling pathway negative regulation of G-protein coupled receptor protein signaling pathway negative regulation of G-protein coupled receptor protein signalling pathway negative regulation of G-protein-coupled receptor protein signalling pathway negative regulation of GPCR protein signaling pathway negative regulation of GPCR protein signalling pathway inhibition of G-protein coupled receptor protein signaling pathway biological_process GO:0045744 negative regulation of G protein-coupled receptor signaling pathway Any process that stops, prevents, or reduces the frequency, rate or extent of G protein-coupled receptor signaling pathway. GOC:go_curators Any process that activates or increases the frequency, rate or extent of G protein-coupled receptor signaling pathway activity. positive regulation of G protein coupled receptor protein signaling pathway positive regulation of G protein coupled receptor protein signalling pathway positive regulation of G-protein coupled receptor protein signaling pathway positive regulation of G-protein coupled receptor protein signalling pathway positive regulation of G-protein-coupled receptor protein signaling pathway positive regulation of G-protein-coupled receptor protein signalling pathway positive regulation of GPCR protein signaling pathway positive regulation of GPCR protein signalling pathway up regulation of G-protein coupled receptor protein signaling pathway up-regulation of G-protein coupled receptor protein signaling pathway upregulation of G-protein coupled receptor protein signaling pathway activation of G-protein coupled receptor protein signaling pathway stimulation of G-protein coupled receptor protein signaling pathway biological_process GO:0045745 positive regulation of G protein-coupled receptor signaling pathway Any process that activates or increases the frequency, rate or extent of G protein-coupled receptor signaling pathway activity. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. down regulation of action potential down-regulation of action potential downregulation of action potential inhibition of action potential biological_process GO:0045759 negative regulation of action potential Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:go_curators Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. up regulation of action potential up-regulation of action potential upregulation of action potential activation of action potential stimulation of action potential biological_process GO:0045760 positive regulation of action potential Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. down regulation of amino acid metabolic process down-regulation of amino acid metabolic process downregulation of amino acid metabolic process negative regulation of amino acid metabolism inhibition of amino acid metabolic process biological_process GO:0045763 negative regulation of cellular amino acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. positive regulation of amino acid metabolism positive regulation of cellular amino acid metabolic process up regulation of amino acid metabolic process up-regulation of amino acid metabolic process upregulation of amino acid metabolic process activation of amino acid metabolic process stimulation of amino acid metabolic process biological_process GO:0045764 positive regulation of amino acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. positive regulation of bone biosynthesis positive regulation of bone formation up regulation of ossification up-regulation of ossification upregulation of ossification activation of ossification stimulation of ossification biological_process GO:0045778 positive regulation of ossification Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell adhesion. up regulation of cell adhesion up-regulation of cell adhesion upregulation of cell adhesion activation of cell adhesion stimulation of cell adhesion biological_process GO:0045785 positive regulation of cell adhesion Any process that activates or increases the frequency, rate or extent of cell adhesion. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. down regulation of progression through cell cycle down-regulation of progression through cell cycle downregulation of progression through cell cycle negative regulation of cell cycle progression negative regulation of progression through cell cycle inhibition of progression through cell cycle biological_process GO:0045786 negative regulation of cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the rate or extent of progression through the cell cycle. positive regulation of cell cycle progression positive regulation of progression through cell cycle up regulation of progression through cell cycle up-regulation of progression through cell cycle upregulation of progression through cell cycle activation of progression through cell cycle stimulation of progression through cell cycle biological_process GO:0045787 positive regulation of cell cycle Any process that activates or increases the rate or extent of progression through the cell cycle. GOC:go_curators positive regulation of progression through cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. down regulation of endocytosis down-regulation of endocytosis downregulation of endocytosis inhibition of endocytosis biological_process GO:0045806 negative regulation of endocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of endocytosis. up regulation of endocytosis up-regulation of endocytosis upregulation of endocytosis activation of endocytosis stimulation of endocytosis biological_process GO:0045807 positive regulation of endocytosis Any process that activates or increases the frequency, rate or extent of endocytosis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. down regulation of glycogen catabolic process down-regulation of glycogen catabolic process downregulation of glycogen catabolic process negative regulation of glycogen breakdown negative regulation of glycogen catabolism negative regulation of glycogen degradation negative regulation of glycogenolysis inhibition of glycogen catabolic process biological_process GO:0045818 negative regulation of glycogen catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. GOC:go_curators negative regulation of glycogenolysis GOC:sl Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. positive regulation of glycogen breakdown positive regulation of glycogen catabolism positive regulation of glycogen degradation positive regulation of glycogenolysis up regulation of glycogen catabolic process up-regulation of glycogen catabolic process upregulation of glycogen catabolic process activation of glycogen catabolic process stimulation of glycogen catabolic process biological_process GO:0045819 positive regulation of glycogen catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen. GOC:go_curators positive regulation of glycogenolysis GOC:sl Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis. down regulation of glycolysis down-regulation of glycolysis downregulation of glycolysis inhibition of glycolysis biological_process GO:0045820 negative regulation of glycolytic process Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of glycolysis. up regulation of glycolysis up-regulation of glycolysis upregulation of glycolysis activation of glycolysis stimulation of glycolysis biological_process GO:0045821 positive regulation of glycolytic process Any process that activates or increases the frequency, rate or extent of glycolysis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction. down regulation of heart contraction down-regulation of heart contraction downregulation of heart contraction inhibition of heart contraction biological_process negative regulation of cardiac contraction GO:0045822 negative regulation of heart contraction Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of heart contraction. positive regulation of cardiac contraction up regulation of heart contraction up-regulation of heart contraction upregulation of heart contraction activation of heart contraction stimulation of heart contraction biological_process GO:0045823 positive regulation of heart contraction Any process that activates or increases the frequency, rate or extent of heart contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response. down regulation of innate immune response down-regulation of innate immune response downregulation of innate immune response inhibition of innate immune response biological_process GO:0045824 negative regulation of innate immune response Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid. down regulation of isoprenoid metabolic process down-regulation of isoprenoid metabolic process downregulation of isoprenoid metabolic process negative regulation of isoprenoid metabolism inhibition of isoprenoid metabolic process biological_process GO:0045827 negative regulation of isoprenoid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid. positive regulation of isoprenoid metabolism up regulation of isoprenoid metabolic process up-regulation of isoprenoid metabolic process upregulation of isoprenoid metabolic process activation of isoprenoid metabolic process stimulation of isoprenoid metabolic process biological_process GO:0045828 positive regulation of isoprenoid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching. down regulation of isotype switching down-regulation of isotype switching downregulation of isotype switching negative regulation of class switch recombination negative regulation of class switching negative regulation of isotype switch recombination inhibition of isotype switching biological_process GO:0045829 negative regulation of isotype switching Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching. GOC:go_curators Any process that activates or increases the frequency, rate or extent of isotype switching. positive regulation of class switch recombination positive regulation of class switching positive regulation of isotype switch recombination up regulation of isotype switching up-regulation of isotype switching upregulation of isotype switching activation of isotype switching stimulation of isotype switching biological_process GO:0045830 positive regulation of isotype switching Any process that activates or increases the frequency, rate or extent of isotype switching. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. down regulation of lipid metabolic process down-regulation of lipid metabolic process downregulation of lipid metabolic process negative regulation of lipid metabolism inhibition of lipid metabolic process biological_process GO:0045833 negative regulation of lipid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. positive regulation of lipid metabolism up regulation of lipid metabolic process up-regulation of lipid metabolic process upregulation of lipid metabolic process activation of lipid metabolic process stimulation of lipid metabolic process biological_process GO:0045834 positive regulation of lipid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis. down regulation of meiosis down-regulation of meiosis downregulation of meiosis negative regulation of meiosis inhibition of meiosis biological_process GO:0045835 negative regulation of meiotic nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis. GOC:go_curators Any process that activates or increases the frequency, rate or extent of meiosis. positive regulation of meiosis up regulation of meiosis up-regulation of meiosis upregulation of meiosis activation of meiosis stimulation of meiosis biological_process GO:0045836 positive regulation of meiotic nuclear division Any process that activates or increases the frequency, rate or extent of meiosis. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. down regulation of mitosis down-regulation of mitosis downregulation of mitosis negative regulation of mitosis inhibition of mitosis biological_process GO:0045839 negative regulation of mitotic nuclear division Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother. GOC:dph GOC:go_curators GOC:tb Any process that activates or increases the frequency, rate or extent of mitosis. positive regulation of mitosis up regulation of mitosis up-regulation of mitosis upregulation of mitosis activation of mitosis mitogenic activity stimulation of mitosis biological_process GO:0045840 positive regulation of mitotic nuclear division Any process that activates or increases the frequency, rate or extent of mitosis. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. down regulation of proteolysis down-regulation of proteolysis downregulation of proteolysis negative regulation of peptidolysis inhibition of proteolysis biological_process GO:0045861 negative regulation of proteolysis Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. positive regulation of peptidolysis up regulation of proteolysis up-regulation of proteolysis upregulation of proteolysis activation of proteolysis stimulation of proteolysis biological_process GO:0045862 positive regulation of proteolysis Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. down regulation of translational elongation down-regulation of translational elongation downregulation of translational elongation inhibition of translational elongation biological_process GO:0045900 negative regulation of translational elongation Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. GOC:go_curators Any process that activates or increases the frequency, rate or extent of translational elongation. up regulation of translational elongation up-regulation of translational elongation upregulation of translational elongation activation of translational elongation stimulation of translational elongation biological_process GO:0045901 positive regulation of translational elongation Any process that activates or increases the frequency, rate or extent of translational elongation. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination. down regulation of DNA recombination down-regulation of DNA recombination downregulation of DNA recombination inhibition of DNA recombination biological_process GO:0045910 negative regulation of DNA recombination Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination. GOC:go_curators Any process that activates or increases the frequency, rate or extent of DNA recombination. up regulation of DNA recombination up-regulation of DNA recombination upregulation of DNA recombination activation of DNA recombination stimulation of DNA recombination biological_process GO:0045911 positive regulation of DNA recombination Any process that activates or increases the frequency, rate or extent of DNA recombination. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. down regulation of carbohydrate metabolic process down-regulation of carbohydrate metabolic process downregulation of carbohydrate metabolic process negative regulation of carbohydrate metabolism inhibition of carbohydrate metabolic process biological_process GO:0045912 negative regulation of carbohydrate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. positive regulation of carbohydrate metabolism up regulation of carbohydrate metabolic process up-regulation of carbohydrate metabolic process upregulation of carbohydrate metabolic process activation of carbohydrate metabolic process stimulation of carbohydrate metabolic process biological_process GO:0045913 positive regulation of carbohydrate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. down regulation of fatty acid metabolic process down-regulation of fatty acid metabolic process downregulation of fatty acid metabolic process negative regulation of fatty acid metabolism inhibition of fatty acid metabolic process biological_process GO:0045922 negative regulation of fatty acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. positive regulation of fatty acid metabolism up regulation of fatty acid metabolic process up-regulation of fatty acid metabolic process upregulation of fatty acid metabolic process activation of fatty acid metabolic process stimulation of fatty acid metabolic process biological_process GO:0045923 positive regulation of fatty acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. down regulation of growth down-regulation of growth downregulation of growth inhibition of growth biological_process GO:0045926 negative regulation of growth Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. up regulation of growth up-regulation of growth upregulation of growth activation of growth stimulation of growth biological_process GO:0045927 positive regulation of growth Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. down regulation of progression through mitotic cell cycle down-regulation of progression through mitotic cell cycle downregulation of progression through mitotic cell cycle negative regulation of mitotic cell cycle progression negative regulation of progression through mitotic cell cycle inhibition of progression through mitotic cell cycle biological_process GO:0045930 negative regulation of mitotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb negative regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. positive regulation of mitotic cell cycle progression positive regulation of progression through mitotic cell cycle up regulation of progression through mitotic cell cycle up-regulation of progression through mitotic cell cycle upregulation of progression through mitotic cell cycle activation of progression through mitotic cell cycle stimulation of progression through mitotic cell cycle biological_process GO:0045931 positive regulation of mitotic cell cycle Any process that activates or increases the rate or extent of progression through the mitotic cell cycle. GOC:dph GOC:go_curators GOC:tb positive regulation of progression through mitotic cell cycle GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction. down regulation of muscle contraction down-regulation of muscle contraction downregulation of muscle contraction inhibition of muscle contraction biological_process GO:0045932 negative regulation of muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of muscle contraction. up regulation of muscle contraction up-regulation of muscle contraction upregulation of muscle contraction activation of muscle contraction stimulation of muscle contraction biological_process GO:0045933 positive regulation of muscle contraction Any process that activates or increases the frequency, rate or extent of muscle contraction. GOC:go_curators Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045934 negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045935 positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. down regulation of phosphate metabolic process down-regulation of phosphate metabolic process downregulation of phosphate metabolic process negative regulation of phosphate metabolism inhibition of phosphate metabolic process biological_process GO:0045936 negative regulation of phosphate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. positive regulation of phosphate metabolism up regulation of phosphate metabolic process up-regulation of phosphate metabolic process upregulation of phosphate metabolic process activation of phosphate metabolic process stimulation of phosphate metabolic process biological_process GO:0045937 positive regulation of phosphate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. down regulation of steroid metabolic process down-regulation of steroid metabolic process downregulation of steroid metabolic process negative regulation of steroid metabolism inhibition of steroid metabolic process biological_process GO:0045939 negative regulation of steroid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. positive regulation of steroid metabolism up regulation of steroid metabolic process up-regulation of steroid metabolic process upregulation of steroid metabolic process activation of steroid metabolic process stimulation of steroid metabolic process biological_process GO:0045940 positive regulation of steroid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleotides. down regulation of nucleotide metabolic process down-regulation of nucleotide metabolic process downregulation of nucleotide metabolic process negative regulation of nucleotide metabolism inhibition of nucleotide metabolic process biological_process GO:0045980 negative regulation of nucleotide metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleotides. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleotides. positive regulation of nucleotide metabolism up regulation of nucleotide metabolic process up-regulation of nucleotide metabolic process upregulation of nucleotide metabolic process activation of nucleotide metabolic process stimulation of nucleotide metabolic process biological_process GO:0045981 positive regulation of nucleotide metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleotides. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases. down regulation of purine base metabolic process down-regulation of purine base metabolic process downregulation of purine base metabolic process negative regulation of purine base metabolic process negative regulation of purine base metabolism inhibition of purine base metabolic process biological_process GO:0045982 negative regulation of purine nucleobase metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases. GOC:go_curators negative regulation of purine base metabolic process GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving purine bases. positive regulation of purine base metabolic process positive regulation of purine base metabolism up regulation of purine base metabolic process up-regulation of purine base metabolic process upregulation of purine base metabolic process activation of purine base metabolic process stimulation of purine base metabolic process biological_process GO:0045983 positive regulation of purine nucleobase metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving purine bases. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction. down regulation of smooth muscle contraction down-regulation of smooth muscle contraction downregulation of smooth muscle contraction inhibition of smooth muscle contraction biological_process smooth muscle relaxation GO:0045986 negative regulation of smooth muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of smooth muscle contraction. up regulation of smooth muscle contraction up-regulation of smooth muscle contraction upregulation of smooth muscle contraction activation of smooth muscle contraction stimulation of smooth muscle contraction biological_process GO:0045987 positive regulation of smooth muscle contraction Any process that activates or increases the frequency, rate or extent of smooth muscle contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction. down regulation of striated muscle contraction down-regulation of striated muscle contraction downregulation of striated muscle contraction inhibition of striated muscle contraction biological_process GO:0045988 negative regulation of striated muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction. GOC:go_curators Any process that activates or increases the frequency, rate or extent of striated muscle contraction. up regulation of striated muscle contraction up-regulation of striated muscle contraction upregulation of striated muscle contraction activation of striated muscle contraction stimulation of striated muscle contraction biological_process GO:0045989 positive regulation of striated muscle contraction Any process that activates or increases the frequency, rate or extent of striated muscle contraction. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. down regulation of embryonic development down-regulation of embryonic development downregulation of embryonic development inhibition of embryonic development biological_process GO:0045992 negative regulation of embryonic development Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development. GOC:go_curators Any process that modulates the frequency, rate or extent of embryonic development. biological_process GO:0045995 regulation of embryonic development Any process that modulates the frequency, rate or extent of embryonic development. GOC:go_curators The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate. ADP metabolism biological_process GO:0046031 ADP metabolic process The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate. ADP breakdown ADP catabolism ADP degradation biological_process GO:0046032 ADP catabolic process The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate. GOC:go_curators The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. ATP metabolism biological_process GO:0046034 ATP metabolic process The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. positive regulation of vitamin metabolism up regulation of vitamin metabolic process up-regulation of vitamin metabolic process upregulation of vitamin metabolic process activation of vitamin metabolic process stimulation of vitamin metabolic process biological_process GO:0046136 positive regulation of vitamin metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. down regulation of vitamin metabolic process down-regulation of vitamin metabolic process downregulation of vitamin metabolic process negative regulation of vitamin metabolism inhibition of vitamin metabolic process biological_process GO:0046137 negative regulation of vitamin metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. GOC:ai The directed movement of the hexose monosaccharide glucose into a cell or organelle. Wikipedia:Glucose_uptake glucose uptake biological_process GO:0046323 glucose import The directed movement of the hexose monosaccharide glucose into a cell or organelle. GOC:ai glucose uptake GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. regulation of glucose uptake biological_process GO:0046324 regulation of glucose import Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. GOC:ai regulation of glucose uptake GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. down regulation of glucose import down-regulation of glucose import downregulation of glucose import negative regulation of glucose uptake inhibition of glucose import biological_process GO:0046325 negative regulation of glucose import Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. GOC:ai negative regulation of glucose uptake GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. positive regulation of glucose uptake up regulation of glucose import up-regulation of glucose import upregulation of glucose import activation of glucose import stimulation of glucose import biological_process GO:0046326 positive regulation of glucose import Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. GOC:ai GOC:dph GOC:tb positive regulation of glucose uptake GOC:dph GOC:tb The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. carboxylic acid anabolism carboxylic acid biosynthesis carboxylic acid formation carboxylic acid synthesis biological_process GO:0046394 carboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups. ISBN:0198506732 The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound. organophosphate breakdown organophosphate catabolism organophosphate degradation biological_process GO:0046434 organophosphate catabolic process The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound. GOC:ai The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198506732 The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide. nicotinamide nucleotide metabolism biological_process GO:0046496 nicotinamide nucleotide metabolic process The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide. ISBN:0198506732 The regulated release of saliva from the salivary glands. In man, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin. Wikipedia:Salivation salivation biological_process GO:0046541 saliva secretion The regulated release of saliva from the salivary glands. In man, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin. GOC:curators UBERON:0001836 Any process that modulates the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046620 regulation of organ growth Any process that modulates the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046621 negative regulation of organ growth Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046622 positive regulation of organ growth Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. biological_process GO:0046649 lymphocyte activation A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. GOC:mgi_curators ISBN:0781735149 Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin. down regulation of insulin secretion down-regulation of insulin secretion downregulation of insulin secretion inhibition of insulin secretion biological_process GO:0046676 negative regulation of insulin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin. GOC:ai The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle breakdown heterocycle catabolism heterocycle degradation biological_process GO:0046700 heterocycle catabolic process The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). GOC:ai The controlled release of acid by a cell or a tissue. biological_process GO:0046717 acid secretion The controlled release of acid by a cell or a tissue. GOC:ai Any process that modulates the frequency, rate or extent of the regulated release of saliva from a cell or a tissue. biological_process GO:0046877 regulation of saliva secretion Any process that modulates the frequency, rate or extent of the regulated release of saliva from a cell or a tissue. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of saliva. up regulation of saliva secretion up-regulation of saliva secretion upregulation of saliva secretion activation of saliva secretion stimulation of saliva secretion biological_process GO:0046878 positive regulation of saliva secretion Any process that activates or increases the frequency, rate or extent of the regulated release of saliva. GOC:ai The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. biological_process GO:0046879 hormone secretion The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. biological_process GO:0046883 regulation of hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. regulation of hormone anabolism regulation of hormone biosynthesis regulation of hormone formation regulation of hormone synthesis biological_process GO:0046885 regulation of hormone biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. positive regulation of hormone anabolism positive regulation of hormone biosynthesis positive regulation of hormone formation positive regulation of hormone synthesis up regulation of hormone biosynthetic process up-regulation of hormone biosynthetic process upregulation of hormone biosynthetic process activation of hormone biosynthetic process stimulation of hormone biosynthetic process biological_process GO:0046886 positive regulation of hormone biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. up regulation of hormone secretion up-regulation of hormone secretion upregulation of hormone secretion activation of hormone secretion stimulation of hormone secretion biological_process GO:0046887 positive regulation of hormone secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell. down regulation of hormone secretion down-regulation of hormone secretion downregulation of hormone secretion inhibition of hormone secretion biological_process GO:0046888 negative regulation of hormone secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. positive regulation of lipid anabolism positive regulation of lipid biosynthesis positive regulation of lipid formation positive regulation of lipid synthesis positive regulation of lipogenesis up regulation of lipid biosynthetic process up-regulation of lipid biosynthetic process upregulation of lipid biosynthetic process activation of lipid biosynthetic process stimulation of lipid biosynthetic process biological_process GO:0046889 positive regulation of lipid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai positive regulation of lipogenesis GOC:sl Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. regulation of lipid anabolism regulation of lipid biosynthesis regulation of lipid formation regulation of lipid synthesis regulation of lipogenesis biological_process GO:0046890 regulation of lipid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai regulation of lipogenesis GOC:sl The controlled release of a substance by a cell or a tissue. biological_process GO:0046903 secretion The controlled release of a substance by a cell or a tissue. GOC:ai The directed movement of substances within a cell. jl 2013-12-18T14:04:50Z GO:1902582 biological_process single organism intracellular transport single-organism intracellular transport GO:0046907 intracellular transport The directed movement of substances within a cell. GOC:ai single organism intracellular transport GOC:TermGenie Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell. biological_process GO:0046928 regulation of neurotransmitter secretion Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter. down regulation of neurotransmitter secretion down-regulation of neurotransmitter secretion downregulation of neurotransmitter secretion conotoxin activity inhibition of neurotransmitter secretion biological_process GO:0046929 negative regulation of neurotransmitter secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter. GOC:ai The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). biological_process GO:0046942 carboxylic acid transport The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). GOC:ai The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism. cellular ketone body metabolism biological_process GO:0046950 cellular ketone body metabolic process The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA. ketone body anabolism ketone body biosynthesis ketone body formation ketone body synthesis biological_process GO:0046951 ketone body biosynthetic process The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA. ISBN:0198506732 The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. somatic stem cell renewal biological_process GO:0048103 somatic stem cell division The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line. GOC:jid ISBN:0582227089 The meiotic divisions undergone by the primary and secondary spermatocytes to produce haploid spermatids. spermatocyte cell division biological_process GO:0048137 spermatocyte division The meiotic divisions undergone by the primary and secondary spermatocytes to produce haploid spermatids. GOC:jid GOC:pr ISBN:0879694238 The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. biological_process Golgi-derived vesicle transport GO:0048193 Golgi vesicle transport The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. GOC:jid ISBN:0716731363 PMID:10219233 The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. Golgi vesicle targeting dictyosome vesicle targeting vesicle targeting, to, from or within dictyosome biological_process GO:0048199 vesicle targeting, to, from or within Golgi The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. regulation of Golgi vesicle targeting biological_process GO:0048209 regulation of vesicle targeting, to, from or within Golgi Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus. GOC:jid GOC:mah ISBN:0716731363 PMID:10219233 Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction. biological_process GO:0048232 male gamete generation Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction. GOC:dph GOC:jid A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium. biological_process sperm activation GO:0048240 Avian spermatozoa do not require a period of capacitation, since they are competent to fertilize the egg without a prolonged sojourn in the oviduct or in a capacitation medium in vitro. Therefore, sperm capacitation can only be applied to Aves to refer to gene products involved in processes that occur prior to sperm being deposited from the avian male. The term cannot apply to processes occurring in the avian female reproductive tract. sperm capacitation A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium. GOC:jid ISBN:978-3-642-58301-8 PMID:11820818 sperm activation PMID:23180860 The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. adrenaline transport biological_process GO:0048241 epinephrine transport The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jid The regulated release of epinephrine by a cell. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system. adrenaline secretion biological_process GO:0048242 epinephrine secretion The regulated release of epinephrine by a cell. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system. GOC:ef GOC:jid The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system. noradrenaline secretion biological_process GO:0048243 norepinephrine secretion The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system. GOC:ef GOC:jid The creation of two or more organelles by division of one organelle. biological_process GO:0048285 organelle fission The creation of two or more organelles by division of one organelle. GOC:jid The process in which the anatomical structures of the mesoderm are generated and organized. biological_process GO:0048332 mesoderm morphogenesis The process in which the anatomical structures of the mesoderm are generated and organized. GOC:go_curators The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. https://github.com/geneontology/go-ontology/issues/24390 biological_process terminal differentiation GO:0048468 cell development The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place. GOC:go_curators terminal differentiation GOC:dph GOC:tb The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state. https://github.com/geneontology/go-ontology/issues/24390 biological_process functional differentiation GO:0048469 cell maturation The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state. GOC:go_curators functional differentiation GOC:dph The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. GO:0009993 GO:0048157 Wikipedia:Oogenesis ovum development biological_process GO:0048477 oogenesis The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster. GOC:kmv GOC:mtg_sensu GOC:pr ovum development Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. https://github.com/geneontology/go-ontology/issues/25943 Wikipedia:Organogenesis development of an organ organogenesis biological_process GO:0048513 animal organ development Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dph GOC:jid The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. spermatid cell differentiation biological_process GO:0048515 spermatid differentiation The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. GOC:dph GOC:jid Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. up regulation of behavior up-regulation of behavior upregulation of behavior activation of behavior stimulation of behavior biological_process GO:0048520 positive regulation of behavior Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. GOC:jid GOC:pr Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. down regulation of behavior down-regulation of behavior downregulation of behavior inhibition of behavior biological_process GO:0048521 negative regulation of behavior Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. GOC:jid GOC:pr Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. biological_process GO:0048580 regulation of post-embryonic development Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. down regulation of post-embryonic development down-regulation of post-embryonic development downregulation of post-embryonic development inhibition of post-embryonic development biological_process GO:0048581 negative regulation of post-embryonic development Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. GOC:jid Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. up regulation of post-embryonic development up-regulation of post-embryonic development upregulation of post-embryonic development activation of post-embryonic development stimulation of post-embryonic development biological_process GO:0048582 positive regulation of post-embryonic development Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. GOC:jid Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. biological_process GO:0048583 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process GO:0048584 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process GO:0048585 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. biological_process GO:0048589 developmental growth The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. GOC:go_curators The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. GO:0048828 embryonic anatomical structure morphogenesis biological_process GO:0048598 embryonic morphogenesis The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants. GOC:jid GOC:mtg_sensu embryonic anatomical structure morphogenesis GOC:dph GOC:tb The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. organismal reproductive process reproductive process in a multicellular organism biological_process GO:0048609 multicellular organismal reproductive process The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs. GOC:dph GOC:jid GOC:tb Any process that modulates the frequency, rate or extent of developmental growth. biological_process GO:0048638 regulation of developmental growth Any process that modulates the frequency, rate or extent of developmental growth. GOC:go_curators Any process that activates, maintains or increases the rate of developmental growth. up regulation of developmental growth up-regulation of developmental growth upregulation of developmental growth activation of developmental growth stimulation of developmental growth biological_process GO:0048639 positive regulation of developmental growth Any process that activates, maintains or increases the rate of developmental growth. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth. down regulation of developmental growth down-regulation of developmental growth downregulation of developmental growth inhibition of developmental growth biological_process GO:0048640 negative regulation of developmental growth Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth. GOC:go_curators The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. formation of an anatomical structure involved in morphogenesis biological_process GO:0048646 Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. anatomical structure formation involved in morphogenesis The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GOC:dph GOC:jid GOC:tb formation of an anatomical structure involved in morphogenesis GOC:dph GOC:tb The process in which the anatomical structures of the skeleton are generated and organized. skeletal morphogenesis biological_process GO:0048705 skeletal system morphogenesis The process in which the anatomical structures of the skeleton are generated and organized. GOC:dph GOC:dsf GOC:jid GOC:tb skeletal morphogenesis GOC:dph GOC:tb The process in which the anatomical structures of a tissue are generated and organized. biological_process GO:0048729 tissue morphogenesis The process in which the anatomical structures of a tissue are generated and organized. GOC:dph GOC:jid The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process GO:0048731 system development The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:dph GOC:jid The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion. biological_process GO:0048732 gland development The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion. GOC:jid The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder. biological_process tubulogenesis GO:0048754 branching morphogenesis of an epithelial tube The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder. GOC:dgh GOC:dph GOC:jid tubulogenesis GOC:dph GOC:tb A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. cellular_component GO:0048770 pigment granule A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes. GOC:jid GOC:mh The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. https://github.com/geneontology/go-ontology/issues/26424 development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. https://github.com/geneontology/go-ontology/issues/19809 cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. biological_process GO:0048871 multicellular organismal-level homeostasis Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. GOC:isa_complete Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. https://github.com/geneontology/go-ontology/issues/24218 cell population homeostasis homeostasis of cell number biological_process GO:0048872 homeostasis of number of cells Any biological process involved in the maintenance of the steady-state number of cells within a population of cells. GOC:isa_complete homeostasis of cell number GOC:dph Any biological process involved in the maintenance of an internal steady state of a chemical. biological_process GO:0048878 chemical homeostasis Any biological process involved in the maintenance of an internal steady state of a chemical. GOC:isa_complete The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. biological_process GO:0050432 catecholamine secretion The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:ai GOC:ef Any process that modulates the frequency, rate or extent of the regulated release of catecholamines. biological_process GO:0050433 regulation of catecholamine secretion Any process that modulates the frequency, rate or extent of the regulated release of catecholamines. GOC:ai The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. biological_process GO:0050673 epithelial cell proliferation The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances. ISBN:0721662544 Any process that modulates the frequency, rate or extent of epithelial cell proliferation. biological_process GO:0050678 regulation of epithelial cell proliferation Any process that modulates the frequency, rate or extent of epithelial cell proliferation. GOC:ai Any process that activates or increases the rate or extent of epithelial cell proliferation. up regulation of epithelial cell proliferation up-regulation of epithelial cell proliferation upregulation of epithelial cell proliferation activation of epithelial cell proliferation stimulation of epithelial cell proliferation biological_process GO:0050679 positive regulation of epithelial cell proliferation Any process that activates or increases the rate or extent of epithelial cell proliferation. GOC:ai Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. down regulation of epithelial cell proliferation down-regulation of epithelial cell proliferation downregulation of epithelial cell proliferation inhibition of epithelial cell proliferation biological_process GO:0050680 negative regulation of epithelial cell proliferation Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. biological_process GO:0050708 regulation of protein secretion Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. down regulation of protein secretion down-regulation of protein secretion downregulation of protein secretion inhibition of protein secretion biological_process GO:0050709 negative regulation of protein secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. up regulation of protein secretion up-regulation of protein secretion upregulation of protein secretion activation of protein secretion stimulation of protein secretion biological_process GO:0050714 positive regulation of protein secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. biological_process GO:0050727 regulation of inflammatory response Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. GO:0030236 anti-inflammatory response down regulation of inflammatory response down-regulation of inflammatory response downregulation of inflammatory response inhibition of inflammatory response biological_process GO:0050728 negative regulation of inflammatory response Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. GOC:ai Any process that activates or increases the frequency, rate or extent of the inflammatory response. up regulation of inflammatory response up-regulation of inflammatory response upregulation of inflammatory response activation of inflammatory response stimulation of inflammatory response biological_process GO:0050729 positive regulation of inflammatory response Any process that activates or increases the frequency, rate or extent of the inflammatory response. GOC:ai Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material. biological_process GO:0050764 regulation of phagocytosis Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis. down regulation of phagocytosis down-regulation of phagocytosis downregulation of phagocytosis inhibition of phagocytosis biological_process GO:0050765 negative regulation of phagocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis. GOC:ai Any process that activates or increases the frequency, rate or extent of phagocytosis. up regulation of phagocytosis up-regulation of phagocytosis upregulation of phagocytosis activation of phagocytosis stimulation of phagocytosis biological_process GO:0050766 positive regulation of phagocytosis Any process that activates or increases the frequency, rate or extent of phagocytosis. GOC:ai Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. biological_process GO:0050776 regulation of immune response Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. down regulation of immune response down-regulation of immune response downregulation of immune response inhibition of immune response biological_process GO:0050777 negative regulation of immune response Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. up regulation of immune response up-regulation of immune response upregulation of immune response stimulation of immune response biological_process GO:0050778 positive regulation of immune response Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. GOC:ai Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the activity of an enzyme. GO:0048552 regulation of enzyme activity regulation of metalloenzyme activity biological_process GO:0050790 regulation of catalytic activity Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). biological_process GO:0050793 regulation of developmental process Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:go_curators Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. regulation of behaviour biological_process GO:0050795 regulation of behavior Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. GOC:go_curators GOC:pr Any process that modulates the frequency, rate or extent of the regulated release of insulin. biological_process GO:0050796 regulation of insulin secretion Any process that modulates the frequency, rate or extent of the regulated release of insulin. GOC:ai Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. https://github.com/geneontology/go-ontology/issues/24455 GO:2000021 ion homeostasis biological_process electrolyte homeostasis negative regulation of crystal formation regulation of ion homeostasis GO:0050801 monoatomic ion homeostasis Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GOC:ai Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. modulation of synaptic transmission regulation of chemical synaptic transmission regulation of synaptic transmission biological_process GO:0050804 modulation of chemical synaptic transmission Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. down regulation of synaptic transmission down-regulation of synaptic transmission downregulation of synaptic transmission inhibition of synaptic transmission biological_process GO:0050805 negative regulation of synaptic transmission Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. GOC:ai Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. up regulation of synaptic transmission up-regulation of synaptic transmission upregulation of synaptic transmission activation of synaptic transmission stimulation of synaptic transmission biological_process GO:0050806 positive regulation of synaptic transmission Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. regulation of steroid anabolism regulation of steroid biosynthesis regulation of steroid formation regulation of steroid synthesis regulation of steroidogenesis biological_process GO:0050810 regulation of steroid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. GOC:ai The process in which a fluid solution, or part of it, changes into a solid or semisolid mass. clotting biological_process GO:0050817 coagulation The process in which a fluid solution, or part of it, changes into a solid or semisolid mass. ISBN:0198506732 Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass. regulation of clotting biological_process GO:0050818 regulation of coagulation Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation. down regulation of coagulation down-regulation of coagulation downregulation of coagulation negative regulation of clotting inhibition of coagulation biological_process anticoagulant activity GO:0050819 negative regulation of coagulation Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation. GOC:ai Any process that activates or increases the frequency, rate or extent of coagulation. positive regulation of clotting up regulation of coagulation up-regulation of coagulation upregulation of coagulation activation of coagulation stimulation of coagulation biological_process GO:0050820 positive regulation of coagulation Any process that activates or increases the frequency, rate or extent of coagulation. GOC:ai Any process that modulates the frequency, rate or extent of T cell activation. regulation of T lymphocyte activation regulation of T-cell activation regulation of T-lymphocyte activation biological_process GO:0050863 regulation of T cell activation Any process that modulates the frequency, rate or extent of T cell activation. GOC:ai Any process that modulates the frequency, rate or extent of B cell activation. regulation of B lymphocyte activation regulation of B-cell activation regulation of B-lymphocyte activation biological_process GO:0050864 regulation of B cell activation Any process that modulates the frequency, rate or extent of B cell activation. GOC:ai Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. biological_process GO:0050865 regulation of cell activation Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation. down regulation of cell activation down-regulation of cell activation downregulation of cell activation inhibition of cell activation biological_process GO:0050866 negative regulation of cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of activation. up regulation of cell activation up-regulation of cell activation upregulation of cell activation activation of cell activation stimulation of cell activation biological_process GO:0050867 positive regulation of cell activation Any process that activates or increases the frequency, rate or extent of activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation. down regulation of T cell activation down-regulation of T cell activation downregulation of T cell activation negative regulation of T lymphocyte activation negative regulation of T-cell activation negative regulation of T-lymphocyte activation inhibition of T cell activation biological_process GO:0050868 negative regulation of T cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation. down regulation of B cell activation down-regulation of B cell activation downregulation of B cell activation negative regulation of B lymphocyte activation negative regulation of B-cell activation negative regulation of B-lymphocyte activation inhibition of B cell activation biological_process GO:0050869 negative regulation of B cell activation Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of T cell activation. positive regulation of T lymphocyte activation positive regulation of T-cell activation positive regulation of T-lymphocyte activation up regulation of T cell activation up-regulation of T cell activation upregulation of T cell activation activation of T cell activation stimulation of T cell activation biological_process GO:0050870 positive regulation of T cell activation Any process that activates or increases the frequency, rate or extent of T cell activation. GOC:ai Any process that activates or increases the frequency, rate or extent of B cell activation. positive regulation of B lymphocyte activation positive regulation of B-cell activation positive regulation of B-lymphocyte activation up regulation of B cell activation up-regulation of B cell activation upregulation of B cell activation activation of B cell activation stimulation of B cell activation biological_process GO:0050871 positive regulation of B cell activation Any process that activates or increases the frequency, rate or extent of B cell activation. GOC:ai A organ system process carried out by any of the organs or tissues of neurological system. https://github.com/geneontology/go-ontology/issues/13824 neurological system process neurophysiological process biological_process pan-neural process GO:0050877 nervous system process A organ system process carried out by any of the organs or tissues of neurological system. GOC:ai GOC:mtg_cardio Any process that modulates the levels of body fluids. biological_process GO:0050878 regulation of body fluid levels Any process that modulates the levels of body fluids. GOC:ai GOC:dph GOC:tb Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. biological_process GO:0050879 multicellular organismal movement Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism. GOC:dph GOC:mtg_muscle GOC:tb The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system. biological_process GO:0050881 musculoskeletal movement The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system. GOC:dph The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system that can be controlled at will. biological_process GO:0050882 voluntary musculoskeletal movement The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system that can be controlled at will. GOC:dph Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors. biological_process regulation of balance GO:0050885 neuromuscular process controlling balance Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors. GOC:ai GOC:dph The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. endocrine physiological process endocrine physiology biological_process GO:0050886 endocrine process The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. ISBN:0721662544 The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory. Wikipedia:Cognition biological_process GO:0050890 cognition The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory. ISBN:0721619908 A chemical homeostatic process involved in the maintenance of a steady state level of water within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell. https://github.com/geneontology/go-ontology/issues/24554 multicellular organismal water homeostasis biological_process body fluid osmoregulation GO:0050891 multicellular organismal-level water homeostasis A chemical homeostatic process involved in the maintenance of a steady state level of water within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell. GOC:dph GOC:tb body fluid osmoregulation GOC:dph GOC:tb Any process in which nutrients are taken up from the contents of the intestine. biological_process GO:0050892 intestinal absorption Any process in which nutrients are taken up from the contents of the intestine. GOC:ai GOC:dph Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf The movement of a leukocyte within or between different tissues and organs of the body. immune cell migration immune cell trafficking leucocyte migration leucocyte trafficking leukocyte trafficking biological_process GO:0050900 leukocyte migration The movement of a leukocyte within or between different tissues and organs of the body. GOC:add ISBN:0781735149 PMID:14680625 PMID:14708592 PMID:7507411 PMID:8600538 Any process pertaining to the functions of the nervous and muscular systems of an organism. neuromotor process neuromuscular physiological process biological_process GO:0050905 neuromuscular process Any process pertaining to the functions of the nervous and muscular systems of an organism. GOC:ai The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. Wikipedia:Transduction_(physiology) sensory detection of stimulus sensory perception, sensory transduction of stimulus sensory perception, stimulus detection sensory transduction biological_process GO:0050906 detection of stimulus involved in sensory perception The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal. GOC:ai GOC:dos GOC:dph The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of chemical stimulus sensory detection of chemical stimulus during sensory perception sensory perception, sensory detection of chemical stimulus sensory perception, sensory transduction of chemical stimulus sensory transduction of chemical stimulus sensory transduction of chemical stimulus during sensory perception biological_process GO:0050907 detection of chemical stimulus involved in sensory perception The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. sensory detection of light during visual perception sensory detection of light stimulus during visual perception sensory transduction of light during visual perception sensory transduction of light stimulus during visual perception visual perception, detection of light stimulus visual perception, sensory transduction during perception of light visual perception, sensory transduction of light stimulus biological_process GO:0050908 detection of light stimulus involved in visual perception The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. GOC:ai GOC:dos The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process. Wikipedia:Taste gustation sense of taste taste taste perception biological_process GO:0050909 sensory perception of taste The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process. GOC:ai The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal. GO:0009592 GO:0055128 detection of sound hearing, sensory transduction of sound perception of sound, detection of mechanical stimulus perception of sound, sensory detection of mechanical stimulus perception of sound, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during perception of sound sensory transduction of mechanical stimulus during perception of sound sensory transduction of sound biological_process GO:0050910 detection of mechanical stimulus involved in sensory perception of sound The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal. GOC:ai The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. perception of smell, detection of chemical stimulus perception of smell, sensory detection of chemical stimulus perception of smell, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of smell sensory detection of scent sensory detection of smell sensory transduction of chemical stimulus during perception of smell sensory transduction of scent sensory transduction of smell biological_process GO:0050911 detection of chemical stimulus involved in sensory perception of smell The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal. GOC:ai The series of events involved in the perception of taste in which a gustatory chemical stimulus is received and converted into a molecular signal. taste perception perception of taste, detection of chemical stimulus perception of taste, sensory detection of chemical stimulus perception of taste, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of taste sensory detection of taste sensory transduction of chemical stimulus during perception of taste sensory transduction of taste biological_process GO:0050912 detection of chemical stimulus involved in sensory perception of taste The series of events involved in the perception of taste in which a gustatory chemical stimulus is received and converted into a molecular signal. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. biological_process GO:0050920 regulation of chemotaxis Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. up regulation of chemotaxis up-regulation of chemotaxis upregulation of chemotaxis activation of chemotaxis stimulation of chemotaxis biological_process GO:0050921 positive regulation of chemotaxis Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. down regulation of chemotaxis down-regulation of chemotaxis downregulation of chemotaxis inhibition of chemotaxis biological_process GO:0050922 negative regulation of chemotaxis Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient. GOC:ai The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. biological_process GO:0050953 sensory perception of light stimulus The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. mechanosensory perception perception of mechanical stimulus biological_process chemi-mechanical coupling GO:0050954 sensory perception of mechanical stimulus The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GOC:ai The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion. Wikipedia:Equilibrioception sensory perception of orientation with respect to gravity biological_process GO:0050957 equilibrioception The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion. http://www.medterms.com The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light. sensory detection of light stimulus sensory detection of light stimulus during sensory perception sensory perception, sensory detection of light stimulus sensory perception, sensory transduction of light stimulus sensory transduction of light stimulus sensory transduction of light stimulus during sensory perception biological_process GO:0050962 detection of light stimulus involved in sensory perception The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light. GOC:ai GOC:dos The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal. perception of pain, detection of mechanical stimulus perception of pain, sensory detection of mechanical stimulus perception of pain, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during perception of pain sensory transduction of mechanical stimulus during perception of pain biological_process mechanical nociception GO:0050966 detection of mechanical stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos mechanical nociception GOC:pr The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal. perception of pain, detection of chemical stimulus perception of pain, sensory detection of chemical stimulus perception of pain, sensory transduction of chemical stimulus sensory detection of chemical stimulus during perception of pain sensory transduction of chemical stimulus during perception of pain biological_process chemical nociception GO:0050968 detection of chemical stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal. GOC:ai chemical nociception GOC:pr The series of events involved in equilibrioception in which a mechanical stimulus is received and converted into a molecular signal. During equilibrioception, mechanical stimuli may be in the form of input from pressure receptors or from the labyrinth system of the inner ears. equilibrioception, detection of mechanical stimulus equilibrioception, sensory detection of mechanical stimulus equilibrioception, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during equilibrioception sensory transduction of mechanical stimulus during equilibrioception biological_process GO:0050973 detection of mechanical stimulus involved in equilibrioception The series of events involved in equilibrioception in which a mechanical stimulus is received and converted into a molecular signal. During equilibrioception, mechanical stimuli may be in the form of input from pressure receptors or from the labyrinth system of the inner ears. GOC:ai GOC:dos The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception. sensory detection of mechanical stimulus sensory detection of mechanical stimulus during sensory perception sensory perception, sensory detection of mechanical stimulus sensory perception, sensory transduction of mechanical stimulus sensory transduction of mechanical stimulus sensory transduction of mechanical stimulus during sensory perception biological_process GO:0050974 detection of mechanical stimulus involved in sensory perception The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception. GOC:ai GOC:dos The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach). Wikipedia:Touch perception of touch tactile sense taction tactition biological_process GO:0050975 sensory perception of touch The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach). GOC:ai The series of events involved in the perception of touch in which a mechanical stimulus is received and converted into a molecular signal. perception of touch, detection of mechanical stimulus perception of touch, sensory detection of mechanical stimulus perception of touch, sensory transduction of mechanical stimulus sensory detection of mechanical stimulus during perception of touch sensory transduction of mechanical stimulus during perception of touch tactition, sensory detection of mechanical stimulus biological_process GO:0050976 detection of mechanical stimulus involved in sensory perception of touch The series of events involved in the perception of touch in which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos The series of events by which a mechanical stimulus is received and converted into a molecular signal. biological_process GO:0050982 detection of mechanical stimulus The series of events by which a mechanical stimulus is received and converted into a molecular signal. GOC:ai GOC:dos Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. biological_process GO:0051046 regulation of secretion Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. up regulation of secretion up-regulation of secretion upregulation of secretion activation of secretion stimulation of secretion biological_process GO:0051047 positive regulation of secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. down regulation of secretion down-regulation of secretion downregulation of secretion inhibition of secretion biological_process GO:0051048 negative regulation of secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051049 regulation of transport Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process GO:0051050 positive regulation of transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolism biological_process GO:0051052 regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. down regulation of DNA metabolic process down-regulation of DNA metabolic process downregulation of DNA metabolic process negative regulation of DNA metabolism inhibition of DNA metabolic process biological_process GO:0051053 negative regulation of DNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. positive regulation of DNA metabolism up regulation of DNA metabolic process up-regulation of DNA metabolic process upregulation of DNA metabolic process activation of DNA metabolic process stimulation of DNA metabolic process biological_process GO:0051054 positive regulation of DNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. down regulation of lipid biosynthetic process down-regulation of lipid biosynthetic process downregulation of lipid biosynthetic process negative regulation of lipid anabolism negative regulation of lipid biosynthesis negative regulation of lipid formation negative regulation of lipid synthesis negative regulation of lipogenesis inhibition of lipid biosynthetic process biological_process GO:0051055 negative regulation of lipid biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GOC:ai negative regulation of lipogenesis GOC:sl Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). down regulation of developmental process down-regulation of developmental process downregulation of developmental process inhibition of developmental process biological_process GO:0051093 negative regulation of developmental process Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). up regulation of developmental process up-regulation of developmental process upregulation of developmental process activation of developmental process stimulation of developmental process biological_process GO:0051094 positive regulation of developmental process Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. regulation of cellular component organisation biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis GO:0051128 regulation of cellular component organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai regulation of cell organisation GOC:mah regulation of cell organization GOC:mah regulation of cellular component organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. down regulation of cell organization down-regulation of cell organization downregulation of cell organization inhibition of cell organization biological_process negative regulation of cell organisation negative regulation of cellular component organization and biogenesis GO:0051129 negative regulation of cellular component organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai negative regulation of cell organisation GOC:mah negative regulation of cellular component organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. positive regulation of cell organisation up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis GO:0051130 positive regulation of cellular component organization Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai positive regulation of cellular component organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process GO:0051171 regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism inhibition of nitrogen metabolic process biological_process GO:0051172 negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process activation of nitrogen metabolic process stimulation of nitrogen metabolic process biological_process GO:0051173 positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. regulation of phosphorus metabolism biological_process GO:0051174 regulation of phosphorus metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. down regulation of sulfur metabolic process down-regulation of sulfur metabolic process downregulation of sulfur metabolic process negative regulation of sulfur metabolism negative regulation of sulphur metabolic process negative regulation of sulphur metabolism inhibition of sulfur metabolic process biological_process GO:0051175 negative regulation of sulfur metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. positive regulation of sulfur metabolism positive regulation of sulphur metabolic process positive regulation of sulphur metabolism up regulation of sulfur metabolic process up-regulation of sulfur metabolic process upregulation of sulfur metabolic process activation of sulfur metabolic process stimulation of sulfur metabolic process biological_process GO:0051176 positive regulation of sulfur metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GOC:ai GOC:dos localisation GOC:mah single organism localization GOC:TermGenie The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. Wikipedia:Chondrogenesis cartilage biogenesis cartilage biosynthesis cartilage element development cartilage formation cartilage organ development chondrogenesis biological_process GO:0051216 cartilage development The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:cjm PMID:23251424 Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process GO:0051222 positive regulation of protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051223 regulation of protein transport Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process GO:0051224 negative regulation of protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. https://github.com/geneontology/go-ontology/issues/24200 establishment of localisation biological_process GO:0051234 establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. biological_process GO:0051239 regulation of multicellular organismal process Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. up regulation of multicellular organismal process up-regulation of multicellular organismal process upregulation of multicellular organismal process activation of multicellular organismal process stimulation of multicellular organismal process biological_process GO:0051240 positive regulation of multicellular organismal process Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. down regulation of multicellular organismal process down-regulation of multicellular organismal process downregulation of multicellular organismal process inhibition of multicellular organismal process biological_process GO:0051241 negative regulation of multicellular organismal process Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032268 regulation of protein metabolism biological_process regulation of cellular protein metabolic process regulation of cellular protein metabolism GO:0051246 regulation of protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032270 positive regulation of cellular protein metabolic process positive regulation of cellular protein metabolism positive regulation of protein metabolism up regulation of cellular protein metabolic process up regulation of protein metabolic process up-regulation of cellular protein metabolic process up-regulation of protein metabolic process upregulation of cellular protein metabolic process upregulation of protein metabolic process activation of cellular protein metabolic process activation of protein metabolic process stimulation of cellular protein metabolic process stimulation of protein metabolic process biological_process GO:0051247 positive regulation of protein metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. https://github.com/geneontology/go-ontology/issues/23112 GO:0032269 down regulation of cellular protein metabolic process down regulation of protein metabolic process down-regulation of cellular protein metabolic process down-regulation of protein metabolic process downregulation of cellular protein metabolic process downregulation of protein metabolic process negative regulation of cellular protein metabolic process negative regulation of cellular protein metabolism negative regulation of protein metabolism inhibition of cellular protein metabolic process inhibition of protein metabolic process biological_process GO:0051248 negative regulation of protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. GOC:ai Any process that modulates the frequency, rate or extent of lymphocyte activation. biological_process GO:0051249 regulation of lymphocyte activation Any process that modulates the frequency, rate or extent of lymphocyte activation. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation. down regulation of lymphocyte activation down-regulation of lymphocyte activation downregulation of lymphocyte activation inhibition of lymphocyte activation biological_process GO:0051250 negative regulation of lymphocyte activation Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation. GOC:ai Any process that activates or increases the frequency, rate or extent of lymphocyte activation. up regulation of lymphocyte activation up-regulation of lymphocyte activation upregulation of lymphocyte activation activation of lymphocyte activation stimulation of lymphocyte activation biological_process GO:0051251 positive regulation of lymphocyte activation Any process that activates or increases the frequency, rate or extent of lymphocyte activation. GOC:ai A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. https://github.com/geneontology/go-ontology/issues/22811 https://github.com/geneontology/go-ontology/issues/4585 GO:0006323 GO:0007001 GO:0051277 DNA condensation chromosome organisation DNA packaging biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance GO:0051276 chromosome organization A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. GOC:ai GOC:dph GOC:jl GOC:mah chromosome organization and biogenesis GOC:mah The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. Wikipedia:Cell_division biological_process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GOC:di GOC:go_curators GOC:pr Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. biological_process GO:0051302 regulation of cell division Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells. GOC:go_curators Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. https://github.com/geneontology/go-ontology/issues/24599 GO:0007126 Wikipedia:Meiosis biological_process meiosis GO:0051321 Note that this term should not be confused with 'GO:0140013 ; meiotic nuclear division'. 'GO:0051321 ; meiotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140013 meiotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. meiotic cell cycle Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions. GOC:ai Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. transferase regulator biological_process GO:0051338 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GOC:ai Any process that modulates the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. lyase regulator biological_process GO:0051339 regulation of lyase activity Any process that modulates the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. GOC:ai Any process that modulates the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. oxidoreductase regulator biological_process GO:0051341 regulation of oxidoreductase activity Any process that modulates the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GOC:ai Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. transferase activator up regulation of transferase activity up-regulation of transferase activity upregulation of transferase activity activation of transferase activity stimulation of transferase activity biological_process GO:0051347 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. down regulation of transferase activity down-regulation of transferase activity downregulation of transferase activity transferase inhibitor inhibition of transferase activity biological_process GO:0051348 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that activates or increases the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. lyase activator up regulation of lyase activity up-regulation of lyase activity upregulation of lyase activity activation of lyase activity stimulation of lyase activity biological_process GO:0051349 positive regulation of lyase activity Any process that activates or increases the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. GOC:ai Any process that stops or reduces the rate of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. down regulation of lyase activity down-regulation of lyase activity downregulation of lyase activity lyase inhibitor inhibition of lyase activity biological_process GO:0051350 negative regulation of lyase activity Any process that stops or reduces the rate of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. GOC:ai Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. GO:0009391 oxidoreductase activator up regulation of oxidoreductase activity up-regulation of oxidoreductase activity upregulation of oxidoreductase activity activation of oxidoreductase activity ribonucleotide reductase activating enzyme activity stimulation of oxidoreductase activity biological_process GO:0051353 positive regulation of oxidoreductase activity Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. GOC:ai Any process that stops or reduces the rate of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. down regulation of oxidoreductase activity down-regulation of oxidoreductase activity downregulation of oxidoreductase activity oxidoreductase inhibitor inhibition of oxidoreductase activity biological_process GO:0051354 negative regulation of oxidoreductase activity Any process that stops or reduces the rate of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. GOC:ai The series of events during equilibrioception required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual input plays an important role in the ability of an organism to perceive its orientation with respect to gravity. perception of orientation with respect to gravity by visual perception equilibrioception by visual perception biological_process visual perception during equilibrioception GO:0051356 visual perception involved in equilibrioception The series of events during equilibrioception required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual input plays an important role in the ability of an organism to perceive its orientation with respect to gravity. GOC:ai visual perception during equilibrioception GOC:dph GOC:tb Any process that modulates the rate or extent of progression through the meiotic cell cycle. meiotic cell cycle modulation meiotic cell cycle regulation modulation of meiotic cell cycle progression regulation of meiotic cell cycle progression regulation of progression through meiotic cell cycle biological_process meiotic cell cycle regulator GO:0051445 regulation of meiotic cell cycle Any process that modulates the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. positive regulation of meiotic cell cycle progression positive regulation of progression through meiotic cell cycle up regulation of progression through meiotic cell cycle up-regulation of progression through meiotic cell cycle upregulation of progression through meiotic cell cycle activation of progression through meiotic cell cycle stimulation of progression through meiotic cell cycle biological_process GO:0051446 positive regulation of meiotic cell cycle Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb positive regulation of progression through meiotic cell cycle GOC:dph GOC:tb Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle. down regulation of progression through meiotic cell cycle down-regulation of progression through meiotic cell cycle downregulation of progression through meiotic cell cycle negative regulation of meiotic cell cycle progression negative regulation of progression through meiotic cell cycle inhibition of progression through meiotic cell cycle biological_process GO:0051447 negative regulation of meiotic cell cycle Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle. GOC:ai GOC:dph GOC:tb negative regulation of progression through meiotic cell cycle GOC:dph GOC:tb The regulated release of corticotropin by a cell. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus. ACTH secretion adrenocorticotropic hormone secretion adrenotropic hormone secretion adrenotropin secretion corticotropic hormone secretion biological_process adrenocorticotropin secretion GO:0051458 corticotropin secretion The regulated release of corticotropin by a cell. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus. GOC:cjm PMID:11027914 adrenocorticotropin secretion GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. regulation of ACTH secretion regulation of adrenocorticotropic hormone secretion regulation of adrenocorticotropin secretion regulation of adrenotropin hormone secretion regulation of adrenotropin secretion regulation of corticotropic hormone secretion biological_process GO:0051459 regulation of corticotropin secretion Any process that modulates the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. GOC:ai GOC:dph regulation of adrenocorticotropic hormone secretion GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. down regulation of adrenocorticotropin secretion down-regulation of adrenocorticotropin secretion downregulation of adrenocorticotropin secretion negative regulation of ACTH secretion negative regulation of adrenocorticotropic hormone secretion negative regulation of adrenocorticotropin secretion negative regulation of adrenotropic hormone secretion negative regulation of adrenotropin secretion negative regulation of corticotropic hormone secretion inhibition of adrenocorticotropin secretion biological_process GO:0051460 negative regulation of corticotropin secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of corticotropic hormone from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin hormone from a cell. positive regulation of ACTH secretion positive regulation of adrenocorticotropic hormone secretion positive regulation of adrenocorticotropin secretion positive regulation of adrenotropic hormone secretion positive regulation of adrenotropin secretion positive regulation of corticotropic hormone secretion up regulation of adrenocorticotropin secretion up-regulation of adrenocorticotropin secretion upregulation of adrenocorticotropin secretion activation of adrenocorticotropin secretion stimulation of adrenocorticotropin secretion biological_process GO:0051461 positive regulation of corticotropin secretion Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin hormone from a cell. GOC:ai positive regulation of adrenocorticotropin secretion GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. regulation of cytoskeleton organisation biological_process regulation of cytoskeleton organization and biogenesis GO:0051493 regulation of cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai regulation of cytoskeleton organisation GOC:mah regulation of cytoskeleton organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. down regulation of cytoskeleton organization down-regulation of cytoskeleton organization downregulation of cytoskeleton organization negative regulation of cytoskeleton organisation inhibition of cytoskeleton organization biological_process negative regulation of cytoskeleton organization and biogenesis GO:0051494 negative regulation of cytoskeleton organization Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai negative regulation of cytoskeleton organisation GOC:mah negative regulation of cytoskeleton organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. positive regulation of cytoskeleton organisation up regulation of cytoskeleton organization up-regulation of cytoskeleton organization upregulation of cytoskeleton organization activation of cytoskeleton organization stimulation of cytoskeleton organization biological_process positive regulation of cytoskeleton organization and biogenesis GO:0051495 positive regulation of cytoskeleton organization Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GOC:ai positive regulation of cytoskeleton organisation GOC:mah positive regulation of cytoskeleton organization and biogenesis GOC:mah Any process involved in the maintenance of an internal steady state of calcium ions within the cytoplasm of a cell or between mitochondria and their surroundings. calcium ion homeostasis in mitochondria calcium ion homeostasis in mitochondrion mitochondrial calcium ion concentration regulation regulation of calcium ion concentration in mitochondria regulation of calcium ion concentration in mitochondrion regulation of mitochondrial calcium ion concentration biological_process GO:0051560 mitochondrial calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions within the cytoplasm of a cell or between mitochondria and their surroundings. GOC:ai GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051588 regulation of neurotransmitter transport Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of neurotransmitter transport down-regulation of neurotransmitter transport downregulation of neurotransmitter transport inhibition of neurotransmitter transport biological_process GO:0051589 negative regulation of neurotransmitter transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of neurotransmitter transport up-regulation of neurotransmitter transport upregulation of neurotransmitter transport activation of neurotransmitter transport stimulation of neurotransmitter transport biological_process GO:0051590 positive regulation of neurotransmitter transport Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process leading to the attainment of the full functional capacity of a protein. biological_process GO:0051604 protein maturation Any process leading to the attainment of the full functional capacity of a protein. GOC:ai The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. stimulus detection biological_process perception of stimulus stimulus sensing GO:0051606 detection of stimulus The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal. GOC:add GOC:ai GOC:dph GOC:mah The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans. biological_process GO:0051608 histamine transport The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans. GOC:ai Any process in which an organelle is transported to, and/or maintained in, a specific location. https://github.com/geneontology/go-ontology/issues/19809 establishment and maintenance of organelle localization organelle localisation biological_process GO:0051640 organelle localization Any process in which an organelle is transported to, and/or maintained in, a specific location. GOC:ai organelle localisation GOC:mah A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization GO:0051641 cellular localization A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. GOC:tb GOC:vw cellular localisation GOC:mah single organism cellular localization GOC:TermGenie Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. cytoplasmic vesicle localization establishment and maintenance of vesicle localization vesicle localisation biological_process GO:0051648 vesicle localization Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. GOC:ai vesicle localisation GOC:mah Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization GO:0051649 establishment of localization in cell Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph GOC:tb establishment of localisation in cell GOC:mah establishment of cellular localization GOC:dph GOC:tb The directed movement of a vesicle to a specific location. establishment of vesicle localisation biological_process GO:0051650 establishment of vesicle localization The directed movement of a vesicle to a specific location. GOC:ai establishment of vesicle localisation GOC:mah The directed movement of an organelle to a specific location. establishment of organelle localisation biological_process GO:0051656 establishment of organelle localization The directed movement of an organelle to a specific location. GOC:ai establishment of organelle localisation GOC:mah Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. GO:0009613 GO:0042828 biological_process GO:0051707 response to other organism Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism. GOC:ai Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl Any process that modulates the rate or extent of progression through the cell cycle. GO:0000074 GO:0007050 GO:0071156 GO:0071157 GO:0071158 GO:0071850 cell cycle modulation cell cycle regulation control of cell cycle progression modulation of cell cycle progression regulation of cell cycle progression regulation of progression through cell cycle arrest of mitotic cell cycle progression cell cycle arrest mitotic cell cycle arrest negative regulation of cell cycle arrest positive regulation of cell cycle arrest regulation of cell cycle arrest biological_process cell cycle regulator tumor suppressor GO:0051726 regulation of cell cycle Any process that modulates the rate or extent of progression through the cell cycle. GOC:ai GOC:dph GOC:tb arrest of mitotic cell cycle progression GOC:mah Any process that activates or increases the frequency, rate or extent of cell division. up regulation of cell division up-regulation of cell division upregulation of cell division activation of cell division stimulation of cell division biological_process GO:0051781 positive regulation of cell division Any process that activates or increases the frequency, rate or extent of cell division. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. down regulation of cell division down-regulation of cell division downregulation of cell division inhibition of cell division biological_process GO:0051782 negative regulation of cell division Any process that stops, prevents, or reduces the frequency, rate or extent of cell division. GOC:ai Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. biological_process GO:0051783 regulation of nuclear division Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. down regulation of nuclear division down-regulation of nuclear division downregulation of nuclear division inhibition of nuclear division biological_process GO:0051784 negative regulation of nuclear division Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. up regulation of nuclear division up-regulation of nuclear division upregulation of nuclear division activation of nuclear division stimulation of nuclear division biological_process GO:0051785 positive regulation of nuclear division Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information. GOC:ai Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots. biological_process GO:0051917 regulation of fibrinolysis Any process that modulates the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots. down regulation of fibrinolysis down-regulation of fibrinolysis downregulation of fibrinolysis inhibition of fibrinolysis biological_process GO:0051918 negative regulation of fibrinolysis Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots. up regulation of fibrinolysis up-regulation of fibrinolysis upregulation of fibrinolysis activation of fibrinolysis stimulation of fibrinolysis biological_process GO:0051919 positive regulation of fibrinolysis Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots. GOC:ai Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. biological_process GO:0051930 regulation of sensory perception of pain Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. GOC:ai Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. biological_process GO:0051931 regulation of sensory perception Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. GOC:ai The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. biological_process GO:0051937 catecholamine transport The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine. GOC:ai ISBN:0198506732 Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051952 regulation of amine transport Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of amine transport down-regulation of amine transport downregulation of amine transport inhibition of amine transport biological_process GO:0051953 negative regulation of amine transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of amine transport up-regulation of amine transport upregulation of amine transport activation of amine transport stimulation of amine transport biological_process GO:0051954 positive regulation of amine transport Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. biological_process GO:0051960 regulation of nervous system development Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. down regulation of nervous system development down-regulation of nervous system development downregulation of nervous system development inhibition of nervous system development biological_process GO:0051961 negative regulation of nervous system development Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. up regulation of nervous system development up-regulation of nervous system development upregulation of nervous system development activation of nervous system development stimulation of nervous system development biological_process GO:0051962 positive regulation of nervous system development Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue. GOC:ai Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. regulation of conduction of nerve impulse biological_process GO:0051969 regulation of transmission of nerve impulse Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai regulation of conduction of nerve impulse GOC:dph Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. down regulation of transmission of nerve impulse down-regulation of transmission of nerve impulse downregulation of transmission of nerve impulse negative regulation of conduction of nerve impulse inhibition of transmission of nerve impulse biological_process GO:0051970 negative regulation of transmission of nerve impulse Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai negative regulation of conduction of nerve impulse GOC:dph Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. positive regulation of conduction of nerve impulse up regulation of transmission of nerve impulse up-regulation of transmission of nerve impulse upregulation of transmission of nerve impulse activation of transmission of nerve impulse stimulation of transmission of nerve impulse biological_process GO:0051971 positive regulation of transmission of nerve impulse Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation. GOC:ai positive regulation of conduction of nerve impulse GOC:dph Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. biological_process GO:0051983 regulation of chromosome segregation Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. up regulation of chromosome segregation up-regulation of chromosome segregation upregulation of chromosome segregation activation of chromosome segregation stimulation of chromosome segregation biological_process GO:0051984 positive regulation of chromosome segregation Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. down regulation of chromosome segregation down-regulation of chromosome segregation downregulation of chromosome segregation inhibition of chromosome segregation biological_process GO:0051985 negative regulation of chromosome segregation Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets. GOC:ai Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell. https://github.com/geneontology/go-ontology/issues/26429 phosphate homeostasis Pi homeostasis biological_process GO:0055062 phosphate ion homeostasis Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell. GOC:jid GOC:mah OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell. GO:0055080 biological_process GO:0055067 This term was obsoleted because it is an unnecessary grouping class. obsolete monovalent inorganic cation homeostasis true OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell. GOC:ai GOC:jid GOC:mah OBSOLETE. Any process involved in the maintenance of an internal steady state of zinc ions within an organism or cell. https://github.com/geneontology/go-ontology/issues/24464 GO:0006882 GO:0180002 zinc homeostasis biological_process GO:0055069 The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. For homeostasis terms, we would like to specify whether the homeostasis takes place intracellularly or at the level of the organism. obsolete zinc ion homeostasis true OBSOLETE. Any process involved in the maintenance of an internal steady state of zinc ions within an organism or cell. GOC:ai GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell. regulation of calcium ion concentration biological_process GO:0055074 calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell. GOC:ceb GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of monoatomic cations within an organism or cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom. https://github.com/geneontology/go-ontology/issues/24455 cation homeostasis biological_process GO:0055080 monoatomic cation homeostasis Any process involved in the maintenance of an internal steady state of monoatomic cations within an organism or cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom. GOC:ceb GOC:jid GOC:mah A homeostatic process involved in the maintenance of a steady state level of a chemical within a cell. https://github.com/geneontology/go-ontology/issues/24514 cellular chemical homeostasis biological_process GO:0055082 intracellular chemical homeostasis A homeostatic process involved in the maintenance of a steady state level of a chemical within a cell. GOC:isa_complete GOC:jid The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. tb 2015-10-21T13:22:47Z GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process GO:0055085 Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. transmembrane transport The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GOC:dph GOC:jid The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. nucleobase, nucleoside and nucleotide metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process GO:0055086 nucleobase-containing small molecule metabolic process The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. GOC:vw Any process that modulates the frequency, rate or extent of cardiac muscle contraction. biological_process GO:0055117 regulation of cardiac muscle contraction Any process that modulates the frequency, rate or extent of cardiac muscle contraction. GOC:ecd Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction. biological_process GO:0055118 negative regulation of cardiac muscle contraction Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction. GOC:ecd The transmission of vibrations via ossicles to the inner ear. jid 2009-10-13T10:59:39Z biological_process GO:0055127 vibrational conductance of sound to the inner ear The transmission of vibrations via ossicles to the inner ear. GOC:mh An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness. Wikipedia:Reflex biological_process GO:0060004 reflex An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness. GOC:dph ISBN:0877797099 A reflex process in which a response to an angular or linear acceleration stimulus begins with an afferent nerve impulse from a receptor in the inner ear and ends with the compensatory action of eye muscles. Signaling never reaches a level of consciousness. biological_process GO:0060005 vestibular reflex A reflex process in which a response to an angular or linear acceleration stimulus begins with an afferent nerve impulse from a receptor in the inner ear and ends with the compensatory action of eye muscles. Signaling never reaches a level of consciousness. PMID:11784757 The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. heart beating biological_process cardiac contraction hemolymph circulation GO:0060047 heart contraction The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body. GOC:dph Muscle contraction of cardiac muscle tissue. heart muscle contraction biological_process GO:0060048 cardiac muscle contraction Muscle contraction of cardiac muscle tissue. GOC:dph Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury. biological_process GO:0060054 positive regulation of epithelial cell proliferation involved in wound healing Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury. GOC:dph The regulation of body fluids process in which parasympathetic nerves stimulate the bladder wall muscle to contract and expel urine from the body. Wikipedia:Urination urination urine voiding biological_process GO:0060073 micturition The regulation of body fluids process in which parasympathetic nerves stimulate the bladder wall muscle to contract and expel urine from the body. GOC:dph The process leading to shortening and/or development of tension in the urinary bladder smooth muscle tissue involved in the expulsion urine from the body. biological_process smooth muscle contraction involved in urination urinary bladder smooth muscle contraction involved in micturition GO:0060083 smooth muscle contraction involved in micturition The process leading to shortening and/or development of tension in the urinary bladder smooth muscle tissue involved in the expulsion urine from the body. GOC:dph PMID:15827347 urinary bladder smooth muscle contraction involved in micturition GOC:dph The process of communication from a neuron to a smooth muscle in the bladder that contributes to the expulsion of urine from the body. biological_process synaptic transmission involved in urination GO:0060084 synaptic transmission involved in micturition The process of communication from a neuron to a smooth muscle in the bladder that contributes to the expulsion of urine from the body. GOC:dph PMID:15827347 A compound molecular function in which an effector function is controlled by one or more regulatory components. molecular_function GO:0060089 molecular transducer activity A compound molecular function in which an effector function is controlled by one or more regulatory components. GOC:dos GOC:pdt Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell. biological_process GO:0060123 regulation of growth hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell. GOC:dph Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell. biological_process GO:0060124 positive regulation of growth hormone secretion Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell. GOC:dph Any process that decreases or stops the frequency, rate or extent of the regulated release of growth hormone from a cell. biological_process GO:0060125 negative regulation of growth hormone secretion Any process that decreases or stops the frequency, rate or extent of the regulated release of growth hormone from a cell. GOC:dph A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. biological_process GO:0060136 embryonic process involved in female pregnancy A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. GOC:dph A reflex that occurs in response to suckling, beginning with a nerve impulse from a receptor in the mammary gland and ending with the ejection of milk from the gland. Signaling never reaches a level of consciousness. milk ejection biological_process GO:0060156 milk ejection reflex A reflex that occurs in response to suckling, beginning with a nerve impulse from a receptor in the mammary gland and ending with the ejection of milk from the gland. Signaling never reaches a level of consciousness. GOC:cjm GOC:dph GOC:mr GOC:st Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. biological_process GO:0060255 regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GO:0042384 Reactome:R-HSA-5617833.2 ciliogenesis cilium formation microtubule-based flagellum assembly biological_process cilium biogenesis cilium morphogenesis cilium organization GO:0060271 Note that we deem cilium and microtubule-based flagellum to be equivalent. cilium assembly The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:BHF GOC:cilia GOC:dph GOC:kmv GOC:pr GOC:vw ISBN:0198506732 PMID:13978319 PMID:27350441 Reactome:R-HSA-5617833.2 cilium biogenesis GOC:mah cilium organization GOC:dph Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. biological_process GO:0060284 regulation of cell development Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. GOC:dph GOC:tb Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GO:0071974 cilium cell motility microtubule-based flagellar cell motility biological_process ciliary cell motility GO:0060285 Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent. cilium-dependent cell motility Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. GOC:cilia GOC:dgh GOC:dph GOC:krc GOC:mlg GOC:mtg_cambridge_2013 Movement of cilia mediated by motor proteins that contributes to the movement of a cell. biological_process GO:0060294 cilium movement involved in cell motility Movement of cilia mediated by motor proteins that contributes to the movement of a cell. GOC:BHF GOC:dph GOC:tb Any process that modulates the rate frequency or extent of cilium movement involved in ciliary motility. biological_process GO:0060295 regulation of cilium movement involved in cell motility Any process that modulates the rate frequency or extent of cilium movement involved in ciliary motility. GOC:BHF GOC:dph GOC:tb The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). biological_process GO:0060326 cell chemotaxis The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). GOC:dph Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. regulation of cellular localisation biological_process GO:0060341 regulation of cellular localization Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. GOC:dph GOC:tb regulation of cellular localisation GOC:mah The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. biological_process GO:0060348 bone development The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. GOC:dph The process in which bones are generated and organized. biological_process GO:0060349 bone morphogenesis The process in which bones are generated and organized. GOC:dph The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone. biological_process GO:0060350 endochondral bone morphogenesis The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone. GOC:dph PMID:11680679 The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones. biological_process GO:0060351 cartilage development involved in endochondral bone morphogenesis The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones. GOC:dph Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement. biological_process GO:0060361 flight Self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement. GOC:dph The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060374 mast cell differentiation The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that modulates the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060375 regulation of mast cell differentiation Any process that modulates the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060376 positive regulation of mast cell differentiation Any process that increases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. biological_process GO:0060377 negative regulation of mast cell differentiation Any process that decreases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. GOC:dph GOC:tb The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. biological_process GO:0060429 epithelium development The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. GOC:dph GOC:mtg_lung Any process that increases the frequency, rate or extent of cardiac muscle contraction. biological_process GO:0060452 positive regulation of cardiac muscle contraction Any process that increases the frequency, rate or extent of cardiac muscle contraction. GOC:dph GOC:tb Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. biological_process GO:0060453 regulation of gastric acid secretion Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:dph GOC:tb Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. biological_process GO:0060454 positive regulation of gastric acid secretion Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:dph GOC:tb Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. biological_process GO:0060455 negative regulation of gastric acid secretion Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0060456 positive regulation of digestive system process Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0060457 negative regulation of digestive system process Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:dph GOC:tb Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). biological_process GO:0060467 negative regulation of fertilization Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:dph The process in which the controlled movement of a flagellated sperm cell is initiated as part of the process required for flagellated sperm to reach fertilization competence. biological_process positive regulation of sperm motility involved in capacitation GO:0060474 positive regulation of flagellated sperm motility involved in capacitation The process in which the controlled movement of a flagellated sperm cell is initiated as part of the process required for flagellated sperm to reach fertilization competence. GOC:cilia GOC:dph GOC:krc Any process that modulates the rate, frequency, or extent of cell projection assembly. biological_process regulation of cell projection formation GO:0060491 regulation of cell projection assembly Any process that modulates the rate, frequency, or extent of cell projection assembly. GOC:dph GOC:tb regulation of cell projection formation GOC:dph GOC:tb The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. dph 2009-04-28T08:42:53Z differential growth biological_process GO:0060560 developmental growth involved in morphogenesis The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. GOC:dph differential growth GOC:dph Any apoptotic process that contributes to the shaping of an anatomical structure. dph 2009-04-28T09:17:27Z apoptosis involved in morphogenesis biological_process apoptosis involved in development morphogenetic apoptosis GO:0060561 apoptotic process involved in morphogenesis Any apoptotic process that contributes to the shaping of an anatomical structure. GOC:dph GOC:mtg_apoptosis morphogenetic apoptosis GOC:dph The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. dph 2009-04-28T09:33:36Z biological_process GO:0060562 epithelial tube morphogenesis The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GOC:dph Creation of the central hole of a tube in an anatomical structure by sealing the edges of an epithelial fold. dph 2009-05-15T09:44:07Z biological_process GO:0060606 tube closure Creation of the central hole of a tube in an anatomical structure by sealing the edges of an epithelial fold. GOC:dph Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. dph 2009-05-18T02:12:13Z biological_process GO:0060623 regulation of chromosome condensation Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. dph 2009-05-18T02:29:43Z biological_process GO:0060627 regulation of vesicle-mediated transport Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. dph 2009-05-18T03:07:02Z biological_process GO:0060632 regulation of microtubule-based movement Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized. dph 2009-06-05T12:41:44Z biological_process GO:0060688 regulation of morphogenesis of a branching structure Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized. GOC:dph Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mammary gland, from its initial state to the mature structure. dph 2009-07-06T09:24:53Z cell-cell signalling involved in mammary gland development biological_process GO:0060764 cell-cell signaling involved in mammary gland development Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mammary gland, from its initial state to the mature structure. GOC:dph cell-cell signalling involved in mammary gland development GOC:mah The regulated release of a hormone into the circulatory system. dph 2010-01-11T09:03:48Z biological_process GO:0060986 endocrine hormone secretion The regulated release of a hormone into the circulatory system. GOC:dph An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. dph 2010-01-22T09:09:10Z hepatobiliary system process biological_process GO:0061007 hepaticobiliary system process An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. GOC:dph hepatobiliary system process GOC:dph A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. jl 2010-02-08T02:43:11Z GO:0016044 GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis single-organism membrane organization GO:0061024 membrane organization A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GOC:dph GOC:tb membrane organisation GOC:mah membrane organization and biogenesis GOC:mah Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. dph 2010-02-09T03:41:35Z biological_process GO:0061035 regulation of cartilage development Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:dph Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. dph 2010-02-09T03:41:35Z biological_process GO:0061036 positive regulation of cartilage development Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:dph Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. dph 2010-02-09T03:41:35Z biological_process GO:0061037 negative regulation of cartilage development Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate. GOC:dph Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. dph 2010-02-25T10:14:37Z biological_process GO:0061041 regulation of wound healing Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:BHF GOC:dph Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. dph 2010-02-25T10:33:30Z biological_process GO:0061045 negative regulation of wound healing Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:dph The process in which the anatomical structures of a branched epithelium are generated and organized. dph 2010-05-25T09:05:34Z biological_process GO:0061138 morphogenesis of a branching epithelium The process in which the anatomical structures of a branched epithelium are generated and organized. GOC:dph The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. dph 2010-09-28T12:50:43Z biological_process GO:0061326 renal tubule development The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. GOC:dph GOC:mtg_kidney_jan10 The process in which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. dph 2010-09-28T01:43:04Z biological_process GO:0061333 renal tubule morphogenesis The process in which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. GOC:dph GOC:mtg_kidney_jan10 The progression of a connective tissue over time, from its formation to the mature structure. dph 2012-03-22T12:53:41Z biological_process GO:0061448 connective tissue development The progression of a connective tissue over time, from its formation to the mature structure. GOC:BHF A process in which a protein is transported to, or maintained in, a location within a cilium. dph 2013-03-22T15:41:44Z biological_process GO:0061512 protein localization to cilium A process in which a protein is transported to, or maintained in, a location within a cilium. GOC:dph The regulated release of acetylcholine by a cell. dph 2013-06-21T15:40:39Z biological_process GO:0061526 acetylcholine secretion The regulated release of acetylcholine by a cell. GOC:dph A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes. dph 2018-02-14T22:37:44Z second meiotic division biological_process GO:0061983 meiosis II cell cycle process A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes. PMID:29385397 second meiotic division PMID:29385397 Any process that modulates the rate, frequency or extent of a small molecule metabolic process. dph 2018-03-19T14:11:54Z regulation of small molecule metabolism biological_process GO:0062012 regulation of small molecule metabolic process Any process that modulates the rate, frequency or extent of a small molecule metabolic process. GOC:vw Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:25:10Z positive regulation of small molecule metabolism biological_process GO:0062013 positive regulation of small molecule metabolic process Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. GOC:vw Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:27:23Z negative regulation of small molecule metabolism biological_process GO:0062014 negative regulation of small molecule metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. GOC:vw An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. dph 2018-04-13T12:47:21Z cellular_component GO:0062023 collagen-containing extracellular matrix An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells. GOC:BHF GOC:rph PMID:21123617 Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis. dph 2018-04-23T14:32:23Z biological_process GO:0062033 positive regulation of mitotic sister chromatid segregation Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis. PMID:12773390 Any process that modulates the frequency, rate or extent of mitochondrial gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). dph 2019-05-30T16:45:04Z biological_process GO:0062125 regulation of mitochondrial gene expression Any process that modulates the frequency, rate or extent of mitochondrial gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA). PMID:28285835 The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal. dph 2019-09-13T13:48:47Z biological_process GO:0062149 detection of stimulus involved in sensory perception of pain The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal. PMID:19837031 Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function biological_process GO:0065009 regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell. extracellular membrane-enclosed organelle cellular_component GO:0065010 extracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell. GOC:isa_complete An organelle lumen that is part of an intracellular organelle. cellular_component GO:0070013 intracellular organelle lumen An organelle lumen that is part of an intracellular organelle. GOC:mah The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). biological_process GO:0070091 glucagon secretion The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans). GOC:BHF GOC:rl Any process that modulates the frequency, rate or extent of the regulated release of glucagon. biological_process GO:0070092 regulation of glucagon secretion Any process that modulates the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon. down regulation of glucagon secretion down-regulation of glucagon secretion downregulation of glucagon secretion inhibition of glucagon secretion biological_process GO:0070093 negative regulation of glucagon secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon. up regulation of glucagon secretion up-regulation of glucagon secretion upregulation of glucagon secretion activation of glucagon secretion stimulation of glucagon secretion biological_process GO:0070094 positive regulation of glucagon secretion Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon. GOC:BHF GOC:mah The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion. mitochondrial translation elongation biological_process GO:0070125 mitochondrial translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in a mitochondrion. GOC:mah mitochondrial translation elongation GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. regulation of mitochondrial protein anabolism regulation of mitochondrial protein biosynthesis regulation of mitochondrial protein formation regulation of mitochondrial protein synthesis biological_process GO:0070129 regulation of mitochondrial translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. GOC:mah regulation of mitochondrial protein anabolism GOC:mah regulation of mitochondrial protein biosynthesis GOC:mah regulation of mitochondrial protein formation GOC:mah regulation of mitochondrial protein synthesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. negative regulation of mitochondrial protein anabolism negative regulation of mitochondrial protein biosynthesis negative regulation of mitochondrial protein formation negative regulation of mitochondrial protein synthesis biological_process GO:0070130 negative regulation of mitochondrial translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. GOC:mah negative regulation of mitochondrial protein anabolism GOC:mah negative regulation of mitochondrial protein biosynthesis GOC:mah negative regulation of mitochondrial protein formation GOC:mah negative regulation of mitochondrial protein synthesis GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. positive regulation of mitochondrial protein anabolism positive regulation of mitochondrial protein biosynthesis positive regulation of mitochondrial protein formation positive regulation of mitochondrial protein synthesis biological_process GO:0070131 positive regulation of mitochondrial translation Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion. GOC:mah positive regulation of mitochondrial protein anabolism GOC:mah positive regulation of mitochondrial protein biosynthesis GOC:mah positive regulation of mitochondrial protein formation GOC:mah positive regulation of mitochondrial protein synthesis GOC:mah A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix. anchoring cell junction cellular_component GO:0070161 anchoring junction A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix. ISBN:0815332181 anchoring cell junction GOC:mah A process of chromosome organization that is involved in a meiotic cell cycle. chromosome organisation involved in meiosis meiotic chromosome organization biological_process GO:0070192 chromosome organization involved in meiotic cell cycle A process of chromosome organization that is involved in a meiotic cell cycle. GOC:mah chromosome organisation involved in meiosis GOC:mah meiotic chromosome organization GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. regulation of establishment of protein localisation biological_process GO:0070201 regulation of establishment of protein localization Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah The regulated release of somatostatin from secretory granules in the D cells of the pancreas. biological_process GO:0070253 somatostatin secretion The regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:mah The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function. mucus production biological_process GO:0070254 mucus secretion The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function. GOC:add ISBN:068340007X ISBN:0721662544 mucus production GOC:add Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. regulation of mucus production biological_process GO:0070255 regulation of mucus secretion Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add regulation of mucus production GOC:add Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. negative regulation of mucus production biological_process GO:0070256 negative regulation of mucus secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add negative regulation of mucus production GOC:add Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. positive regulation of mucus production biological_process GO:0070257 positive regulation of mucus secretion Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue. GOC:add positive regulation of mucus production GOC:add The controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell. ECM constituent secretion ECM secretion biological_process GO:0070278 extracellular matrix constituent secretion The controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell. GOC:mah ECM constituent secretion GOC:mah ECM secretion GOC:mah A renal system process in which water, ions, glucose and proteins are taken up from the collecting ducts, glomerulus and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures (e.g. protein absorption is observed in nephrocytes in Drosophila, see PMID:23264686). nephron absorption renal reabsorption biological_process GO:0070293 renal absorption A renal system process in which water, ions, glucose and proteins are taken up from the collecting ducts, glomerulus and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures (e.g. protein absorption is observed in nephrocytes in Drosophila, see PMID:23264686). GOC:dph GOC:mah GOC:yaf nephron absorption GOC:mah renal reabsorption GOC:dph A renal system process in which water is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures. nephron water absorption renal water reabsorption biological_process GO:0070295 renal water absorption A renal system process in which water is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures. GOC:dph GOC:mah nephron water absorption GOC:mah renal water reabsorption GOC:dph The regulated release of prolactin, a peptide hormone that stimulates lactation, from secretory granules in the anterior pituitary. biological_process GO:0070459 prolactin secretion The regulated release of prolactin, a peptide hormone that stimulates lactation, from secretory granules in the anterior pituitary. GOC:mah ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen. biological_process GO:0070482 response to oxygen levels Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen. GOC:BHF GOC:mah The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. detection of reduced oxygen levels biological_process GO:0070483 detection of hypoxia The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. GOC:BHF GOC:mah detection of reduced oxygen levels GOC:vk Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. regulation of microtubule cytoskeleton organisation regulation of microtubule dynamics biological_process GO:0070507 regulation of microtubule cytoskeleton organization Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. GOC:mah regulation of microtubule cytoskeleton organisation GOC:mah regulation of microtubule dynamics GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of protein processing, a protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. mah 2009-04-29T02:49:14Z GO:0010953 regulation of protein maturation by peptide bond cleavage biological_process GO:0070613 regulation of protein processing Any process that modulates the frequency, rate or extent of protein processing, a protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. GOC:mah Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:09:02Z regulation of bile acid anabolism regulation of bile acid biosynthesis regulation of bile acid formation regulation of bile acid synthesis biological_process GO:0070857 regulation of bile acid biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah regulation of bile acid anabolism GOC:mah regulation of bile acid biosynthesis GOC:mah regulation of bile acid formation GOC:mah regulation of bile acid synthesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:16:40Z down regulation of bile acid biosynthetic process down-regulation of bile acid biosynthetic process downregulation of bile acid biosynthetic process negative regulation of bile acid anabolism negative regulation of bile acid biosynthesis negative regulation of bile acid formation negative regulation of bile acid synthesis inhibition of bile acid biosynthetic process biological_process GO:0070858 negative regulation of bile acid biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah down regulation of bile acid biosynthetic process GOC:mah down-regulation of bile acid biosynthetic process GOC:mah downregulation of bile acid biosynthetic process GOC:mah negative regulation of bile acid anabolism GOC:mah negative regulation of bile acid biosynthesis GOC:mah negative regulation of bile acid formation GOC:mah negative regulation of bile acid synthesis GOC:mah inhibition of bile acid biosynthetic process GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. mah 2009-08-14T03:22:58Z positive regulation of bile acid anabolism positive regulation of bile acid biosynthesis positive regulation of bile acid formation positive regulation of bile acid synthesis up regulation of bile acid biosynthetic process up-regulation of bile acid biosynthetic process upregulation of bile acid biosynthetic process activation of bile acid biosynthetic process stimulation of bile acid biosynthetic process biological_process GO:0070859 positive regulation of bile acid biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids. GOC:BHF GOC:mah positive regulation of bile acid anabolism GOC:mah positive regulation of bile acid biosynthesis GOC:mah positive regulation of bile acid formation GOC:mah positive regulation of bile acid synthesis GOC:mah up regulation of bile acid biosynthetic process GOC:mah up-regulation of bile acid biosynthetic process GOC:mah upregulation of bile acid biosynthetic process GOC:mah activation of bile acid biosynthetic process GOC:mah stimulation of bile acid biosynthetic process GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen. mah 2009-08-20T02:44:53Z regulation of glycogen metabolism biological_process GO:0070873 regulation of glycogen metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen. GOC:mah regulation of glycogen metabolism GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen. mah 2009-08-20T02:50:41Z negative regulation of glycogen metabolism biological_process GO:0070874 negative regulation of glycogen metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen. GOC:mah negative regulation of glycogen metabolism GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen. mah 2009-08-20T02:53:55Z positive regulation of glycogen metabolism biological_process GO:0070875 positive regulation of glycogen metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen. GOC:mah positive regulation of glycogen metabolism GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. mah 2009-08-27T04:41:45Z biological_process GO:0070887 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to chemical stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:mah The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. mah 2009-09-15T03:00:51Z biological_process GO:0070925 organelle assembly The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah The process of biting and mashing food with the teeth prior to swallowing. mah 2010-02-10T11:19:48Z chewing biological_process GO:0071626 mastication The process of biting and mashing food with the teeth prior to swallowing. GOC:gvg chewing GOC:mah Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. mah 2010-02-25T04:00:13Z protein localisation in extracellular region protein localization in extracellular region biological_process GO:0071692 protein localization to extracellular region Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. GOC:mah protein localisation in extracellular region GOC:mah A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state. mah 2010-03-02T11:43:38Z biological_process GO:0071695 anatomical structure maturation A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state. GOC:mah The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. mah 2010-03-08T02:15:14Z biological_process GO:0071702 organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. https://github.com/geneontology/go-ontology/issues/26424 mah 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. mah 2010-03-08T03:56:28Z biological_process GO:0071705 nitrogen compound transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). mah 2010-03-09T04:20:31Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination immunoglobulin V-D-J joining biological_process GO:0071707 immunoglobulin heavy chain V-D-J recombination The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). GOC:add ISBN:0781735149 immunoglobulin V(D)J joining GOC:add immunoglobulin V(D)J recombination GOC:add immunoglobulin V-D-J joining GOC:add The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). mah 2010-03-09T04:22:29Z immunoglobulin V(D)J joining immunoglobulin V(D)J recombination immunoglobulin V-J joining biological_process GO:0071708 immunoglobulin light chain V-J recombination The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). GOC:add ISBN:0781735149 immunoglobulin V(D)J joining GOC:add immunoglobulin V(D)J recombination GOC:add immunoglobulin V-J joining GOC:add A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z cellular_component GO:0071738 Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgD immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:11282392 A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. mah 2010-03-24T01:44:53Z cellular_component GO:0071753 Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. IgM immunoglobulin complex A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. GOC:add ISBN:0781765196 PMID:20176268 A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z cellular_component GO:0071944 cell periphery The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures. GOC:pdt An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. mah 2010-10-11T11:44:57Z elastic fibre elastin fiber cellular_component GO:0071953 elastic fiber An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain. GOC:BHF GOC:mah PMID:20236620 elastic fibre GOC:mah elastin fiber GOC:BHF The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. mah 2010-10-18T03:44:18Z extracellular vesicular exosome assembly biological_process GO:0071971 extracellular exosome assembly The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm. GOC:mah GOC:tfm PMID:19442504 PMID:27462458 extracellular vesicular exosome assembly GOC:vesicles The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels. mah 2010-01-25T10:31:00Z urinary system development urinary tract development biological_process GO:0072001 renal system development The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels. GOC:mtg_kidney_jan10 GOC:yaf http://en.wikibooks.org/wiki/Human_Physiology/The_Urinary_System urinary system development GOC:yaf urinary tract development GOC:yaf PMID:17881463 The developmental process pertaining to the initial formation of an epithelial tube. https://github.com/geneontology/go-ontology/issues/22302 mah 2010-02-26T02:15:40Z biological_process GO:0072175 epithelial tube formation The developmental process pertaining to the initial formation of an epithelial tube. GOC:mtg_kidney_jan10 Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. mah 2010-03-01T03:43:29Z biological_process GO:0072201 negative regulation of mesenchymal cell proliferation Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets. GOC:mtg_kidney_jan10 The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. mah 2010-11-02T04:51:32Z monocarboxylic acid anabolism monocarboxylic acid biosynthesis monocarboxylic acid formation monocarboxylic acid synthesis biological_process GO:0072330 monocarboxylic acid biosynthetic process The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group. GOC:mah monocarboxylic acid anabolism GOC:mah monocarboxylic acid biosynthesis GOC:mah monocarboxylic acid formation GOC:mah monocarboxylic acid synthesis GOC:mah OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell. GO:0055080 mah 2010-12-16T03:22:48Z biological_process GO:0072507 This term was obsoleted because it is an unnecessary grouping class. obsolete divalent inorganic cation homeostasis true OBSOLETE. Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell. GOC:mah The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. mah 2011-01-04T03:03:59Z purine and derivative metabolic process purine-containing compound metabolism biological_process GO:0072521 purine-containing compound metabolic process The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. GOC:mah purine-containing compound metabolism GOC:mah The chemical reactions and pathways resulting in the breakdown of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. mah 2011-01-04T03:17:20Z purine and derivative catabolic process purine-containing compound breakdown purine-containing compound catabolism purine-containing compound degradation biological_process GO:0072523 purine-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. GOC:mah purine-containing compound breakdown GOC:mah purine-containing compound catabolism GOC:mah purine-containing compound degradation GOC:mah The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof. mah 2011-01-04T03:21:47Z pyridine and derivative metabolic process pyridine-containing compound metabolism biological_process GO:0072524 pyridine-containing compound metabolic process The chemical reactions and pathways involving a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof. GOC:mah pyridine-containing compound metabolism GOC:mah The chemical reactions and pathways resulting in the breakdown of a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof. mah 2011-01-04T03:23:14Z pyridine and derivative catabolic process pyridine-containing compound breakdown pyridine-containing compound catabolism pyridine-containing compound degradation biological_process GO:0072526 pyridine-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of a pyridine-containing compound, i.e. any compound that contains pyridine or a formal derivative thereof. GOC:mah pyridine-containing compound breakdown GOC:mah pyridine-containing compound catabolism GOC:mah pyridine-containing compound degradation GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. dhl 2009-04-22T04:30:52Z biological_process GO:0080090 regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. PMID:19211694 Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). dhl 2009-05-06T04:51:28Z biological_process GO:0080134 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stress Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:dhl Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). dhl 2010-09-01T03:44:27Z biological_process GO:0080154 regulation of fertilization Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). GOC:DHL PMID:20478994 An G protein-coupled receptor signaling pathway which contributes to a circulatory system process carried out by the heart. bf 2012-03-19T01:28:23Z G-protein coupled receptor signaling pathway involved in heart process G-protein coupled receptor signalling pathway involved in heart process GPCR signaling pathway involved in cardiac process GPCR signaling pathway involved in heart process biological_process GO:0086103 G protein-coupled receptor signaling pathway involved in heart process An G protein-coupled receptor signaling pathway which contributes to a circulatory system process carried out by the heart. GOC:BHF GOC:mtg_cardiac_conduct_nov11 PMID:17376402 G-protein coupled receptor signaling pathway involved in heart process GOC:bf G-protein coupled receptor signalling pathway involved in heart process GOC:bf GPCR signaling pathway involved in cardiac process GOC:bf GPCR signaling pathway involved in heart process GOC:bf Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones. tb 2009-08-03T10:38:27Z biological_process GO:0090030 regulation of steroid hormone biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones. tb 2009-08-03T10:40:32Z biological_process GO:0090031 positive regulation of steroid hormone biosynthetic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones. tb 2009-08-03T10:41:35Z biological_process GO:0090032 negative regulation of steroid hormone biosynthetic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones. GOC:dph GOC:tb Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. tb 2009-09-09T11:39:52Z biological_process GO:0090068 positive regulation of cell cycle process Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. tb 2009-10-23T11:21:38Z biological_process GO:0090087 regulation of peptide transport Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb A process in which mitochondrial chromosomal DNA and associated proteins organize into a compact, orderly structure. tb 2009-12-08T02:12:19Z mitochondrial DNA packaging biological_process GO:0090139 mitochondrial chromosome packaging A process in which mitochondrial chromosomal DNA and associated proteins organize into a compact, orderly structure. GOC:ascb_2009 GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. tb 2009-12-18T10:33:49Z biological_process GO:0090181 regulation of cholesterol metabolic process Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. tb 2009-12-23T10:27:37Z biological_process GO:0090205 positive regulation of cholesterol metabolic process Any process that increases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. GOC:dph GOC:sl GOC:tb Any process that decreases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. tb 2009-12-23T10:27:37Z biological_process GO:0090206 negative regulation of cholesterol metabolic process Any process that decreases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. GOC:dph GOC:sl GOC:tb Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system. tb 2010-02-03T11:48:13Z biological_process GO:0090257 regulation of muscle system process Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system. GOC:dph GOC:tb Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090273 regulation of somatostatin secretion Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090274 positive regulation of somatostatin secretion Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. tb 2010-02-05T02:54:14Z biological_process GO:0090275 negative regulation of somatostatin secretion Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas. GOC:BHF Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090276 regulation of peptide hormone secretion Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090277 positive regulation of peptide hormone secretion Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. tb 2010-02-05T02:56:39Z biological_process GO:0090278 negative regulation of peptide hormone secretion Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules. GOC:tb Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. tb 2010-03-22T02:12:03Z biological_process GO:0090303 positive regulation of wound healing Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:BHF Any cellular metabolic process involving nucleic acids. https://github.com/geneontology/go-ontology/issues/26133 tb 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090316 positive regulation of intracellular protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090317 negative regulation of intracellular protein transport Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. tb 2010-05-14T10:24:29Z biological_process GO:0090325 regulation of locomotion involved in locomotory behavior Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:dph GOC:kmv GOC:tb Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. tb 2010-05-14T10:26:58Z biological_process GO:0090326 positive regulation of locomotion involved in locomotory behavior Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:dph GOC:kmv GOC:tb Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. tb 2010-05-14T10:26:58Z biological_process GO:0090327 negative regulation of locomotion involved in locomotory behavior Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement. GOC:dph GOC:kmv GOC:tb Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. tb 2010-07-12T11:14:12Z biological_process GO:0090368 regulation of ornithine metabolic process Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. GOC:dph GOC:jp GOC:tb The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents. tb 2014-08-12T12:13:53Z biological_process GO:0090594 inflammatory response to wounding The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents. GOC:add All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. pr 2011-03-23T01:52:31Z cilium plasm microtubule-based flagellar matrix microtubule-based flagellum matrix cellular_component cilial cytoplasm ciliary cytoplasm cilium cytoplasm microtubule-based flagellar cytoplasm microtubule-based flagellum cytoplasm GO:0097014 Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". ciliary plasm All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. GOC:BHF GOC:cilia GOC:dos PMID:17895364 The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. pr 2011-04-01T10:08:42Z biological_process GO:0097028 Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'. dendritic cell differentiation The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. CL:0000451 GOC:pr A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. pr 2011-06-07T11:22:09Z cellular_component GO:0097060 synaptic membrane A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. GOC:BHF PMID:20410104 The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage. pr 2011-11-21T09:01:24Z enamel development biological_process GO:0097186 amelogenesis The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage. GOC:cjm GOC:sl PMID:10206335 PMID:21196346 A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. pr 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis biological_process GO:0097194 execution phase of apoptosis A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:mtg_apoptosis PMID:21760595 A renal system process in which fluid circulating through the body is filtered through a barrier system. pr 2012-01-03T03:10:17Z biological_process GO:0097205 renal filtration A renal system process in which fluid circulating through the body is filtered through a barrier system. GOC:pr GOC:sart The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs. https://github.com/geneontology/go-ontology/issues/22368 pr 2012-03-05T02:03:58Z biological_process GO:0097254 renal tubular secretion The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs. GOC:rph PMID:25287933 Wikipedia:Renal_secretion#Secretion Any vesicle that is part of the intracellular region. pr 2016-03-29T17:39:45Z cellular_component GO:0097708 intracellular vesicle Any vesicle that is part of the intracellular region. GOC:vesicles The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. pr 2016-08-05T16:16:28Z biological_process GO:0097712 vesicle targeting, trans-Golgi to periciliary membrane compartment The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. GOC:cilia PMID:20106869 PMID:23351793 PMID:24814148 PMID:26485645 Reactome:R-HSA-5620920.1 Any process involved in the controlled movement of a sperm cell. pr 2016-09-01T12:00:45Z sperm movement biological_process GO:0097722 sperm motility Any process involved in the controlled movement of a sperm cell. GOC:cilia GOC:krc The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. pr 2016-10-03T14:35:25Z exosome assembly or secretion exosome biogenesis exosome production biological_process ILV assembly intraluminal vesicle assembly GO:0097734 extracellular exosome biogenesis The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. GOC:PARL GOC:bf PMID:19442504 PMID:25392495 Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. https://github.com/geneontology/go-ontology/issues/22173 dos 2013-11-11T12:59:11Z GO:0009814 defence response incompatible interaction defence response to pathogen, incompatible interaction defense response, incompatible interaction resistance response to pathogen biological_process GO:0098542 defense response to other organism Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism. GOC:dos The lipid bilayer that forms the outer-most layer of an organelle. dos 2014-02-26T13:41:31Z cellular_component GO:0098588 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. bounding membrane of organelle The lipid bilayer that forms the outer-most layer of an organelle. GOC:dos A membrane that is a (regional) part of the plasma membrane. dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component GO:0098590 Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. plasma membrane region A membrane that is a (regional) part of the plasma membrane. GOC:dos The attachment of one cell to another cell via adhesion molecules. dos 2014-04-16T13:40:03Z GO:0016337 biological_process single organismal cell-cell adhesion GO:0098609 cell-cell adhesion The attachment of one cell to another cell via adhesion molecules. GOC:dos A collagen trimer that forms networks. cellular_component GO:0098642 network-forming collagen trimer A collagen trimer that forms networks. PMID:21421911 A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands). cellular_component GO:0098643 banded collagen fibril A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands). GOC:dos PMID:21421911 A complex of collagen trimers such as a fibril or collagen network. Supramolecular aggregate of collagen Supramolecular collagen assembly cellular_component GO:0098644 complex of collagen trimers A complex of collagen trimers such as a fibril or collagen network. GOC:dos Supramolecular aggregate of collagen PMID:19693541 Supramolecular collagen assembly PMID:21421911 A supramolecular complex that consists of collagen triple helices associated to form a network. cellular_component GO:0098645 collagen network A supramolecular complex that consists of collagen triple helices associated to form a network. GOC:dos PMID:21421911 Any collagen timer that is part of a basement membrane. cellular_component GO:0098651 basement membrane collagen trimer Any collagen timer that is part of a basement membrane. GOC:dos PMID:21421911 The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. uptake biological_process GO:0098657 import into cell The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis. GOC:dos Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. biological_process GO:0098754 detoxification Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance. GOC:dos Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell. https://github.com/geneontology/go-ontology/issues/24455 biological_process GO:0098771 inorganic ion homeostasis Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell. GOC:dos The part of a synapse that is part of the presynaptic cell. presynaptic terminal cellular_component GO:0098793 presynapse The part of a synapse that is part of the presynaptic cell. GOC:dos Any protein complex that is part of a membrane. cellular_component GO:0098796 membrane protein complex Any protein complex that is part of a membrane. GOC:dos Any protein complex that is part of the plasma membrane. cellular_component GO:0098797 plasma membrane protein complex Any protein complex that is part of the plasma membrane. GOC:dos A protein complex that is part of a mitochondrion. cellular_component mitochondrial protein complex GO:0098798 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. mitochondrial protein-containing complex A protein complex that is part of a mitochondrion. GOC:dos Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system. biological_process GO:0098801 regulation of renal system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system. GOC:dos Any protein complex that is part of the plasma membrane and which functions as a signaling receptor. cellular_component GO:0098802 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. plasma membrane signaling receptor complex Any protein complex that is part of the plasma membrane and which functions as a signaling receptor. GOC:dos The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. biological_process GO:0098813 nuclear chromosome segregation The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles. GOC:dos A cell projection supported by an assembly of actin filaments, and which lacks microtubules. cellular_component GO:0098858 actin-based cell projection A cell projection supported by an assembly of actin filaments, and which lacks microtubules. PMID:15661519 Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. biological_process GO:0098900 The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term. regulation of action potential Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels. GOC:dos GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Cell-cell signaling from pre to post-synapse, across the synaptic cleft. biological_process GO:0098916 anterograde trans-synaptic signaling Cell-cell signaling from pre to post-synapse, across the synaptic cleft. GOC:dos Any vesicle-mediated transport that occurs in a synapse. biological_process GO:0099003 vesicle-mediated transport in synapse Any vesicle-mediated transport that occurs in a synapse. GOC:dos A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. cellular_component GO:0099080 supramolecular complex A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber. GOC:dos A polymeric supramolecular structure. cellular_component GO:0099081 supramolecular polymer A polymeric supramolecular structure. GOC:dos A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. biological_process GO:0099111 microtubule-based transport A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. GOC:cjm ISBN:0815316194 The regulated release of dopamine from the somatodendritic compartment (cell body or dendrites) of a neuron. STD DA release STD dopamine release somatodendritic dopamine release biological_process GO:0099123 somato-dendritic dopamine secretion The regulated release of dopamine from the somatodendritic compartment (cell body or dendrites) of a neuron. GOC:PARL GOC:bf PMID:21576241 STD DA release PMID:21576241 STD dopamine release PMID:21576241 somatodendritic dopamine release PMID:21576241 The actin cytoskeleton that is part of a presynapse. dos 2017-06-09T18:36:19Z cellular_component GO:0099143 presynaptic actin cytoskeleton The actin cytoskeleton that is part of a presynapse. GOC:dos Any process, acting in the presynapse that results in modulation of chemical synaptic transmission. dos 2017-09-11T17:09:31Z biological_process GO:0099171 presynaptic modulation of chemical synaptic transmission Any process, acting in the presynapse that results in modulation of chemical synaptic transmission. GOC:dos Any process that modulates the frequency, rate or extent of trans-synaptic signaling. biological_process GO:0099177 regulation of trans-synaptic signaling Any process that modulates the frequency, rate or extent of trans-synaptic signaling. GOC:dos The intermediate filament cytoskeleton that is part of a presynapse. dos 2017-12-01T18:10:21Z cellular_component GO:0099182 presynaptic intermediate filament cytoskeleton The intermediate filament cytoskeleton that is part of a presynapse. GOC:dos A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. cellular_component GO:0099503 secretory vesicle A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GOC:dos A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GO:0043205 cellular_component fibril GO:0099512 supramolecular fiber A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. GOC:dos A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. cellular_component GO:0099513 polymeric cytoskeletal fiber A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. GOC:dos The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission. biological_process GO:0099531 presynaptic process involved in chemical synaptic transmission The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission. GOC:dos Cell-cell signaling to, from or within a synapse. biological_process GO:0099536 synaptic signaling Cell-cell signaling to, from or within a synapse. GOC:dos Cell-cell signaling in either direction across the synaptic cleft. biological_process GO:0099537 trans-synaptic signaling Cell-cell signaling in either direction across the synaptic cleft. GOC:dos Any process that modulates synaptic transmission by regulating translation occurring at the synapse. biological_process GO:0099547 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at synapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating translation occurring at the synapse. GOC:dos Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse. biological_process GO:0099550 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. trans-synaptic signaling, modulating synaptic transmission Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse. GOC:dos Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 cytoplasmic region Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. GOC:dos The portion of the cytoskeleton contained within the presynapse. cellular_component GO:0099569 presynaptic cytoskeleton The portion of the cytoskeleton contained within the presynapse. GOC:dos Any process that modulates synaptic transmission by regulating translation occurring at the presynapse. biological_process GO:0099577 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at presynapse, modulating synaptic transmission Any process that modulates synaptic transmission by regulating translation occurring at the presynapse. GOC:dos Any signal release from a synapse. biological_process GO:0099643 signal release from synapse Any signal release from a synapse. GOC:dos The complete extent of cell cortex that underlies some some region of the plasma membrane. perimembrane region cellular_component GO:0099738 cell cortex region The complete extent of cell cortex that underlies some some region of the plasma membrane. GOC:dos Any process that modulates the frequency, rate or extent of the inflammatory response to wounding. hjd 2017-04-28T20:03:14Z biological_process GO:0106014 regulation of inflammatory response to wounding Any process that modulates the frequency, rate or extent of the inflammatory response to wounding. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26022821 Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response to wounding. hjd 2017-04-28T20:09:46Z biological_process GO:0106015 negative regulation of inflammatory response to wounding Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response to wounding. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26022821 Any process that activates or increases the frequency, rate or extent of the inflammatory response to wounding. hjd 2017-04-28T20:16:31Z biological_process GO:0106016 positive regulation of inflammatory response to wounding Any process that activates or increases the frequency, rate or extent of the inflammatory response to wounding. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:26022821 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. hjd 2017-10-27T17:33:05Z biological_process GO:0106064 regulation of cobalamin metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. PMID:29056341 Any process that activates or increases the frequency, rate or extent of a cobalamin metabolic process. hjd 2018-05-01T18:07:12Z biological_process GO:0106121 positive regulation of cobalamin metabolic process Any process that activates or increases the frequency, rate or extent of a cobalamin metabolic process. PMID:29056341 Any process that stops, prevents or reduces the frequency, rate or extent of a cobalamin metabolic process. hjd 2018-05-01T18:12:48Z biological_process GO:0106122 negative regulation of cobalamin metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of a cobalamin metabolic process. PMID:29056341 Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis. kmv 2018-07-05T14:10:14Z biological_process GO:0110110 positive regulation of animal organ morphogenesis Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis. GOC:kmv Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis. kmv 2018-07-05T14:25:21Z biological_process GO:0110111 negative regulation of animal organ morphogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis. GOC:kmv A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. https://github.com/geneontology/go-ontology/issues/24200 https://github.com/geneontology/go-ontology/issues/26424 kmv 2019-08-12T18:01:37Z cellular_component GO:0110165 cellular anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GOC:kmv A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 krc 2017-03-21T17:26:07Z cellular_component GO:0120025 plasma membrane bounded cell projection A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-24T23:56:08Z eupodium biological_process GO:0120031 plasma membrane bounded cell projection assembly Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc eupodium GOC:krc GOC:rjd PMID:10328951 PMID:9096956 Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:27:04Z biological_process GO:0120032 regulation of plasma membrane bounded cell projection assembly Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:34:31Z biological_process GO:0120033 negative regulation of plasma membrane bounded cell projection assembly Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T04:34:45Z biological_process GO:0120034 positive regulation of plasma membrane bounded cell projection assembly Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T16:02:06Z biological_process GO:0120035 regulation of plasma membrane bounded cell projection organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections. GOC:krc A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. https://github.com/geneontology/go-ontology/issues/13298 krc 2017-04-26T16:07:02Z biological_process GO:0120036 plasma membrane bounded cell projection organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon. GOC:krc All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. https://github.com/geneontology/go-ontology/issues/14472 krc 2017-11-01T18:58:12Z cellular_component GO:0120111 neuron projection cytoplasm All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. GOC:ha The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. https://github.com/geneontology/go-ontology/issues/16000 krc 2019-05-20T22:34:00Z biological_process GO:0120178 steroid hormone biosynthetic process The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. GOC:krc GOC:nln Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. https://github.com/geneontology/go-ontology/issues/16040 krc 2018-07-16T22:28:58Z biological_process GO:0120188 regulation of bile acid secretion Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. https://github.com/geneontology/go-ontology/issues/16040 krc 2018-07-16T22:36:17Z biological_process GO:0120189 positive regulation of bile acid secretion Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. https://github.com/geneontology/go-ontology/issues/16040 krc 2018-07-16T22:38:34Z biological_process GO:0120190 negative regulation of bile acid secretion Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue. GOC:BHF GOC:BHF_miRNA GOC:rph PMID:22767443 The assembly and organization of the sperm flagellum, the microtubule-based axoneme and associated structures that are part of a sperm flagellum (or cilium). https://github.com/geneontology/go-ontology/issues/21361 krc 2021-04-29T01:27:27Z biological_process GO:0120316 sperm flagellum assembly The assembly and organization of the sperm flagellum, the microtubule-based axoneme and associated structures that are part of a sperm flagellum (or cilium). GOC:krc PMID:32791035 One of the two nuclear divisions that occur as part of the meiotic cell cycle. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T09:40:00Z meiosis biological_process GO:0140013 meiotic nuclear division One of the two nuclear divisions that occur as part of the meiotic cell cycle. PMID:9334324 A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. https://github.com/geneontology/go-ontology/issues/19910 pg 2017-03-23T14:44:23Z mitosis biological_process GO:0140014 mitotic nuclear division A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell. ISBN:0198547684 The process in which a mitochondrial gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. pg 2017-06-26T10:57:45Z biological_process GO:0140053 mitochondrial gene expression The process in which a mitochondrial gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. PMID:27058308 The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. https://github.com/geneontology/go-ontology/issues/14256 pg 2017-10-23T11:53:42Z extracellular vesicle assembly biological_process GO:0140112 extracellular vesicle biogenesis The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content. PMID:28736435 Translation that occurs at the presynapse. https://github.com/geneontology/synapse/issues/216 pg 2018-07-13T13:00:33Z biological_process GO:0140236 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at presynapse Translation that occurs at the presynapse. PMID:27321671 Translation that occurs at the presynapse, and that modulates chemical synaptic transmission. https://github.com/geneontology/synapse/issues/216 pg 2018-07-13T13:07:23Z biological_process GO:0140237 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at presynapse, modulating chemical synaptic transmission Translation that occurs at the presynapse, and that modulates chemical synaptic transmission. PMID:27321671 A vesicle-mediated transport process in which the presynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. https://github.com/geneontology/synapse/issues/230 pg 2018-07-15T07:33:55Z biological_process GO:0140238 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. presynaptic endocytosis A vesicle-mediated transport process in which the presynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle. PMID:24719103 Translation that occurs at the synapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:23:12Z biological_process GO:0140241 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. translation at synapse Translation that occurs at the synapse. PMID:23083742 Any process that regulates translation occurring at the synapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:38:26Z biological_process GO:0140243 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at synapse Any process that regulates translation occurring at the synapse. PMID:20427644 Any process that regulates translation occurring at the presynapse. https://github.com/geneontology/synapse/issues/210 pg 2018-07-15T09:38:33Z biological_process GO:0140244 Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. regulation of translation at presynapse Any process that regulates translation occurring at the presynapse. PMID:20427644 The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. pg 2019-05-22T11:20:45Z efflux biological_process GO:0140352 export from cell The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. GOC:pg The directed movement of a lipid from a cell, into the extracellular region. pg 2019-05-22T11:33:07Z lipid efflux biological_process GO:0140353 lipid export from cell The directed movement of a lipid from a cell, into the extracellular region. GOC:pg A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. pg 2020-09-09T05:12:38Z nuclear complex cellular_component GO:0140513 nuclear protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. GOC:pg Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host. https://github.com/geneontology/go-ontology/issues/20261 pg 2020-11-11T17:19:06Z biological_process GO:0140546 defense response to symbiont Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host. GOC:pg A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell. https://github.com/geneontology/go-ontology/issues/24554 pg 2022-12-12T09:11:06Z multicellular organism level chemical homeostasis organismal level chemical homeostasis biological_process GO:0140962 multicellular organismal-level chemical homeostasis A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell. GOC:curators The chemical reactions and pathways involving an L-amino acid. https://github.com/geneontology/go-ontology/issues/23268 ew 2023-11-20T23:41:23Z L-alpha-amino acid metabolism L-amino acid metabolism biological_process GO:0170033 L-amino acid metabolic process The chemical reactions and pathways involving an L-amino acid. GOC:edw The chemical reactions and pathways involving any amino acid that is incorporated into protein naturally by ribosomal translation of mRNA, and that has a specific codon for translation from mRNA to protein. https://github.com/geneontology/go-ontology/issues/23268 ew 2023-12-18T17:31:08Z proteinogenic amino acid metabolism biological_process GO:0170039 proteinogenic amino acid metabolic process The chemical reactions and pathways involving any amino acid that is incorporated into protein naturally by ribosomal translation of mRNA, and that has a specific codon for translation from mRNA to protein. GOC:ew The chemical reactions and pathways involving non-proteingenic amino acids. https://github.com/geneontology/go-ontology/issues/23269 ew 2023-12-18T17:57:55Z non-proteinogenic amino acid metabolism biological_process GO:0170041 non-proteinogenic amino acid metabolic process The chemical reactions and pathways involving non-proteingenic amino acids. GOC:ew Any process that modulates the frequency, rate or extent of cytokine production involved in inflammatory response. rph 2012-01-11T09:34:27Z regulation of cytokine production involved in acute inflammatory response biological_process GO:1900015 regulation of cytokine production involved in inflammatory response Any process that modulates the frequency, rate or extent of cytokine production involved in inflammatory response. GOC:TermGenie regulation of cytokine production involved in acute inflammatory response GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response. rph 2012-01-11T09:34:31Z down regulation of cytokine production involved in acute inflammatory response negative regulation of cytokine production involved in acute inflammatory response biological_process down regulation of cytokine production involved in inflammatory response GO:1900016 negative regulation of cytokine production involved in inflammatory response Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response. GOC:TermGenie down regulation of cytokine production involved in acute inflammatory response GOC:TermGenie negative regulation of cytokine production involved in acute inflammatory response GOC:TermGenie down regulation of cytokine production involved in inflammatory response GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response. rph 2012-01-11T09:34:35Z up regulation of cytokine production involved in acute inflammatory response positive regulation of cytokine production involved in acute inflammatory response biological_process up regulation of cytokine production involved in inflammatory response GO:1900017 positive regulation of cytokine production involved in inflammatory response Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response. GOC:TermGenie up regulation of cytokine production involved in acute inflammatory response GOC:TermGenie positive regulation of cytokine production involved in acute inflammatory response GOC:TermGenie up regulation of cytokine production involved in inflammatory response GOC:TermGenie Any process that modulates the frequency, rate or extent of hemostasis. jl 2012-01-19T03:23:38Z biological_process GO:1900046 regulation of hemostasis Any process that modulates the frequency, rate or extent of hemostasis. GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis. jl 2012-01-19T03:23:42Z down regulation of hemostasis down-regulation of hemostasis downregulation of hemostasis inhibition of hemostasis biological_process GO:1900047 negative regulation of hemostasis Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis. GOC:TermGenie down regulation of hemostasis GOC:TermGenie down-regulation of hemostasis GOC:TermGenie downregulation of hemostasis GOC:TermGenie inhibition of hemostasis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hemostasis. jl 2012-01-19T03:23:45Z up regulation of hemostasis up-regulation of hemostasis upregulation of hemostasis activation of hemostasis biological_process GO:1900048 positive regulation of hemostasis Any process that activates or increases the frequency, rate or extent of hemostasis. GOC:TermGenie up regulation of hemostasis GOC:TermGenie up-regulation of hemostasis GOC:TermGenie upregulation of hemostasis GOC:TermGenie activation of hemostasis GOC:TermGenie Any process that modulates the frequency, rate or extent of neuromuscular synaptic transmission. kmv 2012-01-26T10:14:10Z biological_process GO:1900073 regulation of neuromuscular synaptic transmission Any process that modulates the frequency, rate or extent of neuromuscular synaptic transmission. GOC:TermGenie GOC:kmv Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular synaptic transmission. kmv 2012-01-26T10:14:18Z biological_process down regulation of neuromuscular synaptic transmission down-regulation of neuromuscular synaptic transmission downregulation of neuromuscular synaptic transmission inhibition of neuromuscular synaptic transmission GO:1900074 negative regulation of neuromuscular synaptic transmission Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular synaptic transmission. GOC:TermGenie GOC:kmv down regulation of neuromuscular synaptic transmission GOC:TermGenie down-regulation of neuromuscular synaptic transmission GOC:TermGenie downregulation of neuromuscular synaptic transmission GOC:TermGenie inhibition of neuromuscular synaptic transmission GOC:TermGenie Any process that activates or increases the frequency, rate or extent of neuromuscular synaptic transmission. kmv 2012-01-26T10:14:22Z biological_process activation of neuromuscular synaptic transmission up regulation of neuromuscular synaptic transmission up-regulation of neuromuscular synaptic transmission upregulation of neuromuscular synaptic transmission GO:1900075 positive regulation of neuromuscular synaptic transmission Any process that activates or increases the frequency, rate or extent of neuromuscular synaptic transmission. GOC:TermGenie GOC:kmv activation of neuromuscular synaptic transmission GOC:TermGenie up regulation of neuromuscular synaptic transmission GOC:TermGenie up-regulation of neuromuscular synaptic transmission GOC:TermGenie upregulation of neuromuscular synaptic transmission GOC:TermGenie Any regulation of signal transduction that takes place in the extracellular region. bf 2012-02-22T10:21:48Z regulation of signaling pathway in extracellular region regulation of signalling pathway in extracellular region biological_process GO:1900115 extracellular regulation of signal transduction Any regulation of signal transduction that takes place in the extracellular region. GOC:TermGenie GOC:signaling regulation of signaling pathway in extracellular region GOC:TermGenie regulation of signalling pathway in extracellular region GOC:TermGenie Any negative regulation of signal transduction that takes place in extracellular region. bf 2012-02-22T10:27:56Z down regulation of signal transduction in extracellular region down-regulation of signal transduction in extracellular region downregulation of signal transduction in extracellular region negative regulation of signaling pathway in extracellular region negative regulation of signalling pathway in extracellular region extracellular inhibition of signaling pathway inhibition of signal transduction in extracellular region biological_process GO:1900116 extracellular negative regulation of signal transduction Any negative regulation of signal transduction that takes place in extracellular region. GOC:TermGenie GOC:signaling down regulation of signal transduction in extracellular region GOC:TermGenie down-regulation of signal transduction in extracellular region GOC:TermGenie downregulation of signal transduction in extracellular region GOC:TermGenie negative regulation of signaling pathway in extracellular region GOC:TermGenie negative regulation of signalling pathway in extracellular region GOC:TermGenie extracellular inhibition of signaling pathway GOC:bf inhibition of signal transduction in extracellular region GOC:TermGenie Any process that modulates the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:20Z biological_process GO:1900117 regulation of execution phase of apoptosis Any process that modulates the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:24Z down regulation of execution phase of apoptosis down-regulation of execution phase of apoptosis downregulation of execution phase of apoptosis inhibition of execution phase of apoptosis biological_process GO:1900118 negative regulation of execution phase of apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis down regulation of execution phase of apoptosis GOC:TermGenie down-regulation of execution phase of apoptosis GOC:TermGenie downregulation of execution phase of apoptosis GOC:TermGenie inhibition of execution phase of apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:27Z up regulation of execution phase of apoptosis up-regulation of execution phase of apoptosis upregulation of execution phase of apoptosis activation of execution phase of apoptosis biological_process GO:1900119 positive regulation of execution phase of apoptosis Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis up regulation of execution phase of apoptosis GOC:TermGenie up-regulation of execution phase of apoptosis GOC:TermGenie upregulation of execution phase of apoptosis GOC:TermGenie activation of execution phase of apoptosis GOC:TermGenie Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process. yaf 2012-02-23T01:09:21Z regulation of hyaluronan anabolism regulation of hyaluronan biosynthesis regulation of hyaluronan formation regulation of hyaluronan synthesis biological_process GO:1900125 regulation of hyaluronan biosynthetic process Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process. GOC:TermGenie GOC:yaf regulation of hyaluronan anabolism GOC:TermGenie regulation of hyaluronan biosynthesis GOC:TermGenie regulation of hyaluronan formation GOC:TermGenie regulation of hyaluronan synthesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process. yaf 2012-02-23T01:09:29Z down regulation of hyaluronan anabolism down regulation of hyaluronan biosynthesis down regulation of hyaluronan biosynthetic process down regulation of hyaluronan formation down regulation of hyaluronan synthesis down-regulation of hyaluronan anabolism down-regulation of hyaluronan biosynthesis down-regulation of hyaluronan biosynthetic process down-regulation of hyaluronan formation down-regulation of hyaluronan synthesis downregulation of hyaluronan anabolism downregulation of hyaluronan biosynthesis downregulation of hyaluronan biosynthetic process downregulation of hyaluronan formation downregulation of hyaluronan synthesis inhibition of hyaluronan anabolism inhibition of hyaluronan biosynthesis inhibition of hyaluronan formation inhibition of hyaluronan synthesis negative regulation of hyaluronan anabolism negative regulation of hyaluronan biosynthesis negative regulation of hyaluronan formation negative regulation of hyaluronan synthesis inhibition of hyaluronan biosynthetic process biological_process GO:1900126 negative regulation of hyaluronan biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process. GOC:TermGenie GOC:yaf down regulation of hyaluronan anabolism GOC:TermGenie down regulation of hyaluronan biosynthesis GOC:TermGenie down regulation of hyaluronan biosynthetic process GOC:TermGenie down regulation of hyaluronan formation GOC:TermGenie down regulation of hyaluronan synthesis GOC:TermGenie down-regulation of hyaluronan anabolism GOC:TermGenie down-regulation of hyaluronan biosynthesis GOC:TermGenie down-regulation of hyaluronan biosynthetic process GOC:TermGenie down-regulation of hyaluronan formation GOC:TermGenie down-regulation of hyaluronan synthesis GOC:TermGenie downregulation of hyaluronan anabolism GOC:TermGenie downregulation of hyaluronan biosynthesis GOC:TermGenie downregulation of hyaluronan biosynthetic process GOC:TermGenie downregulation of hyaluronan formation GOC:TermGenie downregulation of hyaluronan synthesis GOC:TermGenie inhibition of hyaluronan anabolism GOC:TermGenie inhibition of hyaluronan biosynthesis GOC:TermGenie inhibition of hyaluronan formation GOC:TermGenie inhibition of hyaluronan synthesis GOC:TermGenie negative regulation of hyaluronan anabolism GOC:TermGenie negative regulation of hyaluronan biosynthesis GOC:TermGenie negative regulation of hyaluronan formation GOC:TermGenie negative regulation of hyaluronan synthesis GOC:TermGenie inhibition of hyaluronan biosynthetic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process. yaf 2012-02-23T01:09:33Z activation of hyaluronan anabolism activation of hyaluronan biosynthesis activation of hyaluronan formation activation of hyaluronan synthesis positive regulation of hyaluronan anabolism positive regulation of hyaluronan biosynthesis positive regulation of hyaluronan formation positive regulation of hyaluronan synthesis up regulation of hyaluronan anabolism up regulation of hyaluronan biosynthesis up regulation of hyaluronan biosynthetic process up regulation of hyaluronan formation up regulation of hyaluronan synthesis up-regulation of hyaluronan anabolism up-regulation of hyaluronan biosynthesis up-regulation of hyaluronan biosynthetic process up-regulation of hyaluronan formation up-regulation of hyaluronan synthesis upregulation of hyaluronan anabolism upregulation of hyaluronan biosynthesis upregulation of hyaluronan biosynthetic process upregulation of hyaluronan formation upregulation of hyaluronan synthesis activation of hyaluronan biosynthetic process biological_process GO:1900127 positive regulation of hyaluronan biosynthetic process Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process. GOC:TermGenie GOC:yaf activation of hyaluronan anabolism GOC:TermGenie activation of hyaluronan biosynthesis GOC:TermGenie activation of hyaluronan formation GOC:TermGenie activation of hyaluronan synthesis GOC:TermGenie positive regulation of hyaluronan anabolism GOC:TermGenie positive regulation of hyaluronan biosynthesis GOC:TermGenie positive regulation of hyaluronan formation GOC:TermGenie positive regulation of hyaluronan synthesis GOC:TermGenie up regulation of hyaluronan anabolism GOC:TermGenie up regulation of hyaluronan biosynthesis GOC:TermGenie up regulation of hyaluronan biosynthetic process GOC:TermGenie up regulation of hyaluronan formation GOC:TermGenie up regulation of hyaluronan synthesis GOC:TermGenie up-regulation of hyaluronan anabolism GOC:TermGenie up-regulation of hyaluronan biosynthesis GOC:TermGenie up-regulation of hyaluronan biosynthetic process GOC:TermGenie up-regulation of hyaluronan formation GOC:TermGenie up-regulation of hyaluronan synthesis GOC:TermGenie upregulation of hyaluronan anabolism GOC:TermGenie upregulation of hyaluronan biosynthesis GOC:TermGenie upregulation of hyaluronan biosynthetic process GOC:TermGenie upregulation of hyaluronan formation GOC:TermGenie upregulation of hyaluronan synthesis GOC:TermGenie activation of hyaluronan biosynthetic process GOC:TermGenie Any process that modulates the frequency, rate or extent of purine nucleotide metabolic process. krc 2012-05-11T05:43:15Z regulation of purine nucleotide metabolism regulation of purine metabolic process regulation of purine metabolism biological_process GO:1900542 regulation of purine nucleotide metabolic process Any process that modulates the frequency, rate or extent of purine nucleotide metabolic process. GOC:TermGenie regulation of purine nucleotide metabolism GOC:TermGenie regulation of purine metabolic process GOC:TermGenie regulation of purine metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of purine nucleotide metabolic process. krc 2012-05-11T05:44:21Z down regulation of purine nucleotide metabolic process down regulation of purine nucleotide metabolism down-regulation of purine nucleotide metabolic process down-regulation of purine nucleotide metabolism downregulation of purine nucleotide metabolic process downregulation of purine nucleotide metabolism negative regulation of purine nucleotide metabolism down regulation of purine metabolic process down regulation of purine metabolism down-regulation of purine metabolic process down-regulation of purine metabolism downregulation of purine metabolic process downregulation of purine metabolism inhibition of purine metabolic process inhibition of purine metabolism inhibition of purine nucleotide metabolic process inhibition of purine nucleotide metabolism negative regulation of purine metabolic process negative regulation of purine metabolism biological_process GO:1900543 negative regulation of purine nucleotide metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of purine nucleotide metabolic process. GOC:TermGenie down regulation of purine nucleotide metabolic process GOC:TermGenie down regulation of purine nucleotide metabolism GOC:TermGenie down-regulation of purine nucleotide metabolic process GOC:TermGenie down-regulation of purine nucleotide metabolism GOC:TermGenie downregulation of purine nucleotide metabolic process GOC:TermGenie downregulation of purine nucleotide metabolism GOC:TermGenie negative regulation of purine nucleotide metabolism GOC:TermGenie down regulation of purine metabolic process GOC:TermGenie down regulation of purine metabolism GOC:TermGenie down-regulation of purine metabolic process GOC:TermGenie down-regulation of purine metabolism GOC:TermGenie downregulation of purine metabolic process GOC:TermGenie downregulation of purine metabolism GOC:TermGenie inhibition of purine metabolic process GOC:TermGenie inhibition of purine metabolism GOC:TermGenie inhibition of purine nucleotide metabolic process GOC:TermGenie inhibition of purine nucleotide metabolism GOC:TermGenie negative regulation of purine metabolic process GOC:TermGenie negative regulation of purine metabolism GOC:TermGenie Any process that activates or increases the frequency, rate or extent of purine nucleotide metabolic process. krc 2012-05-11T05:44:43Z positive regulation of purine nucleotide metabolism up regulation of purine nucleotide metabolic process up regulation of purine nucleotide metabolism up-regulation of purine nucleotide metabolic process up-regulation of purine nucleotide metabolism upregulation of purine nucleotide metabolic process upregulation of purine nucleotide metabolism activation of purine metabolic process activation of purine metabolism activation of purine nucleotide metabolic process activation of purine nucleotide metabolism positive regulation of purine metabolic process positive regulation of purine metabolism up regulation of purine metabolic process up regulation of purine metabolism up-regulation of purine metabolic process up-regulation of purine metabolism upregulation of purine metabolic process upregulation of purine metabolism biological_process GO:1900544 positive regulation of purine nucleotide metabolic process Any process that activates or increases the frequency, rate or extent of purine nucleotide metabolic process. GOC:TermGenie positive regulation of purine nucleotide metabolism GOC:TermGenie up regulation of purine nucleotide metabolic process GOC:TermGenie up regulation of purine nucleotide metabolism GOC:TermGenie up-regulation of purine nucleotide metabolic process GOC:TermGenie up-regulation of purine nucleotide metabolism GOC:TermGenie upregulation of purine nucleotide metabolic process GOC:TermGenie upregulation of purine nucleotide metabolism GOC:TermGenie activation of purine metabolic process GOC:TermGenie activation of purine metabolism GOC:TermGenie activation of purine nucleotide metabolic process GOC:TermGenie activation of purine nucleotide metabolism GOC:TermGenie positive regulation of purine metabolic process GOC:TermGenie positive regulation of purine metabolism GOC:TermGenie up regulation of purine metabolic process GOC:TermGenie up regulation of purine metabolism GOC:TermGenie up-regulation of purine metabolic process GOC:TermGenie up-regulation of purine metabolism GOC:TermGenie upregulation of purine metabolic process GOC:TermGenie upregulation of purine metabolism GOC:TermGenie The chemical reactions and pathways involving carbohydrate derivative. bf 2012-07-12T04:05:09Z carbohydrate derivative metabolism biological_process GO:1901135 carbohydrate derivative metabolic process The chemical reactions and pathways involving carbohydrate derivative. GOC:TermGenie carbohydrate derivative metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative. bf 2012-07-12T04:05:31Z carbohydrate derivative breakdown carbohydrate derivative catabolism carbohydrate derivative degradation biological_process GO:1901136 carbohydrate derivative catabolic process The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative. GOC:TermGenie carbohydrate derivative breakdown GOC:TermGenie carbohydrate derivative catabolism GOC:TermGenie carbohydrate derivative degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of carbohydrate derivative. bf 2012-07-12T04:05:39Z carbohydrate derivative anabolism carbohydrate derivative biosynthesis carbohydrate derivative formation carbohydrate derivative synthesis biological_process GO:1901137 carbohydrate derivative biosynthetic process The chemical reactions and pathways resulting in the formation of carbohydrate derivative. GOC:TermGenie carbohydrate derivative anabolism GOC:TermGenie carbohydrate derivative biosynthesis GOC:TermGenie carbohydrate derivative formation GOC:TermGenie carbohydrate derivative synthesis GOC:TermGenie Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form. bf 2012-07-16T03:29:30Z expression of extracellular matrix proteins biological_process extracellular matrix protein production GO:1901148 gene expression involved in extracellular matrix organization Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form. GOC:TermGenie GOC:pg PMID:18668558 expression of extracellular matrix proteins GOC:bf extracellular matrix protein production GOC:pg The chemical reactions and pathways resulting in the breakdown of a nucleoside phosphate. bf 2012-08-20T12:33:25Z nucleoside phosphate breakdown nucleoside phosphate catabolism nucleoside phosphate degradation biological_process GO:1901292 nucleoside phosphate catabolic process The chemical reactions and pathways resulting in the breakdown of a nucleoside phosphate. GOC:TermGenie nucleoside phosphate breakdown GOC:TermGenie nucleoside phosphate catabolism GOC:TermGenie nucleoside phosphate degradation GOC:TermGenie Any process that modulates the frequency, rate or extent of flagellated sperm motility. hjd 2012-08-22T20:50:14Z regulation of sperm motility regulation of sperm movement biological_process GO:1901317 regulation of flagellated sperm motility Any process that modulates the frequency, rate or extent of flagellated sperm motility. GOC:TermGenie GOC:cilia GOC:krc regulation of sperm movement GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility. hjd 2012-08-22T20:50:35Z down regulation of sperm motility down regulation of sperm movement down-regulation of sperm motility down-regulation of sperm movement downregulation of sperm motility downregulation of sperm movement inhibition of sperm movement negative regulation of sperm motility negative regulation of sperm movement inhibition of sperm motility biological_process GO:1901318 negative regulation of flagellated sperm motility Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility. GOC:TermGenie GOC:cilia GOC:krc down regulation of sperm motility GOC:TermGenie down regulation of sperm movement GOC:TermGenie down-regulation of sperm motility GOC:TermGenie down-regulation of sperm movement GOC:TermGenie downregulation of sperm motility GOC:TermGenie downregulation of sperm movement GOC:TermGenie inhibition of sperm movement GOC:TermGenie negative regulation of sperm movement GOC:TermGenie inhibition of sperm motility GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. bf 2012-09-14T09:05:04Z organic cyclic compound breakdown organic cyclic compound catabolism organic cyclic compound degradation biological_process GO:1901361 organic cyclic compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. GOC:TermGenie organic cyclic compound breakdown GOC:TermGenie organic cyclic compound catabolism GOC:TermGenie organic cyclic compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic cyclic compound. bf 2012-09-14T09:05:22Z organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis biological_process GO:1901362 organic cyclic compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic cyclic compound. GOC:TermGenie organic cyclic compound anabolism GOC:TermGenie organic cyclic compound biosynthesis GOC:TermGenie organic cyclic compound formation GOC:TermGenie organic cyclic compound synthesis GOC:TermGenie The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bf 2012-09-28T10:42:13Z biological_process GO:1901374 acetate ester transport The directed movement of an acetate ester into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:TermGenie Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:34:03Z regulation of tetrapyrrole metabolism biological_process GO:1901401 regulation of tetrapyrrole metabolic process Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators regulation of tetrapyrrole metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:35:11Z down regulation of tetrapyrrole metabolic process down regulation of tetrapyrrole metabolism down-regulation of tetrapyrrole metabolic process down-regulation of tetrapyrrole metabolism downregulation of tetrapyrrole metabolic process downregulation of tetrapyrrole metabolism inhibition of tetrapyrrole metabolism negative regulation of tetrapyrrole metabolism inhibition of tetrapyrrole metabolic process biological_process GO:1901402 negative regulation of tetrapyrrole metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators down regulation of tetrapyrrole metabolic process GOC:TermGenie down regulation of tetrapyrrole metabolism GOC:TermGenie down-regulation of tetrapyrrole metabolic process GOC:TermGenie down-regulation of tetrapyrrole metabolism GOC:TermGenie downregulation of tetrapyrrole metabolic process GOC:TermGenie downregulation of tetrapyrrole metabolism GOC:TermGenie inhibition of tetrapyrrole metabolism GOC:TermGenie negative regulation of tetrapyrrole metabolism GOC:TermGenie inhibition of tetrapyrrole metabolic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:35:29Z activation of tetrapyrrole metabolism positive regulation of tetrapyrrole metabolism up regulation of tetrapyrrole metabolic process up regulation of tetrapyrrole metabolism up-regulation of tetrapyrrole metabolic process up-regulation of tetrapyrrole metabolism upregulation of tetrapyrrole metabolic process upregulation of tetrapyrrole metabolism activation of tetrapyrrole metabolic process biological_process GO:1901403 positive regulation of tetrapyrrole metabolic process Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators activation of tetrapyrrole metabolism GOC:TermGenie positive regulation of tetrapyrrole metabolism GOC:TermGenie up regulation of tetrapyrrole metabolic process GOC:TermGenie up regulation of tetrapyrrole metabolism GOC:TermGenie up-regulation of tetrapyrrole metabolic process GOC:TermGenie up-regulation of tetrapyrrole metabolism GOC:TermGenie upregulation of tetrapyrrole metabolic process GOC:TermGenie upregulation of tetrapyrrole metabolism GOC:TermGenie activation of tetrapyrrole metabolic process GOC:TermGenie Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:01Z regulation of haematopoietic progenitor cell differentiation regulation of haemopoietic progenitor cell differentiation regulation of hemopoietic progenitor cell differentiation biological_process GO:1901532 regulation of hematopoietic progenitor cell differentiation Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl regulation of haematopoietic progenitor cell differentiation GOC:TermGenie regulation of haemopoietic progenitor cell differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:06Z down regulation of haematopoietic progenitor cell differentiation down regulation of haemopoietic progenitor cell differentiation down regulation of hemopoietic progenitor cell differentiation down-regulation of haematopoietic progenitor cell differentiation down-regulation of haemopoietic progenitor cell differentiation down-regulation of hemopoietic progenitor cell differentiation downregulation of haematopoietic progenitor cell differentiation downregulation of haemopoietic progenitor cell differentiation downregulation of hemopoietic progenitor cell differentiation inhibition of haematopoietic progenitor cell differentiation inhibition of haemopoietic progenitor cell differentiation negative regulation of haematopoietic progenitor cell differentiation negative regulation of haemopoietic progenitor cell differentiation negative regulation of hemopoietic progenitor cell differentiation inhibition of hemopoietic progenitor cell differentiation biological_process down regulation of hematopoietic progenitor cell differentiation down-regulation of hematopoietic progenitor cell differentiation downregulation of hematopoietic progenitor cell differentiation inhibition of hematopoietic progenitor cell differentiation GO:1901533 negative regulation of hematopoietic progenitor cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl down regulation of haematopoietic progenitor cell differentiation GOC:TermGenie down regulation of haemopoietic progenitor cell differentiation GOC:TermGenie down regulation of hemopoietic progenitor cell differentiation GOC:TermGenie down-regulation of haematopoietic progenitor cell differentiation GOC:TermGenie down-regulation of haemopoietic progenitor cell differentiation GOC:TermGenie down-regulation of hemopoietic progenitor cell differentiation GOC:TermGenie downregulation of haematopoietic progenitor cell differentiation GOC:TermGenie downregulation of haemopoietic progenitor cell differentiation GOC:TermGenie downregulation of hemopoietic progenitor cell differentiation GOC:TermGenie inhibition of haematopoietic progenitor cell differentiation GOC:TermGenie inhibition of haemopoietic progenitor cell differentiation GOC:TermGenie negative regulation of haematopoietic progenitor cell differentiation GOC:TermGenie negative regulation of haemopoietic progenitor cell differentiation GOC:TermGenie inhibition of hemopoietic progenitor cell differentiation GOC:TermGenie down regulation of hematopoietic progenitor cell differentiation GOC:TermGenie down-regulation of hematopoietic progenitor cell differentiation GOC:TermGenie downregulation of hematopoietic progenitor cell differentiation GOC:TermGenie inhibition of hematopoietic progenitor cell differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation. vk 2012-10-24T11:23:14Z activation of haematopoietic progenitor cell differentiation activation of haemopoietic progenitor cell differentiation positive regulation of haematopoietic progenitor cell differentiation positive regulation of haemopoietic progenitor cell differentiation positive regulation of hemopoietic progenitor cell differentiation up regulation of haematopoietic progenitor cell differentiation up regulation of haemopoietic progenitor cell differentiation up regulation of hemopoietic progenitor cell differentiation up-regulation of haematopoietic progenitor cell differentiation up-regulation of haemopoietic progenitor cell differentiation up-regulation of hemopoietic progenitor cell differentiation upregulation of haematopoietic progenitor cell differentiation upregulation of haemopoietic progenitor cell differentiation upregulation of hemopoietic progenitor cell differentiation activation of hemopoietic progenitor cell differentiation biological_process activation of hematopoietic progenitor cell differentiation up regulation of hematopoietic progenitor cell differentiation up-regulation of hematopoietic progenitor cell differentiation upregulation of hematopoietic progenitor cell differentiation GO:1901534 positive regulation of hematopoietic progenitor cell differentiation Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation. GOC:BHF GOC:TermGenie GOC:rl activation of haematopoietic progenitor cell differentiation GOC:TermGenie activation of haemopoietic progenitor cell differentiation GOC:TermGenie positive regulation of haematopoietic progenitor cell differentiation GOC:TermGenie positive regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up regulation of haematopoietic progenitor cell differentiation GOC:TermGenie up regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up regulation of hemopoietic progenitor cell differentiation GOC:TermGenie up-regulation of haematopoietic progenitor cell differentiation GOC:TermGenie up-regulation of haemopoietic progenitor cell differentiation GOC:TermGenie up-regulation of hemopoietic progenitor cell differentiation GOC:TermGenie upregulation of haematopoietic progenitor cell differentiation GOC:TermGenie upregulation of haemopoietic progenitor cell differentiation GOC:TermGenie upregulation of hemopoietic progenitor cell differentiation GOC:TermGenie activation of hemopoietic progenitor cell differentiation GOC:TermGenie activation of hematopoietic progenitor cell differentiation GOC:TermGenie up regulation of hematopoietic progenitor cell differentiation GOC:TermGenie up-regulation of hematopoietic progenitor cell differentiation GOC:TermGenie upregulation of hematopoietic progenitor cell differentiation GOC:TermGenie The chemical reactions and pathways involving organonitrogen compound. https://github.com/geneontology/go-ontology/issues/26424 pr 2012-11-04T15:17:52Z organonitrogen compound metabolism biological_process GO:1901564 organonitrogen compound metabolic process The chemical reactions and pathways involving organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. pr 2012-11-04T15:17:56Z organonitrogen compound breakdown organonitrogen compound catabolism organonitrogen compound degradation biological_process GO:1901565 organonitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound breakdown GOC:TermGenie organonitrogen compound catabolism GOC:TermGenie organonitrogen compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organonitrogen compound. pr 2012-11-04T15:18:00Z organonitrogen compound anabolism organonitrogen compound biosynthesis organonitrogen compound formation organonitrogen compound synthesis biological_process GO:1901566 organonitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound anabolism GOC:TermGenie organonitrogen compound biosynthesis GOC:TermGenie organonitrogen compound formation GOC:TermGenie organonitrogen compound synthesis GOC:TermGenie The chemical reactions and pathways involving fatty acid derivative. pr 2012-11-04T17:13:36Z fatty acid derivative metabolism biological_process GO:1901568 fatty acid derivative metabolic process The chemical reactions and pathways involving fatty acid derivative. GOC:TermGenie GOC:pr fatty acid derivative metabolism GOC:TermGenie The chemical reactions and pathways resulting in the formation of fatty acid derivative. pr 2012-11-04T17:13:44Z fatty acid derivative anabolism fatty acid derivative biosynthesis fatty acid derivative formation fatty acid derivative synthesis biological_process GO:1901570 fatty acid derivative biosynthetic process The chemical reactions and pathways resulting in the formation of fatty acid derivative. GOC:TermGenie GOC:pr fatty acid derivative anabolism GOC:TermGenie fatty acid derivative biosynthesis GOC:TermGenie fatty acid derivative formation GOC:TermGenie fatty acid derivative synthesis GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:36Z organic molecular entity breakdown organic molecular entity catabolic process organic molecular entity catabolism organic molecular entity degradation organic substance breakdown organic substance catabolism organic substance degradation biological_process GO:1901575 organic substance catabolic process The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity breakdown GOC:TermGenie organic molecular entity catabolism GOC:TermGenie organic molecular entity degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:40Z organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis biological_process GO:1901576 organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity anabolism GOC:TermGenie organic molecular entity biosynthesis GOC:TermGenie organic molecular entity formation GOC:TermGenie organic molecular entity synthesis GOC:TermGenie The chemical reactions and pathways involving an alpha-amino acid. tb 2012-11-08T17:39:50Z alpha-amino acid metabolism biological_process GO:1901605 alpha-amino acid metabolic process The chemical reactions and pathways involving an alpha-amino acid. GOC:TermGenie alpha-amino acid metabolism GOC:TermGenie The chemical reactions and pathways involving organic hydroxy compound. pr 2012-11-13T12:54:27Z organic hydroxy compound metabolism biological_process GO:1901615 organic hydroxy compound metabolic process The chemical reactions and pathways involving organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic hydroxy compound. pr 2012-11-13T12:54:36Z organic hydroxy compound anabolism organic hydroxy compound biosynthesis organic hydroxy compound formation organic hydroxy compound synthesis biological_process GO:1901617 organic hydroxy compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound anabolism GOC:TermGenie organic hydroxy compound biosynthesis GOC:TermGenie organic hydroxy compound formation GOC:TermGenie organic hydroxy compound synthesis GOC:TermGenie The chemical reactions and pathways involving quinone. pr 2012-11-20T14:44:39Z GO:0042375 quinone metabolism biological_process quinone cofactor metabolic process quinone cofactor metabolism GO:1901661 quinone metabolic process The chemical reactions and pathways involving quinone. GOC:TermGenie GOC:go_curators GOC:pr quinone metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of vitamin A metabolic process. dph 2013-01-11T15:29:43Z regulation of vitamin A metabolism biological_process GO:1901738 regulation of vitamin A metabolic process Any process that modulates the frequency, rate or extent of vitamin A metabolic process. GOC:TermGenie PMID:18093975 regulation of vitamin A metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of mitochondrial DNA metabolic process. yaf 2013-02-01T10:05:04Z regulation of mitochondrial DNA metabolism regulation of mtDNA metabolic process regulation of mtDNA metabolism biological_process GO:1901858 regulation of mitochondrial DNA metabolic process Any process that modulates the frequency, rate or extent of mitochondrial DNA metabolic process. GOC:TermGenie GOC:yaf PMID:23150719 regulation of mitochondrial DNA metabolism GOC:TermGenie regulation of mtDNA metabolic process GOC:TermGenie regulation of mtDNA metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial DNA metabolic process. yaf 2013-02-01T10:05:09Z down regulation of mitochondrial DNA metabolic process down regulation of mitochondrial DNA metabolism down regulation of mtDNA metabolic process down regulation of mtDNA metabolism down-regulation of mitochondrial DNA metabolic process down-regulation of mitochondrial DNA metabolism down-regulation of mtDNA metabolic process down-regulation of mtDNA metabolism downregulation of mitochondrial DNA metabolic process downregulation of mitochondrial DNA metabolism downregulation of mtDNA metabolic process downregulation of mtDNA metabolism inhibition of mitochondrial DNA metabolism inhibition of mtDNA metabolic process inhibition of mtDNA metabolism negative regulation of mitochondrial DNA metabolism negative regulation of mtDNA metabolic process negative regulation of mtDNA metabolism inhibition of mitochondrial DNA metabolic process biological_process GO:1901859 negative regulation of mitochondrial DNA metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial DNA metabolic process. GOC:TermGenie GOC:yaf PMID:23150719 down regulation of mitochondrial DNA metabolic process GOC:TermGenie down regulation of mitochondrial DNA metabolism GOC:TermGenie down regulation of mtDNA metabolic process GOC:TermGenie down regulation of mtDNA metabolism GOC:TermGenie down-regulation of mitochondrial DNA metabolic process GOC:TermGenie down-regulation of mitochondrial DNA metabolism GOC:TermGenie down-regulation of mtDNA metabolic process GOC:TermGenie down-regulation of mtDNA metabolism GOC:TermGenie downregulation of mitochondrial DNA metabolic process GOC:TermGenie downregulation of mitochondrial DNA metabolism GOC:TermGenie downregulation of mtDNA metabolic process GOC:TermGenie downregulation of mtDNA metabolism GOC:TermGenie inhibition of mitochondrial DNA metabolism GOC:TermGenie inhibition of mtDNA metabolic process GOC:TermGenie inhibition of mtDNA metabolism GOC:TermGenie negative regulation of mitochondrial DNA metabolism GOC:TermGenie negative regulation of mtDNA metabolic process GOC:TermGenie negative regulation of mtDNA metabolism GOC:TermGenie inhibition of mitochondrial DNA metabolic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of mitochondrial DNA metabolic process. yaf 2013-02-01T10:05:14Z activation of mitochondrial DNA metabolism activation of mtDNA metabolic process activation of mtDNA metabolism positive regulation of mitochondrial DNA metabolism positive regulation of mtDNA metabolic process positive regulation of mtDNA metabolism up regulation of mitochondrial DNA metabolic process up regulation of mitochondrial DNA metabolism up regulation of mtDNA metabolic process up regulation of mtDNA metabolism up-regulation of mitochondrial DNA metabolic process up-regulation of mitochondrial DNA metabolism up-regulation of mtDNA metabolic process up-regulation of mtDNA metabolism upregulation of mitochondrial DNA metabolic process upregulation of mitochondrial DNA metabolism upregulation of mtDNA metabolic process upregulation of mtDNA metabolism activation of mitochondrial DNA metabolic process biological_process GO:1901860 positive regulation of mitochondrial DNA metabolic process Any process that activates or increases the frequency, rate or extent of mitochondrial DNA metabolic process. GOC:TermGenie GOC:yaf PMID:23150719 activation of mitochondrial DNA metabolism GOC:TermGenie activation of mtDNA metabolic process GOC:TermGenie activation of mtDNA metabolism GOC:TermGenie positive regulation of mitochondrial DNA metabolism GOC:TermGenie positive regulation of mtDNA metabolic process GOC:TermGenie positive regulation of mtDNA metabolism GOC:TermGenie up regulation of mitochondrial DNA metabolic process GOC:TermGenie up regulation of mitochondrial DNA metabolism GOC:TermGenie up regulation of mtDNA metabolic process GOC:TermGenie up regulation of mtDNA metabolism GOC:TermGenie up-regulation of mitochondrial DNA metabolic process GOC:TermGenie up-regulation of mitochondrial DNA metabolism GOC:TermGenie up-regulation of mtDNA metabolic process GOC:TermGenie up-regulation of mtDNA metabolism GOC:TermGenie upregulation of mitochondrial DNA metabolic process GOC:TermGenie upregulation of mitochondrial DNA metabolism GOC:TermGenie upregulation of mtDNA metabolic process GOC:TermGenie upregulation of mtDNA metabolism GOC:TermGenie activation of mitochondrial DNA metabolic process GOC:TermGenie Any process that modulates the frequency, rate or extent of cilium assembly. dph 2013-03-26T18:10:51Z regulation of ciliogenesis biological_process regulation of cilium biogenesis GO:1902017 regulation of cilium assembly Any process that modulates the frequency, rate or extent of cilium assembly. GOC:TermGenie GOC:cilia GOC:dph PMID:17719545 regulation of ciliogenesis GOC:TermGenie regulation of cilium biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly. dph 2013-03-26T18:10:56Z down regulation of ciliogenesis down regulation of cilium assembly down-regulation of ciliogenesis down-regulation of cilium assembly downregulation of ciliogenesis downregulation of cilium assembly inhibition of ciliogenesis negative regulation of ciliogenesis inhibition of cilium assembly biological_process down regulation of cilium biogenesis down-regulation of cilium biogenesis downregulation of cilium biogenesis inhibition of cilium biogenesis negative regulation of cilium biogenesis GO:1902018 negative regulation of cilium assembly Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly. GOC:TermGenie GOC:cilia GOC:dph PMID:17719545 down regulation of ciliogenesis GOC:TermGenie down regulation of cilium assembly GOC:TermGenie down-regulation of ciliogenesis GOC:TermGenie down-regulation of cilium assembly GOC:TermGenie downregulation of ciliogenesis GOC:TermGenie downregulation of cilium assembly GOC:TermGenie inhibition of ciliogenesis GOC:TermGenie negative regulation of ciliogenesis GOC:TermGenie inhibition of cilium assembly GOC:TermGenie down regulation of cilium biogenesis GOC:TermGenie down-regulation of cilium biogenesis GOC:TermGenie downregulation of cilium biogenesis GOC:TermGenie inhibition of cilium biogenesis GOC:TermGenie negative regulation of cilium biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of cilium-dependent cell motility. jl 2013-03-27T14:42:38Z regulation of cilium cell motility biological_process regulation of ciliary cell motility GO:1902019 regulation of cilium-dependent cell motility Any process that modulates the frequency, rate or extent of cilium-dependent cell motility. GOC:TermGenie GOC:cilia GOC:jl Any process that stops, prevents or reduces the frequency, rate or extent of cilium-dependent cell motility. jl 2013-03-27T14:42:42Z down regulation of ciliary cell motility down-regulation of ciliary cell motility downregulation of ciliary cell motility negative regulation of cilium cell motility inhibition of ciliary cell motility biological_process negative regulation of ciliary cell motility GO:1902020 negative regulation of cilium-dependent cell motility Any process that stops, prevents or reduces the frequency, rate or extent of cilium-dependent cell motility. GOC:TermGenie GOC:cilia GOC:jl down regulation of ciliary cell motility GOC:TermGenie down-regulation of ciliary cell motility GOC:TermGenie downregulation of ciliary cell motility GOC:TermGenie inhibition of ciliary cell motility GOC:TermGenie Any process that activates or increases the frequency, rate or extent of flagellated sperm motility. bf 2013-04-29T09:15:25Z activation of sperm movement positive regulation of sperm motility positive regulation of sperm movement up regulation of sperm motility up regulation of sperm movement up-regulation of sperm motility up-regulation of sperm movement upregulation of sperm motility upregulation of sperm movement activation of sperm motility biological_process GO:1902093 positive regulation of flagellated sperm motility Any process that activates or increases the frequency, rate or extent of flagellated sperm motility. GOC:TermGenie GOC:cilia GOC:jh2 GOC:krc PMID:7513657 activation of sperm movement GOC:TermGenie positive regulation of sperm movement GOC:TermGenie up regulation of sperm motility GOC:TermGenie up regulation of sperm movement GOC:TermGenie up-regulation of sperm motility GOC:TermGenie up-regulation of sperm movement GOC:TermGenie upregulation of sperm motility GOC:TermGenie upregulation of sperm movement GOC:TermGenie activation of sperm motility GOC:TermGenie Any process that modulates the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:42Z regulation of immune cell differentiation regulation of leucocyte differentiation biological_process GO:1902105 regulation of leukocyte differentiation Any process that modulates the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add regulation of immune cell differentiation GOC:TermGenie regulation of leucocyte differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:47Z down regulation of immune cell differentiation down regulation of leucocyte differentiation down regulation of leukocyte differentiation down-regulation of immune cell differentiation down-regulation of leucocyte differentiation down-regulation of leukocyte differentiation downregulation of immune cell differentiation downregulation of leucocyte differentiation downregulation of leukocyte differentiation negative regulation of immune cell differentiation negative regulation of leucocyte differentiation inhibition of immune cell differentiation inhibition of leucocyte differentiation inhibition of leukocyte differentiation biological_process GO:1902106 negative regulation of leukocyte differentiation Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add down regulation of immune cell differentiation GOC:TermGenie down regulation of leucocyte differentiation GOC:TermGenie down regulation of leukocyte differentiation GOC:TermGenie down-regulation of immune cell differentiation GOC:TermGenie down-regulation of leucocyte differentiation GOC:TermGenie down-regulation of leukocyte differentiation GOC:TermGenie downregulation of immune cell differentiation GOC:TermGenie downregulation of leucocyte differentiation GOC:TermGenie downregulation of leukocyte differentiation GOC:TermGenie negative regulation of immune cell differentiation GOC:TermGenie negative regulation of leucocyte differentiation GOC:TermGenie inhibition of immune cell differentiation GOC:TermGenie inhibition of leucocyte differentiation GOC:TermGenie inhibition of leukocyte differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of leukocyte differentiation. pr 2013-05-02T17:32:52Z positive regulation of immune cell differentiation positive regulation of leucocyte differentiation up regulation of immune cell differentiation up regulation of leucocyte differentiation up regulation of leukocyte differentiation up-regulation of immune cell differentiation up-regulation of leucocyte differentiation up-regulation of leukocyte differentiation upregulation of immune cell differentiation upregulation of leucocyte differentiation upregulation of leukocyte differentiation activation of immune cell differentiation activation of leucocyte differentiation activation of leukocyte differentiation biological_process GO:1902107 positive regulation of leukocyte differentiation Any process that activates or increases the frequency, rate or extent of leukocyte differentiation. GOC:TermGenie GOC:add positive regulation of immune cell differentiation GOC:TermGenie positive regulation of leucocyte differentiation GOC:TermGenie up regulation of immune cell differentiation GOC:TermGenie up regulation of leucocyte differentiation GOC:TermGenie up regulation of leukocyte differentiation GOC:TermGenie up-regulation of immune cell differentiation GOC:TermGenie up-regulation of leucocyte differentiation GOC:TermGenie up-regulation of leukocyte differentiation GOC:TermGenie upregulation of immune cell differentiation GOC:TermGenie upregulation of leucocyte differentiation GOC:TermGenie upregulation of leukocyte differentiation GOC:TermGenie activation of immune cell differentiation GOC:TermGenie activation of leucocyte differentiation GOC:TermGenie activation of leukocyte differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:21Z biological_process GO:1902115 regulation of organelle assembly Any process that modulates the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:31Z down regulation of organelle assembly down-regulation of organelle assembly downregulation of organelle assembly inhibition of organelle assembly biological_process GO:1902116 negative regulation of organelle assembly Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr down regulation of organelle assembly GOC:TermGenie down-regulation of organelle assembly GOC:TermGenie downregulation of organelle assembly GOC:TermGenie inhibition of organelle assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of organelle assembly. pr 2013-05-14T09:43:36Z up regulation of organelle assembly up-regulation of organelle assembly upregulation of organelle assembly activation of organelle assembly biological_process GO:1902117 positive regulation of organelle assembly Any process that activates or increases the frequency, rate or extent of organelle assembly. GOC:TermGenie GOC:pr up regulation of organelle assembly GOC:TermGenie up-regulation of organelle assembly GOC:TermGenie upregulation of organelle assembly GOC:TermGenie activation of organelle assembly GOC:TermGenie The chemical reactions and pathways involving erythrose 4-phosphate/phosphoenolpyruvate family amino acid. pr 2013-06-13T10:37:38Z erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolism biological_process GO:1902221 erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process The chemical reactions and pathways involving erythrose 4-phosphate/phosphoenolpyruvate family amino acid. GOC:TermGenie GOC:pr erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolism GOC:TermGenie The chemical reactions and pathways involving ketone body. pr 2013-06-13T10:37:54Z ketone body metabolism biological_process GO:1902224 ketone body metabolic process The chemical reactions and pathways involving ketone body. GOC:TermGenie GOC:pr ketone body metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:16Z regulation of apoptosis involved in morphogenesis biological_process regulation of apoptosis involved in development regulation of morphogenetic apoptosis GO:1902337 regulation of apoptotic process involved in morphogenesis Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 regulation of apoptosis involved in morphogenesis GOC:TermGenie regulation of apoptosis involved in development GOC:TermGenie regulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:25Z down regulation of apoptotic process involved in morphogenesis down-regulation of apoptotic process involved in morphogenesis downregulation of apoptotic process involved in morphogenesis down regulation of apoptosis involved in morphogenesis down-regulation of apoptosis involved in morphogenesis downregulation of apoptosis involved in morphogenesis inhibition of apoptosis involved in morphogenesis inhibition of apoptotic process involved in morphogenesis negative regulation of apoptosis involved in morphogenesis biological_process down regulation of apoptosis involved in development down regulation of morphogenetic apoptosis down-regulation of apoptosis involved in development down-regulation of morphogenetic apoptosis downregulation of apoptosis involved in development downregulation of morphogenetic apoptosis inhibition of apoptosis involved in development inhibition of morphogenetic apoptosis negative regulation of apoptosis involved in development negative regulation of morphogenetic apoptosis GO:1902338 negative regulation of apoptotic process involved in morphogenesis Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 down regulation of apoptotic process involved in morphogenesis GOC:TermGenie down-regulation of apoptotic process involved in morphogenesis GOC:TermGenie downregulation of apoptotic process involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in morphogenesis GOC:TermGenie down-regulation of apoptosis involved in morphogenesis GOC:TermGenie downregulation of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptotic process involved in morphogenesis GOC:TermGenie negative regulation of apoptosis involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in development GOC:TermGenie down regulation of morphogenetic apoptosis GOC:TermGenie down-regulation of apoptosis involved in development GOC:TermGenie down-regulation of morphogenetic apoptosis GOC:TermGenie downregulation of apoptosis involved in development GOC:TermGenie downregulation of morphogenetic apoptosis GOC:TermGenie inhibition of apoptosis involved in development GOC:TermGenie inhibition of morphogenetic apoptosis GOC:TermGenie negative regulation of apoptosis involved in development GOC:TermGenie negative regulation of morphogenetic apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:33Z up regulation of apoptotic process involved in morphogenesis up-regulation of apoptotic process involved in morphogenesis upregulation of apoptotic process involved in morphogenesis activation of apoptosis involved in morphogenesis activation of apoptotic process involved in morphogenesis positive regulation of apoptosis involved in morphogenesis up regulation of apoptosis involved in morphogenesis up-regulation of apoptosis involved in morphogenesis upregulation of apoptosis involved in morphogenesis biological_process activation of apoptosis involved in development activation of morphogenetic apoptosis positive regulation of apoptosis involved in development positive regulation of morphogenetic apoptosis up regulation of apoptosis involved in development up regulation of morphogenetic apoptosis up-regulation of apoptosis involved in development up-regulation of morphogenetic apoptosis upregulation of apoptosis involved in development upregulation of morphogenetic apoptosis GO:1902339 positive regulation of apoptotic process involved in morphogenesis Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 up regulation of apoptotic process involved in morphogenesis GOC:TermGenie up-regulation of apoptotic process involved in morphogenesis GOC:TermGenie upregulation of apoptotic process involved in morphogenesis GOC:TermGenie activation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptotic process involved in morphogenesis GOC:TermGenie positive regulation of apoptosis involved in morphogenesis GOC:TermGenie up regulation of apoptosis involved in morphogenesis GOC:TermGenie up-regulation of apoptosis involved in morphogenesis GOC:TermGenie upregulation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptosis involved in development GOC:TermGenie activation of morphogenetic apoptosis GOC:TermGenie positive regulation of apoptosis involved in development GOC:TermGenie positive regulation of morphogenetic apoptosis GOC:TermGenie up regulation of apoptosis involved in development GOC:TermGenie up regulation of morphogenetic apoptosis GOC:TermGenie up-regulation of apoptosis involved in development GOC:TermGenie up-regulation of morphogenetic apoptosis GOC:TermGenie upregulation of apoptosis involved in development GOC:TermGenie upregulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. dgf 2013-07-29T20:54:14Z down regulation of chromosome condensation down regulation of eukaryotic chromosome condensation down regulation of nuclear chromosome condensation down-regulation of chromosome condensation down-regulation of eukaryotic chromosome condensation down-regulation of nuclear chromosome condensation downregulation of chromosome condensation downregulation of eukaryotic chromosome condensation downregulation of nuclear chromosome condensation negative regulation of eukaryotic chromosome condensation negative regulation of nuclear chromosome condensation inhibition of chromosome condensation inhibition of eukaryotic chromosome condensation inhibition of nuclear chromosome condensation biological_process GO:1902340 negative regulation of chromosome condensation Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation. GOC:TermGenie PMID:23219725 down regulation of chromosome condensation GOC:TermGenie down regulation of eukaryotic chromosome condensation GOC:TermGenie down regulation of nuclear chromosome condensation GOC:TermGenie down-regulation of chromosome condensation GOC:TermGenie down-regulation of eukaryotic chromosome condensation GOC:TermGenie down-regulation of nuclear chromosome condensation GOC:TermGenie downregulation of chromosome condensation GOC:TermGenie downregulation of eukaryotic chromosome condensation GOC:TermGenie downregulation of nuclear chromosome condensation GOC:TermGenie negative regulation of eukaryotic chromosome condensation GOC:TermGenie negative regulation of nuclear chromosome condensation GOC:TermGenie inhibition of chromosome condensation GOC:TermGenie inhibition of eukaryotic chromosome condensation GOC:TermGenie inhibition of nuclear chromosome condensation GOC:TermGenie Any process that modulates the frequency, rate or extent of sperm capacitation. hjd 2013-11-12T21:17:03Z biological_process regulation of sperm activation GO:1902490 regulation of sperm capacitation Any process that modulates the frequency, rate or extent of sperm capacitation. GOC:TermGenie GOC:hjd PMID:22539676 regulation of sperm activation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of sperm capacitation. hjd 2013-11-12T21:17:12Z down regulation of sperm capacitation down-regulation of sperm capacitation downregulation of sperm capacitation inhibition of sperm capacitation biological_process down regulation of sperm activation down-regulation of sperm activation downregulation of sperm activation inhibition of sperm activation negative regulation of sperm activation GO:1902491 negative regulation of sperm capacitation Any process that stops, prevents or reduces the frequency, rate or extent of sperm capacitation. GOC:TermGenie GOC:hjd PMID:22539676 down regulation of sperm capacitation GOC:TermGenie down-regulation of sperm capacitation GOC:TermGenie downregulation of sperm capacitation GOC:TermGenie inhibition of sperm capacitation GOC:TermGenie down regulation of sperm activation GOC:TermGenie down-regulation of sperm activation GOC:TermGenie downregulation of sperm activation GOC:TermGenie inhibition of sperm activation GOC:TermGenie negative regulation of sperm activation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of sperm capacitation. hjd 2013-11-12T21:17:21Z up regulation of sperm capacitation up-regulation of sperm capacitation upregulation of sperm capacitation activation of sperm capacitation biological_process activation of sperm activation positive regulation of sperm activation up regulation of sperm activation up-regulation of sperm activation upregulation of sperm activation GO:1902492 positive regulation of sperm capacitation Any process that activates or increases the frequency, rate or extent of sperm capacitation. GOC:TermGenie GOC:hjd PMID:22539676 up regulation of sperm capacitation GOC:TermGenie up-regulation of sperm capacitation GOC:TermGenie upregulation of sperm capacitation GOC:TermGenie activation of sperm capacitation GOC:TermGenie activation of sperm activation GOC:TermGenie positive regulation of sperm activation GOC:TermGenie up regulation of sperm activation GOC:TermGenie up-regulation of sperm activation GOC:TermGenie upregulation of sperm activation GOC:TermGenie Any process that modulates the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:32:52Z GO:0010627 regulation of intracellular signaling cascade regulation of intracellular signaling chain regulation of intracellular protein kinase cascade regulation of intracellular signal transduction pathway regulation of signal transmission via intracellular cascade biological_process regulation of intracellular signaling pathway regulation of signal transduction via intracellular signaling cascade GO:1902531 regulation of intracellular signal transduction Any process that modulates the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb regulation of intracellular signaling cascade GOC:TermGenie regulation of intracellular signaling chain GOC:TermGenie regulation of intracellular signal transduction pathway GOC:TermGenie regulation of signal transmission via intracellular cascade GOC:TermGenie regulation of intracellular signaling pathway GOC:TermGenie regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:01Z GO:0010741 down regulation of intracellular signal transduction down regulation of intracellular signaling chain down-regulation of intracellular signal transduction down-regulation of intracellular signaling chain downregulation of intracellular signal transduction downregulation of intracellular signaling chain negative regulation of intracellular protein kinase cascade negative regulation of intracellular signaling cascade negative regulation of intracellular signaling chain down regulation of intracellular signal transduction pathway down regulation of intracellular signaling cascade down regulation of signal transmission via intracellular cascade down-regulation of intracellular signal transduction pathway downregulation of intracellular signal transduction pathway downregulation of intracellular signaling cascade downregulation of signal transmission via intracellular cascade inhibition of intracellular signal transduction inhibition of intracellular signal transduction pathway inhibition of intracellular signaling cascade inhibition of intracellular signaling chain inhibition of signal transmission via intracellular cascade negative regulation of intracellular signal transduction pathway negative regulation of signal transmission via intracellular cascade biological_process down regulation of intracellular signaling pathway down regulation of signal transduction via intracellular signaling cascade down-regulation of intracellular signaling cascade down-regulation of intracellular signaling pathway down-regulation of signal transduction via intracellular signaling cascade down-regulation of signal transmission via intracellular cascade downregulation of intracellular signaling pathway downregulation of signal transduction via intracellular signaling cascade inhibition of intracellular signaling pathway inhibition of signal transduction via intracellular signaling cascade negative regulation of intracellular signaling pathway negative regulation of signal transduction via intracellular signaling cascade GO:1902532 negative regulation of intracellular signal transduction Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb down regulation of intracellular signal transduction GOC:TermGenie down regulation of intracellular signaling chain GOC:TermGenie down-regulation of intracellular signal transduction GOC:TermGenie down-regulation of intracellular signaling chain GOC:TermGenie downregulation of intracellular signal transduction GOC:TermGenie downregulation of intracellular signaling chain GOC:TermGenie negative regulation of intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling chain GOC:TermGenie down regulation of intracellular signal transduction pathway GOC:TermGenie down regulation of intracellular signaling cascade GOC:TermGenie down regulation of signal transmission via intracellular cascade GOC:TermGenie down-regulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signaling cascade GOC:TermGenie downregulation of signal transmission via intracellular cascade GOC:TermGenie inhibition of intracellular signal transduction GOC:TermGenie inhibition of intracellular signal transduction pathway GOC:TermGenie inhibition of intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling chain GOC:TermGenie inhibition of signal transmission via intracellular cascade GOC:TermGenie negative regulation of intracellular signal transduction pathway GOC:TermGenie negative regulation of signal transmission via intracellular cascade GOC:TermGenie down regulation of intracellular signaling pathway GOC:TermGenie down regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling pathway GOC:TermGenie down-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of signal transmission via intracellular cascade GOC:TermGenie downregulation of intracellular signaling pathway GOC:TermGenie downregulation of signal transduction via intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling pathway GOC:TermGenie inhibition of signal transduction via intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling pathway GOC:TermGenie negative regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:10Z GO:0010740 positive regulation of intracellular signaling chain up regulation of intracellular signal transduction up regulation of intracellular signaling chain up-regulation of intracellular signal transduction up-regulation of intracellular signaling chain upregulation of intracellular signal transduction upregulation of intracellular signaling chain activation of intracellular signal transduction activation of intracellular signal transduction pathway activation of intracellular signaling cascade activation of intracellular signaling chain activation of signal transmission via intracellular cascade positive regulation of intracellular protein kinase cascade positive regulation of intracellular signal transduction pathway positive regulation of signal transmission via intracellular cascade up regulation of intracellular signal transduction pathway up regulation of signal transmission via intracellular cascade up-regulation of intracellular signal transduction pathway up-regulation of signal transmission via intracellular cascade upregulation of intracellular signal transduction pathway upregulation of signal transmission via intracellular cascade biological_process activation of intracellular signaling pathway activation of signal transduction via intracellular signaling cascade positive regulation of intracellular signaling cascade positive regulation of intracellular signaling pathway positive regulation of signal transduction via intracellular signaling cascade up regulation of intracellular signaling cascade up regulation of intracellular signaling pathway up regulation of signal transduction via intracellular signaling cascade up-regulation of intracellular signaling cascade up-regulation of intracellular signaling pathway up-regulation of signal transduction via intracellular signaling cascade upregulation of intracellular signaling cascade upregulation of intracellular signaling pathway upregulation of signal transduction via intracellular signaling cascade GO:1902533 positive regulation of intracellular signal transduction Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. GOC:BHF GOC:TermGenie GOC:dph GOC:signaling GOC:tb positive regulation of intracellular signaling chain GOC:TermGenie up regulation of intracellular signal transduction GOC:TermGenie up regulation of intracellular signaling chain GOC:TermGenie up-regulation of intracellular signal transduction GOC:TermGenie up-regulation of intracellular signaling chain GOC:TermGenie upregulation of intracellular signal transduction GOC:TermGenie upregulation of intracellular signaling chain GOC:TermGenie activation of intracellular signal transduction GOC:TermGenie activation of intracellular signal transduction pathway GOC:TermGenie activation of intracellular signaling cascade GOC:TermGenie activation of intracellular signaling chain GOC:TermGenie activation of signal transmission via intracellular cascade GOC:TermGenie positive regulation of intracellular signal transduction pathway GOC:TermGenie positive regulation of signal transmission via intracellular cascade GOC:TermGenie up regulation of intracellular signal transduction pathway GOC:TermGenie up regulation of signal transmission via intracellular cascade GOC:TermGenie up-regulation of intracellular signal transduction pathway GOC:TermGenie up-regulation of signal transmission via intracellular cascade GOC:TermGenie upregulation of intracellular signal transduction pathway GOC:TermGenie upregulation of signal transmission via intracellular cascade GOC:TermGenie activation of intracellular signaling pathway GOC:TermGenie activation of signal transduction via intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling pathway GOC:TermGenie positive regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling pathway GOC:TermGenie up regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling pathway GOC:TermGenie up-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling pathway GOC:TermGenie upregulation of signal transduction via intracellular signaling cascade GOC:TermGenie The chemical reactions and pathways involving secondary alcohol. tt 2014-01-22T10:14:52Z secondary alcohol metabolism biological_process GO:1902652 secondary alcohol metabolic process The chemical reactions and pathways involving secondary alcohol. GOC:TermGenie GOC:mengo_curators GO_REF:0000068 PMID:11288200 secondary alcohol metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion. mr 2014-02-24T16:09:28Z down regulation of prolactin secretion down-regulation of prolactin secretion downregulation of prolactin secretion inhibition of prolactin secretion biological_process GO:1902721 negative regulation of prolactin secretion Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion. GOC:TermGenie GO_REF:0000058 PMID:16159377 down regulation of prolactin secretion GOC:TermGenie down-regulation of prolactin secretion GOC:TermGenie downregulation of prolactin secretion GOC:TermGenie inhibition of prolactin secretion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of prolactin secretion. mr 2014-02-24T16:09:37Z up regulation of prolactin secretion up-regulation of prolactin secretion upregulation of prolactin secretion activation of prolactin secretion biological_process GO:1902722 positive regulation of prolactin secretion Any process that activates or increases the frequency, rate or extent of prolactin secretion. GOC:TermGenie GO_REF:0000058 PMID:16159377 up regulation of prolactin secretion GOC:TermGenie up-regulation of prolactin secretion GOC:TermGenie upregulation of prolactin secretion GOC:TermGenie activation of prolactin secretion GOC:TermGenie Any apoptotic process that is involved in anatomical structure development. pr 2014-02-28T13:09:43Z apoptotic cell death involved in anatomical structure development apoptotic cell death involved in development of an anatomical structure apoptotic process involved in anatomical structure development apoptotic process involved in development of an anatomical structure apoptotic programmed cell death involved in anatomical structure development apoptotic programmed cell death involved in development of an anatomical structure programmed cell death by apoptosis involved in anatomical structure development programmed cell death by apoptosis involved in development of an anatomical structure activation of apoptosis involved in anatomical structure development activation of apoptosis involved in development of an anatomical structure apoptosis involved in anatomical structure development apoptosis involved in development of an anatomical structure apoptosis signaling involved in anatomical structure development apoptosis signaling involved in development of an anatomical structure apoptotic program involved in anatomical structure development apoptotic program involved in development of an anatomical structure type I programmed cell death involved in anatomical structure development type I programmed cell death involved in development of an anatomical structure biological_process apoptosis activator activity involved in anatomical structure development apoptosis activator activity involved in development of an anatomical structure commitment to apoptosis involved in anatomical structure development commitment to apoptosis involved in development of an anatomical structure induction of apoptosis by p53 involved in anatomical structure development induction of apoptosis by p53 involved in development of an anatomical structure induction of apoptosis involved in anatomical structure development induction of apoptosis involved in development of an anatomical structure signaling (initiator) caspase activity involved in anatomical structure development signaling (initiator) caspase activity involved in development of an anatomical structure GO:1902742 apoptotic process involved in development Any apoptotic process that is involved in anatomical structure development. GOC:TermGenie GOC:mtg_apoptosis GOC:pg GO_REF:0000060 apoptotic cell death involved in anatomical structure development GOC:TermGenie apoptotic cell death involved in development of an anatomical structure GOC:TermGenie apoptotic process involved in development of an anatomical structure GOC:TermGenie apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis involved in anatomical structure development GOC:TermGenie apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis signaling involved in anatomical structure development GOC:TermGenie apoptosis signaling involved in development of an anatomical structure GOC:TermGenie apoptotic program involved in anatomical structure development GOC:TermGenie apoptotic program involved in development of an anatomical structure GOC:TermGenie type I programmed cell death involved in anatomical structure development GOC:TermGenie type I programmed cell death involved in development of an anatomical structure GOC:TermGenie apoptosis activator activity involved in anatomical structure development GOC:TermGenie apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie commitment to apoptosis involved in anatomical structure development GOC:TermGenie commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie induction of apoptosis involved in anatomical structure development GOC:TermGenie induction of apoptosis involved in development of an anatomical structure GOC:TermGenie signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any microtubule cytoskeleton organization that is involved in mitosis. vw 2014-04-02T14:19:38Z microtubule cytoskeleton organisation involved in mitosis microtubule dynamics involved in mitosis biological_process microtubule cytoskeleton organization and biogenesis involved in mitosis GO:1902850 microtubule cytoskeleton organization involved in mitosis Any microtubule cytoskeleton organization that is involved in mitosis. GOC:TermGenie GO_REF:0000060 PMID:18799626 microtubule cytoskeleton organisation involved in mitosis GOC:TermGenie microtubule dynamics involved in mitosis GOC:TermGenie microtubule cytoskeleton organization and biogenesis involved in mitosis GOC:TermGenie Any process that modulates the frequency, rate or extent of bone development. mr 2014-05-13T22:41:53Z biological_process GO:1903010 regulation of bone development Any process that modulates the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 Any process that stops, prevents or reduces the frequency, rate or extent of bone development. mr 2014-05-13T22:42:00Z down regulation of bone development down-regulation of bone development downregulation of bone development inhibition of bone development biological_process GO:1903011 negative regulation of bone development Any process that stops, prevents or reduces the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 down regulation of bone development GOC:TermGenie down-regulation of bone development GOC:TermGenie downregulation of bone development GOC:TermGenie inhibition of bone development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bone development. mr 2014-05-13T22:42:06Z up regulation of bone development up-regulation of bone development upregulation of bone development activation of bone development biological_process GO:1903012 positive regulation of bone development Any process that activates or increases the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 up regulation of bone development GOC:TermGenie up-regulation of bone development GOC:TermGenie upregulation of bone development GOC:TermGenie activation of bone development GOC:TermGenie Any process that modulates the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:46Z regulation of physiological response to wounding biological_process GO:1903034 regulation of response to wounding Any process that modulates the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 PMID:19164535 regulation of physiological response to wounding GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:52Z down regulation of physiological response to wounding down regulation of response to wounding down-regulation of physiological response to wounding down-regulation of response to wounding downregulation of physiological response to wounding downregulation of response to wounding negative regulation of physiological response to wounding inhibition of physiological response to wounding inhibition of response to wounding biological_process GO:1903035 negative regulation of response to wounding Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 PMID:19164535 down regulation of physiological response to wounding GOC:TermGenie down regulation of response to wounding GOC:TermGenie down-regulation of physiological response to wounding GOC:TermGenie down-regulation of response to wounding GOC:TermGenie downregulation of physiological response to wounding GOC:TermGenie downregulation of response to wounding GOC:TermGenie negative regulation of physiological response to wounding GOC:TermGenie inhibition of physiological response to wounding GOC:TermGenie inhibition of response to wounding GOC:TermGenie Any process that activates or increases the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:58Z positive regulation of physiological response to wounding up regulation of physiological response to wounding up regulation of response to wounding up-regulation of physiological response to wounding up-regulation of response to wounding upregulation of physiological response to wounding upregulation of response to wounding activation of physiological response to wounding activation of response to wounding biological_process GO:1903036 positive regulation of response to wounding Any process that activates or increases the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 PMID:19164535 positive regulation of physiological response to wounding GOC:TermGenie up regulation of physiological response to wounding GOC:TermGenie up regulation of response to wounding GOC:TermGenie up-regulation of physiological response to wounding GOC:TermGenie up-regulation of response to wounding GOC:TermGenie upregulation of physiological response to wounding GOC:TermGenie upregulation of response to wounding GOC:TermGenie activation of physiological response to wounding GOC:TermGenie activation of response to wounding GOC:TermGenie Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion. rl 2014-05-19T15:29:58Z regulation of leukocyte adhesion regulation of leukocyte cell adhesion biological_process GO:1903037 Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion regulation of leukocyte cell-cell adhesion Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21106532 regulation of leukocyte adhesion GOC:TermGenie regulation of leukocyte cell adhesion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion. rl 2014-05-19T15:30:05Z down regulation of leukocyte adhesion down regulation of leukocyte cell adhesion down regulation of leukocyte cell-cell adhesion down-regulation of leukocyte adhesion down-regulation of leukocyte cell adhesion down-regulation of leukocyte cell-cell adhesion downregulation of leukocyte adhesion downregulation of leukocyte cell adhesion downregulation of leukocyte cell-cell adhesion negative regulation of leukocyte adhesion negative regulation of leukocyte cell adhesion inhibition of leukocyte adhesion inhibition of leukocyte cell adhesion inhibition of leukocyte cell-cell adhesion biological_process GO:1903038 Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion negative regulation of leukocyte cell-cell adhesion Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21106532 down regulation of leukocyte adhesion GOC:TermGenie down regulation of leukocyte cell adhesion GOC:TermGenie down regulation of leukocyte cell-cell adhesion GOC:TermGenie down-regulation of leukocyte adhesion GOC:TermGenie down-regulation of leukocyte cell adhesion GOC:TermGenie down-regulation of leukocyte cell-cell adhesion GOC:TermGenie downregulation of leukocyte adhesion GOC:TermGenie downregulation of leukocyte cell adhesion GOC:TermGenie downregulation of leukocyte cell-cell adhesion GOC:TermGenie negative regulation of leukocyte adhesion GOC:TermGenie negative regulation of leukocyte cell adhesion GOC:TermGenie inhibition of leukocyte adhesion GOC:TermGenie inhibition of leukocyte cell adhesion GOC:TermGenie inhibition of leukocyte cell-cell adhesion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion. rl 2014-05-19T15:30:15Z positive regulation of leukocyte adhesion positive regulation of leukocyte cell adhesion up regulation of leukocyte adhesion up regulation of leukocyte cell adhesion up regulation of leukocyte cell-cell adhesion up-regulation of leukocyte adhesion up-regulation of leukocyte cell adhesion up-regulation of leukocyte cell-cell adhesion upregulation of leukocyte adhesion upregulation of leukocyte cell adhesion upregulation of leukocyte cell-cell adhesion activation of leukocyte adhesion activation of leukocyte cell adhesion activation of leukocyte cell-cell adhesion biological_process GO:1903039 Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion positive regulation of leukocyte cell-cell adhesion Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:21106532 positive regulation of leukocyte adhesion GOC:TermGenie positive regulation of leukocyte cell adhesion GOC:TermGenie up regulation of leukocyte adhesion GOC:TermGenie up regulation of leukocyte cell adhesion GOC:TermGenie up regulation of leukocyte cell-cell adhesion GOC:TermGenie up-regulation of leukocyte adhesion GOC:TermGenie up-regulation of leukocyte cell adhesion GOC:TermGenie up-regulation of leukocyte cell-cell adhesion GOC:TermGenie upregulation of leukocyte adhesion GOC:TermGenie upregulation of leukocyte cell adhesion GOC:TermGenie upregulation of leukocyte cell-cell adhesion GOC:TermGenie activation of leukocyte adhesion GOC:TermGenie activation of leukocyte cell adhesion GOC:TermGenie activation of leukocyte cell-cell adhesion GOC:TermGenie A process that is part of the meiotic cell cycle. jl 2014-05-22T14:22:28Z biological_process GO:1903046 meiotic cell cycle process A process that is part of the meiotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 A process that is part of the mitotic cell cycle. jl 2014-05-22T14:22:34Z biological_process GO:1903047 mitotic cell cycle process A process that is part of the mitotic cell cycle. GOC:TermGenie GOC:mtg_cell_cycle GO_REF:0000060 Any process that modulates the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:41Z regulation of extracellular matrix organisation biological_process regulation of extracellular matrix organization and biogenesis GO:1903053 regulation of extracellular matrix organization Any process that modulates the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 regulation of extracellular matrix organisation GOC:TermGenie regulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:47Z down regulation of extracellular matrix organisation down regulation of extracellular matrix organization down-regulation of extracellular matrix organisation down-regulation of extracellular matrix organization downregulation of extracellular matrix organisation downregulation of extracellular matrix organization negative regulation of extracellular matrix organisation inhibition of extracellular matrix organisation inhibition of extracellular matrix organization biological_process down regulation of extracellular matrix organization and biogenesis down-regulation of extracellular matrix organization and biogenesis downregulation of extracellular matrix organization and biogenesis inhibition of extracellular matrix organization and biogenesis negative regulation of extracellular matrix organization and biogenesis GO:1903054 negative regulation of extracellular matrix organization Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 down regulation of extracellular matrix organisation GOC:TermGenie down regulation of extracellular matrix organization GOC:TermGenie down-regulation of extracellular matrix organisation GOC:TermGenie down-regulation of extracellular matrix organization GOC:TermGenie downregulation of extracellular matrix organisation GOC:TermGenie downregulation of extracellular matrix organization GOC:TermGenie negative regulation of extracellular matrix organisation GOC:TermGenie inhibition of extracellular matrix organisation GOC:TermGenie inhibition of extracellular matrix organization GOC:TermGenie down regulation of extracellular matrix organization and biogenesis GOC:TermGenie down-regulation of extracellular matrix organization and biogenesis GOC:TermGenie downregulation of extracellular matrix organization and biogenesis GOC:TermGenie inhibition of extracellular matrix organization and biogenesis GOC:TermGenie negative regulation of extracellular matrix organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular matrix organization. rl 2014-05-23T17:15:53Z positive regulation of extracellular matrix organisation up regulation of extracellular matrix organisation up regulation of extracellular matrix organization up-regulation of extracellular matrix organisation up-regulation of extracellular matrix organization upregulation of extracellular matrix organisation upregulation of extracellular matrix organization activation of extracellular matrix organisation activation of extracellular matrix organization biological_process activation of extracellular matrix organization and biogenesis positive regulation of extracellular matrix organization and biogenesis up regulation of extracellular matrix organization and biogenesis up-regulation of extracellular matrix organization and biogenesis upregulation of extracellular matrix organization and biogenesis GO:1903055 positive regulation of extracellular matrix organization Any process that activates or increases the frequency, rate or extent of extracellular matrix organization. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:22357537 positive regulation of extracellular matrix organisation GOC:TermGenie up regulation of extracellular matrix organisation GOC:TermGenie up regulation of extracellular matrix organization GOC:TermGenie up-regulation of extracellular matrix organisation GOC:TermGenie up-regulation of extracellular matrix organization GOC:TermGenie upregulation of extracellular matrix organisation GOC:TermGenie upregulation of extracellular matrix organization GOC:TermGenie activation of extracellular matrix organisation GOC:TermGenie activation of extracellular matrix organization GOC:TermGenie activation of extracellular matrix organization and biogenesis GOC:TermGenie positive regulation of extracellular matrix organization and biogenesis GOC:TermGenie up regulation of extracellular matrix organization and biogenesis GOC:TermGenie up-regulation of extracellular matrix organization and biogenesis GOC:TermGenie upregulation of extracellular matrix organization and biogenesis GOC:TermGenie The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. cls 2014-06-25T15:47:09Z biological_process GO:1903131 mononuclear cell differentiation The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell. CL:0000842 GOC:TermGenie GO_REF:0000086 PMID:24759906 Any process that modulates the frequency, rate or extent of protein maturation. vw 2014-08-18T12:59:07Z biological_process GO:1903317 regulation of protein maturation Any process that modulates the frequency, rate or extent of protein maturation. GOC:TermGenie GOC:vw GO_REF:0000058 Any process that stops, prevents or reduces the frequency, rate or extent of protein maturation. vw 2014-08-18T12:59:15Z down regulation of protein maturation down-regulation of protein maturation downregulation of protein maturation inhibition of protein maturation biological_process GO:1903318 negative regulation of protein maturation Any process that stops, prevents or reduces the frequency, rate or extent of protein maturation. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of protein maturation GOC:TermGenie down-regulation of protein maturation GOC:TermGenie downregulation of protein maturation GOC:TermGenie inhibition of protein maturation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein maturation. vw 2014-08-18T12:59:23Z up regulation of protein maturation up-regulation of protein maturation upregulation of protein maturation activation of protein maturation biological_process GO:1903319 positive regulation of protein maturation Any process that activates or increases the frequency, rate or extent of protein maturation. GOC:TermGenie GOC:vw GO_REF:0000058 up regulation of protein maturation GOC:TermGenie up-regulation of protein maturation GOC:TermGenie upregulation of protein maturation GOC:TermGenie activation of protein maturation GOC:TermGenie Any process that modulates the frequency, rate or extent of nucleus organization. hjd 2014-08-20T19:36:16Z regulation of nuclear organisation regulation of nuclear organization biological_process regulation of nuclear morphology regulation of nuclear organization and biogenesis regulation of nucleus organization and biogenesis GO:1903353 regulation of nucleus organization Any process that modulates the frequency, rate or extent of nucleus organization. GOC:TermGenie GO_REF:0000058 PMID:16943282 regulation of nuclear organisation GOC:TermGenie regulation of nuclear organization GOC:TermGenie regulation of nuclear morphology GOC:TermGenie regulation of nuclear organization and biogenesis GOC:TermGenie regulation of nucleus organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:13Z biological_process GO:1903379 regulation of mitotic chromosome condensation Any process that modulates the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation. al 2014-08-26T13:57:29Z up regulation of mitotic chromosome condensation up-regulation of mitotic chromosome condensation upregulation of mitotic chromosome condensation activation of mitotic chromosome condensation biological_process GO:1903380 positive regulation of mitotic chromosome condensation Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:9490640 up regulation of mitotic chromosome condensation GOC:TermGenie up-regulation of mitotic chromosome condensation GOC:TermGenie upregulation of mitotic chromosome condensation GOC:TermGenie activation of mitotic chromosome condensation GOC:TermGenie Any process that modulates the frequency, rate or extent of cell maturation. jl 2014-09-15T13:31:23Z biological_process regulation of functional differentiation GO:1903429 regulation of cell maturation Any process that modulates the frequency, rate or extent of cell maturation. GOC:TermGenie GO_REF:0000058 PMID:17459944 regulation of functional differentiation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation. jl 2014-09-15T13:31:32Z down regulation of cell maturation down-regulation of cell maturation downregulation of cell maturation inhibition of cell maturation biological_process down regulation of functional differentiation down-regulation of functional differentiation downregulation of functional differentiation inhibition of functional differentiation negative regulation of functional differentiation GO:1903430 negative regulation of cell maturation Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation. GOC:TermGenie GO_REF:0000058 PMID:17459944 down regulation of cell maturation GOC:TermGenie down-regulation of cell maturation GOC:TermGenie downregulation of cell maturation GOC:TermGenie inhibition of cell maturation GOC:TermGenie down regulation of functional differentiation GOC:TermGenie down-regulation of functional differentiation GOC:TermGenie downregulation of functional differentiation GOC:TermGenie inhibition of functional differentiation GOC:TermGenie negative regulation of functional differentiation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cell maturation. jl 2014-09-15T13:31:41Z up regulation of cell maturation up-regulation of cell maturation upregulation of cell maturation activation of cell maturation biological_process activation of functional differentiation positive regulation of functional differentiation up regulation of functional differentiation up-regulation of functional differentiation upregulation of functional differentiation GO:1903431 positive regulation of cell maturation Any process that activates or increases the frequency, rate or extent of cell maturation. GOC:TermGenie GO_REF:0000058 PMID:17459944 up regulation of cell maturation GOC:TermGenie up-regulation of cell maturation GOC:TermGenie upregulation of cell maturation GOC:TermGenie activation of cell maturation GOC:TermGenie activation of functional differentiation GOC:TermGenie positive regulation of functional differentiation GOC:TermGenie up regulation of functional differentiation GOC:TermGenie up-regulation of functional differentiation GOC:TermGenie upregulation of functional differentiation GOC:TermGenie Any process that modulates the frequency, rate or extent of lactation. mr 2014-09-24T14:44:13Z biological_process GO:1903487 regulation of lactation Any process that modulates the frequency, rate or extent of lactation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:19563620 Any process that stops, prevents or reduces the frequency, rate or extent of lactation. mr 2014-09-24T14:44:22Z down regulation of lactation down-regulation of lactation downregulation of lactation inhibition of lactation biological_process GO:1903488 negative regulation of lactation Any process that stops, prevents or reduces the frequency, rate or extent of lactation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:19563620 down regulation of lactation GOC:TermGenie down-regulation of lactation GOC:TermGenie downregulation of lactation GOC:TermGenie inhibition of lactation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lactation. mr 2014-09-24T14:44:30Z up regulation of lactation up-regulation of lactation upregulation of lactation activation of lactation biological_process GO:1903489 positive regulation of lactation Any process that activates or increases the frequency, rate or extent of lactation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:19563620 up regulation of lactation GOC:TermGenie up-regulation of lactation GOC:TermGenie upregulation of lactation GOC:TermGenie activation of lactation GOC:TermGenie The chemical reactions and pathways involving mucopolysaccharide. dph 2014-10-01T21:55:47Z mucopolysaccharide metabolism biological_process GO:1903510 mucopolysaccharide metabolic process The chemical reactions and pathways involving mucopolysaccharide. GOC:TermGenie GOC:dph GO_REF:0000068 PMID:4236091 mucopolysaccharide metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of blood circulation. mr 2014-10-06T18:38:56Z biological_process regulation of hemolymph circulation GO:1903522 regulation of blood circulation Any process that modulates the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 regulation of hemolymph circulation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation. mr 2014-10-06T18:39:05Z down regulation of blood circulation down-regulation of blood circulation downregulation of blood circulation inhibition of blood circulation biological_process down regulation of hemolymph circulation down-regulation of hemolymph circulation downregulation of hemolymph circulation inhibition of hemolymph circulation negative regulation of hemolymph circulation GO:1903523 negative regulation of blood circulation Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 down regulation of blood circulation GOC:TermGenie down-regulation of blood circulation GOC:TermGenie downregulation of blood circulation GOC:TermGenie inhibition of blood circulation GOC:TermGenie down regulation of hemolymph circulation GOC:TermGenie down-regulation of hemolymph circulation GOC:TermGenie downregulation of hemolymph circulation GOC:TermGenie inhibition of hemolymph circulation GOC:TermGenie negative regulation of hemolymph circulation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of blood circulation. mr 2014-10-06T18:39:13Z up regulation of blood circulation up-regulation of blood circulation upregulation of blood circulation activation of blood circulation biological_process activation of hemolymph circulation positive regulation of hemolymph circulation up regulation of hemolymph circulation up-regulation of hemolymph circulation upregulation of hemolymph circulation GO:1903524 positive regulation of blood circulation Any process that activates or increases the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 up regulation of blood circulation GOC:TermGenie up-regulation of blood circulation GOC:TermGenie upregulation of blood circulation GOC:TermGenie activation of blood circulation GOC:TermGenie activation of hemolymph circulation GOC:TermGenie positive regulation of hemolymph circulation GOC:TermGenie up regulation of hemolymph circulation GOC:TermGenie up-regulation of hemolymph circulation GOC:TermGenie upregulation of hemolymph circulation GOC:TermGenie Any process that modulates the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:24:59Z regulation of cellular secretion biological_process GO:1903530 regulation of secretion by cell Any process that modulates the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 regulation of cellular secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:08Z down regulation of cellular secretion down regulation of secretion by cell down-regulation of cellular secretion down-regulation of secretion by cell downregulation of cellular secretion downregulation of secretion by cell negative regulation of cellular secretion inhibition of cellular secretion inhibition of secretion by cell biological_process GO:1903531 negative regulation of secretion by cell Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 down regulation of cellular secretion GOC:TermGenie down regulation of secretion by cell GOC:TermGenie down-regulation of cellular secretion GOC:TermGenie down-regulation of secretion by cell GOC:TermGenie downregulation of cellular secretion GOC:TermGenie downregulation of secretion by cell GOC:TermGenie negative regulation of cellular secretion GOC:TermGenie inhibition of cellular secretion GOC:TermGenie inhibition of secretion by cell GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:17Z positive regulation of cellular secretion up regulation of cellular secretion up regulation of secretion by cell up-regulation of cellular secretion up-regulation of secretion by cell upregulation of cellular secretion upregulation of secretion by cell activation of cellular secretion activation of secretion by cell biological_process GO:1903532 positive regulation of secretion by cell Any process that activates or increases the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 positive regulation of cellular secretion GOC:TermGenie up regulation of cellular secretion GOC:TermGenie up regulation of secretion by cell GOC:TermGenie up-regulation of cellular secretion GOC:TermGenie up-regulation of secretion by cell GOC:TermGenie upregulation of cellular secretion GOC:TermGenie upregulation of secretion by cell GOC:TermGenie activation of cellular secretion GOC:TermGenie activation of secretion by cell GOC:TermGenie Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:25Z regulation of extracellular vesicular exosome assembly biological_process GO:1903551 regulation of extracellular exosome assembly Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 regulation of extracellular vesicular exosome assembly GOC:vesicles Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:33Z down regulation of extracellular vesicular exosome assembly down-regulation of extracellular vesicular exosome assembly downregulation of extracellular vesicular exosome assembly negative regulation of extracellular vesicular exosome assembly inhibition of extracellular vesicular exosome assembly biological_process GO:1903552 negative regulation of extracellular exosome assembly Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 down regulation of extracellular vesicular exosome assembly GOC:TermGenie down-regulation of extracellular vesicular exosome assembly GOC:TermGenie downregulation of extracellular vesicular exosome assembly GOC:TermGenie negative regulation of extracellular vesicular exosome assembly GOC:vesicles inhibition of extracellular vesicular exosome assembly GOC:TermGenie Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. pga 2014-10-20T15:37:42Z up regulation of extracellular vesicular exosome assembly up-regulation of extracellular vesicular exosome assembly upregulation of extracellular vesicular exosome assembly activation of extracellular vesicular exosome assembly biological_process positive regulation of extracellular vesicular exosome assembly GO:1903553 positive regulation of extracellular exosome assembly Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly. GOC:TermGenie GO_REF:0000058 PMID:24105262 up regulation of extracellular vesicular exosome assembly GOC:TermGenie up-regulation of extracellular vesicular exosome assembly GOC:TermGenie upregulation of extracellular vesicular exosome assembly GOC:TermGenie activation of extracellular vesicular exosome assembly GOC:TermGenie positive regulation of extracellular vesicular exosome assembly GOC:vesicles Any vesicle that is part of the extracellular region. jl 2014-10-22T14:26:11Z cellular_component microparticle GO:1903561 extracellular vesicle Any vesicle that is part of the extracellular region. GOC:TermGenie GOC:pm GO_REF:0000064 PMID:24769233 microparticle GOC:vesicles Any process that modulates the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:11Z biological_process GO:1903564 regulation of protein localization to cilium Any process that modulates the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:20Z down regulation of protein localization to cilium down-regulation of protein localization to cilium downregulation of protein localization to cilium inhibition of protein localization to cilium biological_process GO:1903565 negative regulation of protein localization to cilium Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 down regulation of protein localization to cilium GOC:TermGenie down-regulation of protein localization to cilium GOC:TermGenie downregulation of protein localization to cilium GOC:TermGenie inhibition of protein localization to cilium GOC:TermGenie Any process that activates or increases the frequency, rate or extent of protein localization to cilium. krc 2014-10-24T20:58:28Z up regulation of protein localization to cilium up-regulation of protein localization to cilium upregulation of protein localization to cilium activation of protein localization to cilium biological_process GO:1903566 positive regulation of protein localization to cilium Any process that activates or increases the frequency, rate or extent of protein localization to cilium. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:22072986 up regulation of protein localization to cilium GOC:TermGenie up-regulation of protein localization to cilium GOC:TermGenie upregulation of protein localization to cilium GOC:TermGenie activation of protein localization to cilium GOC:TermGenie Any process that modulates the frequency, rate or extent of ATP metabolic process. sl 2014-10-30T19:04:24Z regulation of ATP metabolism biological_process GO:1903578 regulation of ATP metabolic process Any process that modulates the frequency, rate or extent of ATP metabolic process. GOC:TermGenie GO_REF:0000058 PMID:20695849 regulation of ATP metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of ATP metabolic process. sl 2014-10-30T19:04:33Z down regulation of ATP metabolic process down regulation of ATP metabolism down-regulation of ATP metabolic process down-regulation of ATP metabolism downregulation of ATP metabolic process downregulation of ATP metabolism negative regulation of ATP metabolism inhibition of ATP metabolic process inhibition of ATP metabolism biological_process GO:1903579 negative regulation of ATP metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of ATP metabolic process. GOC:TermGenie GO_REF:0000058 PMID:20695849 down regulation of ATP metabolic process GOC:TermGenie down regulation of ATP metabolism GOC:TermGenie down-regulation of ATP metabolic process GOC:TermGenie down-regulation of ATP metabolism GOC:TermGenie downregulation of ATP metabolic process GOC:TermGenie downregulation of ATP metabolism GOC:TermGenie negative regulation of ATP metabolism GOC:TermGenie inhibition of ATP metabolic process GOC:TermGenie inhibition of ATP metabolism GOC:TermGenie Any process that activates or increases the frequency, rate or extent of ATP metabolic process. sl 2014-10-30T19:04:42Z positive regulation of ATP metabolism up regulation of ATP metabolic process up regulation of ATP metabolism up-regulation of ATP metabolic process up-regulation of ATP metabolism upregulation of ATP metabolic process upregulation of ATP metabolism activation of ATP metabolic process activation of ATP metabolism biological_process GO:1903580 positive regulation of ATP metabolic process Any process that activates or increases the frequency, rate or extent of ATP metabolic process. GOC:TermGenie GO_REF:0000058 PMID:20695849 positive regulation of ATP metabolism GOC:TermGenie up regulation of ATP metabolic process GOC:TermGenie up regulation of ATP metabolism GOC:TermGenie up-regulation of ATP metabolic process GOC:TermGenie up-regulation of ATP metabolism GOC:TermGenie upregulation of ATP metabolic process GOC:TermGenie upregulation of ATP metabolism GOC:TermGenie activation of ATP metabolic process GOC:TermGenie activation of ATP metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:13Z regulation of blood cell biosynthesis regulation of blood cell formation regulation of haemopoiesis regulation of hematopoiesis biological_process GO:1903706 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. regulation of hemopoiesis Any process that modulates the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 regulation of blood cell biosynthesis GOC:TermGenie regulation of blood cell formation GOC:TermGenie regulation of haemopoiesis GOC:TermGenie regulation of hematopoiesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:21Z down regulation of blood cell biosynthesis down regulation of blood cell formation down regulation of haemopoiesis down regulation of hematopoiesis down regulation of hemopoiesis down-regulation of blood cell biosynthesis down-regulation of blood cell formation down-regulation of haemopoiesis down-regulation of hematopoiesis down-regulation of hemopoiesis downregulation of blood cell biosynthesis downregulation of blood cell formation downregulation of haemopoiesis downregulation of hematopoiesis downregulation of hemopoiesis negative regulation of blood cell biosynthesis negative regulation of blood cell formation negative regulation of haemopoiesis negative regulation of hematopoiesis inhibition of blood cell biosynthesis inhibition of blood cell formation inhibition of haemopoiesis inhibition of hematopoiesis inhibition of hemopoiesis biological_process GO:1903707 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. negative regulation of hemopoiesis Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 down regulation of blood cell biosynthesis GOC:TermGenie down regulation of blood cell formation GOC:TermGenie down regulation of haemopoiesis GOC:TermGenie down regulation of hematopoiesis GOC:TermGenie down regulation of hemopoiesis GOC:TermGenie down-regulation of blood cell biosynthesis GOC:TermGenie down-regulation of blood cell formation GOC:TermGenie down-regulation of haemopoiesis GOC:TermGenie down-regulation of hematopoiesis GOC:TermGenie down-regulation of hemopoiesis GOC:TermGenie downregulation of blood cell biosynthesis GOC:TermGenie downregulation of blood cell formation GOC:TermGenie downregulation of haemopoiesis GOC:TermGenie downregulation of hematopoiesis GOC:TermGenie downregulation of hemopoiesis GOC:TermGenie negative regulation of blood cell biosynthesis GOC:TermGenie negative regulation of blood cell formation GOC:TermGenie negative regulation of haemopoiesis GOC:TermGenie negative regulation of hematopoiesis GOC:TermGenie inhibition of blood cell biosynthesis GOC:TermGenie inhibition of blood cell formation GOC:TermGenie inhibition of haemopoiesis GOC:TermGenie inhibition of hematopoiesis GOC:TermGenie inhibition of hemopoiesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of hemopoiesis. pad 2014-12-04T15:34:30Z positive regulation of blood cell biosynthesis positive regulation of blood cell formation positive regulation of haemopoiesis positive regulation of hematopoiesis up regulation of blood cell biosynthesis up regulation of blood cell formation up regulation of haemopoiesis up regulation of hematopoiesis up regulation of hemopoiesis up-regulation of blood cell biosynthesis up-regulation of blood cell formation up-regulation of haemopoiesis up-regulation of hematopoiesis up-regulation of hemopoiesis upregulation of blood cell biosynthesis upregulation of blood cell formation upregulation of haemopoiesis upregulation of hematopoiesis upregulation of hemopoiesis activation of blood cell biosynthesis activation of blood cell formation activation of haemopoiesis activation of hematopoiesis activation of hemopoiesis biological_process GO:1903708 An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype. positive regulation of hemopoiesis Any process that activates or increases the frequency, rate or extent of hemopoiesis. GOC:PARL GOC:TermGenie GOC:pad GO_REF:0000058 PMID:20080761 positive regulation of blood cell biosynthesis GOC:TermGenie positive regulation of blood cell formation GOC:TermGenie positive regulation of haemopoiesis GOC:TermGenie positive regulation of hematopoiesis GOC:TermGenie up regulation of blood cell biosynthesis GOC:TermGenie up regulation of blood cell formation GOC:TermGenie up regulation of haemopoiesis GOC:TermGenie up regulation of hematopoiesis GOC:TermGenie up regulation of hemopoiesis GOC:TermGenie up-regulation of blood cell biosynthesis GOC:TermGenie up-regulation of blood cell formation GOC:TermGenie up-regulation of haemopoiesis GOC:TermGenie up-regulation of hematopoiesis GOC:TermGenie up-regulation of hemopoiesis GOC:TermGenie upregulation of blood cell biosynthesis GOC:TermGenie upregulation of blood cell formation GOC:TermGenie upregulation of haemopoiesis GOC:TermGenie upregulation of hematopoiesis GOC:TermGenie upregulation of hemopoiesis GOC:TermGenie activation of blood cell biosynthesis GOC:TermGenie activation of blood cell formation GOC:TermGenie activation of haemopoiesis GOC:TermGenie activation of hematopoiesis GOC:TermGenie activation of hemopoiesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:24Z down regulation of cellular protein localisation down regulation of cellular protein localization down-regulation of cellular protein localisation down-regulation of cellular protein localization downregulation of cellular protein localisation downregulation of cellular protein localization negative regulation of cellular protein localisation negative regulation of cellular protein localization inhibition of cellular protein localisation inhibition of cellular protein localization biological_process GO:1903828 negative regulation of protein localization Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of cellular protein localisation GOC:TermGenie down regulation of cellular protein localization GOC:TermGenie down-regulation of cellular protein localisation GOC:TermGenie down-regulation of cellular protein localization GOC:TermGenie downregulation of cellular protein localisation GOC:TermGenie downregulation of cellular protein localization GOC:TermGenie negative regulation of cellular protein localisation GOC:TermGenie inhibition of cellular protein localisation GOC:TermGenie inhibition of cellular protein localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of a protein localization. https://github.com/geneontology/go-ontology/issues/22021 jl 2015-01-20T14:32:33Z positive regulation of cellular protein localisation positive regulation of cellular protein localization up regulation of cellular protein localisation up regulation of cellular protein localization up-regulation of cellular protein localisation up-regulation of cellular protein localization upregulation of cellular protein localisation upregulation of cellular protein localization biological_process GO:1903829 positive regulation of protein localization Any process that activates or increases the frequency, rate or extent of a protein localization. GOC:TermGenie GOC:vw GO_REF:0000058 positive regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localization GOC:TermGenie up-regulation of cellular protein localisation GOC:TermGenie up-regulation of cellular protein localization GOC:TermGenie upregulation of cellular protein localisation GOC:TermGenie upregulation of cellular protein localization GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange. sl 2015-02-17T20:26:24Z down regulation of respiratory gaseous exchange down-regulation of respiratory gaseous exchange downregulation of respiratory gaseous exchange inhibition of respiratory gaseous exchange biological_process GO:1903941 negative regulation of respiratory gaseous exchange Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange. GOC:TermGenie GO_REF:0000058 PMID:22819705 down regulation of respiratory gaseous exchange GOC:TermGenie down-regulation of respiratory gaseous exchange GOC:TermGenie downregulation of respiratory gaseous exchange GOC:TermGenie inhibition of respiratory gaseous exchange GOC:TermGenie Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange. sl 2015-02-17T20:26:35Z up regulation of respiratory gaseous exchange up-regulation of respiratory gaseous exchange upregulation of respiratory gaseous exchange activation of respiratory gaseous exchange biological_process GO:1903942 positive regulation of respiratory gaseous exchange Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange. GOC:TermGenie GO_REF:0000058 PMID:22819705 up regulation of respiratory gaseous exchange GOC:TermGenie up-regulation of respiratory gaseous exchange GOC:TermGenie upregulation of respiratory gaseous exchange GOC:TermGenie activation of respiratory gaseous exchange GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain. sl 2015-03-18T20:33:57Z down regulation of nociception down regulation of sensory perception of pain down-regulation of nociception down-regulation of sensory perception of pain downregulation of nociception downregulation of sensory perception of pain negative regulation of nociception down regulation of perception of physiological pain down-regulation of perception of physiological pain downregulation of perception of physiological pain inhibition of nociception inhibition of perception of physiological pain inhibition of sensory perception of pain negative regulation of perception of physiological pain biological_process GO:1904057 negative regulation of sensory perception of pain Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain. GOC:TermGenie GO_REF:0000058 PMID:17167094 down regulation of nociception GOC:TermGenie down regulation of sensory perception of pain GOC:TermGenie down-regulation of nociception GOC:TermGenie down-regulation of sensory perception of pain GOC:TermGenie downregulation of nociception GOC:TermGenie downregulation of sensory perception of pain GOC:TermGenie negative regulation of nociception GOC:TermGenie down regulation of perception of physiological pain GOC:TermGenie down-regulation of perception of physiological pain GOC:TermGenie downregulation of perception of physiological pain GOC:TermGenie inhibition of nociception GOC:TermGenie inhibition of perception of physiological pain GOC:TermGenie inhibition of sensory perception of pain GOC:TermGenie negative regulation of perception of physiological pain GOC:TermGenie Any process that activates or increases the frequency, rate or extent of sensory perception of pain. sl 2015-03-18T20:34:03Z positive regulation of nociception up regulation of nociception up regulation of sensory perception of pain up-regulation of nociception up-regulation of sensory perception of pain upregulation of nociception upregulation of sensory perception of pain activation of nociception activation of perception of physiological pain activation of sensory perception of pain positive regulation of perception of physiological pain up regulation of perception of physiological pain up-regulation of perception of physiological pain upregulation of perception of physiological pain biological_process GO:1904058 positive regulation of sensory perception of pain Any process that activates or increases the frequency, rate or extent of sensory perception of pain. GOC:TermGenie GO_REF:0000058 PMID:17167094 positive regulation of nociception GOC:TermGenie up regulation of nociception GOC:TermGenie up regulation of sensory perception of pain GOC:TermGenie up-regulation of nociception GOC:TermGenie up-regulation of sensory perception of pain GOC:TermGenie upregulation of nociception GOC:TermGenie upregulation of sensory perception of pain GOC:TermGenie activation of nociception GOC:TermGenie activation of perception of physiological pain GOC:TermGenie activation of sensory perception of pain GOC:TermGenie positive regulation of perception of physiological pain GOC:TermGenie up regulation of perception of physiological pain GOC:TermGenie up-regulation of perception of physiological pain GOC:TermGenie upregulation of perception of physiological pain GOC:TermGenie Any process that modulates the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:19Z regulation of cell blebbing biological_process GO:1904170 regulation of bleb assembly Any process that modulates the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 regulation of cell blebbing GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:25Z down regulation of bleb assembly down regulation of cell blebbing down-regulation of bleb assembly down-regulation of cell blebbing downregulation of bleb assembly downregulation of cell blebbing negative regulation of cell blebbing inhibition of bleb assembly inhibition of cell blebbing biological_process GO:1904171 negative regulation of bleb assembly Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 down regulation of bleb assembly GOC:TermGenie down regulation of cell blebbing GOC:TermGenie down-regulation of bleb assembly GOC:TermGenie down-regulation of cell blebbing GOC:TermGenie downregulation of bleb assembly GOC:TermGenie downregulation of cell blebbing GOC:TermGenie negative regulation of cell blebbing GOC:TermGenie inhibition of bleb assembly GOC:TermGenie inhibition of cell blebbing GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:31Z positive regulation of cell blebbing up regulation of bleb assembly up regulation of cell blebbing up-regulation of bleb assembly up-regulation of cell blebbing upregulation of bleb assembly upregulation of cell blebbing activation of bleb assembly activation of cell blebbing biological_process GO:1904172 positive regulation of bleb assembly Any process that activates or increases the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 positive regulation of cell blebbing GOC:TermGenie up regulation of bleb assembly GOC:TermGenie up regulation of cell blebbing GOC:TermGenie up-regulation of bleb assembly GOC:TermGenie up-regulation of cell blebbing GOC:TermGenie upregulation of bleb assembly GOC:TermGenie upregulation of cell blebbing GOC:TermGenie activation of bleb assembly GOC:TermGenie activation of cell blebbing GOC:TermGenie Any process that modulates the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:28Z regulation of bile acid metabolism biological_process GO:1904251 regulation of bile acid metabolic process Any process that modulates the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 regulation of bile acid metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:35Z down regulation of bile acid metabolic process down regulation of bile acid metabolism down-regulation of bile acid metabolic process down-regulation of bile acid metabolism downregulation of bile acid metabolic process downregulation of bile acid metabolism negative regulation of bile acid metabolism inhibition of bile acid metabolic process inhibition of bile acid metabolism biological_process GO:1904252 negative regulation of bile acid metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 down regulation of bile acid metabolic process GOC:TermGenie down regulation of bile acid metabolism GOC:TermGenie down-regulation of bile acid metabolic process GOC:TermGenie down-regulation of bile acid metabolism GOC:TermGenie downregulation of bile acid metabolic process GOC:TermGenie downregulation of bile acid metabolism GOC:TermGenie negative regulation of bile acid metabolism GOC:TermGenie inhibition of bile acid metabolic process GOC:TermGenie inhibition of bile acid metabolism GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bile acid metabolic process. bf 2015-05-20T11:04:40Z positive regulation of bile acid metabolism up regulation of bile acid metabolic process up regulation of bile acid metabolism up-regulation of bile acid metabolic process up-regulation of bile acid metabolism upregulation of bile acid metabolic process upregulation of bile acid metabolism activation of bile acid metabolic process activation of bile acid metabolism biological_process GO:1904253 positive regulation of bile acid metabolic process Any process that activates or increases the frequency, rate or extent of bile acid metabolic process. GOC:TermGenie GOC:bf GO_REF:0000058 positive regulation of bile acid metabolism GOC:TermGenie up regulation of bile acid metabolic process GOC:TermGenie up regulation of bile acid metabolism GOC:TermGenie up-regulation of bile acid metabolic process GOC:TermGenie up-regulation of bile acid metabolism GOC:TermGenie upregulation of bile acid metabolic process GOC:TermGenie upregulation of bile acid metabolism GOC:TermGenie activation of bile acid metabolic process GOC:TermGenie activation of bile acid metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. sl 2015-06-09T23:18:42Z biological_process GO:1904304 regulation of gastro-intestinal system smooth muscle contraction Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:10821044 Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. sl 2015-06-09T23:18:48Z down regulation of gastro-intestinal system smooth muscle contraction down-regulation of gastro-intestinal system smooth muscle contraction downregulation of gastro-intestinal system smooth muscle contraction inhibition of gastro-intestinal system smooth muscle contraction biological_process GO:1904305 negative regulation of gastro-intestinal system smooth muscle contraction Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:10821044 down regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie down-regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie downregulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie inhibition of gastro-intestinal system smooth muscle contraction GOC:TermGenie Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. sl 2015-06-09T23:18:54Z up regulation of gastro-intestinal system smooth muscle contraction up-regulation of gastro-intestinal system smooth muscle contraction upregulation of gastro-intestinal system smooth muscle contraction activation of gastro-intestinal system smooth muscle contraction biological_process GO:1904306 positive regulation of gastro-intestinal system smooth muscle contraction Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction. GOC:TermGenie GO_REF:0000058 PMID:10821044 up regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie up-regulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie upregulation of gastro-intestinal system smooth muscle contraction GOC:TermGenie activation of gastro-intestinal system smooth muscle contraction GOC:TermGenie Any process that modulates the frequency, rate or extent of smooth muscle contraction involved in micturition. sl 2015-06-10T18:46:11Z biological_process regulation of smooth muscle contraction involved in urination regulation of urinary bladder smooth muscle contraction involved in micturition GO:1904318 regulation of smooth muscle contraction involved in micturition Any process that modulates the frequency, rate or extent of smooth muscle contraction involved in micturition. GOC:TermGenie GO_REF:0000058 PMID:18562635 regulation of smooth muscle contraction involved in urination GOC:TermGenie regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle contraction involved in micturition. sl 2015-06-10T18:46:17Z down regulation of smooth muscle contraction involved in micturition down-regulation of smooth muscle contraction involved in micturition downregulation of smooth muscle contraction involved in micturition inhibition of smooth muscle contraction involved in micturition biological_process down regulation of smooth muscle contraction involved in urination down regulation of urinary bladder smooth muscle contraction involved in micturition down-regulation of smooth muscle contraction involved in urination down-regulation of urinary bladder smooth muscle contraction involved in micturition downregulation of smooth muscle contraction involved in urination downregulation of urinary bladder smooth muscle contraction involved in micturition inhibition of smooth muscle contraction involved in urination inhibition of urinary bladder smooth muscle contraction involved in micturition negative regulation of smooth muscle contraction involved in urination negative regulation of urinary bladder smooth muscle contraction involved in micturition GO:1904319 negative regulation of smooth muscle contraction involved in micturition Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle contraction involved in micturition. GOC:TermGenie GO_REF:0000058 PMID:18562635 down regulation of smooth muscle contraction involved in micturition GOC:TermGenie down-regulation of smooth muscle contraction involved in micturition GOC:TermGenie downregulation of smooth muscle contraction involved in micturition GOC:TermGenie inhibition of smooth muscle contraction involved in micturition GOC:TermGenie down regulation of smooth muscle contraction involved in urination GOC:TermGenie down regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie down-regulation of smooth muscle contraction involved in urination GOC:TermGenie down-regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie downregulation of smooth muscle contraction involved in urination GOC:TermGenie downregulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie inhibition of smooth muscle contraction involved in urination GOC:TermGenie inhibition of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie negative regulation of smooth muscle contraction involved in urination GOC:TermGenie negative regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie Any process that activates or increases the frequency, rate or extent of smooth muscle contraction involved in micturition. sl 2015-06-10T18:46:23Z up regulation of smooth muscle contraction involved in micturition up-regulation of smooth muscle contraction involved in micturition upregulation of smooth muscle contraction involved in micturition activation of smooth muscle contraction involved in micturition biological_process activation of smooth muscle contraction involved in urination activation of urinary bladder smooth muscle contraction involved in micturition positive regulation of smooth muscle contraction involved in urination positive regulation of urinary bladder smooth muscle contraction involved in micturition up regulation of smooth muscle contraction involved in urination up regulation of urinary bladder smooth muscle contraction involved in micturition up-regulation of smooth muscle contraction involved in urination up-regulation of urinary bladder smooth muscle contraction involved in micturition upregulation of smooth muscle contraction involved in urination upregulation of urinary bladder smooth muscle contraction involved in micturition GO:1904320 positive regulation of smooth muscle contraction involved in micturition Any process that activates or increases the frequency, rate or extent of smooth muscle contraction involved in micturition. GOC:TermGenie GO_REF:0000058 PMID:18562635 up regulation of smooth muscle contraction involved in micturition GOC:TermGenie up-regulation of smooth muscle contraction involved in micturition GOC:TermGenie upregulation of smooth muscle contraction involved in micturition GOC:TermGenie activation of smooth muscle contraction involved in micturition GOC:TermGenie activation of smooth muscle contraction involved in urination GOC:TermGenie activation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie positive regulation of smooth muscle contraction involved in urination GOC:TermGenie positive regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie up regulation of smooth muscle contraction involved in urination GOC:TermGenie up regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie up-regulation of smooth muscle contraction involved in urination GOC:TermGenie up-regulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie upregulation of smooth muscle contraction involved in urination GOC:TermGenie upregulation of urinary bladder smooth muscle contraction involved in micturition GOC:TermGenie Any process that modulates the frequency, rate or extent of calcitonin secretion. sl 2015-06-15T17:54:52Z biological_process GO:1904362 regulation of calcitonin secretion Any process that modulates the frequency, rate or extent of calcitonin secretion. GOC:TermGenie GO_REF:0000058 PMID:11278900 Any process that stops, prevents or reduces the frequency, rate or extent of calcitonin secretion. sl 2015-06-15T17:54:58Z down regulation of calcitonin secretion down-regulation of calcitonin secretion downregulation of calcitonin secretion inhibition of calcitonin secretion biological_process GO:1904363 negative regulation of calcitonin secretion Any process that stops, prevents or reduces the frequency, rate or extent of calcitonin secretion. GOC:TermGenie GO_REF:0000058 PMID:11278900 down regulation of calcitonin secretion GOC:TermGenie down-regulation of calcitonin secretion GOC:TermGenie downregulation of calcitonin secretion GOC:TermGenie inhibition of calcitonin secretion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of calcitonin secretion. sl 2015-06-15T17:55:05Z up regulation of calcitonin secretion up-regulation of calcitonin secretion upregulation of calcitonin secretion activation of calcitonin secretion biological_process GO:1904364 positive regulation of calcitonin secretion Any process that activates or increases the frequency, rate or extent of calcitonin secretion. GOC:TermGenie GO_REF:0000058 PMID:11278900 up regulation of calcitonin secretion GOC:TermGenie up-regulation of calcitonin secretion GOC:TermGenie upregulation of calcitonin secretion GOC:TermGenie activation of calcitonin secretion GOC:TermGenie Any process that modulates the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:42Z regulation of secretory granule organisation biological_process regulation of secretory granule organization and biogenesis GO:1904409 regulation of secretory granule organization Any process that modulates the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 regulation of secretory granule organisation GOC:TermGenie regulation of secretory granule organization and biogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:49Z down regulation of secretory granule organisation down regulation of secretory granule organization down-regulation of secretory granule organisation down-regulation of secretory granule organization downregulation of secretory granule organisation downregulation of secretory granule organization negative regulation of secretory granule organisation inhibition of secretory granule organisation inhibition of secretory granule organization biological_process down regulation of secretory granule organization and biogenesis down-regulation of secretory granule organization and biogenesis downregulation of secretory granule organization and biogenesis inhibition of secretory granule organization and biogenesis negative regulation of secretory granule organization and biogenesis GO:1904410 negative regulation of secretory granule organization Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 down regulation of secretory granule organisation GOC:TermGenie down regulation of secretory granule organization GOC:TermGenie down-regulation of secretory granule organisation GOC:TermGenie down-regulation of secretory granule organization GOC:TermGenie downregulation of secretory granule organisation GOC:TermGenie downregulation of secretory granule organization GOC:TermGenie negative regulation of secretory granule organisation GOC:TermGenie inhibition of secretory granule organisation GOC:TermGenie inhibition of secretory granule organization GOC:TermGenie down regulation of secretory granule organization and biogenesis GOC:TermGenie down-regulation of secretory granule organization and biogenesis GOC:TermGenie downregulation of secretory granule organization and biogenesis GOC:TermGenie inhibition of secretory granule organization and biogenesis GOC:TermGenie negative regulation of secretory granule organization and biogenesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretory granule organization. sl 2015-06-25T19:40:55Z positive regulation of secretory granule organisation up regulation of secretory granule organisation up regulation of secretory granule organization up-regulation of secretory granule organisation up-regulation of secretory granule organization upregulation of secretory granule organisation upregulation of secretory granule organization activation of secretory granule organisation activation of secretory granule organization biological_process activation of secretory granule organization and biogenesis positive regulation of secretory granule organization and biogenesis up regulation of secretory granule organization and biogenesis up-regulation of secretory granule organization and biogenesis upregulation of secretory granule organization and biogenesis GO:1904411 positive regulation of secretory granule organization Any process that activates or increases the frequency, rate or extent of secretory granule organization. GOC:TermGenie GO_REF:0000058 PMID:15039777 positive regulation of secretory granule organisation GOC:TermGenie up regulation of secretory granule organisation GOC:TermGenie up regulation of secretory granule organization GOC:TermGenie up-regulation of secretory granule organisation GOC:TermGenie up-regulation of secretory granule organization GOC:TermGenie upregulation of secretory granule organisation GOC:TermGenie upregulation of secretory granule organization GOC:TermGenie activation of secretory granule organisation GOC:TermGenie activation of secretory granule organization GOC:TermGenie activation of secretory granule organization and biogenesis GOC:TermGenie positive regulation of secretory granule organization and biogenesis GOC:TermGenie up regulation of secretory granule organization and biogenesis GOC:TermGenie up-regulation of secretory granule organization and biogenesis GOC:TermGenie upregulation of secretory granule organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of intestinal absorption. rl 2015-07-13T15:58:47Z biological_process GO:1904478 regulation of intestinal absorption Any process that modulates the frequency, rate or extent of intestinal absorption. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:12469120 Any process that stops, prevents or reduces the frequency, rate or extent of intestinal absorption. rl 2015-07-13T15:58:54Z down regulation of intestinal absorption down-regulation of intestinal absorption downregulation of intestinal absorption inhibition of intestinal absorption biological_process GO:1904479 negative regulation of intestinal absorption Any process that stops, prevents or reduces the frequency, rate or extent of intestinal absorption. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:12469120 down regulation of intestinal absorption GOC:TermGenie down-regulation of intestinal absorption GOC:TermGenie downregulation of intestinal absorption GOC:TermGenie inhibition of intestinal absorption GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intestinal absorption. rl 2015-07-13T15:59:00Z up regulation of intestinal absorption up-regulation of intestinal absorption upregulation of intestinal absorption activation of intestinal absorption biological_process GO:1904480 positive regulation of intestinal absorption Any process that activates or increases the frequency, rate or extent of intestinal absorption. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:12469120 up regulation of intestinal absorption GOC:TermGenie up-regulation of intestinal absorption GOC:TermGenie upregulation of intestinal absorption GOC:TermGenie activation of intestinal absorption GOC:TermGenie The process in which glucose is transported across a membrane. vw 2015-09-04T17:20:16Z GO:0015758 biological_process glucose transport GO:1904659 glucose transmembrane transport The process in which glucose is transported across a membrane. GOC:TermGenie GO_REF:0000069 PMID:9090050 Any process that modulates the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:22Z regulation of somatic stem cell renewal biological_process GO:1904675 regulation of somatic stem cell division Any process that modulates the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 regulation of somatic stem cell renewal GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:28Z down regulation of somatic stem cell division down regulation of somatic stem cell renewal down-regulation of somatic stem cell division down-regulation of somatic stem cell renewal downregulation of somatic stem cell division downregulation of somatic stem cell renewal negative regulation of somatic stem cell renewal inhibition of somatic stem cell division inhibition of somatic stem cell renewal biological_process GO:1904676 negative regulation of somatic stem cell division Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 down regulation of somatic stem cell division GOC:TermGenie down regulation of somatic stem cell renewal GOC:TermGenie down-regulation of somatic stem cell division GOC:TermGenie down-regulation of somatic stem cell renewal GOC:TermGenie downregulation of somatic stem cell division GOC:TermGenie downregulation of somatic stem cell renewal GOC:TermGenie negative regulation of somatic stem cell renewal GOC:TermGenie inhibition of somatic stem cell division GOC:TermGenie inhibition of somatic stem cell renewal GOC:TermGenie Any process that activates or increases the frequency, rate or extent of somatic stem cell division. rph 2015-09-14T08:47:34Z positive regulation of somatic stem cell renewal up regulation of somatic stem cell division up regulation of somatic stem cell renewal up-regulation of somatic stem cell division up-regulation of somatic stem cell renewal upregulation of somatic stem cell division upregulation of somatic stem cell renewal activation of somatic stem cell division activation of somatic stem cell renewal biological_process GO:1904677 positive regulation of somatic stem cell division Any process that activates or increases the frequency, rate or extent of somatic stem cell division. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:19409607 positive regulation of somatic stem cell renewal GOC:TermGenie up regulation of somatic stem cell division GOC:TermGenie up regulation of somatic stem cell renewal GOC:TermGenie up-regulation of somatic stem cell division GOC:TermGenie up-regulation of somatic stem cell renewal GOC:TermGenie upregulation of somatic stem cell division GOC:TermGenie upregulation of somatic stem cell renewal GOC:TermGenie activation of somatic stem cell division GOC:TermGenie activation of somatic stem cell renewal GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:27Z down regulation of apoptotic cell death involved in anatomical structure development down regulation of apoptotic cell death involved in development of an anatomical structure down regulation of apoptotic process involved in anatomical structure development down regulation of apoptotic process involved in development down regulation of apoptotic process involved in development of an anatomical structure down regulation of apoptotic programmed cell death involved in anatomical structure development down regulation of apoptotic programmed cell death involved in development of an anatomical structure down regulation of programmed cell death by apoptosis involved in anatomical structure development down regulation of programmed cell death by apoptosis involved in development of an anatomical structure down-regulation of apoptotic cell death involved in anatomical structure development down-regulation of apoptotic cell death involved in development of an anatomical structure down-regulation of apoptotic process involved in anatomical structure development down-regulation of apoptotic process involved in development down-regulation of apoptotic process involved in development of an anatomical structure down-regulation of apoptotic programmed cell death involved in anatomical structure development down-regulation of apoptotic programmed cell death involved in development of an anatomical structure down-regulation of programmed cell death by apoptosis involved in anatomical structure development down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure downregulation of apoptotic cell death involved in anatomical structure development downregulation of apoptotic cell death involved in development of an anatomical structure downregulation of apoptotic process involved in anatomical structure development downregulation of apoptotic process involved in development downregulation of apoptotic process involved in development of an anatomical structure downregulation of apoptotic programmed cell death involved in anatomical structure development downregulation of apoptotic programmed cell death involved in development of an anatomical structure downregulation of programmed cell death by apoptosis involved in anatomical structure development downregulation of programmed cell death by apoptosis involved in development of an anatomical structure negative regulation of apoptotic cell death involved in anatomical structure development negative regulation of apoptotic cell death involved in development of an anatomical structure negative regulation of apoptotic process involved in anatomical structure development negative regulation of apoptotic process involved in development of an anatomical structure negative regulation of apoptotic programmed cell death involved in anatomical structure development negative regulation of apoptotic programmed cell death involved in development of an anatomical structure negative regulation of programmed cell death by apoptosis involved in anatomical structure development negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure down regulation of activation of apoptosis involved in anatomical structure development down regulation of activation of apoptosis involved in development of an anatomical structure down regulation of apoptosis involved in anatomical structure development down regulation of apoptosis involved in development of an anatomical structure down regulation of apoptosis signaling involved in anatomical structure development down regulation of apoptosis signaling involved in development of an anatomical structure down regulation of apoptotic program involved in anatomical structure development down regulation of apoptotic program involved in development of an anatomical structure down regulation of type I programmed cell death involved in anatomical structure development down regulation of type I programmed cell death involved in development of an anatomical structure down-regulation of activation of apoptosis involved in anatomical structure development down-regulation of activation of apoptosis involved in development of an anatomical structure down-regulation of apoptosis involved in anatomical structure development down-regulation of apoptosis involved in development of an anatomical structure down-regulation of apoptosis signaling involved in anatomical structure development down-regulation of apoptosis signaling involved in development of an anatomical structure down-regulation of apoptotic program involved in anatomical structure development down-regulation of apoptotic program involved in development of an anatomical structure down-regulation of type I programmed cell death involved in anatomical structure development down-regulation of type I programmed cell death involved in development of an anatomical structure downregulation of activation of apoptosis involved in anatomical structure development downregulation of activation of apoptosis involved in development of an anatomical structure downregulation of apoptosis involved in anatomical structure development downregulation of apoptosis involved in development of an anatomical structure downregulation of apoptosis signaling involved in anatomical structure development downregulation of apoptosis signaling involved in development of an anatomical structure downregulation of apoptotic program involved in anatomical structure development downregulation of apoptotic program involved in development of an anatomical structure downregulation of type I programmed cell death involved in anatomical structure development downregulation of type I programmed cell death involved in development of an anatomical structure inhibition of activation of apoptosis involved in anatomical structure development inhibition of activation of apoptosis involved in development of an anatomical structure inhibition of apoptosis involved in anatomical structure development inhibition of apoptosis involved in development of an anatomical structure inhibition of apoptosis signaling involved in anatomical structure development inhibition of apoptosis signaling involved in development of an anatomical structure inhibition of apoptotic cell death involved in anatomical structure development inhibition of apoptotic cell death involved in development of an anatomical structure inhibition of apoptotic process involved in anatomical structure development inhibition of apoptotic process involved in development inhibition of apoptotic process involved in development of an anatomical structure inhibition of apoptotic program involved in anatomical structure development inhibition of apoptotic program involved in development of an anatomical structure inhibition of apoptotic programmed cell death involved in anatomical structure development inhibition of apoptotic programmed cell death involved in development of an anatomical structure inhibition of programmed cell death by apoptosis involved in anatomical structure development inhibition of programmed cell death by apoptosis involved in development of an anatomical structure inhibition of type I programmed cell death involved in anatomical structure development inhibition of type I programmed cell death involved in development of an anatomical structure negative regulation of activation of apoptosis involved in anatomical structure development negative regulation of activation of apoptosis involved in development of an anatomical structure negative regulation of apoptosis involved in anatomical structure development negative regulation of apoptosis involved in development of an anatomical structure negative regulation of apoptosis signaling involved in anatomical structure development negative regulation of apoptosis signaling involved in development of an anatomical structure negative regulation of apoptotic program involved in anatomical structure development negative regulation of apoptotic program involved in development of an anatomical structure negative regulation of type I programmed cell death involved in anatomical structure development negative regulation of type I programmed cell death involved in development of an anatomical structure biological_process down regulation of apoptosis activator activity involved in anatomical structure development down regulation of apoptosis activator activity involved in development of an anatomical structure down regulation of commitment to apoptosis involved in anatomical structure development down regulation of commitment to apoptosis involved in development of an anatomical structure down regulation of induction of apoptosis by p53 involved in anatomical structure development down regulation of induction of apoptosis by p53 involved in development of an anatomical structure down regulation of induction of apoptosis involved in anatomical structure development down regulation of induction of apoptosis involved in development of an anatomical structure down regulation of signaling (initiator) caspase activity involved in anatomical structure development down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure down-regulation of apoptosis activator activity involved in anatomical structure development down-regulation of apoptosis activator activity involved in development of an anatomical structure down-regulation of commitment to apoptosis involved in anatomical structure development down-regulation of commitment to apoptosis involved in development of an anatomical structure down-regulation of induction of apoptosis by p53 involved in anatomical structure development down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure down-regulation of induction of apoptosis involved in anatomical structure development down-regulation of induction of apoptosis involved in development of an anatomical structure down-regulation of signaling (initiator) caspase activity involved in anatomical structure development down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure downregulation of apoptosis activator activity involved in anatomical structure development downregulation of apoptosis activator activity involved in development of an anatomical structure downregulation of commitment to apoptosis involved in anatomical structure development downregulation of commitment to apoptosis involved in development of an anatomical structure downregulation of induction of apoptosis by p53 involved in anatomical structure development downregulation of induction of apoptosis by p53 involved in development of an anatomical structure downregulation of induction of apoptosis involved in anatomical structure development downregulation of induction of apoptosis involved in development of an anatomical structure downregulation of signaling (initiator) caspase activity involved in anatomical structure development downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure inhibition of apoptosis activator activity involved in anatomical structure development inhibition of apoptosis activator activity involved in development of an anatomical structure inhibition of commitment to apoptosis involved in anatomical structure development inhibition of commitment to apoptosis involved in development of an anatomical structure inhibition of induction of apoptosis by p53 involved in anatomical structure development inhibition of induction of apoptosis by p53 involved in development of an anatomical structure inhibition of induction of apoptosis involved in anatomical structure development inhibition of induction of apoptosis involved in development of an anatomical structure inhibition of signaling (initiator) caspase activity involved in anatomical structure development inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure negative regulation of apoptosis activator activity involved in anatomical structure development negative regulation of apoptosis activator activity involved in development of an anatomical structure negative regulation of commitment to apoptosis involved in anatomical structure development negative regulation of commitment to apoptosis involved in development of an anatomical structure negative regulation of induction of apoptosis by p53 involved in anatomical structure development negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure negative regulation of induction of apoptosis involved in anatomical structure development negative regulation of induction of apoptosis involved in development of an anatomical structure negative regulation of signaling (initiator) caspase activity involved in anatomical structure development negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904746 U4PR86 in PMID:22801495 inferred from mutant phenotype negative regulation of apoptotic process involved in development Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 down regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down regulation of apoptotic process involved in development GOC:TermGenie down regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic process involved in development GOC:TermGenie down-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic process involved in anatomical structure development GOC:TermGenie downregulation of apoptotic process involved in development GOC:TermGenie downregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie downregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic process involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie downregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic program involved in anatomical structure development GOC:TermGenie downregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie downregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of activation of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis signaling involved in anatomical structure development GOC:TermGenie inhibition of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic process involved in anatomical structure development GOC:TermGenie inhibition of apoptotic process involved in development GOC:TermGenie inhibition of apoptotic process involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic program involved in anatomical structure development GOC:TermGenie inhibition of apoptotic program involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie inhibition of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of type I programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic program involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie negative regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie downregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie downregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie downregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis activator activity involved in anatomical structure development GOC:TermGenie inhibition of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie inhibition of commitment to apoptosis involved in anatomical structure development GOC:TermGenie inhibition of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie negative regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:34Z positive regulation of apoptotic cell death involved in anatomical structure development positive regulation of apoptotic cell death involved in development of an anatomical structure positive regulation of apoptotic process involved in anatomical structure development positive regulation of apoptotic process involved in development of an anatomical structure positive regulation of apoptotic programmed cell death involved in anatomical structure development positive regulation of apoptotic programmed cell death involved in development of an anatomical structure positive regulation of programmed cell death by apoptosis involved in anatomical structure development positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure up regulation of apoptotic cell death involved in anatomical structure development up regulation of apoptotic cell death involved in development of an anatomical structure up regulation of apoptotic process involved in anatomical structure development up regulation of apoptotic process involved in development up regulation of apoptotic process involved in development of an anatomical structure up regulation of apoptotic programmed cell death involved in anatomical structure development up regulation of apoptotic programmed cell death involved in development of an anatomical structure up regulation of programmed cell death by apoptosis involved in anatomical structure development up regulation of programmed cell death by apoptosis involved in development of an anatomical structure up-regulation of apoptotic cell death involved in anatomical structure development up-regulation of apoptotic cell death involved in development of an anatomical structure up-regulation of apoptotic process involved in anatomical structure development up-regulation of apoptotic process involved in development up-regulation of apoptotic process involved in development of an anatomical structure up-regulation of apoptotic programmed cell death involved in anatomical structure development up-regulation of apoptotic programmed cell death involved in development of an anatomical structure up-regulation of programmed cell death by apoptosis involved in anatomical structure development up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure upregulation of apoptotic cell death involved in anatomical structure development upregulation of apoptotic cell death involved in development of an anatomical structure upregulation of apoptotic process involved in anatomical structure development upregulation of apoptotic process involved in development upregulation of apoptotic process involved in development of an anatomical structure upregulation of apoptotic programmed cell death involved in anatomical structure development upregulation of apoptotic programmed cell death involved in development of an anatomical structure upregulation of programmed cell death by apoptosis involved in anatomical structure development upregulation of programmed cell death by apoptosis involved in development of an anatomical structure activation of activation of apoptosis involved in anatomical structure development activation of activation of apoptosis involved in development of an anatomical structure activation of apoptosis involved in anatomical structure development activation of apoptosis involved in development of an anatomical structure activation of apoptosis signaling involved in anatomical structure development activation of apoptosis signaling involved in development of an anatomical structure activation of apoptotic cell death involved in anatomical structure development activation of apoptotic cell death involved in development of an anatomical structure activation of apoptotic process involved in anatomical structure development activation of apoptotic process involved in development activation of apoptotic process involved in development of an anatomical structure activation of apoptotic program involved in anatomical structure development activation of apoptotic program involved in development of an anatomical structure activation of apoptotic programmed cell death involved in anatomical structure development activation of apoptotic programmed cell death involved in development of an anatomical structure activation of programmed cell death by apoptosis involved in anatomical structure development activation of programmed cell death by apoptosis involved in development of an anatomical structure activation of type I programmed cell death involved in anatomical structure development activation of type I programmed cell death involved in development of an anatomical structure positive regulation of activation of apoptosis involved in anatomical structure development positive regulation of activation of apoptosis involved in development of an anatomical structure positive regulation of apoptosis involved in anatomical structure development positive regulation of apoptosis involved in development of an anatomical structure positive regulation of apoptosis signaling involved in anatomical structure development positive regulation of apoptosis signaling involved in development of an anatomical structure positive regulation of apoptotic program involved in anatomical structure development positive regulation of apoptotic program involved in development of an anatomical structure positive regulation of type I programmed cell death involved in anatomical structure development positive regulation of type I programmed cell death involved in development of an anatomical structure up regulation of activation of apoptosis involved in anatomical structure development up regulation of activation of apoptosis involved in development of an anatomical structure up regulation of apoptosis involved in anatomical structure development up regulation of apoptosis involved in development of an anatomical structure up regulation of apoptosis signaling involved in anatomical structure development up regulation of apoptosis signaling involved in development of an anatomical structure up regulation of apoptotic program involved in anatomical structure development up regulation of apoptotic program involved in development of an anatomical structure up regulation of type I programmed cell death involved in anatomical structure development up regulation of type I programmed cell death involved in development of an anatomical structure up-regulation of activation of apoptosis involved in anatomical structure development up-regulation of activation of apoptosis involved in development of an anatomical structure up-regulation of apoptosis involved in anatomical structure development up-regulation of apoptosis involved in development of an anatomical structure up-regulation of apoptosis signaling involved in anatomical structure development up-regulation of apoptosis signaling involved in development of an anatomical structure up-regulation of apoptotic program involved in anatomical structure development up-regulation of apoptotic program involved in development of an anatomical structure up-regulation of type I programmed cell death involved in anatomical structure development up-regulation of type I programmed cell death involved in development of an anatomical structure upregulation of activation of apoptosis involved in anatomical structure development upregulation of activation of apoptosis involved in development of an anatomical structure upregulation of apoptosis involved in anatomical structure development upregulation of apoptosis involved in development of an anatomical structure upregulation of apoptosis signaling involved in anatomical structure development upregulation of apoptosis signaling involved in development of an anatomical structure upregulation of apoptotic program involved in anatomical structure development upregulation of apoptotic program involved in development of an anatomical structure upregulation of type I programmed cell death involved in anatomical structure development upregulation of type I programmed cell death involved in development of an anatomical structure biological_process activation of apoptosis activator activity involved in anatomical structure development activation of apoptosis activator activity involved in development of an anatomical structure activation of commitment to apoptosis involved in anatomical structure development activation of commitment to apoptosis involved in development of an anatomical structure activation of induction of apoptosis by p53 involved in anatomical structure development activation of induction of apoptosis by p53 involved in development of an anatomical structure activation of induction of apoptosis involved in anatomical structure development activation of induction of apoptosis involved in development of an anatomical structure activation of signaling (initiator) caspase activity involved in anatomical structure development activation of signaling (initiator) caspase activity involved in development of an anatomical structure positive regulation of apoptosis activator activity involved in anatomical structure development positive regulation of apoptosis activator activity involved in development of an anatomical structure positive regulation of commitment to apoptosis involved in anatomical structure development positive regulation of commitment to apoptosis involved in development of an anatomical structure positive regulation of induction of apoptosis by p53 involved in anatomical structure development positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure positive regulation of induction of apoptosis involved in anatomical structure development positive regulation of induction of apoptosis involved in development of an anatomical structure positive regulation of signaling (initiator) caspase activity involved in anatomical structure development positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure up regulation of apoptosis activator activity involved in anatomical structure development up regulation of apoptosis activator activity involved in development of an anatomical structure up regulation of commitment to apoptosis involved in anatomical structure development up regulation of commitment to apoptosis involved in development of an anatomical structure up regulation of induction of apoptosis by p53 involved in anatomical structure development up regulation of induction of apoptosis by p53 involved in development of an anatomical structure up regulation of induction of apoptosis involved in anatomical structure development up regulation of induction of apoptosis involved in development of an anatomical structure up regulation of signaling (initiator) caspase activity involved in anatomical structure development up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure up-regulation of apoptosis activator activity involved in anatomical structure development up-regulation of apoptosis activator activity involved in development of an anatomical structure up-regulation of commitment to apoptosis involved in anatomical structure development up-regulation of commitment to apoptosis involved in development of an anatomical structure up-regulation of induction of apoptosis by p53 involved in anatomical structure development up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure up-regulation of induction of apoptosis involved in anatomical structure development up-regulation of induction of apoptosis involved in development of an anatomical structure up-regulation of signaling (initiator) caspase activity involved in anatomical structure development up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure upregulation of apoptosis activator activity involved in anatomical structure development upregulation of apoptosis activator activity involved in development of an anatomical structure upregulation of commitment to apoptosis involved in anatomical structure development upregulation of commitment to apoptosis involved in development of an anatomical structure upregulation of induction of apoptosis by p53 involved in anatomical structure development upregulation of induction of apoptosis by p53 involved in development of an anatomical structure upregulation of induction of apoptosis involved in anatomical structure development upregulation of induction of apoptosis involved in development of an anatomical structure upregulation of signaling (initiator) caspase activity involved in anatomical structure development upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904747 U4PR86 in PMID:22801495 inferred from mutant phenotype positive regulation of apoptotic process involved in development Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 positive regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic process involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up regulation of apoptotic process involved in development GOC:TermGenie up regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic process involved in development GOC:TermGenie up-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic process involved in anatomical structure development GOC:TermGenie upregulation of apoptotic process involved in development GOC:TermGenie upregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie upregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis signaling involved in anatomical structure development GOC:TermGenie activation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie activation of apoptotic cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptotic process involved in anatomical structure development GOC:TermGenie activation of apoptotic process involved in development GOC:TermGenie activation of apoptotic process involved in development of an anatomical structure GOC:TermGenie activation of apoptotic program involved in anatomical structure development GOC:TermGenie activation of apoptotic program involved in development of an anatomical structure GOC:TermGenie activation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie activation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of type I programmed cell death involved in anatomical structure development GOC:TermGenie activation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic program involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie positive regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie upregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic program involved in anatomical structure development GOC:TermGenie upregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie upregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie activation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie activation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie activation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie activation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie positive regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie upregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie upregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie upregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T15:02:28Z regulation of apoptotic cell death involved in anatomical structure development regulation of apoptotic cell death involved in development of an anatomical structure regulation of apoptotic process involved in anatomical structure development regulation of apoptotic process involved in development of an anatomical structure regulation of apoptotic programmed cell death involved in anatomical structure development regulation of apoptotic programmed cell death involved in development of an anatomical structure regulation of programmed cell death by apoptosis involved in anatomical structure development regulation of programmed cell death by apoptosis involved in development of an anatomical structure regulation of activation of apoptosis involved in anatomical structure development regulation of activation of apoptosis involved in development of an anatomical structure regulation of apoptosis involved in anatomical structure development regulation of apoptosis involved in development of an anatomical structure regulation of apoptosis signaling involved in anatomical structure development regulation of apoptosis signaling involved in development of an anatomical structure regulation of apoptotic program involved in anatomical structure development regulation of apoptotic program involved in development of an anatomical structure regulation of type I programmed cell death involved in anatomical structure development regulation of type I programmed cell death involved in development of an anatomical structure biological_process regulation of apoptosis activator activity involved in anatomical structure development regulation of apoptosis activator activity involved in development of an anatomical structure regulation of commitment to apoptosis involved in anatomical structure development regulation of commitment to apoptosis involved in development of an anatomical structure regulation of induction of apoptosis by p53 involved in anatomical structure development regulation of induction of apoptosis by p53 involved in development of an anatomical structure regulation of induction of apoptosis involved in anatomical structure development regulation of induction of apoptosis involved in development of an anatomical structure regulation of signaling (initiator) caspase activity involved in anatomical structure development regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GO:1904748 Q10943 in PMID:22801495, inferred from mutant phenotype regulation of apoptotic process involved in development Any process that modulates the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic process involved in anatomical structure development GOC:TermGenie regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic program involved in anatomical structure development GOC:TermGenie regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:24Z down regulation of establishment of protein localisation down regulation of establishment of protein localization down regulation of protein positioning down regulation of protein recruitment down-regulation of establishment of protein localisation down-regulation of establishment of protein localization down-regulation of protein positioning down-regulation of protein recruitment downregulation of establishment of protein localisation downregulation of establishment of protein localization downregulation of protein positioning downregulation of protein recruitment negative regulation of establishment of protein localisation negative regulation of protein positioning negative regulation of protein recruitment inhibition of establishment of protein localisation inhibition of establishment of protein localization inhibition of protein positioning inhibition of protein recruitment biological_process GO:1904950 negative regulation of establishment of protein localization Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 down regulation of establishment of protein localisation GOC:TermGenie down regulation of establishment of protein localization GOC:TermGenie down regulation of protein positioning GOC:TermGenie down regulation of protein recruitment GOC:TermGenie down-regulation of establishment of protein localisation GOC:TermGenie down-regulation of establishment of protein localization GOC:TermGenie down-regulation of protein positioning GOC:TermGenie down-regulation of protein recruitment GOC:TermGenie downregulation of establishment of protein localisation GOC:TermGenie downregulation of establishment of protein localization GOC:TermGenie downregulation of protein positioning GOC:TermGenie downregulation of protein recruitment GOC:TermGenie negative regulation of establishment of protein localisation GOC:TermGenie negative regulation of protein positioning GOC:TermGenie negative regulation of protein recruitment GOC:TermGenie inhibition of establishment of protein localisation GOC:TermGenie inhibition of establishment of protein localization GOC:TermGenie inhibition of protein positioning GOC:TermGenie inhibition of protein recruitment GOC:TermGenie Any process that activates or increases the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:32Z positive regulation of establishment of protein localisation positive regulation of protein positioning positive regulation of protein recruitment up regulation of establishment of protein localisation up regulation of establishment of protein localization up regulation of protein positioning up regulation of protein recruitment up-regulation of establishment of protein localisation up-regulation of establishment of protein localization up-regulation of protein positioning up-regulation of protein recruitment upregulation of establishment of protein localisation upregulation of establishment of protein localization upregulation of protein positioning upregulation of protein recruitment activation of establishment of protein localisation activation of establishment of protein localization activation of protein positioning activation of protein recruitment biological_process GO:1904951 positive regulation of establishment of protein localization Any process that activates or increases the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 positive regulation of establishment of protein localisation GOC:TermGenie positive regulation of protein positioning GOC:TermGenie positive regulation of protein recruitment GOC:TermGenie up regulation of establishment of protein localisation GOC:TermGenie up regulation of establishment of protein localization GOC:TermGenie up regulation of protein positioning GOC:TermGenie up regulation of protein recruitment GOC:TermGenie up-regulation of establishment of protein localisation GOC:TermGenie up-regulation of establishment of protein localization GOC:TermGenie up-regulation of protein positioning GOC:TermGenie up-regulation of protein recruitment GOC:TermGenie upregulation of establishment of protein localisation GOC:TermGenie upregulation of establishment of protein localization GOC:TermGenie upregulation of protein positioning GOC:TermGenie upregulation of protein recruitment GOC:TermGenie activation of establishment of protein localisation GOC:TermGenie activation of establishment of protein localization GOC:TermGenie activation of protein positioning GOC:TermGenie activation of protein recruitment GOC:TermGenie Any process that modulates the frequency, rate or extent of mitochondrial translational elongation. hjd 2016-03-25T17:37:03Z regulation of mitochondrial translation elongation biological_process GO:1905082 regulation of mitochondrial translational elongation Any process that modulates the frequency, rate or extent of mitochondrial translational elongation. GOC:TermGenie GO_REF:0000058 PMID:25738458 regulation of mitochondrial translation elongation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial translational elongation. hjd 2016-03-25T17:37:13Z down regulation of mitochondrial translation elongation down regulation of mitochondrial translational elongation down-regulation of mitochondrial translation elongation down-regulation of mitochondrial translational elongation downregulation of mitochondrial translation elongation downregulation of mitochondrial translational elongation negative regulation of mitochondrial translation elongation inhibition of mitochondrial translation elongation inhibition of mitochondrial translational elongation biological_process GO:1905083 negative regulation of mitochondrial translational elongation Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial translational elongation. GOC:TermGenie GO_REF:0000058 PMID:25738458 down regulation of mitochondrial translation elongation GOC:TermGenie down regulation of mitochondrial translational elongation GOC:TermGenie down-regulation of mitochondrial translation elongation GOC:TermGenie down-regulation of mitochondrial translational elongation GOC:TermGenie downregulation of mitochondrial translation elongation GOC:TermGenie downregulation of mitochondrial translational elongation GOC:TermGenie negative regulation of mitochondrial translation elongation GOC:TermGenie inhibition of mitochondrial translation elongation GOC:TermGenie inhibition of mitochondrial translational elongation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of mitochondrial translational elongation. hjd 2016-03-25T17:37:22Z positive regulation of mitochondrial translation elongation up regulation of mitochondrial translation elongation up regulation of mitochondrial translational elongation up-regulation of mitochondrial translation elongation up-regulation of mitochondrial translational elongation upregulation of mitochondrial translation elongation upregulation of mitochondrial translational elongation activation of mitochondrial translation elongation activation of mitochondrial translational elongation biological_process GO:1905084 positive regulation of mitochondrial translational elongation Any process that activates or increases the frequency, rate or extent of mitochondrial translational elongation. GOC:TermGenie GO_REF:0000058 PMID:25738458 positive regulation of mitochondrial translation elongation GOC:TermGenie up regulation of mitochondrial translation elongation GOC:TermGenie up regulation of mitochondrial translational elongation GOC:TermGenie up-regulation of mitochondrial translation elongation GOC:TermGenie up-regulation of mitochondrial translational elongation GOC:TermGenie upregulation of mitochondrial translation elongation GOC:TermGenie upregulation of mitochondrial translational elongation GOC:TermGenie activation of mitochondrial translation elongation GOC:TermGenie activation of mitochondrial translational elongation GOC:TermGenie Any process that modulates the frequency, rate or extent of membrane invagination. bf 2016-04-18T15:43:54Z biological_process GO:1905153 regulation of membrane invagination Any process that modulates the frequency, rate or extent of membrane invagination. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:26589353 Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. bf 2016-04-18T15:44:04Z down regulation of membrane invagination down-regulation of membrane invagination downregulation of membrane invagination inhibition of membrane invagination biological_process GO:1905154 negative regulation of membrane invagination Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 PMID:26589353 down regulation of membrane invagination GOC:TermGenie down-regulation of membrane invagination GOC:TermGenie downregulation of membrane invagination GOC:TermGenie inhibition of membrane invagination GOC:TermGenie Any process that activates or increases the frequency, rate or extent of membrane invagination. bf 2016-04-18T15:44:12Z up regulation of membrane invagination up-regulation of membrane invagination upregulation of membrane invagination activation of membrane invagination biological_process GO:1905155 positive regulation of membrane invagination Any process that activates or increases the frequency, rate or extent of membrane invagination. GOC:PARL GOC:TermGenie GOC:bf GO_REF:0000058 up regulation of membrane invagination GOC:TermGenie up-regulation of membrane invagination GOC:TermGenie upregulation of membrane invagination GOC:TermGenie activation of membrane invagination GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. vw 2016-06-03T08:41:08Z biological_process GO:1905213 negative regulation of mitotic chromosome condensation Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation. GOC:TermGenie GO_REF:0000058 PMID:23219725 Any process that modulates the frequency, rate or extent of epithelial tube formation. bhm 2016-06-20T09:35:41Z biological_process GO:1905276 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of epithelial tube formation Any process that modulates the frequency, rate or extent of epithelial tube formation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation. bhm 2016-06-20T09:35:49Z down regulation of epithelial tube formation down-regulation of epithelial tube formation downregulation of epithelial tube formation inhibition of epithelial tube formation biological_process GO:1905277 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of epithelial tube formation Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 down regulation of epithelial tube formation GOC:TermGenie down-regulation of epithelial tube formation GOC:TermGenie downregulation of epithelial tube formation GOC:TermGenie inhibition of epithelial tube formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of epithelial tube formation. bhm 2016-06-20T09:35:57Z up regulation of epithelial tube formation up-regulation of epithelial tube formation upregulation of epithelial tube formation activation of epithelial tube formation biological_process GO:1905278 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of epithelial tube formation Any process that activates or increases the frequency, rate or extent of epithelial tube formation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 up regulation of epithelial tube formation GOC:TermGenie up-regulation of epithelial tube formation GOC:TermGenie upregulation of epithelial tube formation GOC:TermGenie activation of epithelial tube formation GOC:TermGenie Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium. bhm 2016-07-22T07:13:49Z regulation of epithelium morphogenesis biological_process GO:1905330 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of morphogenesis of an epithelium Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 regulation of epithelium morphogenesis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium. bhm 2016-07-22T07:13:57Z down regulation of epithelium morphogenesis down regulation of morphogenesis of an epithelium down-regulation of epithelium morphogenesis down-regulation of morphogenesis of an epithelium downregulation of epithelium morphogenesis downregulation of morphogenesis of an epithelium negative regulation of epithelium morphogenesis inhibition of epithelium morphogenesis inhibition of morphogenesis of an epithelium biological_process GO:1905331 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of morphogenesis of an epithelium Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 down regulation of epithelium morphogenesis GOC:TermGenie down regulation of morphogenesis of an epithelium GOC:TermGenie down-regulation of epithelium morphogenesis GOC:TermGenie down-regulation of morphogenesis of an epithelium GOC:TermGenie downregulation of epithelium morphogenesis GOC:TermGenie downregulation of morphogenesis of an epithelium GOC:TermGenie negative regulation of epithelium morphogenesis GOC:TermGenie inhibition of epithelium morphogenesis GOC:TermGenie inhibition of morphogenesis of an epithelium GOC:TermGenie Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium. bhm 2016-07-22T07:14:05Z positive regulation of epithelium morphogenesis up regulation of epithelium morphogenesis up regulation of morphogenesis of an epithelium up-regulation of epithelium morphogenesis up-regulation of morphogenesis of an epithelium upregulation of epithelium morphogenesis upregulation of morphogenesis of an epithelium activation of epithelium morphogenesis activation of morphogenesis of an epithelium biological_process GO:1905332 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of morphogenesis of an epithelium Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:25745997 positive regulation of epithelium morphogenesis GOC:TermGenie up regulation of epithelium morphogenesis GOC:TermGenie up regulation of morphogenesis of an epithelium GOC:TermGenie up-regulation of epithelium morphogenesis GOC:TermGenie up-regulation of morphogenesis of an epithelium GOC:TermGenie upregulation of epithelium morphogenesis GOC:TermGenie upregulation of morphogenesis of an epithelium GOC:TermGenie activation of epithelium morphogenesis GOC:TermGenie activation of morphogenesis of an epithelium GOC:TermGenie The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. pr 2016-08-04T14:49:43Z cilial transition zone assembly cilial transition zone formation ciliary transition zone formation cilium transition zone assembly cilium transition zone formation biological_process GO:1905349 ciliary transition zone assembly The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. GOC:TermGenie GOC:cilia GO_REF:0000079 PMID:21725307 PMID:23644468 PMID:24448408 PMID:26595381 PMID:26982032 cilial transition zone assembly GOC:TermGenie cilial transition zone formation GOC:TermGenie ciliary transition zone formation GOC:TermGenie cilium transition zone assembly GOC:TermGenie cilium transition zone formation GOC:TermGenie Any process that modulates the frequency, rate or extent of motile cilium assembly. krc 2016-09-27T18:27:47Z biological_process regulation of motile primary cilia assembly regulation of motile primary cilia formation regulation of motile primary cilium assembly regulation of motile primary cilium formation regulation of nodal cilium assembly regulation of nodal cilium formation GO:1905503 regulation of motile cilium assembly Any process that modulates the frequency, rate or extent of motile cilium assembly. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:25294941 regulation of motile primary cilia assembly GOC:TermGenie regulation of motile primary cilia formation GOC:TermGenie regulation of motile primary cilium formation GOC:TermGenie regulation of nodal cilium assembly GOC:TermGenie regulation of nodal cilium formation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of motile cilium assembly. krc 2016-09-27T18:27:55Z inhibition of motile primary cilia assembly inhibition of motile primary cilia formation inhibition of motile primary cilium assembly inhibition of motile primary cilium formation biological_process down regulation of motile primary cilia assembly down regulation of motile primary cilia formation down regulation of motile primary cilium assembly down regulation of motile primary cilium formation down regulation of nodal cilium assembly down regulation of nodal cilium formation down-regulation of motile primary cilia assembly down-regulation of motile primary cilia formation down-regulation of motile primary cilium assembly down-regulation of motile primary cilium formation down-regulation of nodal cilium assembly down-regulation of nodal cilium formation downregulation of motile primary cilia assembly downregulation of motile primary cilia formation downregulation of motile primary cilium assembly downregulation of motile primary cilium formation downregulation of nodal cilium assembly downregulation of nodal cilium formation inhibition of nodal cilium assembly inhibition of nodal cilium formation negative regulation of motile primary cilia assembly negative regulation of motile primary cilia formation negative regulation of motile primary cilium assembly negative regulation of motile primary cilium formation negative regulation of nodal cilium assembly negative regulation of nodal cilium formation GO:1905504 negative regulation of motile cilium assembly Any process that stops, prevents or reduces the frequency, rate or extent of motile cilium assembly. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:25294941 inhibition of motile primary cilia assembly GOC:TermGenie inhibition of motile primary cilia formation GOC:TermGenie inhibition of motile primary cilium assembly GOC:TermGenie inhibition of motile primary cilium formation GOC:TermGenie down regulation of motile primary cilia assembly GOC:TermGenie down regulation of motile primary cilia formation GOC:TermGenie down regulation of motile primary cilium assembly GOC:TermGenie down regulation of motile primary cilium formation GOC:TermGenie down regulation of nodal cilium assembly GOC:TermGenie down regulation of nodal cilium formation GOC:TermGenie down-regulation of motile primary cilia assembly GOC:TermGenie down-regulation of motile primary cilia formation GOC:TermGenie down-regulation of motile primary cilium assembly GOC:TermGenie down-regulation of motile primary cilium formation GOC:TermGenie down-regulation of nodal cilium assembly GOC:TermGenie down-regulation of nodal cilium formation GOC:TermGenie downregulation of motile primary cilia assembly GOC:TermGenie downregulation of motile primary cilia formation GOC:TermGenie downregulation of motile primary cilium assembly GOC:TermGenie downregulation of motile primary cilium formation GOC:TermGenie downregulation of nodal cilium assembly GOC:TermGenie downregulation of nodal cilium formation GOC:TermGenie inhibition of nodal cilium assembly GOC:TermGenie inhibition of nodal cilium formation GOC:TermGenie negative regulation of motile primary cilia assembly GOC:TermGenie negative regulation of motile primary cilia formation GOC:TermGenie negative regulation of motile primary cilium formation GOC:TermGenie negative regulation of nodal cilium assembly GOC:TermGenie negative regulation of nodal cilium formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of motile cilium assembly. krc 2016-09-27T18:28:03Z activation of motile primary cilia assembly activation of motile primary cilia formation activation of motile primary cilium assembly activation of motile primary cilium formation biological_process activation of nodal cilium assembly activation of nodal cilium formation positive regulation of motile primary cilia assembly positive regulation of motile primary cilia formation positive regulation of motile primary cilium assembly positive regulation of motile primary cilium formation positive regulation of nodal cilium assembly positive regulation of nodal cilium formation up regulation of motile primary cilia assembly up regulation of motile primary cilia formation up regulation of motile primary cilium assembly up regulation of motile primary cilium formation up regulation of nodal cilium assembly up regulation of nodal cilium formation up-regulation of motile primary cilia assembly up-regulation of motile primary cilia formation up-regulation of motile primary cilium assembly up-regulation of motile primary cilium formation up-regulation of nodal cilium assembly up-regulation of nodal cilium formation upregulation of motile primary cilia assembly upregulation of motile primary cilia formation upregulation of motile primary cilium assembly upregulation of motile primary cilium formation upregulation of nodal cilium assembly upregulation of nodal cilium formation GO:1905505 positive regulation of motile cilium assembly Any process that activates or increases the frequency, rate or extent of motile cilium assembly. GOC:TermGenie GOC:cilia GOC:krc GO_REF:0000058 PMID:25294941 activation of motile primary cilia assembly GOC:TermGenie activation of motile primary cilia formation GOC:TermGenie activation of motile primary cilium assembly GOC:TermGenie activation of motile primary cilium formation GOC:TermGenie activation of nodal cilium assembly GOC:TermGenie activation of nodal cilium formation GOC:TermGenie positive regulation of motile primary cilia assembly GOC:TermGenie positive regulation of motile primary cilia formation GOC:TermGenie positive regulation of motile primary cilium formation GOC:TermGenie positive regulation of nodal cilium assembly GOC:TermGenie positive regulation of nodal cilium formation GOC:TermGenie up regulation of motile primary cilia assembly GOC:TermGenie up regulation of motile primary cilia formation GOC:TermGenie up regulation of motile primary cilium assembly GOC:TermGenie up regulation of motile primary cilium formation GOC:TermGenie up regulation of nodal cilium assembly GOC:TermGenie up regulation of nodal cilium formation GOC:TermGenie up-regulation of motile primary cilia assembly GOC:TermGenie up-regulation of motile primary cilia formation GOC:TermGenie up-regulation of motile primary cilium assembly GOC:TermGenie up-regulation of motile primary cilium formation GOC:TermGenie up-regulation of nodal cilium assembly GOC:TermGenie up-regulation of nodal cilium formation GOC:TermGenie upregulation of motile primary cilia assembly GOC:TermGenie upregulation of motile primary cilia formation GOC:TermGenie upregulation of motile primary cilium assembly GOC:TermGenie upregulation of motile primary cilium formation GOC:TermGenie upregulation of nodal cilium assembly GOC:TermGenie upregulation of nodal cilium formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of fertilization. pr 2016-09-30T14:32:32Z positive regulation of syngamy up regulation of fertilization up regulation of syngamy up-regulation of fertilization up-regulation of syngamy upregulation of fertilization upregulation of syngamy activation of fertilization activation of syngamy biological_process GO:1905516 positive regulation of fertilization Any process that activates or increases the frequency, rate or extent of fertilization. GOC:TermGenie GOC:hbye GO_REF:0000058 PMID:27564576 positive regulation of syngamy GOC:TermGenie up regulation of fertilization GOC:TermGenie up regulation of syngamy GOC:TermGenie up-regulation of fertilization GOC:TermGenie up-regulation of syngamy GOC:TermGenie upregulation of fertilization GOC:TermGenie upregulation of syngamy GOC:TermGenie activation of fertilization GOC:TermGenie activation of syngamy GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of saliva secretion. pga 2016-12-09T10:24:00Z down regulation of saliva secretion down regulation of salivation down-regulation of saliva secretion down-regulation of salivation downregulation of saliva secretion downregulation of salivation negative regulation of salivation inhibition of saliva secretion inhibition of salivation biological_process GO:1905747 negative regulation of saliva secretion Any process that stops, prevents or reduces the frequency, rate or extent of saliva secretion. GOC:TermGenie GO_REF:0000058 PMID:23419067 down regulation of saliva secretion GOC:TermGenie down regulation of salivation GOC:TermGenie down-regulation of saliva secretion GOC:TermGenie down-regulation of salivation GOC:TermGenie downregulation of saliva secretion GOC:TermGenie downregulation of salivation GOC:TermGenie negative regulation of salivation GOC:TermGenie inhibition of saliva secretion GOC:TermGenie inhibition of salivation GOC:TermGenie Any process that modulates the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. hbye 2017-01-09T15:11:04Z regulation of perception of touch, detection of mechanical stimulus regulation of perception of touch, sensory detection of mechanical stimulus regulation of perception of touch, sensory transduction of mechanical stimulus regulation of sensory detection of mechanical stimulus during perception of touch regulation of sensory transduction of mechanical stimulus during perception of touch regulation of tactition, sensory detection of mechanical stimulus biological_process GO:1905787 regulation of detection of mechanical stimulus involved in sensory perception of touch Any process that modulates the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. GOC:TermGenie GO_REF:0000058 PMID:8692859 regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. hbye 2017-01-09T15:11:14Z down regulation of detection of mechanical stimulus involved in sensory perception of touch down regulation of perception of touch, detection of mechanical stimulus down regulation of perception of touch, sensory detection of mechanical stimulus down regulation of perception of touch, sensory transduction of mechanical stimulus down regulation of sensory detection of mechanical stimulus during perception of touch down regulation of sensory transduction of mechanical stimulus during perception of touch down regulation of tactition, sensory detection of mechanical stimulus down-regulation of detection of mechanical stimulus involved in sensory perception of touch down-regulation of perception of touch, detection of mechanical stimulus down-regulation of perception of touch, sensory detection of mechanical stimulus down-regulation of perception of touch, sensory transduction of mechanical stimulus down-regulation of sensory detection of mechanical stimulus during perception of touch down-regulation of sensory transduction of mechanical stimulus during perception of touch down-regulation of tactition, sensory detection of mechanical stimulus downregulation of detection of mechanical stimulus involved in sensory perception of touch downregulation of perception of touch, detection of mechanical stimulus downregulation of perception of touch, sensory detection of mechanical stimulus downregulation of perception of touch, sensory transduction of mechanical stimulus downregulation of sensory detection of mechanical stimulus during perception of touch downregulation of sensory transduction of mechanical stimulus during perception of touch downregulation of tactition, sensory detection of mechanical stimulus negative regulation of perception of touch, detection of mechanical stimulus negative regulation of perception of touch, sensory detection of mechanical stimulus negative regulation of perception of touch, sensory transduction of mechanical stimulus negative regulation of sensory detection of mechanical stimulus during perception of touch negative regulation of sensory transduction of mechanical stimulus during perception of touch negative regulation of tactition, sensory detection of mechanical stimulus inhibition of detection of mechanical stimulus involved in sensory perception of touch inhibition of perception of touch, detection of mechanical stimulus inhibition of perception of touch, sensory detection of mechanical stimulus inhibition of perception of touch, sensory transduction of mechanical stimulus inhibition of sensory detection of mechanical stimulus during perception of touch inhibition of sensory transduction of mechanical stimulus during perception of touch inhibition of tactition, sensory detection of mechanical stimulus biological_process GO:1905788 negative regulation of detection of mechanical stimulus involved in sensory perception of touch Any process that stops, prevents or reduces the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. GOC:TermGenie GO_REF:0000058 PMID:8692859 down regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie down regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie down regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie down regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie down regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie down regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie down regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie down-regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie down-regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie down-regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie down-regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie down-regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie down-regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie down-regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie downregulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie downregulation of perception of touch, detection of mechanical stimulus GOC:TermGenie downregulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie downregulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie downregulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie downregulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie downregulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie negative regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie negative regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie negative regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie negative regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie negative regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie negative regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie inhibition of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie inhibition of perception of touch, detection of mechanical stimulus GOC:TermGenie inhibition of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie inhibition of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie inhibition of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie inhibition of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie inhibition of tactition, sensory detection of mechanical stimulus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. hbye 2017-01-09T15:11:23Z positive regulation of perception of touch, detection of mechanical stimulus positive regulation of perception of touch, sensory detection of mechanical stimulus positive regulation of perception of touch, sensory transduction of mechanical stimulus positive regulation of sensory detection of mechanical stimulus during perception of touch positive regulation of sensory transduction of mechanical stimulus during perception of touch positive regulation of tactition, sensory detection of mechanical stimulus up regulation of detection of mechanical stimulus involved in sensory perception of touch up regulation of perception of touch, detection of mechanical stimulus up regulation of perception of touch, sensory detection of mechanical stimulus up regulation of perception of touch, sensory transduction of mechanical stimulus up regulation of sensory detection of mechanical stimulus during perception of touch up regulation of sensory transduction of mechanical stimulus during perception of touch up regulation of tactition, sensory detection of mechanical stimulus up-regulation of detection of mechanical stimulus involved in sensory perception of touch up-regulation of perception of touch, detection of mechanical stimulus up-regulation of perception of touch, sensory detection of mechanical stimulus up-regulation of perception of touch, sensory transduction of mechanical stimulus up-regulation of sensory detection of mechanical stimulus during perception of touch up-regulation of sensory transduction of mechanical stimulus during perception of touch up-regulation of tactition, sensory detection of mechanical stimulus upregulation of detection of mechanical stimulus involved in sensory perception of touch upregulation of perception of touch, detection of mechanical stimulus upregulation of perception of touch, sensory detection of mechanical stimulus upregulation of perception of touch, sensory transduction of mechanical stimulus upregulation of sensory detection of mechanical stimulus during perception of touch upregulation of sensory transduction of mechanical stimulus during perception of touch upregulation of tactition, sensory detection of mechanical stimulus activation of detection of mechanical stimulus involved in sensory perception of touch activation of perception of touch, detection of mechanical stimulus activation of perception of touch, sensory detection of mechanical stimulus activation of perception of touch, sensory transduction of mechanical stimulus activation of sensory detection of mechanical stimulus during perception of touch activation of sensory transduction of mechanical stimulus during perception of touch activation of tactition, sensory detection of mechanical stimulus biological_process GO:1905789 positive regulation of detection of mechanical stimulus involved in sensory perception of touch Any process that activates or increases the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch. GOC:TermGenie GO_REF:0000058 PMID:8692859 positive regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie positive regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie positive regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie positive regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie positive regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie positive regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie up regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie up regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie up regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie up regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie up regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie up regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie up regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie up-regulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie up-regulation of perception of touch, detection of mechanical stimulus GOC:TermGenie up-regulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie up-regulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie up-regulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie up-regulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie up-regulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie upregulation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie upregulation of perception of touch, detection of mechanical stimulus GOC:TermGenie upregulation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie upregulation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie upregulation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie upregulation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie upregulation of tactition, sensory detection of mechanical stimulus GOC:TermGenie activation of detection of mechanical stimulus involved in sensory perception of touch GOC:TermGenie activation of perception of touch, detection of mechanical stimulus GOC:TermGenie activation of perception of touch, sensory detection of mechanical stimulus GOC:TermGenie activation of perception of touch, sensory transduction of mechanical stimulus GOC:TermGenie activation of sensory detection of mechanical stimulus during perception of touch GOC:TermGenie activation of sensory transduction of mechanical stimulus during perception of touch GOC:TermGenie activation of tactition, sensory detection of mechanical stimulus GOC:TermGenie Any process that activates or increases the frequency, rate or extent of chromosome condensation. bhm 2017-01-13T14:13:44Z positive regulation of eukaryotic chromosome condensation positive regulation of nuclear chromosome condensation up regulation of chromosome condensation up regulation of eukaryotic chromosome condensation up regulation of nuclear chromosome condensation up-regulation of chromosome condensation up-regulation of eukaryotic chromosome condensation up-regulation of nuclear chromosome condensation upregulation of chromosome condensation upregulation of eukaryotic chromosome condensation upregulation of nuclear chromosome condensation activation of chromosome condensation activation of eukaryotic chromosome condensation activation of nuclear chromosome condensation biological_process GO:1905821 positive regulation of chromosome condensation Any process that activates or increases the frequency, rate or extent of chromosome condensation. GOC:TermGenie GOC:bhm GO_REF:0000058 PMID:17268547 positive regulation of eukaryotic chromosome condensation GOC:TermGenie positive regulation of nuclear chromosome condensation GOC:TermGenie up regulation of chromosome condensation GOC:TermGenie up regulation of eukaryotic chromosome condensation GOC:TermGenie up regulation of nuclear chromosome condensation GOC:TermGenie up-regulation of chromosome condensation GOC:TermGenie up-regulation of eukaryotic chromosome condensation GOC:TermGenie up-regulation of nuclear chromosome condensation GOC:TermGenie upregulation of chromosome condensation GOC:TermGenie upregulation of eukaryotic chromosome condensation GOC:TermGenie upregulation of nuclear chromosome condensation GOC:TermGenie activation of chromosome condensation GOC:TermGenie activation of eukaryotic chromosome condensation GOC:TermGenie activation of nuclear chromosome condensation GOC:TermGenie Any process that modulates the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:05Z regulation of ovum development biological_process GO:1905879 regulation of oogenesis Any process that modulates the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 regulation of ovum development GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:15Z down regulation of oogenesis down regulation of ovum development down-regulation of oogenesis down-regulation of ovum development downregulation of oogenesis downregulation of ovum development negative regulation of ovum development inhibition of oogenesis inhibition of ovum development biological_process GO:1905880 negative regulation of oogenesis Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 down regulation of oogenesis GOC:TermGenie down regulation of ovum development GOC:TermGenie down-regulation of oogenesis GOC:TermGenie down-regulation of ovum development GOC:TermGenie downregulation of oogenesis GOC:TermGenie downregulation of ovum development GOC:TermGenie negative regulation of ovum development GOC:TermGenie inhibition of oogenesis GOC:TermGenie inhibition of ovum development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of oogenesis. hbye 2017-01-31T09:31:23Z positive regulation of ovum development up regulation of oogenesis up regulation of ovum development up-regulation of oogenesis up-regulation of ovum development upregulation of oogenesis upregulation of ovum development activation of oogenesis activation of ovum development biological_process GO:1905881 positive regulation of oogenesis Any process that activates or increases the frequency, rate or extent of oogenesis. GOC:TermGenie GO_REF:0000058 PMID:26434723 positive regulation of ovum development GOC:TermGenie up regulation of oogenesis GOC:TermGenie up regulation of ovum development GOC:TermGenie up-regulation of oogenesis GOC:TermGenie up-regulation of ovum development GOC:TermGenie upregulation of oogenesis GOC:TermGenie upregulation of ovum development GOC:TermGenie activation of oogenesis GOC:TermGenie activation of ovum development GOC:TermGenie Any process that modulates the frequency, rate or extent of mesoderm formation. rph 2017-02-03T12:28:20Z biological_process GO:1905902 regulation of mesoderm formation Any process that modulates the frequency, rate or extent of mesoderm formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23939491 Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation. rph 2017-02-03T12:28:29Z down regulation of mesoderm formation down-regulation of mesoderm formation downregulation of mesoderm formation inhibition of mesoderm formation biological_process GO:1905903 negative regulation of mesoderm formation Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23939491 down regulation of mesoderm formation GOC:TermGenie down-regulation of mesoderm formation GOC:TermGenie downregulation of mesoderm formation GOC:TermGenie inhibition of mesoderm formation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of mesoderm formation. rph 2017-02-03T12:28:38Z up regulation of mesoderm formation up-regulation of mesoderm formation upregulation of mesoderm formation activation of mesoderm formation biological_process GO:1905904 positive regulation of mesoderm formation Any process that activates or increases the frequency, rate or extent of mesoderm formation. GOC:BHF GOC:BHF_miRNA GOC:TermGenie GOC:rph GO_REF:0000058 PMID:23939491 up regulation of mesoderm formation GOC:TermGenie up-regulation of mesoderm formation GOC:TermGenie upregulation of mesoderm formation GOC:TermGenie activation of mesoderm formation GOC:TermGenie Any DNA recombination that takes place in mitochondrion. vw 2017-02-19T10:48:17Z DNA recombination in mitochondria biological_process GO:1905951 mitochondrion DNA recombination Any DNA recombination that takes place in mitochondrion. GOC:TermGenie GO_REF:0000062 PMID:8087883 DNA recombination in mitochondria GOC:TermGenie Any process that modulates the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:22Z regulation of lipid localisation biological_process GO:1905952 regulation of lipid localization Any process that modulates the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 regulation of lipid localisation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:41Z down regulation of lipid localisation down regulation of lipid localization down-regulation of lipid localisation down-regulation of lipid localization downregulation of lipid localisation downregulation of lipid localization negative regulation of lipid localisation inhibition of lipid localisation inhibition of lipid localization biological_process GO:1905953 negative regulation of lipid localization Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 down regulation of lipid localisation GOC:TermGenie down regulation of lipid localization GOC:TermGenie down-regulation of lipid localisation GOC:TermGenie down-regulation of lipid localization GOC:TermGenie downregulation of lipid localisation GOC:TermGenie downregulation of lipid localization GOC:TermGenie negative regulation of lipid localisation GOC:TermGenie inhibition of lipid localisation GOC:TermGenie inhibition of lipid localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:49Z positive regulation of lipid localisation up regulation of lipid localisation up regulation of lipid localization up-regulation of lipid localisation up-regulation of lipid localization upregulation of lipid localisation upregulation of lipid localization activation of lipid localisation activation of lipid localization biological_process GO:1905954 positive regulation of lipid localization Any process that activates or increases the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 positive regulation of lipid localisation GOC:TermGenie up regulation of lipid localisation GOC:TermGenie up regulation of lipid localization GOC:TermGenie up-regulation of lipid localisation GOC:TermGenie up-regulation of lipid localization GOC:TermGenie upregulation of lipid localisation GOC:TermGenie upregulation of lipid localization GOC:TermGenie activation of lipid localisation GOC:TermGenie activation of lipid localization GOC:TermGenie Any process that modulates the frequency, rate or extent of multicellular organismal development. tb 2010-08-05T11:25:59Z biological_process GO:2000026 regulation of multicellular organismal development Any process that modulates the frequency, rate or extent of multicellular organismal development. GOC:obol Any process that modulates the frequency, rate or extent of animal organ morphogenesis. tb 2010-08-05T11:26:27Z biological_process regulation of histogenesis and organogenesis GO:2000027 regulation of animal organ morphogenesis Any process that modulates the frequency, rate or extent of animal organ morphogenesis. GOC:obol regulation of histogenesis and organogenesis GOC:obol Any process that modulates the frequency, rate or extent of stem cell division. tb 2010-08-05T11:34:53Z regulation of stem cell renewal biological_process GO:2000035 regulation of stem cell division Any process that modulates the frequency, rate or extent of stem cell division. GOC:obol regulation of stem cell renewal GOC:obol Any process that modulates the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:21Z regulation of cell locomotion regulation of movement of a cell biological_process regulation of cell movement GO:2000145 regulation of cell motility Any process that modulates the frequency, rate or extent of cell motility. GOC:mah regulation of cell locomotion GOC:obol regulation of movement of a cell GOC:obol regulation of cell movement GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:26Z negative regulation of cell locomotion negative regulation of movement of a cell biological_process negative regulation of cell movement GO:2000146 negative regulation of cell motility Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. GOC:mah negative regulation of cell locomotion GOC:obol negative regulation of movement of a cell GOC:obol negative regulation of cell movement GOC:obol Any process that activates or increases the frequency, rate or extent of cell motility. mah 2010-10-01T09:41:30Z positive regulation of cell locomotion positive regulation of movement of a cell biological_process positive regulation of cell movement GO:2000147 positive regulation of cell motility Any process that activates or increases the frequency, rate or extent of cell motility. GOC:mah positive regulation of cell locomotion GOC:obol positive regulation of movement of a cell GOC:obol positive regulation of cell movement GOC:obol Any process that activates or increases the frequency, rate or extent of cilium-dependent cell motility. mah 2010-10-04T12:41:05Z biological_process positive regulation of ciliary cell motility GO:2000155 positive regulation of cilium-dependent cell motility Any process that activates or increases the frequency, rate or extent of cilium-dependent cell motility. GOC:cilia GOC:jl Any process that modulates the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:02Z biological_process GO:2000241 regulation of reproductive process Any process that modulates the frequency, rate or extent of reproductive process. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:05Z biological_process GO:2000242 negative regulation of reproductive process Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process. GOC:mah Any process that activates or increases the frequency, rate or extent of reproductive process. mah 2010-11-10T02:44:08Z biological_process GO:2000243 positive regulation of reproductive process Any process that activates or increases the frequency, rate or extent of reproductive process. GOC:mah Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. bf 2010-12-02T09:28:47Z negative regulation of receptor activity negative regulation of signalling receptor activity biological_process GO:2000272 negative regulation of signaling receptor activity Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity. GOC:obol Any process that activates or increases the frequency, rate or extent of signaling receptor activity. bf 2010-12-02T09:28:50Z positive regulation of signalling receptor activity biological_process GO:2000273 positive regulation of signaling receptor activity Any process that activates or increases the frequency, rate or extent of signaling receptor activity. GOC:obol Any process that modulates the frequency, rate or extent of defecation. bf 2010-12-21T09:23:08Z biological_process GO:2000292 regulation of defecation Any process that modulates the frequency, rate or extent of defecation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of defecation. bf 2010-12-21T09:23:13Z biological_process GO:2000293 negative regulation of defecation Any process that stops, prevents or reduces the frequency, rate or extent of defecation. GOC:obol Any process that activates or increases the frequency, rate or extent of defecation. bf 2010-12-21T09:23:16Z biological_process GO:2000294 positive regulation of defecation Any process that activates or increases the frequency, rate or extent of defecation. GOC:obol Any process that modulates the frequency, rate or extent of mesoderm development. vk 2011-02-15T03:09:46Z biological_process GO:2000380 regulation of mesoderm development Any process that modulates the frequency, rate or extent of mesoderm development. GOC:BHF Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development. vk 2011-02-15T03:10:02Z biological_process GO:2000381 negative regulation of mesoderm development Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development. GOC:BHF Any process that activates or increases the frequency, rate or extent of mesoderm development. vk 2011-02-15T03:10:12Z biological_process GO:2000382 positive regulation of mesoderm development Any process that activates or increases the frequency, rate or extent of mesoderm development. GOC:BHF Any process that modulates the frequency, rate or extent of ectoderm development. vk 2011-02-15T03:17:10Z biological_process GO:2000383 regulation of ectoderm development Any process that modulates the frequency, rate or extent of ectoderm development. GOC:BHF Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development. vk 2011-02-15T03:17:27Z biological_process GO:2000384 negative regulation of ectoderm development Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development. GOC:BHF Any process that activates or increases the frequency, rate or extent of ectoderm development. vk 2011-02-15T03:17:39Z biological_process GO:2000385 positive regulation of ectoderm development Any process that activates or increases the frequency, rate or extent of ectoderm development. GOC:BHF Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation. yaf 2011-04-01T04:10:08Z biological_process GO:2000542 negative regulation of gastrulation Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation. GOC:obol Any process that activates or increases the frequency, rate or extent of gastrulation. yaf 2011-04-01T04:10:15Z biological_process GO:2000543 positive regulation of gastrulation Any process that activates or increases the frequency, rate or extent of gastrulation. GOC:obol Any process that modulates the frequency, rate or extent of thyroid hormone generation. yaf 2011-04-18T10:12:14Z biological_process GO:2000609 regulation of thyroid hormone generation Any process that modulates the frequency, rate or extent of thyroid hormone generation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of thyroid hormone generation. yaf 2011-04-18T10:12:19Z biological_process GO:2000610 negative regulation of thyroid hormone generation Any process that stops, prevents or reduces the frequency, rate or extent of thyroid hormone generation. GOC:obol Any process that activates or increases the frequency, rate or extent of thyroid hormone generation. yaf 2011-04-18T10:12:22Z biological_process GO:2000611 positive regulation of thyroid hormone generation Any process that activates or increases the frequency, rate or extent of thyroid hormone generation. GOC:obol Any process that modulates the frequency, rate or extent of parathyroid hormone secretion. bf 2011-07-26T08:37:53Z regulation of PTH secretion regulation of parathormone secretion regulation of parathyrin secretion biological_process GO:2000828 regulation of parathyroid hormone secretion Any process that modulates the frequency, rate or extent of parathyroid hormone secretion. GOC:obol regulation of PTH secretion GOC:obol regulation of parathormone secretion GOC:obol regulation of parathyrin secretion GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of parathyroid hormone secretion. bf 2011-07-26T08:37:57Z negative regulation of PTH secretion negative regulation of parathormone secretion negative regulation of parathyrin secretion biological_process GO:2000829 negative regulation of parathyroid hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of parathyroid hormone secretion. GOC:obol negative regulation of PTH secretion GOC:obol negative regulation of parathormone secretion GOC:obol negative regulation of parathyrin secretion GOC:obol Any process that activates or increases the frequency, rate or extent of parathyroid hormone secretion. bf 2011-07-26T08:38:00Z positive regulation of PTH secretion positive regulation of parathormone secretion positive regulation of parathyrin secretion biological_process GO:2000830 positive regulation of parathyroid hormone secretion Any process that activates or increases the frequency, rate or extent of parathyroid hormone secretion. GOC:obol positive regulation of PTH secretion GOC:obol positive regulation of parathormone secretion GOC:obol positive regulation of parathyrin secretion GOC:obol Any process that modulates the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:46Z biological_process GO:2000831 regulation of steroid hormone secretion Any process that modulates the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:50Z biological_process GO:2000832 negative regulation of steroid hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:51Z biological_process GO:2000833 positive regulation of steroid hormone secretion Any process that activates or increases the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that modulates the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:45Z biological_process GO:2000834 regulation of androgen secretion Any process that modulates the frequency, rate or extent of androgen secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:48Z biological_process GO:2000835 negative regulation of androgen secretion Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of androgen secretion. bf 2011-07-26T08:39:51Z biological_process GO:2000836 positive regulation of androgen secretion Any process that activates or increases the frequency, rate or extent of androgen secretion. GOC:sl Any process that modulates the frequency, rate or extent of corticosteroid hormone secretion. bf 2011-07-26T08:43:38Z biological_process regulation of corticosteroid secretion GO:2000846 regulation of corticosteroid hormone secretion Any process that modulates the frequency, rate or extent of corticosteroid hormone secretion. GOC:sl regulation of corticosteroid secretion GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of corticosteroid hormone secretion. bf 2011-07-26T08:43:42Z biological_process negative regulation of corticosteroid secretion GO:2000847 negative regulation of corticosteroid hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of corticosteroid hormone secretion. GOC:sl negative regulation of corticosteroid secretion GOC:obol Any process that activates or increases the frequency, rate or extent of corticosteroid hormone secretion. bf 2011-07-26T08:43:45Z biological_process positive regulation of corticosteroid secretion GO:2000848 positive regulation of corticosteroid hormone secretion Any process that activates or increases the frequency, rate or extent of corticosteroid hormone secretion. GOC:sl positive regulation of corticosteroid secretion GOC:obol Any process that modulates the frequency, rate or extent of mineralocorticoid secretion. bf 2011-07-26T08:46:38Z biological_process GO:2000855 regulation of mineralocorticoid secretion Any process that modulates the frequency, rate or extent of mineralocorticoid secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of mineralocorticoid secretion. bf 2011-07-26T08:46:42Z biological_process GO:2000856 negative regulation of mineralocorticoid secretion Any process that stops, prevents or reduces the frequency, rate or extent of mineralocorticoid secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of mineralocorticoid secretion. bf 2011-07-26T08:46:45Z biological_process GO:2000857 positive regulation of mineralocorticoid secretion Any process that activates or increases the frequency, rate or extent of mineralocorticoid secretion. GOC:sl Any process that modulates the frequency, rate or extent of aldosterone secretion. bf 2011-07-26T08:47:27Z biological_process GO:2000858 regulation of aldosterone secretion Any process that modulates the frequency, rate or extent of aldosterone secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of aldosterone secretion. bf 2011-07-26T08:47:31Z biological_process GO:2000859 negative regulation of aldosterone secretion Any process that stops, prevents or reduces the frequency, rate or extent of aldosterone secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of aldosterone secretion. bf 2011-07-26T08:47:34Z biological_process GO:2000860 positive regulation of aldosterone secretion Any process that activates or increases the frequency, rate or extent of aldosterone secretion. GOC:sl Any epithelial cell proliferation that is involved in renal tubule morphogenesis. yaf 2011-08-12T11:37:29Z biological_process GO:2001013 epithelial cell proliferation involved in renal tubule morphogenesis Any epithelial cell proliferation that is involved in renal tubule morphogenesis. GOC:obol Any process that modulates the frequency, rate or extent of renal water transport. yaf 2011-10-24T11:37:51Z biological_process GO:2001151 regulation of renal water transport Any process that modulates the frequency, rate or extent of renal water transport. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of renal water transport. yaf 2011-10-24T11:37:57Z biological_process GO:2001152 negative regulation of renal water transport Any process that stops, prevents or reduces the frequency, rate or extent of renal water transport. GOC:obol Any process that activates or increases the frequency, rate or extent of renal water transport. yaf 2011-10-24T11:38:01Z biological_process GO:2001153 positive regulation of renal water transport Any process that activates or increases the frequency, rate or extent of renal water transport. GOC:obol Any process that modulates the frequency, rate or extent of dendritic cell differentiation. yaf 2011-11-04T02:01:27Z biological_process GO:2001198 regulation of dendritic cell differentiation Any process that modulates the frequency, rate or extent of dendritic cell differentiation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation. yaf 2011-11-04T02:01:33Z biological_process GO:2001199 negative regulation of dendritic cell differentiation Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation. GOC:obol Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation. yaf 2011-11-04T02:01:36Z biological_process GO:2001200 positive regulation of dendritic cell differentiation Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:20Z negative regulation of chromosome organisation biological_process negative regulation of chromosome organization and biogenesis negative regulation of maintenance of genome integrity negative regulation of nuclear genome maintenance GO:2001251 negative regulation of chromosome organization Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. GOC:obol negative regulation of chromosome organisation GOC:obol negative regulation of chromosome organization and biogenesis GOC:obol negative regulation of maintenance of genome integrity GOC:obol negative regulation of nuclear genome maintenance GOC:obol Any process that activates or increases the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:26Z positive regulation of chromosome organisation biological_process positive regulation of chromosome organization and biogenesis positive regulation of maintenance of genome integrity positive regulation of nuclear genome maintenance GO:2001252 positive regulation of chromosome organization Any process that activates or increases the frequency, rate or extent of chromosome organization. GOC:obol positive regulation of chromosome organisation GOC:obol positive regulation of chromosome organization and biogenesis GOC:obol positive regulation of maintenance of genome integrity GOC:obol positive regulation of nuclear genome maintenance GOC:obol UMLS:C0444868 HP:0000001 Root of all terms in the Human Phenotype Ontology. All Deviation from the norm of height with respect to that which is expected according to age and gender norms. 2008-02-27T02:20:00Z UMLS:C4025901 Abnormality of body height HP:0000002 Abnormality of body height Deviation from the norm of height with respect to that which is expected according to age and gender norms. Abnormality of body height An abnormality of the female internal genitalia. UMLS:C4025900 Abnormality of female internal genitalia HP:0000008 Abnormal morphology of female internal genitalia An abnormality of the female internal genitalia. Dysfunction of the urinary bladder. HP:0004424 HP:0008731 UMLS:C3806583 Poor bladder function HP:0000009 Functional abnormality of the bladder Dysfunction of the urinary bladder. Underdevelopment of the uterus. HP:0001154 HP:0008637 SNOMEDCT_US:35850006 UMLS:C0266399 Hypoplastic uterus Rudimentary uterus Small uterus Underdeveloped uterus HP:0000013 Hypoplasia of the uterus Underdevelopment of the uterus. Small uterus Underdeveloped uterus An abnormality of the urinary bladder. UMLS:C0149632 HP:0000014 Abnormality of the bladder An abnormality of the urinary bladder. Diverticulum (sac or pouch) in the wall of the urinary bladder. MSH:C562406 SNOMEDCT_US:197866008 UMLS:C0156273 Bladder diverticula HP:0000015 Bladder diverticulum Diverticulum (sac or pouch) in the wall of the urinary bladder. Bladder diverticula An abnormality of the male internal genitalia. UMLS:C4025899 HP:0000022 The internal genital structures of the male including the testis, epididymis, vas deferens, seminal vesicle, ejaculatory duct, bulbourethral gland, and the prostate. Abnormal male internal genitalia morphology An abnormality of the male internal genitalia. The presence of inflammation of the prostate. MSH:D011472 SNOMEDCT_US:9713002 UMLS:C0033581 Inflammation of the prostate HP:0000024 Prostatitis The presence of inflammation of the prostate. Inflammation of the prostate UMLS:C4025898 HP:0000025 Functional abnormality of male internal genitalia Decreased functionality of the male gonad, i.e., of the testis, with reduced spermatogenesis or testosterone synthesis. HP:0008649 MSH:D005058 SNOMEDCT_US:48723006 UMLS:C0151721 Decreased function of male gonad HP:0000026 Male hypogonadism Decreased functionality of the male gonad, i.e., of the testis, with reduced spermatogenesis or testosterone synthesis. Decreased function of male gonad Absence of any measurable level of sperm,whereby spermatozoa cannot be observed even after centrifugation of the semen pellet. MSH:D053713 SNOMEDCT_US:425558002 SNOMEDCT_US:48188009 UMLS:C0004509 Absent sperm in semen HP:0000027 Azoospermia Absence of any measurable level of sperm,whereby spermatozoa cannot be observed even after centrifugation of the semen pellet. PMID:20514278 Absent sperm in semen Wasting (atrophy) of the testicle (the male gonad) manifested by a decrease in size and potentially by a loss of fertility. SNOMEDCT_US:17585008 UMLS:C0156312 Testicular degeneration HP:0000029 Testicular atrophy Wasting (atrophy) of the testicle (the male gonad) manifested by a decrease in size and potentially by a loss of fertility. Testicular degeneration The presence of inflammation of the epididymis. MSH:D004823 SNOMEDCT_US:31070006 UMLS:C0014534 HP:0000031 Epididymitis The presence of inflammation of the epididymis. Any structural abnormality of male external genitalia. UMLS:C4025897 Abnormality of male external genitalia HP:0000032 Abnormal male external genitalia morphology Any structural abnormality of male external genitalia. An anomaly of the testicle (the male gonad). SNOMEDCT_US:55631001 UMLS:C0266423 Abnormality of the testis Anomaly of the testes HP:0000035 Abnormal testis morphology An anomaly of the testicle (the male gonad). Abnormality of the testis Abnormality of the male external sex organ. UMLS:C4025896 Abnormality of the penis HP:0000036 Abnormal penis morphology Abnormality of the penis Penile length more than 2 SD above the mean for age. SNOMEDCT_US:88673001 UMLS:C0269011 Enlarged penis Long penis HP:0000040 Penile length is the distance between the midline attachment of the gently stretched, flaccid penis above the pubic symphysis and tip of the glans. Long penis Enlarged penis Long penis Lack of external genitalia in a male or female individual. UMLS:C1848869 Absent external genitalia HP:0000042 Absent external genitalia Lack of external genitalia in a male or female individual. Absent external genitalia Any structural abnormality of the scrotum, i.e., the sac that contains the testes, epididymis, and the lower part of the spermatic cord. UMLS:C4025895 Abnormality of the scrotum HP:0000045 Abnormal scrotum morphology Apparently small scrotum for age. HP:0030276 SNOMEDCT_US:204912007 UMLS:C0431659 Hypoplastic scrotum Scrotal hypoplasia Smaller than typical growth of scrotum Underdeveloped scrotum HP:0000046 A small scrotum is often accompanied by Cryptorchidism which should be coded separately. The size of the scrotum is dependent on the ambient temperature: a low temperature may cause the testes to retract, leading to the false impression of a small scrotum. Small scrotum Apparently small scrotum for age. PMID:23650202 Smaller than typical growth of scrotum Underdeveloped scrotum Midline indentation or cleft of the scrotum. SNOMEDCT_US:236780002 UMLS:C0341787 Cleft of scrotum Scrotal cleft HP:0000048 A testis may or may not be present in each half of the scrotum. Bifid scrotum Midline indentation or cleft of the scrotum. PMID:23650202 Cleft of scrotum Underdevelopment of part or all of the male external reproductive organs (which include the penis, the scrotum and the urethra). HP:0008710 HP:0008721 UMLS:C1852534 Hypoplastic male genitalia Small male external genitalia Underdeveloped male genitalia HP:0000050 Hypoplastic male external genitalia Underdevelopment of part or all of the male external reproductive organs (which include the penis, the scrotum and the urethra). Small male external genitalia Underdeveloped male genitalia The presence of abnormally large testes. UMLS:C1263023 Large testicles Large testis HP:0000053 Macroorchidism The presence of abnormally large testes. Large testis Any structural abnormality of the female external genitalia. UMLS:C4021822 Abnormal female external genitalia Abnormality of female external genitalia HP:0000055 Abnormal female external genitalia morphology Any structural abnormality of the female external genitalia. Abnormal female external genitalia Any structural abnormality of the clitoris. UMLS:C4025893 Abnormality of the clit Abnormality of the clitoris HP:0000056 Abnormal clitoris morphology Any structural abnormality of the clitoris. Abnormality of the clit Developmental hypoplasia of the clitoris. UMLS:C1844527 Hypoplastic clitoris Small clitoris Underdeveloped clit HP:0000060 Clitoral hypoplasia Developmental hypoplasia of the clitoris. Small clitoris Underdeveloped clit An abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. HP:0006001 UMLS:C1840382 Abnormality of the ureters Ureter issue Ureteral anomalies HP:0000069 Abnormality of the ureter An abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. A developmental anomaly characterized by the presence of two, instead of one, ureter connecting a kidney to the bladder. SNOMEDCT_US:49496001 UMLS:C0221365 Double ureter HP:0000073 Ureteral duplication A developmental anomaly characterized by the presence of two, instead of one, ureter connecting a kidney to the bladder. Double ureter A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters. 2008-02-25T12:45:00Z SNOMEDCT_US:30275001 UMLS:C0266298 Extra kidney Supernumerary kidney HP:0000075 Renal duplication A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters. Extra kidney An abnormality of the kidney. MSH:D007674 SNOMEDCT_US:44513007 SNOMEDCT_US:90708001 UMLS:C0022658 UMLS:C0266292 Abnormal kidney Abnormality of the kidney Renal anomalies Renal anomaly HP:0000077 The kidney is a paired organ whose primary function is the production of urine. Abnormality of the kidney An abnormality of the kidney. Abnormal kidney Abnormality of the kidney An abnormality of the genital system. UMLS:C0281966 UMLS:C0744356 Genital abnormalities Genital abnormality Genital anomalies Genital defects Abnormality of the reproductive system HP:0000078 Abnormality of the genital system An abnormality of the genital system. Genital abnormalities Genital abnormality Genital anomalies Genital defects Abnormality of the reproductive system An abnormality of the urinary system. UMLS:C4021821 Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies HP:0000079 Abnormality of the urinary system An abnormality of the urinary system. Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies An abnormal functionality of the genital system. Abnormality of genital physiology UMLS:C4020896 UMLS:C4021820 Abnormality of reproductive system physiology Genital functional abnormality HP:0000080 Abnormality of reproductive system physiology An abnormal functionality of the genital system. Abnormality of genital physiology Abnormality of reproductive system physiology Genital functional abnormality A duplication of the collecting system of the kidney, defined as a kidney with two (instead of, normally, one) pyelocaliceal systems. The pyelocaliceal system is comprised of the renal pelvis and calices. The duplicated renal collecting system can be associated with a single ureter or with double ureters. In the latter case, the two ureters empty separately into the bladder or fuse to form a single ureteral orifice. 2008-02-25T12:45:00Z UMLS:C1858565 Double collecting system Double urinary collecting systems on intravenous pyelography Duplex collecting system Duplicated renal collecting system HP:0000081 Duplicated collecting system A duplication of the collecting system of the kidney, defined as a kidney with two (instead of, normally, one) pyelocaliceal systems. The pyelocaliceal system is comprised of the renal pelvis and calices. The duplicated renal collecting system can be associated with a single ureter or with double ureters. In the latter case, the two ureters empty separately into the bladder or fuse to form a single ureteral orifice. Hypoplasia of the kidney. HP:0001968 HP:0004741 HP:0008641 SNOMEDCT_US:32659003 UMLS:C0266295 Hypoplastic kidney Hypoplastic kidneys Small kidneys Underdeveloped kidneys HP:0000089 Oligomeganephronic renal hypoplasia differs from simple hypoplasia, in which the renal mass is reduced but the number of nephrons is normal. Renal hypoplasia Hypoplasia of the kidney. Small kidneys Underdeveloped kidneys An abnormality of the renal tubules. UMLS:C4021826 Abnormality of the renal tubule Morphologic abnormality of the renal tubules HP:0000091 The renal tubules are reabsorptive canals that are involved in the secreting, collecting, and conducting of the urine. Abnormal renal tubule morphology An abnormality of the renal tubules. The presence of renal tubules with thick redundant basement membranes, or a reduction of greater than 50% in tubular diameter compared to surrounding non-atrophic tubules. HP:0005578 UMLS:C1858395 Renal tubular cell atrophy Tubular atrophy HP:0000092 Atrophic tubules must be distinguished from acute tubular injury as both can show extensive tubular epithelial changes. In acute tubular injury, tubules are often dilated and tubular basement membranes are smooth and maintain normal thickness, in contrast to the contracted tubules with thickened and wrinkled tubular basement membranes of tubular atrophy. Further, in acute tubular injury, tubules are usually back-to-back or mildly separated by interstitial edema, while in tubular atrophy tubules can be separated by interstitial fibrosis. Uniform thickening of tubular basement membranes without shrinkage and otherwise healthy epithelial cells can be seen in diabetic nephropathy. Duplication, or lamellation, thickening, and disruption of tubular basement membranes with tubular dilatation can be seen in medullary cystic kidney disease/nephronophthisis. Renal tubular atrophy The presence of renal tubules with thick redundant basement membranes, or a reduction of greater than 50% in tubular diameter compared to surrounding non-atrophic tubules. PMID:27211375 Increased levels of protein in the urine. MSH:D011507 SNOMEDCT_US:29738008 UMLS:C0033687 High urine protein levels Protein in urine HP:0000093 Proteinuria Increased levels of protein in the urine. High urine protein levels Protein in urine A structural anomaly of the glomerulus. UMLS:C4025889 Abnormality of renal glomerulus morphology Morphologic abnormality of the renal glomerulus HP:0000095 Each human kidney contains approximately one million nephrons. The glomerulus is the most proximal component of the nephron. The glomerulus of the mammalian kidney is a highly developed vascular bed that acts as a filter, allowing a filtrate of small molecules, such as water, sugars, electrolytes and small proteins, to pass through a barrier that retains high molecular weight proteins and cells in the circulation. Abnormal renal glomerulus morphology A structural anomaly of the glomerulus. HPO_CONTRIBUTOR:Eurenomics_ewuehl PMID:18184729 A height above that which is expected according to age and gender norms. 2008-02-27T02:21:00Z HP:0001527 HP:0003515 HP:0003516 SNOMEDCT_US:248328003 UMLS:C0241240 Accelerated linear growth Increased body height Increased linear growth Tall stature HP:0000098 Tall stature A height above that which is expected according to age and gender norms. Increased body height Tall stature An increased rate of urine production. HP:0200060 MSH:D011141 SNOMEDCT_US:28442001 SNOMEDCT_US:56574000 SNOMEDCT_US:718402002 UMLS:C0032617 Increased urine output HP:0000103 An excessive volume of urination for an adult is more than 2.5 liters of urine per day. Polyuria An increased rate of urine production. Increased urine output Agenesis, that is, failure of the kidney to develop during embryogenesis and development. HP:0000785 HP:0004745 HP:0008680 Fyler:4503 SNOMEDCT_US:204942005 UMLS:C0542519 Absent kidney Missing kidney Renal aplasia HP:0000104 Renal agenesis can occur as a unilateral or bilateral trait. Renal agenesis Agenesis, that is, failure of the kidney to develop during embryogenesis and development. Absent kidney Missing kidney An abnormal increase in the size of the kidney. SNOMEDCT_US:300444006 UMLS:C0542518 Enlarged kidney Large kidneys Nephromegaly Renal enlargement Large kidney HP:0000105 The main causes of large kidney are hydronephrosis, polycystic disease, renal cell carcinoma, nephroblastoma/Wilms tumor (in children), and solitary cysts. If possible, a specific term should be used instead of this one. There are several ways of diagnosing enlarged kidney including intravenous urography. Enlarged kidney An abnormal increase in the size of the kidney. Enlarged kidney Large kidneys A fluid filled sac in the kidney. HP:0000088 HP:0000109 MSH:D052177 UMLS:C0022679 UMLS:C3887499 Kidney cyst Cystic kidney disease Cystic kidneys Renal cysts HP:0000107 Renal cyst A fluid filled sac in the kidney. HPO_CONTRIBUTOR:Eurenomics_fschaefer Kidney cyst Cystic kidney disease Cystic kidneys Renal cysts The presence of developmental dysplasia of the kidney. HP:0000116 HP:0004721 MSH:C563261 SNOMEDCT_US:204949001 UMLS:C1619700 UMLS:C3536714 Dysplastic kidneys Renal adysplasia HP:0000110 Renal dysplasia The presence of developmental dysplasia of the kidney. A phenotypic abnormality. UMLS:C4021819 Organ abnormality HP:0000118 This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality A phenotypic abnormality. The presence of any abnormality of the genitourinary system. HP:0008658 HP:0008688 HP:0008704 HP:0008713 MSH:D014564 SNOMEDCT_US:287085006 SNOMEDCT_US:42030000 UMLS:C0042063 UMLS:C0080276 UMLS:C4020895 Abnormality of the GU system Genitourinary abnormality Genitourinary tract anomalies Genitourinary tract malformation Urogenital abnormalities Urogenital anomalies Genitourinary disease Genitourinary dysplasia HP:0000119 Abnormality of the genitourinary system The presence of any abnormality of the genitourinary system. Abnormality of the GU system Nephrocalcinosis is the deposition of calcium salts in renal parenchyma. MSH:D009397 SNOMEDCT_US:48638002 UMLS:C0027709 UMLS:C4280679 Too much calcium deposited in kidneys Increased calcium level in kidney HP:0000121 Nephrocalcinosis can be intratubular or interstitial, and can be diagnosed by means of a radiologic exam (plain radiographs, ultrasonograms, or computed tomography scans) or via microscopic examination of the renal tissues. The term nephrocalcinosis most often applies to a generalized increase in renal calcium content. Nephrocalcinosis Nephrocalcinosis is the deposition of calcium salts in renal parenchyma. Too much calcium deposited in kidneys Increased calcium level in kidney The presence of inflammation affecting the kidney. HP:0008634 MSH:D009393 SNOMEDCT_US:52845002 UMLS:C0027697 Kidney inflammation HP:0000123 Nephritis The presence of inflammation affecting the kidney. Kidney inflammation Abnormal function of the renal tubule. The basic functional unit of the kidney, the nephron, consists of a renal corpuscle attached to a renal tubule, with roughly 0.8 to 1.5 nephrons per adult kidney. The functions of the renal tubule include reabsorption of water, electrolytes, glucose, and amino acids and secretion of substances such as uric acid. SNOMEDCT_US:95568003 UMLS:C0151747 Abnormal function of filtrating structures in kidney Renal tubular defect Renal tubular disease HP:0000124 Renal tubular dysfunction Abnormal function of filtrating structures in kidney An abnormality of the uterus. HP:0008630 HP:0008692 MSH:C562565 SNOMEDCT_US:37849005 UMLS:C0266383 Abnormality of the uterus Uterine abnormalities Uterine malformations HP:0000130 Abnormality of the uterus An abnormality of the uterus. Abnormality of the uterus Uterine abnormalities Uterine malformations The presence of a leiomyoma of the uterus. HP:0008642 MSH:D007889 NCIT:C3157 SNOMEDCT_US:146801000119103 SNOMEDCT_US:44598004 SNOMEDCT_US:95315005 UMLS:C0042133 Benign uterine leiomyomas Uterine fibroid HP:0000131 Leiomyoma is a benign neoplasm derived from smooth muscle cells. Uterine leiomyoma The presence of a leiomyoma of the uterus. HP:0003243 MSH:D006059 MSH:D006060 SNOMEDCT_US:205681004 SNOMEDCT_US:38804009 SNOMEDCT_US:83579008 SNOMEDCT_US:95219002 UMLS:C0018051 UMLS:C0018055 UMLS:C0687149 Mixed gonadal dysgenesis Pure gonadal dysgenesis HP:0000133 Gonadal dysgenesis Decreased functionality of the female gonads, i.e., of the ovary. SNOMEDCT_US:16041008 UMLS:C0271578 Hypogonadism, female HP:0000134 Female hypogonadism Decreased functionality of the female gonads, i.e., of the ovary. A decreased functionality of the gonad. MSH:D007006 SNOMEDCT_US:48130008 UMLS:C0020619 Decreased activity of gonads HP:0000135 Reduced functioning of the gonads (ovaries or testes) with reduced production of sex hormones. Hypogonadism A decreased functionality of the gonad. Decreased activity of gonads The presence of a bifid uterus. UMLS:C1850327 HP:0000136 A uterus that is divided into two lateral horns as a result of imperfect fusion of the paramesonephric ducts. Bifid uterus The presence of a bifid uterus. An abnormality of the ovary. MSH:D010049 SNOMEDCT_US:5552004 UMLS:C0029928 UMLS:C4021818 Abnormality of the ovaries Abnormality of the ovary Ovarian disease HP:0000137 Abnormality of the ovary An abnormality of the ovary. Abnormality of the ovaries Abnormality of the ovary Ovarian disease Any structural abnormality of the vagina. HP:0008650 UMLS:C1856023 Vaginal malformation HP:0000142 Abnormal vagina morphology Any structural abnormality of the vagina. Aplasia of the uterus. SNOMEDCT_US:248942000 UMLS:C0425913 Absent uterus uterus absent HP:0000151 Aplasia of the uterus Aplasia of the uterus. Absent uterus uterus absent An abnormality of head and neck. UMLS:C4021817 Abnormality of head or neck Head and neck abnormality HP:0000152 Abnormality of head or neck An abnormality of head and neck. Abnormality of head or neck Head and neck abnormality An abnormality of the mouth. MSH:D009056 SNOMEDCT_US:128334002 UMLS:C0026633 Abnormal mouth Abnormality of the mouth HP:0000153 Abnormality of the mouth An abnormality of the mouth. Abnormal mouth Abnormality of the mouth Any abnormality of the tongue. UMLS:C0878638 Abnormal tongue Abnormality of the tongue Glossal abnormality Lingual abnormality Tongue abnormality HP:0000157 Abnormality of the tongue Any abnormality of the tongue. Abnormal tongue Abnormality of the tongue Glossal abnormality Lingual abnormality Tongue abnormality Increased length and width of the tongue. HP:0000203 Glossal hypertrophy Lingual hyperplasia Lingual hypertrophy MSH:D008260 SNOMEDCT_US:25273001 UMLS:C0024421 Abnormally large tongue Hyperplasia of the tongue Hypertrophy of the tongue Increased size of tongue Large tongue Tongue hypertrophy HP:0000158 Normal standards do not exist. Large size usually leads to protrusion of the tongue. This is an acknowledged bundled term, but due to its frequent usage and relative paucity of situations that would call for separate individual assessments of tongue dimensions, the bundled term is retained. Micrognathia may give the false appearance of a large tongue. Macroglossia Increased length and width of the tongue. PMID:19125428 Glossal hypertrophy Lingual hyperplasia Lingual hypertrophy Abnormally large tongue Increased size of tongue Large tongue An abnormality of the lip. UMLS:C2183966 Abnormal lip Abnormality of the lip Lip abnormality Anomaly of lip Deformity of lip Malformation of lip HP:0000159 Abnormal lip morphology An abnormality of the lip. Abnormal lip Abnormality of the lip Lip abnormality Anomaly of lip Deformity of lip Malformation of lip Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. UMLS:C4025887 Abnormality of the oral cavity HP:0000163 Abnormal oral cavity morphology Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. Abnormality of the oral cavity Any abnormality of the teeth. HP:0001567 HP:0006296 HP:0006348 MSH:D014071 SNOMEDCT_US:422775003 UMLS:C0040427 UMLS:C0262444 Abnormal dentition Abnormal teeth Dental abnormalities Dental abnormality Dental anomalies Abnormality of the teeth Dental problem Dental problems Tooth abnormalities HP:0000164 Any abnormality of the primary (deciduous) or permanent teeth. Abnormality of the dentition Any abnormality of the teeth. Abnormal dentition Abnormal teeth Dental abnormalities Dental abnormality Dental anomalies Abnormality of the teeth Dental problem Dental problems Tooth abnormalities Any abnormality of the gingiva (also known as gums). UMLS:C4021816 Abnormality of the gums Gingival abnormality HP:0000168 The gingiva consists of the mucosal tissue that lies over the alveolar bone and around the base of the teeth. Abnormality of the gingiva Any abnormality of the gingiva (also known as gums). Abnormality of the gums Decreased length and width of the tongue. HP:0000226 HP:0009079 MSH:D014060 SNOMEDCT_US:249380003 SNOMEDCT_US:32614006 UMLS:C0025988 UMLS:C0426492 Abnormally small tongue Decreased size of tongue Hypoglossia Hypoplasia of the tongue Hypoplastic tongue Lingual hypoplasia Rudimentary tongue Small tongue Underdevelopment of the tongue HP:0000171 Normal standards do not exist. The term aglossia is often used for extremely small tongue, but a nubbin of tongue tissue is almost always present and aglossia in sensu strictu is extremely rare. This is an acknowledged bundled term, but due to its frequent usage and relative paucity of situations that would call for separate individual assessments of tongue dimensions, the bundled term is retained. Microglossia Decreased length and width of the tongue. PMID:19125428 Abnormally small tongue Underdevelopment of the tongue Any abnormality of the palate, i.e., of roof of the mouth. UMLS:C4021815 Abnormality of the palate Abnormality of the roof of the mouth Palatal anomaly Palate abnormality HP:0000174 Abnormal palate morphology Any abnormality of the palate, i.e., of roof of the mouth. Abnormality of the palate Abnormality of the roof of the mouth Palatal anomaly Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate). HP:0410004 Cleft secondary palate Fyler:4876 MSH:D002972 SNOMEDCT_US:63567004 SNOMEDCT_US:87979003 UMLS:C0008925 UMLS:C2981150 Cleft hard and soft palate Cleft of hard and soft palate Cleft of palate Cleft palate Cleft roof of mouth Palatoschisis Uranostaphyloschisis HP:0000175 Cleft palate is a developmental defect that occurs between the 7th and 12th week of pregnancy. Normally, the palatine processes fuse during this time to form the soft and hard palate. A failure of fusion results in a cleft palate. The clinical spectrum ranges from bifid uvula, to (incomplete or complete) cleft of the soft palate, up to (complete or incomplete) cleft of both the soft and hard palate. Cleft palate Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate). Cleft hard and soft palate Cleft of hard and soft palate Cleft palate Cleft roof of mouth Palatoschisis Uranostaphyloschisis An abnormality of the upper lip. UMLS:C4025884 Abnormality of upper lip Anomaly of the upper lip Deformity of the upper lip Malformation of the upper lip HP:0000177 Abnormal upper lip morphology An abnormality of the upper lip. Abnormality of upper lip Anomaly of the upper lip Deformity of the upper lip Malformation of the upper lip An abnormality of the lower lip. UMLS:C4025883 Abnormality of lower lip Anomaly of the lower lip Deformity of the lower lip Malformation of the lower lip HP:0000178 Abnormal lower lip morphology An abnormality of the lower lip. Abnormality of lower lip Anomaly of the lower lip Deformity of the lower lip Malformation of the lower lip Decreased width of the upper lip. HP:0200087 UMLS:C1848977 Decreased height of upper lip Decreased upper labial height Decreased upper labial length Decreased vertical length of upper lip Short upper lip Shortening of upper lip Vertical deficiency of upper lip HP:0000188 Short upper lip Decreased width of the upper lip. Decreased height of upper lip Decreased upper labial height Decreased upper labial length Decreased vertical length of upper lip Short upper lip Shortening of upper lip Vertical deficiency of upper lip A facial appearance characterized by a permanently or nearly permanently opened mouth. SNOMEDCT_US:262016004 UMLS:C0240379 Gaped jawed appearance Gaped mouthed appearance Open mouth Slack jawed appearance Open mouth appearance HP:0000194 Open mouth A facial appearance characterized by a permanently or nearly permanently opened mouth. Gaped jawed appearance Gaped mouthed appearance Open mouth Slack jawed appearance Open mouth appearance The presence of a cleft (gap, opening, or groove) in the oral cavity, including cleft of the upper lip and/or cleft of the palate. Cleft of the upper lip is visible as a groove or fissure in the lip, most frequently due to a congenital failure of the maxillary and median nasal processes to fuse. Cleft palate is characterized by a grooved depression or fissure in the roof of the mouth, most often resulting from a congenital failure of the palate to fuse properly. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately. SNOMEDCT_US:253983005 SNOMEDCT_US:66948001 UMLS:C0158646 UMLS:C4021813 Cleft of the mouth Oral cleft Oral clefting Cleft lip, cleft palate Cleft lip/palate HP:0000202 Orofacial cleft The presence of a cleft (gap, opening, or groove) in the oral cavity, including cleft of the upper lip and/or cleft of the palate. Cleft of the upper lip is visible as a groove or fissure in the lip, most frequently due to a congenital failure of the maxillary and median nasal processes to fuse. Cleft palate is characterized by a grooved depression or fissure in the roof of the mouth, most often resulting from a congenital failure of the palate to fuse properly. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately. PMID:21331089 https://www.cdc.gov/ncbddd/birthdefects/surveillancemanual/chapters/chapter-4/chapter4-6.html Cleft of the mouth A gap or groove in the upper lip. This is a congenital defect resulting from nonfusion of tissues of the lip during embryonal development. Fyler:4875 MSH:D002971 SNOMEDCT_US:80281008 UMLS:C0008924 Cheiloschisis of upper lip Cleft upper lip Harelip Cleft of upper lip HP:0000204 Cleft upper lip A gap or groove in the upper lip. This is a congenital defect resulting from nonfusion of tissues of the lip during embryonal development. Cheiloschisis of upper lip Cleft upper lip Harelip Cleft of upper lip Hyperplasia of the gingiva (that is, a thickening of the soft tissue overlying the alveolar ridge. The degree of thickening ranges from involvement of the interdental papillae alone to gingival overgrowth covering the entire tooth crown. HP:0000195 MSH:D005885 MSH:D005886 MSH:D019214 SNOMEDCT_US:441787004 SNOMEDCT_US:441798003 SNOMEDCT_US:54711002 UMLS:C0017566 UMLS:C0017567 UMLS:C0376480 Gingival enlargement Gingival hyperplasia Gum enlargement Gum hypertrophy Hypertrophic gingivitis Oral soft tissue hyperplasia HP:0000212 This finding is to be distinguished from overgrowth of the alveolar ridge. Gingival overgrowth Hyperplasia of the gingiva (that is, a thickening of the soft tissue overlying the alveolar ridge. The degree of thickening ranges from involvement of the interdental papillae alone to gingival overgrowth covering the entire tooth crown. PMID:19125428 Gingival enlargement Gum enlargement Height of the palate more than 2 SD above the mean (objective) or palatal height at the level of the first permanent molar more than twice the height of the teeth (subjective). HP:0000156 HP:0009080 HP:0009082 HP:0009097 SNOMEDCT_US:27272007 UMLS:C0240635 Elevated palate High arched palate High palate High, arched palate High-arched palate Increased palatal height Palate high-arched Palate, high-arched Ogival palate HP:0000218 The measuring device for this assessment is described in (Hall JG, Froster-Iskenius UG, Allanson JE, Gripp K, Slavotinek A. 2006. Handbook of Normal Physical Measurements. 2nd edition. Oxford Medical, publishers). A high palate is often associated with a narrow palate. However, a narrow palate can easily give a false appearance of a high palate. Height and width of the palate should be assessed and coded separately. We do not recommend the subjective determination because this term can be overused and applied inaccurately. High palate Height of the palate more than 2 SD above the mean (objective) or palatal height at the level of the first permanent molar more than twice the height of the teeth (subjective). PMID:19125428 Elevated palate High palate Increased palatal height Inflammation of the gingiva. MSH:D005891 SNOMEDCT_US:66383009 UMLS:C0017574 Gingival inflammation Inflamed gums Red and swollen gums HP:0000230 Gingivitis Inflammation of the gingiva. Gingival inflammation Inflamed gums Red and swollen gums An abnormality of the head. UMLS:C4021812 Abnormal head Abnormality of the head Head abnormality HP:0000234 Abnormality of the head An abnormality of the head. Abnormal head Abnormality of the head Head abnormality Any abnormality of the fontanelles (the regions covered by a thick membrane that normally ossify in the first two years of life) or the cranial sutures (the fibrous joints in which the articulating bones or cartilages of the skull are connected by sutural ligaments). UMLS:C4025876 HP:0000235 Fontanels are the fibrous, membrane-covered gaps created when more than two cranial bones are juxtaposed, as opposed to sutures, which are narrow seams of fibrous connective tissue that separate the flat bones of the skull. At birth, an infant has six fontanels (the anterior and posterior, two mastoid, and two sphenoid). The anterior fontanel is the largest and most important for clinical evaluation. The average size of the anterior fontanel is 2.1 cm, and the median time of closure is 13.8 months. Abnormality of the fontanelles or cranial sutures Any abnormality of the fontanelles (the regions covered by a thick membrane that normally ossify in the first two years of life) or the cranial sutures (the fibrous joints in which the articulating bones or cartilages of the skull are connected by sutural ligaments). PMID:12825844 Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation. HP:0007189 HP:0008503 MSH:D006849 SNOMEDCT_US:230745008 UMLS:C0020255 Hydrocephaly Nonsyndromal hydrocephalus Too much cerebrospinal fluid in the brain HP:0000238 Hydrocephalus results from an imbalance between the rate of production of cerebrospinal fluid (CSF), mainly in the choroid plexus, and its reabsorption in the subarchnoid space over brain and spinal cord. Hydrocephalus Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation. PMID:18211712 PMID:19410151 Too much cerebrospinal fluid in the brain In newborns, the two frontal bones, two parietal bones, and one occipital bone are joined by fibrous sutures, which form a small posterior fontanelle, and a larger, diamond-shaped anterior fontanelle. These regions allow for the skull to pass the birth canal and for later growth. The fontanelles gradually ossify, whereby the posterior fontanelle usually closes by eight weeks and the anterior fontanelle by the 9th to 16th month of age. Large fontanelles are diagnosed if the fontanelles are larger than age-dependent norms. HP:0004473 SNOMEDCT_US:276709006 UMLS:C0456132 UMLS:C4072820 UMLS:C4072821 UMLS:C4072822 Enlarged fontanelles Large fontanel Large fontanelle Large fontanels Persistent wide fontanel Wide fontanelles Large bregma sutures Large, late-closing fontanelle Wide bregma sutures HP:0000239 There are six membrane-covered openings between the cranial sutures in the incompletely ossified skull of the fetus or newborn infant that normally close sometime after birth (anterior fontanel, cranial fontanel, mastoid fontanel, posterior fontanel, sphenoidal fontanel). Large fontanelles In newborns, the two frontal bones, two parietal bones, and one occipital bone are joined by fibrous sutures, which form a small posterior fontanelle, and a larger, diamond-shaped anterior fontanelle. These regions allow for the skull to pass the birth canal and for later growth. The fontanelles gradually ossify, whereby the posterior fontanelle usually closes by eight weeks and the anterior fontanelle by the 9th to 16th month of age. Large fontanelles are diagnosed if the fontanelles are larger than age-dependent norms. Wide fontanelles Large bregma sutures Large, late-closing fontanelle Wide bregma sutures Any abnormality of the size of the skull. Abnormality of head size UMLS:C4025874 Abnormality of cranium size Abnormality of skull size HP:0000240 Abnormality of skull size Any abnormality of the size of the skull. Abnormality of head size Abnormality of cranium size Abnormality of skull size An abnormal increase of density of the bones making up the calvaria. UMLS:C1854834 Dense skull cap HP:0000250 Dense calvaria An abnormal increase of density of the bones making up the calvaria. Dense skull cap Head circumference below 2 standard deviations below the mean for age and gender. HP:0001366 HP:0005485 HP:0005489 HP:0005497 Abnormally small head Decreased size of head Small head Small skull Fyler:4310 SNOMEDCT_US:271611007 UMLS:C4551563 Abnormally small cranium Abnormally small skull Decreased circumference of cranium Decreased size of cranium Decreased size of skull Reduced head circumference Small head circumference small calvarium small cranium HP:0000252 Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles, others by standard deviations. It is important to add an indication of how far below the normal standard the head circumference is if an accurate assessment of this can be made. Microcephaly is an absolute term. The term relative microcephaly can be used when the head size centile is less than the centile for height, for example, head size at the 3rd centile with height at the 75% for age and sex. On prenatal ultrasound, microcephaly is diagnosed if the head circumference or the biparietal diameter is more than three standard deviations below the mean. Microcephaly is divided into primary microcephaly, which is present at birth, and secondary microcephaly, which develops postnatally. The crucial difference between these groupings is that primary microcephaly is usually a static developmental anomaly, whereas secondary microcephaly indicates a progressive neurodegenerative condition Microcephaly Head circumference below 2 standard deviations below the mean for age and gender. PMID:15806441 PMID:19125436 PMID:25465325 PMID:9683597 Abnormally small head Decreased size of head Small head Small skull Abnormally small cranium Abnormally small skull Decreased circumference of cranium Decreased size of cranium Decreased size of skull Reduced head circumference Small head circumference small calvarium small cranium Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms. UMLS:C1850456 Microcephaly, postnatal, progressive Microcephaly, progressive Progressively abnormally small cranium Progressively abnormally small skull HP:0000253 Progressive microcephaly Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms. Microcephaly, progressive Progressively abnormally small cranium Progressively abnormally small skull Occipitofrontal (head) circumference greater than 97th centile compared to appropriate, age matched, sex-matched normal standards. Alternatively, a apparently increased size of the cranium. HP:0005491 HP:0005496 HP:0200135 Big calvaria Big cranium Big head Big skull Increased size of head Large calvaria Large cranium Large skull Fyler:4335 UMLS:C4083076 UMLS:C4255213 UMLS:C4280663 UMLS:C4280664 Increased size of cranium Increased size of skull Large head Large head circumference Macrocephalus Macrocrania Megacephaly HP:0000256 Macrocephaly can be due to hydrocephalus (increased CFSF), megalencephaly (increased brain volume) or thickening of the skull. Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles [Hall et al. [2007]], others by standard deviations [Farkas, [1981]]. It is important to add an indication of how far above the normal standard the head circumference is if an accurate assessment of this can be made. Macrocephaly is an absolute term. The term relative macrocephaly can be used when the head size centile exceeds the centile for height, for example, head size at the 75th centile with height at the 5th centile for age and sex. Macrocephaly Occipitofrontal (head) circumference greater than 97th centile compared to appropriate, age matched, sex-matched normal standards. Alternatively, a apparently increased size of the cranium. PMID:19125436 Big calvaria Big cranium Big head Big skull Increased size of head Large calvaria Large cranium Large skull Increased size of cranium Increased size of skull Large head Large head circumference Megacephaly An abnormality of the face. Abnormality of the countenance Abnormality of the physiognomy Abnormality of the visage Disorder of face SNOMEDCT_US:118930001 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C1290857 UMLS:C4025871 Abnormal face Abnormality of the face Facial abnormality Disorder of the face Anomaly of face Anomaly of the face Facial anomaly HP:0000271 Abnormality of the face An abnormality of the face. Abnormality of the countenance Abnormality of the physiognomy Abnormality of the visage Disorder of face Abnormal face Abnormality of the face Facial abnormality Disorder of the face Anomaly of face Anomaly of the face Facial anomaly A face that is short and narrow. UMLS:C1855538 Facial hypoplasia Hypoplasia of face Microface Microfacies Short and narrow face Small face Small facies HP:0000274 This term represents a combination of two terms, short face and narrow face. Small face A face that is short and narrow. Facial hypoplasia Hypoplasia of face Microface Microfacies Short and narrow face Small face Small facies Facial height (length) is more than 2 standard deviations above the mean (objective); or, an apparent increase in the height (length) of the face (subjective). HP:0000334 UMLS:C1836047 Elongation of face Increased height of face Increased length of face Increased vertical dimension of face Long face Long facies Vertical Facial Excess Vertical elongation of face Vertical enlargement of face Vertical excess of face Vertical hyperplasia of face Vertical overgrowth of face HP:0000276 Objective measurement of the face height is made with sliding calipers from the nasion, just above the depth of the nasal root, to the gnathion, the inferior border of the mandible, both in the midline. Note that long face is distinct from narrow face. Long face Facial height (length) is more than 2 standard deviations above the mean (objective); or, an apparent increase in the height (length) of the face (subjective). PMID:19125436 Elongation of face Increased height of face Increased length of face Increased vertical dimension of face Long face Long facies Vertical Facial Excess Vertical elongation of face Vertical enlargement of face Vertical excess of face Vertical hyperplasia of face Vertical overgrowth of face An increased amount of subcutaneous fat tissue in the face. UMLS:C4025868 UMLS:C4280649 UMLS:C4280650 Increased amount of facial adipose tissue Increased amount of facial fat Increased volume of facial adipose tissue Facial fat hyperplasia Facial fat hypertrophy Hyperplasia of facial adipose tissue Hypertrophy of facial adipose tissue HP:0000287 Increased facial adipose tissue An increased amount of subcutaneous fat tissue in the face. Increased amount of facial adipose tissue Increased amount of facial fat Increased volume of facial adipose tissue Facial fat hyperplasia Facial fat hypertrophy Hyperplasia of facial adipose tissue Hypertrophy of facial adipose tissue An anomaly of the forehead. UMLS:C4025867 Abnormality of the forehead Abnormality of the frontal region of the face Anomaly of the forehead Deformity of the forehead Malformation of the forehead HP:0000290 Abnormality of the forehead An anomaly of the forehead. Abnormality of the forehead Abnormality of the frontal region of the face Anomaly of the forehead Deformity of the forehead Malformation of the forehead UMLS:C4025866 Abnormality of facial fat Deformity of facial adipose tissue Malformation of facial adipose tissue HP:0000291 Abnormality of facial adipose tissue Abnormality of facial fat Deformity of facial adipose tissue Malformation of facial adipose tissue Loss of normal subcutaneous fat tissue in the face. UMLS:C1837767 Decreased amount of facial adipose tissue Decreased amount of facial fat Decreased volume of facial adipose tissue Loss of facial fat Loss of facial subcutaneous adipose tissue Loss of subcutaneous adipose tissue from face HP:0000292 Loss of facial adipose tissue Loss of normal subcutaneous fat tissue in the face. Decreased amount of facial adipose tissue Decreased amount of facial fat Decreased volume of facial adipose tissue Loss of facial fat Increased prominence or roundness of soft tissues between zygomata and mandible. HP:0002262 HP:0004427 UMLS:C1866231 UMLS:C2748653 UMLS:C3806443 UMLS:C4280647 UMLS:C4280648 Apple cheeks Big cheeks Full cheeks Increased size of cheeks Large cheeks Chubby cheeks Hyperplasia of cheeks Hypertrophy of cheeks Puffy cheeks HP:0000293 Full cheeks Increased prominence or roundness of soft tissues between zygomata and mandible. Apple cheeks Big cheeks Full cheeks Increased size of cheeks Large cheeks Chubby cheeks Hyperplasia of cheeks Hypertrophy of cheeks Puffy cheeks An anomaly of a muscle that is innervated by the facial nerve (the seventh cranial nerve). UMLS:C4025865 Abnormality of facial muscles Facial muscle issue HP:0000301 Facial muscles control facial expression and are innervated by the seventh cranial nerve. Facial muscles around the eye are responsible for eye blink and eyelid closure. Abnormality of facial musculature An anomaly of a muscle that is innervated by the facial nerve (the seventh cranial nerve). Abnormality of facial muscles Facial muscle issue An anomaly of the midface, which is a region and not an anatomical term. It extends, superiorly, from the inferior orbital margin to, inferiorly, the level of nasal base. It is formed by the maxilla (upper jaw) and zygoma and cheeks and malar region. Traditionally, the nose and premaxilla are not included in the midface. HP:0430026 UMLS:C4021811 Abnormal morphology of the midface Abnormality of the midface Anomaly of the midface Deformity of the midface Malformation of the midface HP:0000309 Abnormal midface morphology An anomaly of the midface, which is a region and not an anatomical term. It extends, superiorly, from the inferior orbital margin to, inferiorly, the level of nasal base. It is formed by the maxilla (upper jaw) and zygoma and cheeks and malar region. Traditionally, the nose and premaxilla are not included in the midface. PMID:19125436 Abnormality of the midface Deformity of the midface Malformation of the midface The facial appearance is more circular than usual as viewed from the front. HP:0000304 HP:0004653 Round, full face UMLS:C0239479 UMLS:C1856468 Circular face Round face Round facial appearance Round facial shape Round facies HP:0000311 Round face The facial appearance is more circular than usual as viewed from the front. PMID:19125436 Circular face Round face Round facial appearance Round facial shape HP:0000284 UMLS:C4025863 Abnormality of the eye region Abnormality of the region around the eyes Anomaly of the orbital region of the face Deformity of the orbital region of the face Malformation of the orbital region of the face HP:0000315 Abnormality of the orbital region Abnormality of the eye region Abnormality of the region around the eyes Anomaly of the orbital region of the face Deformity of the orbital region of the face Malformation of the orbital region of the face An abnormally increased height of the forehead. HP:0000342 UMLS:C0239676 UMLS:C2677762 High forehead Tall forehead HP:0000348 High forehead An abnormally increased height of the forehead. High forehead Tall forehead The presence of a forehead that is abnormally small. UMLS:C1845250 UMLS:C4280633 UMLS:C4280634 Decreased size of forehead Decreased size of frontal region of face Small forehead Hypoplasia of forehead Hypotrophic forehead HP:0000350 Small forehead The presence of a forehead that is abnormally small. Decreased size of forehead Decreased size of frontal region of face Small forehead Hypoplasia of forehead Hypotrophic forehead An abnormality of the external ear. HP:0001752 SNOMEDCT_US:275259005 UMLS:C0266589 UMLS:C1846460 Abnormal pinnae Abnormality of the auricle Abnormality of the external ear Abnormality of the outer ear Ear anomalies External ear malformations Malformed pinnae Outer ear abnormality HP:0000356 Abnormality of the outer ear An abnormality of the external ear. Abnormality of the external ear Abnormality of the outer ear Ear anomalies External ear malformations Outer ear abnormality Abnormal location of the ear. UMLS:C4021810 Abnormal location of ears External ear position defect HP:0000357 Abnormal location of ears Abnormal location of the ear. Abnormal location of ears An abnormality of the inner ear. UMLS:C4021809 Abnormality of the inner ear Inner ear abnormality HP:0000359 Abnormality of the inner ear An abnormality of the inner ear. Abnormality of the inner ear Inner ear abnormality An abnormality of the sensory perception of sound. UMLS:C4025860 Abnormal hearing Hearing abnormality HP:0000364 According to the World Health Organization, deafness refers to the complete loss of hearing ability in one or two ears. Hearing impairment refers to both complete and partial loss of the ability to hear. Hearing abnormality An abnormality of the sensory perception of sound. Abnormal hearing Hearing abnormality A decreased magnitude of the sensory perception of sound. HP:0000404 HP:0001728 HP:0001729 HP:0001754 HP:0008560 HP:0008563 Fyler:4868 MSH:D003638 MSH:D034381 SNOMEDCT_US:103276001 SNOMEDCT_US:15188001 SNOMEDCT_US:343087000 SNOMEDCT_US:95828007 UMLS:C0011053 UMLS:C0018772 UMLS:C0339789 UMLS:C1384666 Deafness Hearing defect Hearing impairment Hypacusis Hearing loss Hypoacusis HP:0000365 Hearing loss can be categorized by which part of the auditory system is damaged, as conductive hearing loss, sensorineural hearing loss, and mixed hearing loss. Another axis of classification uses the degree of hearing impairment. The degree of hearing loss is computed by using a three frequency average taken at 500 Hz, 1,000 Hz and 2,000 Hz. The average of these three frequencies is called the Pure Tone Average (PTA). 0-20 dB is considered normal, 21-40 dB mild loss, 41-60 dB moderate loss, 61-70 dB moderately severe loss,71-90 dB severe loss, and greater than 90 dB profound loss. Note that the word deafness is occasionally used to describe partial hearing loss. The World Health Organization uses the word deafness to refer to complete loss of the ability to hear, and hearing impairment to refer to any degree of reduced hearing. Hearing impairment A decreased magnitude of the sensory perception of sound. Deafness Hearing defect Hearing impairment Hearing loss An abnormality of the nose. SNOMEDCT_US:128274005 SNOMEDCT_US:72089000 UMLS:C0240547 UMLS:C0265736 UMLS:C2235909 Abnormality of the nose Anomaly of the nose Nasal abnormality Nasal anomaly Deformity of the nose Malformation of the nose Nasal deformity Nasal malformation HP:0000366 Abnormality of the nose An abnormality of the nose. Abnormality of the nose Anomaly of the nose Nasal abnormality Nasal anomaly Deformity of the nose Malformation of the nose Nasal deformity Nasal malformation Upper insertion of the ear to the scalp below an imaginary horizontal line drawn between the inner canthi of the eye and extending posteriorly to the ear. SNOMEDCT_US:95515009 UMLS:C0239234 Low set ears Low-set ears Low-set pinnae Lowset ears Melotia HP:0000369 Low-set ears Upper insertion of the ear to the scalp below an imaginary horizontal line drawn between the inner canthi of the eye and extending posteriorly to the ear. PMID:19152421 Low set ears Low-set ears Lowset ears An abnormality of the middle ear. UMLS:C1861141 Middle ear abnormalities Middle ear abnormality HP:0000370 Abnormality of the middle ear An abnormality of the middle ear. An abnormality of the External acoustic tube (also known as the auditory canal). UMLS:C4021807 Auditory canal abnormality HP:0000372 Abnormality of the auditory canal An abnormality of the External acoustic tube (also known as the auditory canal). An abnormality of the cochlea. UMLS:C4025858 Abnormality of cochlea HP:0000375 The cochlea is an inner ear structure comprised of a snail-shell like structure divided into three fluid-filled parts. Two are canals for the transmission of pressure and in the third is the organ of Corti, which detects pressure impulses and responds with electrical impulses which travel along the auditory nerve to the brain. Abnormal cochlea morphology An abnormality of the cochlea. An abnormality of the pinna, which is also referred to as the auricle or external ear. HP:0000390 HP:0000398 HP:0004465 HP:0008562 HP:0008566 HP:0008567 HP:0008580 HP:0008582 HP:0008602 HP:0040111 SNOMEDCT_US:253255002 UMLS:C0431483 UMLS:C0857379 Abnormal form of ears Abnormally shaped ears Auricular malformation Deformed auricles Deformed ears Dysplastic ears Malformation of auricle Malformed auricles Malformed ears Malformed external ears Minor malformation of the auricles Poorly defined conchae HP:0000377 The term 'dysplastic' is no longer accepted as a descriptor for an ear with unusual morphology. Each specific anatomical component of the ear should be described when the ear is thought to be abnormal in appearance. Abnormal pinna morphology An abnormality of the pinna, which is also referred to as the auricle or external ear. Abnormally shaped ears Auricular malformation Deformed ears Malformed ears Inflammation or infection of the middle ear. MSH:D010033 SNOMEDCT_US:65363002 UMLS:C0029882 Middle ear infection HP:0000388 Otitis media Inflammation or infection of the middle ear. Middle ear infection Median longitudinal ear length greater than two standard deviations above the mean and median ear width greater than two standard deviations above the mean (objective); or, apparent increase in length and width of the pinna (subjective). HP:0000382 HP:0000386 HP:0000401 HP:0001755 SNOMEDCT_US:275480001 SNOMEDCT_US:69056000 UMLS:C0152421 UMLS:C0554972 UMLS:C1835581 UMLS:C1848570 UMLS:C1850189 UMLS:C1855062 UMLS:C1860838 Large ears Large pinnae HP:0000400 This is acknowledged to be a bundled term but retained here because of its usefulness in practice. Ear length is determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. If only length is increased the term Long ear should be used. Macrotia Median longitudinal ear length greater than two standard deviations above the mean and median ear width greater than two standard deviations above the mean (objective); or, apparent increase in length and width of the pinna (subjective). PMID:19152421 Large ears An abnormality of vibrational conductance of sound to the inner ear leading to impairment of sensory perception of sound. HP:0000367 HP:0008581 MSH:D006314 SNOMEDCT_US:44057004 UMLS:C0018777 Conduction deafness Conductive deafness Conductive hearing loss Hearing loss, conductive HP:0000405 A conductive hearing impariment with greater than 90 dB loss. Conductive hearing impairment An abnormality of vibrational conductance of sound to the inner ear leading to impairment of sensory perception of sound. Conductive deafness Conductive hearing loss A type of hearing impairment in one or both ears related to an abnormal functionality of the cochlear nerve. HP:0000374 HP:0001753 HP:0001916 HP:0008538 HP:0008553 HP:0008565 HP:0008576 HP:0008611 HP:0008613 HP:0008614 MSH:D006319 SNOMEDCT_US:60700002 UMLS:C0018784 Hearing loss, sensorineural Sensorineural deafness Sensorineural hearing loss HP:0000407 Hearing loss caused by damage or dysfunction of the auditory nerve (cranial nerve VIII, also known as the cochlear nerve). Sensorineural hearing impairment A type of hearing impairment in one or both ears related to an abnormal functionality of the cochlear nerve. Hearing loss, sensorineural A progressive form of sensorineural hearing impairment. HP:0000397 HP:0000406 HP:0008592 HP:0008601 HP:0008617 UMLS:C1843156 Bilateral progressive sensorineural hearing loss Hearing loss, progressive sensorineural Hearing loss, sensorineural, bilateral, progressive Hearing loss, sensorineural, progressive Progressive bilateral sensorineural hearing loss Sensorineural hearing loss, progressive HP:0000408 Progressive sensorineural hearing impairment A progressive form of sensorineural hearing impairment. Increased volume and globular shape of the anteroinferior aspect of the nose. HP:0000443 MSH:C538354 UMLS:C0240543 UMLS:C1834118 UMLS:C1855751 Bulbous nose Bulbous nasal tip Potato nose HP:0000414 This is a bundled term, but as it is useful in practice it is kept here. This alteration of size and shape may be limited to the tip, but may involve the lower third of the nose. If only the width of the nasal tip is increased this should be coded as Broad nasal tip. Bulbous nose Increased volume and globular shape of the anteroinferior aspect of the nose. PMID:19152422 Bulbous nose Potato nose Abnormality of the choanae (the posterior nasal apertures). UMLS:C4025855 HP:0000415 Abnormality of the choanae Abnormality of the choanae (the posterior nasal apertures). An abnormality of the nasal septum. SNOMEDCT_US:95433000 UMLS:C0151790 Abnormality of septum of nose Abnormality of the nasal septum Anomaly of nasal septum Anomaly of septum of nose HP:0000419 Abnormal nasal septum morphology An abnormality of the nasal septum. Abnormality of septum of nose Abnormality of the nasal septum Anomaly of nasal septum Anomaly of septum of nose Reduced superior to inferior length of the nasal septum. UMLS:C1844857 Decreased length of nasal septum Decreased length of septum of nose Short nasal septum Short septum of nose HP:0000420 Short nasal septum Reduced superior to inferior length of the nasal septum. Decreased length of nasal septum Decreased length of septum of nose Short nasal septum Short septum of nose An abnormality of the Ala of nose. UMLS:C2227020 UMLS:C4021804 UMLS:C4280631 UMLS:C4280632 Abnormality of the nasal ala Abnormality of the nasal alae Abnormality of the nasal alar cartilage Deformity of the nasal ala Deformity of the nasal alar cartilage Malformation of the nasal ala Malformation of the nasal alar cartilage HP:0000429 The nasal ala is the tissue comprising the lateral boundary of the nose, inferiorly, surrounding the naris. Abnormal morphology of the nasal alae An abnormality of the Ala of nose. PMID:19152422 Abnormality of the nasal alar cartilage Deformity of the nasal ala Deformity of the nasal alar cartilage Malformation of the nasal ala Malformation of the nasal alar cartilage Thinned, deficient, or excessively arched ala nasi. HP:0004497 HP:0004507 HP:0005276 HP:0005277 HP:0005286 UMLS:C1834055 Ala nasi, underdeveloped Alar cartilage hypoplasia Decreased size of nasal alae Hypoplastic alae nasae Hypoplastic alae nasi Hypoplastic alar cartilage Hypoplastic alar nasae Hypoplastic nares Hypoplastic nasal alae Hypoplastic nasal wings Hypoplastic nostrils Nasal cartilage hypoplasia Small nasal alae Thin hypoplastic alae nasi Underdeveloped tissue around nostril HP:0000430 The alae nasi are the lateral portions of the nose or the wings of the nostrils, which partly encircle the nostrils (nares). They are usually about the width of the columella, but vary greatly depending on the shape of the nostril. Note that individuals may be described as having a Cleft ala nasi, but have a severely underdeveloped ala nasi. In an underdeveloped ala the continuity of the tissue encircling the nostril is undisturbed while in a cleft it is disrupted. With severe hypoplasia of the nasal alae, the nasal tip may appear depressed. Underdeveloped nasal alae Thinned, deficient, or excessively arched ala nasi. PMID:19152422 Decreased size of nasal alae Small nasal alae Underdeveloped tissue around nostril UMLS:C4025854 Abnormality of mucosa of nose Abnormality of mucous membrane of nose Abnormality of nasal mucous membrane Abnormality of the nasal mucosa HP:0000433 Abnormal nasal mucosa morphology Abnormality of mucosa of nose Abnormality of mucous membrane of nose Abnormality of nasal mucous membrane Abnormality of the nasal mucosa An abnormality of the nasal tip. UMLS:C4025852 Abnormality of the nasal tip Abnormality of tip of nose Deformity of the nasal tip Deformity of tip of nose Malformation of the nasal tip Malformation of tip of nose HP:0000436 The nasal tip is located at the junction of the inferior margin of the nasal ridge and the columella. Commonly, it is the part of the nose furthest from the plane of the face. In rare circumstances, such as markedly prominent and convex nasal profiles, other parts of the ridge may be further removed from the facial plane. Abnormal nasal tip morphology An abnormality of the nasal tip. PMID:19152422 Abnormality of the nasal tip Abnormality of tip of nose Deformity of the nasal tip Deformity of tip of nose Malformation of the nasal tip Malformation of tip of nose Decreased distance from the nasal tip to the nasal base. HP:0005279 UMLS:C1859717 Caved in nasal tip Depressed nasal tip Depressed tip of nose Flat nasal tip Flat tip of nose Flattened nasal tip Nasal tip, depressed Nasal tip, recessed Nasal tip, retruded Retruded tip of nose HP:0000437 This often accompanies a Short columella, Overhanging nasal tip, and Underdeveloped nasal tip, but these should be assessed and coded separately. Depressed nasal tip Decreased distance from the nasal tip to the nasal base. PMID:19152422 Caved in nasal tip Depressed nasal tip Depressed tip of nose Flat nasal tip Flat tip of nose Flattened nasal tip Nasal tip, depressed Retruded tip of nose A splitting of the nasal tip. Visually assessable vertical indentation, cleft, or depression of the nasal tip. HP:0005282 SNOMEDCT_US:249326006 UMLS:C0426428 UMLS:C4020890 Bifid tip of nose Cleft nasal tip Cleft tip of nose Notched nasal tip Notched tip of nose HP:0000456 This is a rare congenital deformity due to failure of the paired nasal processes to fuse to a single midline organ during early gestation. Bifid nasal tip A splitting of the nasal tip. Visually assessable vertical indentation, cleft, or depression of the nasal tip. PMID:19152422 Bifid tip of nose Cleft nasal tip Cleft tip of nose Notched nasal tip Notched tip of nose Lack of prominence of the nose resulting from a posteriorly-placed nasal ridge. UMLS:C1842876 Depressed dorsum of nose Depressed nasal dorsum Flat dorsum of nose Flat nasal dorsum Flat nose Recessed dorsum of nose Recessed nasal dorsum Recessed nasal ridge Retruded dorsum of nose Retruded nasal dorsum Retruded nasal ridge HP:0000457 The adjective 'depressed' here does not indicate an active process but a status. The feature should be assessed in a profile view. This finding is typically associated with a Short columella, but this should be assessed separately. Depressed nasal ridge Lack of prominence of the nose resulting from a posteriorly-placed nasal ridge. PMID:19152422 Depressed dorsum of nose Depressed nasal dorsum Flat dorsum of nose Flat nasal dorsum Flat nose Recessed dorsum of nose Recessed nasal dorsum Recessed nasal ridge Retruded dorsum of nose Retruded nasal dorsum Retruded nasal ridge An inability to perceive odors. This is a general term describing inability to smell arising in any part of the process of smelling from absorption of odorants into the nasal mucous overlying the olfactory epithelium, diffusion to the cilia, binding to olfactory receptor sites, generation of action potentials in olfactory neurons, and perception of a smell. MSH:D000857 SNOMEDCT_US:44169009 UMLS:C0003126 Loss of smell Lost smell HP:0000458 Anosmia An inability to perceive odors. This is a general term describing inability to smell arising in any part of the process of smelling from absorption of odorants into the nasal mucous overlying the olfactory epithelium, diffusion to the cilia, binding to olfactory receptor sites, generation of action potentials in olfactory neurons, and perception of a smell. Lost smell An abnormality of the neck. SNOMEDCT_US:298390003 SNOMEDCT_US:40052002 UMLS:C0266623 UMLS:C0575167 UMLS:C4280628 Abnormality of the neck Anomaly of the neck Deformity of the neck Malformation of the neck HP:0000464 Abnormality of the neck An abnormality of the neck. Abnormality of the neck Anomaly of the neck Deformity of the neck Malformation of the neck An increased amount of subcutaneous fat tissue around the neck. UMLS:C4025850 Increased fat around the neck HP:0000468 Increased adipose tissue around the neck An increased amount of subcutaneous fat tissue around the neck. Increased fat around the neck Diminished length of the neck. HP:0005992 HP:0200137 SNOMEDCT_US:95427009 UMLS:C0521525 Cervical shortening Decreased cervical height Decreased cervical length Decreased length of neck Short neck HP:0000470 Short neck Diminished length of the neck. Cervical shortening Decreased cervical height Decreased cervical length Decreased length of neck Short neck Dysplasia affecting the vasculature of the gastrointestinal tract. UMLS:C0854242 GI angiodysplasia HP:0000471 Gastrointestinal angiodysplasia Dysplasia affecting the vasculature of the gastrointestinal tract. GI angiodysplasia Increased inferior-superior length of the neck. UMLS:C1839816 Cervical elongation Elongated neck Increased cervical length Increased length of neck Long neck HP:0000472 Long neck Increased inferior-superior length of the neck. Cervical elongation Elongated neck Increased cervical length Increased length of neck Long neck Any abnormality of the eye, including location, spacing, and intraocular abnormalities. MSH:D005124 MSH:D005128 SNOMEDCT_US:19416009 SNOMEDCT_US:371405004 SNOMEDCT_US:371409005 UMLS:C0015393 UMLS:C0015397 Abnormal eye Abnormality of the eye Eye disease HP:0000478 Abnormality of the eye Any abnormality of the eye, including location, spacing, and intraocular abnormalities. Abnormal eye Abnormality of the eye Eye disease A structural abnormality of the retina. HP:0007938 MSH:D012164 SNOMEDCT_US:29555009 UMLS:C0035300 UMLS:C0035309 Abnormal retina Abnormality of the retina Anomaly of the retina Retina issue Retinal disease HP:0000479 Abnormal retinal morphology A structural abnormality of the retina. Abnormal retina Retina issue A notch or cleft of the retina. HP:0007808 UMLS:C3540764 Hole in the back of the eye HP:0000480 Retinal coloboma A notch or cleft of the retina. Hole in the back of the eye Any abnormality of the cornea, which is the transparent tissue at the front of the eye that covers the iris, pupil, and anterior chamber. HP:0007771 HP:0007972 UMLS:C1855670 UMLS:C4020889 Abnormality of the cornea Corneal abnormalities Corneal abnormality Cornela disease HP:0000481 Abnormal cornea morphology Any abnormality of the cornea, which is the transparent tissue at the front of the eye that covers the iris, pupil, and anterior chamber. A congenital abnormality of the cornea in which the cornea and the anterior segment of the eye are smaller than normal. The horizontal diameter of the cornea does not reach 10 mm even in adulthood. HP:0100688 SNOMEDCT_US:26098002 UMLS:C0266544 UMLS:C1167713 Cornea of eye less than 10mm in diameter Decreased corneal diameter HP:0000482 Note that the cornea's diameter is normally about 9.5-10.0 mm at birth and reaches 10.0-12-5 mm in adulthood. Microcornea A congenital abnormality of the cornea in which the cornea and the anterior segment of the eye are smaller than normal. The horizontal diameter of the cornea does not reach 10 mm even in adulthood. Cornea of eye less than 10mm in diameter An enlargement of the cornea with normal clarity and function. Megalocornea is diagnosed with a horizontal corneal diameter of 12 mm or more at birth or 13 mm or more after two years of age. HP:0007660 MSH:C562829 SNOMEDCT_US:204118005 SNOMEDCT_US:268158009 UMLS:C0344530 UMLS:C1167712 Anterior megalophthalmos Enlarged cornea Increased corneal diameter Macrocornea HP:0000485 Megalocornea An enlargement of the cornea with normal clarity and function. Megalocornea is diagnosed with a horizontal corneal diameter of 12 mm or more at birth or 13 mm or more after two years of age. Enlarged cornea Abnormality of eyesight (visual perception). UMLS:C4025846 Abnormality of sight Abnormality of vision Vision issue HP:0000504 Abnormality of vision Abnormality of eyesight (visual perception). Abnormality of sight Abnormality of vision Vision issue Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery. HP:0000516 HP:0000566 HP:0007758 HP:0007860 HP:0007983 MSH:D014786 MSH:D015354 SNOMEDCT_US:246635007 SNOMEDCT_US:397540003 SNOMEDCT_US:7973008 UMLS:C0042798 UMLS:C3665347 Impaired vision Loss of eyesight Poor vision Visual impairment HP:0000505 Visual impairment Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery. Impaired vision Loss of eyesight Poor vision Visual impairment An inherited retinal disease subtype in which the rod photoreceptors appear to be more severely affected than the cone photoreceptors. Typical presentation is with nyctalopia (due to rod dysfunction) followed by loss of mid-peripheral field of vision, which gradually extends and leaves many patients with a small central island of vision due to the preservation of macular cones. HP:0000547 HP:0001127 HP:0007635 HP:0007645 HP:0007742 HP:0007816 HP:0007826 HP:0007927 HP:0008036 MSH:D012174 SNOMEDCT_US:28835009 UMLS:C0035334 Retinitis pigmentosa Rod cone dystrophy HP:0000510 Retinitis pigmentosa is a group of hereditary diseases of the eye. However, the term retinitis pigmentosa has also been used to describe the retinal findings characteristic of these diseases but also seen on other diseases such as Usher syndrome. It is preferable to describe the findings precisely if possible, but this term is kept for convenience. Rod-cone dystrophy An inherited retinal disease subtype in which the rod photoreceptors appear to be more severely affected than the cone photoreceptors. Typical presentation is with nyctalopia (due to rod dysfunction) followed by loss of mid-peripheral field of vision, which gradually extends and leaves many patients with a small central island of vision due to the preservation of macular cones. PMID:20212494 An abnormality of the lens. MSH:D007905 SNOMEDCT_US:10810001 UMLS:C0023308 UMLS:C0549651 Abnormality of the lens Lens issue Lens disease HP:0000517 Abnormal lens morphology An abnormality of the lens. Abnormality of the lens Lens issue Lens disease A cataract is an opacity or clouding that develops in the crystalline lens of the eye or in its capsule. HP:0001113 HP:0007825 HP:0010700 Fyler:4865 MSH:D002386 SNOMEDCT_US:128306009 SNOMEDCT_US:193570009 SNOMEDCT_US:247053007 UMLS:C0086543 UMLS:C1510497 Cataracts Clouding of the lens of the eye Cloudy lens Lens opacities Lens opacity HP:0000518 Note that some ophthalmologists call any opacity in the lens a cataract, while others restrict the term to lens opacities that impair vision. We use the term to refer to the first meaning (any lens opacity). Cataract A cataract is an opacity or clouding that develops in the crystalline lens of the eye or in its capsule. Clouding of the lens of the eye Cloudy lens An abnormality of the iris, which is the pigmented muscular tissue between the cornea and the lens, that is perforated by an opening called the pupil. UMLS:C4025845 Abnormality of the iris HP:0000525 Abnormality iris morphology An abnormality of the iris, which is the pigmented muscular tissue between the cornea and the lens, that is perforated by an opening called the pupil. Abnormality of the iris Abnormality of the iris characterized by, typically bilateral, complete or partial iris hypoplasia. The phenotype ranges from mild defects of anterior iris stroma only to almost complete absence of the iris. HP:0011498 MSH:D015783 SNOMEDCT_US:69278003 UMLS:C0003076 Absent iris HP:0000526 Aniridia Abnormality of the iris characterized by, typically bilateral, complete or partial iris hypoplasia. The phenotype ranges from mild defects of anterior iris stroma only to almost complete absence of the iris. PMID:24138039 PMID:25313118 PMID:29850208 Absent iris Absence of the globe or eyeball. HP:0001485 HP:0007664 Fyler:4864 MSH:D000853 SNOMEDCT_US:204099004 SNOMEDCT_US:7183006 UMLS:C0003119 Absence of eyeballs Absence of globes of eyes Anophthalmia, clinical Clinical anophthalmia, unilateral/bilateral Failure of development of eyeball Missing eyeball Missing globe of eye No eyeball No globe of eye Ocular absence HP:0000528 Anophthalmia Absence of the globe or eyeball. HPO_CONTRIBUTOR:DDD_ncarter Absence of eyeballs Absence of globes of eyes Failure of development of eyeball Missing eyeball Missing globe of eye No eyeball No globe of eye Ocular absence An abnormality of the choroid and retina. HP:0001145 HP:0007888 UMLS:C4025844 Chorioretinal abnormality HP:0000532 The choroid is the vascular layer of the eye, located between the retina and the sclera. Abnormal chorioretinal morphology An abnormality of the choroid and retina. Atrophy of the choroid and retinal layers of the fundus. HP:0001150 HP:0007884 HP:0007918 HP:0007931 SNOMEDCT_US:95686007 UMLS:C4048273 Chorioretinal thinning HP:0000533 Choroidal sclerosis is a descriptive term applied to the ophthalmoscopic appearance of prominent white choroidal vessels in which the blood columns are not seen or are sheathed by white lines. Choroidal sclerosis is a term used to describe a group of genetically heterogeneous retinal dystrophies that share a common funduscopic phenotype of scalloped, well-circumscribed, and confluent chorioretinal atrophic lesions that extend beyond the macula. The term choroidal sclerosis was initially coined because of the sclerotic appearance of choroidal vessels which frequently appear white or light-yellow. However, histologic studies have demonstrated the term to be a misnomer as the principle abnormality is the loss of choriocapillaris, retinal pigment epithelium (RPE), and the outer retina in the absence of abnormal sclerotic changes in the choroidal vasculature. Therefore, we are making choroidal sclerosis a synonym of chorioretinal atrophy. Chorioretinal atrophy Atrophy of the choroid and retinal layers of the fundus. PMID:20224472 A nonspecific term denoting degeneration of the retinal pigment epithelium and/or retinal photoreceptor cells. HP:0007632 HP:0007790 HP:0007863 HP:0007893 MSH:D012162 SNOMEDCT_US:95695004 UMLS:C0035304 Retina degeneration HP:0000546 Retinal degeneration A nonspecific term denoting degeneration of the retinal pigment epithelium and/or retinal photoreceptor cells. Retina degeneration An abnormality of the uvea, the vascular layer of the eyeball. UMLS:C4025842 Abnormality of the uvea HP:0000553 Abnormal uvea morphology An abnormality of the uvea, the vascular layer of the eyeball. Inflammation of one or all portions of the uveal tract. MSH:D014605 SNOMEDCT_US:128473001 UMLS:C0042164 HP:0000554 The uvea is the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid. Uveitis Inflammation of one or all portions of the uveal tract. Retinal dystrophy is an abnormality of the retina associated with a hereditary process. Retinal dystrophies are defined by their predominantly monogenic inheritance and they are frequently associated with loss or dysfunction of photoreceptor cells as a primary or secondary event. HP:0007736 HP:0007910 HP:0007974 HP:0007982 MSH:D058499 SNOMEDCT_US:314407005 UMLS:C0854723 Breakdown of light-sensitive cells in back of eye HP:0000556 Retinal dystrophy Retinal dystrophy is an abnormality of the retina associated with a hereditary process. Retinal dystrophies are defined by their predominantly monogenic inheritance and they are frequently associated with loss or dysfunction of photoreceptor cells as a primary or secondary event. Breakdown of light-sensitive cells in back of eye A developmental anomaly characterized by abnormal smallness of one or both eyes. HP:0007996 Decreased size of eyeball Decreased size of globe of eye Fyler:4877 MSH:D008850 SNOMEDCT_US:204108000 SNOMEDCT_US:61142002 UMLS:C0026010 UMLS:C4280625 UMLS:C4280808 Abnormally small eyeball Abnormally small globe of eye Microphthalmos Nanophthalmos HP:0000568 Microphthalmia A developmental anomaly characterized by abnormal smallness of one or both eyes. Decreased size of eyeball Decreased size of globe of eye Abnormally small eyeball Abnormally small globe of eye A developmental defect characterized by a cleft of some portion of the eye or ocular adnexa. HP:0007767 HP:0007995 Fyler:4311 MSH:D003103 SNOMEDCT_US:92828000 SNOMEDCT_US:93390002 UMLS:C0009363 Notched pupil Ocular coloboma Ocular colobomas HP:0000589 Coloboma A developmental defect characterized by a cleft of some portion of the eye or ocular adnexa. Notched pupil An abnormality of the sclera. Abnormality of the outer white part of eyeball UMLS:C4025840 Abnormality of the sclera HP:0000591 Abnormal sclera morphology An abnormality of the sclera. Abnormality of the outer white part of eyeball Abnormality of the anterior chamber, which is the space in the eye that is behind the cornea and in front of the iris. SNOMEDCT_US:204142009 UMLS:C3152182 Abnormality of the anterior chamber Anterior chamber anomalies Ocular anterior chamber abnormality HP:0000593 Abnormal anterior chamber morphology Abnormality of the anterior chamber, which is the space in the eye that is behind the cornea and in front of the iris. An abnormality of the ear. SNOMEDCT_US:275259005 UMLS:C0266589 Abnormality of the ear Ear anomaly HP:0000598 Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future. Abnormality of the ear An abnormality of the ear. Abnormality of the ear An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. UMLS:C4025838 HP:0000600 The pharynx is tubular structure extending from base of skull superiorly to esophageal inlet inferiorly, and is composed of three distinct areas: the nasopharynx, the oropharynx, and the hypopharynx, with the pharyngeal walls being composed of the superior, middle, and inferior pharyngeal constrictor muscles. It is part of the digestive system and of the conducting zone of the respiratory system. Abnormality of the pharynx An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. Any structural abnormality of the choroid. HP:0001122 MSH:D015862 UMLS:C0008521 UMLS:C4025836 Abnormality of the choroid Choroid disease HP:0000610 Abnormal choroid morphology Any structural abnormality of the choroid. A coloboma of the iris. HP:0007744 HP:0007748 UMLS:C0240063 Cat eye Coloboma of iris Coloboma of the iris Keyhole iris HP:0000612 Iris coloboma A coloboma of the iris. PMID:19369671 Cat eye An abnormality of the nasolacrimal drainage system, which serves as a conduit for tear flow from the external eye to the nasal cavity. UMLS:C4025835 Abnormality of the nasolacrimal system HP:0000614 The nasolacrimal system consists of the puncta, canaliculi, lacrimal sac, and nasolacrimal duct. Abnormal nasolacrimal system morphology An abnormality of the nasolacrimal drainage system, which serves as a conduit for tear flow from the external eye to the nasal cavity. HPO_CONTRIBUTOR:DDD_ncarter Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degrees in radius around central fixation. HP:0007839 Fyler:4866 MSH:D001766 SNOMEDCT_US:65956007 UMLS:C0271215 UMLS:C0456909 Blindness Total vision loss Legal blindness HP:0000618 Various scales have been developed to describe the extent of vision loss and define blindness. Total blindness is the complete lack of form and visual light perception and is clinically recorded as NLP (no light perception). Blindness is frequently used to describe severe visual impairment with residual vision. Those described as having only light perception have no more sight than the ability to tell light from dark and the general direction of a light source. Blindness Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degrees in radius around central fixation. PMID:28779882 Blindness Legal blindness UMLS:C4021802 Abnormality of retinal arteries Retinal arterial abnormality HP:0000630 Abnormal retinal artery morphology Abnormality of retinal arteries Retinal arterial abnormality Atrophy of the eyeball with blindness and decreased intraocular pressure due to end-stage intraocular disease. SNOMEDCT_US:4229009 UMLS:C0271007 HP:0000667 Phthisis bulbi refers to atrophy and degeneration of a blind eye. Phthisis bulbi Atrophy of the eyeball with blindness and decreased intraocular pressure due to end-stage intraocular disease. The absence of all teeth from the normal series by a failure to develop. HP:0006484 MSH:D000848 SNOMEDCT_US:16958000 SNOMEDCT_US:26624006 UMLS:C0399352 UMLS:C4280622 Anodontia vera Complete agenesis of all teeth Complete dental agenesis Failure of development of all teeth Complete anodontia Total anodontia Missing all teeth Total absence of all teeth HP:0000674 Anodontia can affect both primary and permanent teeth. Alternatively, there can be anodontia of just the permanent teeth. Anodontia must be distinguished from non-erupted teeth. Anodontia The absence of all teeth from the normal series by a failure to develop. PMID:31468724 Anodontia vera Complete agenesis of all teeth Failure of development of all teeth Complete anodontia Total anodontia Missing all teeth Total absence of all teeth An abnormality of the dental enamel. HP:0006322 UMLS:C4021800 UMLS:C4280262 UMLS:C4280615 Abnormal tooth enamel Abnormality of dental enamel Enamel abnormalities Enamel abnormality Defective tooth enamel Dystrophic tooth enamel Malformation of dental enamel Malformation of tooth enamel HP:0000682 The dental enamel is the external layer of the teeth, being a highly mineralized substance consisting primarily of hydroxylapatite. Abnormal dental enamel morphology An abnormality of the dental enamel. Abnormal tooth enamel Enamel abnormalities Enamel abnormality Defective tooth enamel Dystrophic tooth enamel Malformation of dental enamel Malformation of tooth enamel Developmental hypoplasia of teeth. HP:0000688 HP:0006281 HP:0006307 Decreased size of teeth Underdevelopment of teeth UMLS:C0235357 UMLS:C4280611 Hypoplastic teeth HP:0000685 Hypoplasia of teeth Developmental hypoplasia of teeth. Decreased size of teeth Underdevelopment of teeth Decreased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD below mean. Alternatively, an apparently decreased maximum width of tooth. Hypotrophic tooth SNOMEDCT_US:32337007 UMLS:C0240340 UMLS:C4280611 UMLS:C4280612 Decreased size of tooth Decreased width of tooth Small teeth Small tooth Tooth hypoplasia Tooth hypotrophy Underdeveloped tooth HP:0000691 Standard reference has means and standard deviations by gender [Moyers et al, 1976]. It is easy to measure the width of teeth, for which reason the definition of microdontia can be made with reference to the width of the tooth. However, microdontia means that the overall size of the tooth is decreased. In microdontia, the gaps between the teeth, particularly the anterior upper and lower teeth, are increased, creating diastemata. This should be assessed and coded separately. Microdontia Decreased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD below mean. Alternatively, an apparently decreased maximum width of tooth. PMID:19125428 Hypotrophic tooth Decreased size of tooth Decreased width of tooth Small tooth Developmental dysplasia of dentin. MSH:D003811 SNOMEDCT_US:196286005 UMLS:C0011436 HP:0000703 This term is kept for convenience since it is often used to refer to the phenotype of discolored, fragile teeth in the medical literature. Dentinogenesis imperfecta is a disorder of tooth development. This condition causes the teeth to be discolored (most often a blue-gray or yellow-brown color) and translucent. Teeth are also weaker than normal, making them prone to rapid wear, breakage, and loss. Dentinogenesis imperfecta Developmental dysplasia of dentin. Inflammation of the periodontium. HP:0000165 HP:0006301 Gum disease Periodontal disease MSH:D005882 MSH:D010510 MSH:D010518 SNOMEDCT_US:18718003 SNOMEDCT_US:2556008 SNOMEDCT_US:41565005 UMLS:C0017563 UMLS:C0031090 UMLS:C0031099 Pyorrhea HP:0000704 Periodontitis Inflammation of the periodontium. Gum disease Pyorrhea A developmental dysplasia of the dental enamel. HP:0006284 HP:0006310 HP:0006325 HP:0006327 HP:0006331 MSH:D000567 SNOMEDCT_US:78494001 UMLS:C0002452 HP:0000705 Amelogenesis imperfecta (AI) is a term for a clinically and genetically heterogeneous group of diseases that affect the dental enamel, occasionally in conjunction with other dental, oral and extraoral tissues. This term has often been used to describe the phenotype associated with AI, but for new annotations it is recommended to describe the individual manifestations. Amelogenesis imperfecta A developmental dysplasia of the dental enamel. PMID:18499550 An abnormality of the nervous system. HP:0001333 HP:0006987 Brain and/or spinal cord issue MSH:D009421 SNOMEDCT_US:88425004 UMLS:C0497552 Abnormality of the nervous system Neurologic abnormalities Neurological abnormality HP:0000707 The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system. Abnormality of the nervous system An abnormality of the nervous system. Brain and/or spinal cord issue Abnormality of the nervous system Neurologic abnormalities Neurological abnormality Atypical behavior is an abnormality in a person's actions, which can be controlled or modulated by the will of the individual. While abnormal behaviors can be difficult to control, they are distinct from other abnormal actions that cannot be affected by the individual's will. HP:0000715 HP:0002368 HP:0002456 MSH:D000066553 MSH:D001526 SNOMEDCT_US:25786006 SNOMEDCT_US:277843001 UMLS:C0004941 UMLS:C0233514 Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral symptoms Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural changes Behavioural disorders Behavioural disturbances Behavioural problems Behavioural symptoms Behavioural/Psychiatric abnormality Behavioural/psychiatric abnormality Psychiatric disorders Psychiatric disturbances HP:0000708 Atypical behaviors should include or directly affect observable actions. While behavioral disorders often encompass abnormal thoughts, feelings, perceptions, or other cognitions, these alone would not be considered atypical behavioral features. Atypical behavior Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral symptoms Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural changes Behavioural disorders Behavioural disturbances Behavioural problems Behavioural symptoms Behavioural/Psychiatric abnormality Psychiatric disorders Psychiatric disturbances A state of unease is characterized by diffuse motor activity or motion, which is subject to limited control, nonproductive, or disorganized behavior. SNOMEDCT_US:162221009 UMLS:C3887611 Fidgetiness Restiveness HP:0000711 Restlessness Fidgetiness Restiveness A state of extreme restlessness and excessive motor activity is associated with mental distress or a feeling of inner tension. SNOMEDCT_US:24199005 UMLS:C0085631 Psychomotor agitation HP:0000713 Agitation An explicit or perceived action, demonstration, conduct, or language (verbal and written) that is contrary to generally accepted norms, rules, procedures, or unacceptable within the context in which it is carried out. Inappropriate behaviors could take place in a sexual or social context and could be aggressive, violent, impulsive, intimidating, or threatening in nature. SNOMEDCT_US:112082005 UMLS:C0233522 Inappropriate behavior Inappropriate behaviour HP:0000719 Inappropriate behavior Inappropriate behavior Inappropriate behaviour Reduced ability to control, or a failure to resist a temptation, urge, or impulse. Examples include disregard for social conventions, general impulsivity, and poor risk assessment. SNOMEDCT_US:247977003 UMLS:C0424296 Impulse control disorders Self-control HP:0000734 Disinhibition affects motor, instinctual, emotional, cognitive, and perceptual aspects, exhibiting signs and symptoms similar to the diagnostic criteria for mania. Hypersexuality, hyperphagia, and aggressive outbursts are indicative of disinhibited instinctual drives. Disinhibition Difficulty interacting with others through emotional, physical, or verbal communication. MSH:D000067404 SNOMEDCT_US:88598008 UMLS:C0150080 Impaired social interaction Impaired social interactions Poor social interactions HP:0000735 Impaired social interactions Impaired social interaction Impaired social interactions Poor social interactions A structural abnormality of the peripheral nervous system, which is composed of the nerves that lead to or branch off from the central nervous system. This includes the cranial nerves (olfactory and optic nerves are technically part of the central nervous system). HP:0003483 MSH:D010523 SNOMEDCT_US:302226006 SNOMEDCT_US:42658009 UMLS:C0031117 UMLS:C4025831 Abnormal peripheral nervous system structure Peripheral nervous system disease HP:0000759 The peripheral nervous system is divided into autonomic and somatic components, which both include afferent (sensory) and efferent (motor) nerves. Abnormal peripheral nervous system morphology A structural abnormality of the peripheral nervous system, which is composed of the nerves that lead to or branch off from the central nervous system. This includes the cranial nerves (olfactory and optic nerves are technically part of the central nervous system). Abnormal peripheral nervous system structure Any abnormality of the thorax (the region of the body formed by the sternum, the thoracic vertebrae and the ribs). HP:0100655 UMLS:C4021797 Abnormality of the chest Abnormality of the thorax Structural abnormality of the chest wall HP:0000765 Abnormal thorax morphology Any abnormality of the thorax (the region of the body formed by the sternum, the thoracic vertebrae and the ribs). Abnormality of the chest An anomaly of the sternum, also known as the breastbone. HP:0000780 HP:0006586 HP:0006594 HP:0006605 HP:0006630 HP:0006708 UMLS:C1860493 Abnormality of the sternum Pectus carinatum or pectus excavatum Pectus deformities Pectus deformity Pectus excavatum or carinatum Pectus excavatum or pectus carinatum Pectus excavatum/carinatum Sternal anomalies HP:0000766 Abnormal sternum morphology An anomaly of the sternum, also known as the breastbone. Abnormality of the sternum Sternal anomalies A defect of the chest wall characterized by a depression of the sternum, giving the chest ("pectus") a caved-in ("excavatum") appearance. HP:0006613 HP:0006617 SNOMEDCT_US:391987005 UMLS:C2051831 Funnel chest HP:0000767 Pectus excavatum A defect of the chest wall characterized by a depression of the sternum, giving the chest ("pectus") a caved-in ("excavatum") appearance. Funnel chest An abnormality of the breast. UMLS:C4025829 Abnormality of the breast HP:0000769 Abnormality of the breast An abnormality of the breast. Abnormality of the breast Abnormal development of large mammary glands in males resulting in breast enlargement. HP:0000770 MSH:D006177 SNOMEDCT_US:4754008 UMLS:C0018418 Enlarged male breast Gynaecomastia HP:0000771 Gynecomastia Abnormal development of large mammary glands in males resulting in breast enlargement. Enlarged male breast An anomaly of the rib. HP:0006618 UMLS:C1842083 Abnormality of the ribs Rib abnormalities Rib anomalies HP:0000772 Abnormal rib morphology An anomaly of the rib. Abnormality of the ribs Rib abnormalities Reduced rib length. HP:0000899 HP:0000908 HP:0009750 SNOMEDCT_US:249696007 UMLS:C0426817 Hypoplastic ribs Rib hypoplasia Short ribs HP:0000773 Short ribs Reduced rib length. Short ribs Any abnormality of the diaphragm, the sheet of skeletal muscle that separates the thoracic cavity from the abdominal cavity. HP:0005204 UMLS:C1848873 Abnormality of the diaphragm Diaphragm issues Diaphragmatic defect HP:0000775 Abnormality of the diaphragm Any abnormality of the diaphragm, the sheet of skeletal muscle that separates the thoracic cavity from the abdominal cavity. Abnormality of the diaphragm Diaphragm issues Diaphragmatic defect Abnormality of the thymus, an organ located in the upper anterior portion of the chest cavity just behind the sternum and whose main function is to provide an environment for T lymphocyte maturation. SNOMEDCT_US:93297002 UMLS:C0262650 UMLS:C0685891 Abnormality of the thymus HP:0000777 Abnormal thymus morphology Abnormality of the thymus, an organ located in the upper anterior portion of the chest cavity just behind the sternum and whose main function is to provide an environment for T lymphocyte maturation. Abnormality of the thymus Underdevelopment of the thymus. SNOMEDCT_US:93297002 UMLS:C0685891 UMLS:C4228227 Small thymus Thymic hypoplasia Thymus hypoplasia HP:0000778 Hypoplasia of the thymus Underdevelopment of the thymus. Small thymus Any abnormality of the scapula, also known as the shoulder blade. UMLS:C4025828 Abnormality of the shoulder blade HP:0000782 Abnormal scapula morphology Any abnormality of the scapula, also known as the shoulder blade. Abnormality of the shoulder blade The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). High urine occult blood MSH:D006417 SNOMEDCT_US:34436003 SNOMEDCT_US:53298000 UMLS:C0018965 Blood in urine HP:0000790 Hematuria The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). High urine occult blood Blood in urine An abnormality of the urethra, i.e., of the tube which connects the urinary bladder to the outside of the body. UMLS:C4025826 Urethra issue HP:0000795 Abnormality of the urethra An abnormality of the urethra, i.e., of the tube which connects the urinary bladder to the outside of the body. Urethra issue UMLS:C4025825 Abnormal external genitalia HP:0000811 Abnormal external genitalia Abnormal external genitalia An anomaly of the adnexa, uterus, and vagina (in female) or seminal tract and prostate (in male). UMLS:C4025824 Abnormal internal genitalia HP:0000812 Abnormal internal genitalia An anomaly of the adnexa, uterus, and vagina (in female) or seminal tract and prostate (in male). Abnormal internal genitalia An abnormality of the endocrine system. MSH:D004700 SNOMEDCT_US:362969004 UMLS:C0014130 UMLS:C4025823 Endocrine system disease HP:0000818 The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions. Abnormality of the endocrine system An abnormality of the endocrine system. A group of abnormalities characterized by hyperglycemia and glucose intolerance. HP:0004908 HP:0008217 HP:0008234 HP:0008260 MSH:D003920 SNOMEDCT_US:73211009 UMLS:C0011849 HP:0000819 Diabetes mellitus A group of abnormalities characterized by hyperglycemia and glucose intolerance. An abnormality of the thyroid gland. MSH:D013959 SNOMEDCT_US:14304000 UMLS:C0040128 Abnormality of the thyroid gland Thyroid abnormality Thyroid disease HP:0000820 Abnormality of the thyroid gland An abnormality of the thyroid gland. Abnormality of the thyroid gland Thyroid abnormality Thyroid disease Deficiency of thyroid hormone. HP:0003222 HP:0008203 MSH:D007037 SNOMEDCT_US:40930008 UMLS:C0020676 Low T4 Underactive thyroid HP:0000821 Hypothyroidism Deficiency of thyroid hormone. Underactive thyroid The presence of chronic increased pressure in the systemic arterial system. HP:0004949 HP:0005126 MSH:D006973 SNOMEDCT_US:24184005 SNOMEDCT_US:38341003 UMLS:C0020538 UMLS:C0497247 Arterial hypertension Systemic hypertension High blood pressure HP:0000822 Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both. Hypertension The presence of chronic increased pressure in the systemic arterial system. High blood pressure Insufficient responses to growth hormone (GH) provocation tests. GH deficiency is defined as a serum peak GH concentration less than 10 ng/mL on provocation with a combination of at least two separate stimulation tests. HP:0000861 HP:0008195 HP:0008206 SNOMEDCT_US:2109003 UMLS:C3714796 Growth hormone deficiency Somatotropin deficiency HP:0000824 GH stimulation tests are performed with various stimuli, such as insulin, L-dopa, arginine, and growth hormone releasing hormone (GHRH). The test using insulin as a stimulus is classically recommended, but this test has potential risks such as hypoglycemia. The effects of growth hormone are mediated almost exclusively by insulin-like growth factor 1(IGF-1), which is produced primarily in the liver. Growth hormone deficiency refers to inadequate levels of GH (and therefore IGF-1), resulting in growth retardation in children and metabolic disturbances in adults. Decreased response to growth hormone stimulation test Insufficient responses to growth hormone (GH) provocation tests. GH deficiency is defined as a serum peak GH concentration less than 10 ng/mL on provocation with a combination of at least two separate stimulation tests. PMID:25914878 Growth hormone deficiency An increased concentration of insulin combined with a decreased concentration of glucose in the blood. UMLS:C1864903 Hyperinsulinaemic hypoglycaemia Hyperinsulinemia hypoglycemia HP:0000825 Hyperinsulinemic hypoglycemia describes a situation in which the level of insulin is inappropriate for the low level of blood sugar. Hyperinsulinemic hypoglycemia An increased concentration of insulin combined with a decreased concentration of glucose in the blood. An abnormality of the parathyroid gland. MSH:D010279 SNOMEDCT_US:73132005 UMLS:C0030517 UMLS:C4025822 Parathyroid disease HP:0000828 There are four parathyroid glands, which are small endocrine glands located in the neck behind the thyroid gland that produce parathyroid hormone. Abnormality of the parathyroid gland An abnormality of the parathyroid gland. A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia. HP:0000856 HP:0008292 MSH:D007011 SNOMEDCT_US:36976004 UMLS:C0020626 Decreased parathyroid hormone secretion Low parathyroid hormone HP:0000829 Hypoparathyroidism A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia. Decreased parathyroid hormone secretion A condition of reduced function of the anterior pituitary gland characterized by decreased secretion of one or more of the pituitary hormones growth hormone, thyroid-stimulating hormone, adrenocorticotropic hormone, prolactin, luteinizing hormone, and follicle-stimulating hormone. UMLS:C4025821 HP:0000830 Anterior hypopituitarism A condition of reduced function of the anterior pituitary gland characterized by decreased secretion of one or more of the pituitary hormones growth hormone, thyroid-stimulating hormone, adrenocorticotropic hormone, prolactin, luteinizing hormone, and follicle-stimulating hormone. A type of hypothyroidism that results from a defect in the thyroid gland. SNOMEDCT_US:111566002 UMLS:C0700502 HP:0000832 Primary hypothyroidism A type of hypothyroidism that results from a defect in the thyroid gland. Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kindneys. MSH:D000307 SNOMEDCT_US:30171000 UMLS:C0001621 UMLS:C4021794 Adrenal abnormalities Adrenal gland disease HP:0000834 Abnormality of the adrenal glands Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kindneys. Adrenal abnormalities Adrenal gland disease Developmental hypoplasia of the adrenal glands. MSH:C538429 SNOMEDCT_US:237774001 UMLS:C0342491 UMLS:C1846223 Adrenal gland hypoplasia Hypoplastic adrenal glands Small adrenal glands Underdeveloped adrenal glands HP:0000835 Adrenal hypoplasia Developmental hypoplasia of the adrenal glands. Small adrenal glands An abnormality of thyroid physiology characterized by excessive secretion of the thyroid hormones thyroxine (i.e., T4) and/or 3,3',5-triiodo-L-thyronine zwitterion (i.e., triiodothyronine or T3). HP:0008241 MSH:D006980 SNOMEDCT_US:34486009 UMLS:C0020550 Overactive thyroid HP:0000836 Hyperthyroidism An abnormality of thyroid physiology characterized by excessive secretion of the thyroid hormones thyroxine (i.e., T4) and/or 3,3',5-triiodo-L-thyronine zwitterion (i.e., triiodothyronine or T3). Overactive thyroid http://www.mayoclinic.org/diseases-conditions/hyperthyroidism/basics/definition/con-20020986 An increased concentration of insulin in the blood. MSH:D006946 SNOMEDCT_US:83469008 UMLS:C0020459 Elevated insulin level HP:0000842 Hyperinsulinemia An increased concentration of insulin in the blood. Excessive production of parathyroid hormone (PTH) by the parathyroid glands. MSH:D006961 SNOMEDCT_US:66999008 UMLS:C0020502 Elevated blood parathyroid hormone level HP:0000843 Hyperparathyroidism Excessive production of parathyroid hormone (PTH) by the parathyroid glands. Elevated blood parathyroid hormone level Acromegaly is a condition resulting from overproduction of growth hormone by the pituitary gland in persons with closed epiphyses, and consists chiefly in the enlargement of the distal parts of the body. The circumference of the skull increases, the nose becomes broad, the tongue becomes enlarged, the facial features become coarsened, the mandible grows excessively, and the teeth become separated. The fingers and toes grow chiefly in thickness. HP:0008856 MSH:C531600 MSH:D000172 SNOMEDCT_US:74107003 UMLS:C0001206 UMLS:C0235986 Elevated circulating somatotropin concentration Growth hormone excess Somatotropin excess HP:0000845 Disorder resulting from excess pituitary gland production of growth hormone (hGH). Elevated circulating growth hormone concentration Acromegaly is a condition resulting from overproduction of growth hormone by the pituitary gland in persons with closed epiphyses, and consists chiefly in the enlargement of the distal parts of the body. The circumference of the skull increases, the nose becomes broad, the tongue becomes enlarged, the facial features become coarsened, the mandible grows excessively, and the teeth become separated. The fingers and toes grow chiefly in thickness. Growth hormone excess Insufficient production of steroid hormones (primarily cortisol) by the adrenal glands. HP:0000865 HP:0008218 MSH:D000309 SNOMEDCT_US:111563005 SNOMEDCT_US:237785004 SNOMEDCT_US:386584007 UMLS:C0001623 Hypoadrenalism HP:0000846 Adrenal insufficiency may cause persistent vomiting, anorexia, hypoglycemia, poor weight gain in a child, or unexplained weight loss in an adult, malaise, fatigue, muscular weakness, unexplained isotonic or hyponatremic dehydration, hyperkalemia, hypotension, hypoglycemia and especially generalized hyperpigmentation. Adrenal insufficiency Insufficient production of steroid hormones (primarily cortisol) by the adrenal glands. PMID:11443143 UMLS:C4025820 HP:0000849 Adrenocortical abnormality An enlargement of the thyroid gland. MSH:D006042 SNOMEDCT_US:3716002 UMLS:C0018021 Enlarged thyroid gland in neck Goitre Thyroid goiter Thyroid goitre HP:0000853 Goiter An enlargement of the thyroid gland. Enlarged thyroid gland in neck Goitre Thyroid goitre Developmental hypoplasia of the parathyroid gland. UMLS:C1389851 Small parathyroid glands Underdeveloped parathyroid glands HP:0000860 Parathyroid hypoplasia Developmental hypoplasia of the parathyroid gland. Small parathyroid glands Underdeveloped parathyroid glands Abnormality of the pituitary gland (also known as hypophysis), which is an endocrine gland that protrudes from the bottom of the hypothalamus at the base of the brain. The pituitary gland secretes the hormones ACTH, TSH, PRL, GH, endorphins, FSH, LH, oxytocin, and antidiuretic hormone. The secretion of hormones from the anterior pituitary is under the strict control of hypothalamic hormones, and the posterior pituitary is essentially an extension of the hypothalamus, so that hypothalamus and pituitary gland may be regarded as a functional unit. HP:0000838 HP:0000844 UMLS:C4025819 HP:0000864 Abnormality of the hypothalamus-pituitary axis Abnormality of the pituitary gland (also known as hypophysis), which is an endocrine gland that protrudes from the bottom of the hypothalamus at the base of the brain. The pituitary gland secretes the hormones ACTH, TSH, PRL, GH, endorphins, FSH, LH, oxytocin, and antidiuretic hormone. The secretion of hormones from the anterior pituitary is under the strict control of hypothalamic hormones, and the posterior pituitary is essentially an extension of the hypothalamus, so that hypothalamus and pituitary gland may be regarded as a functional unit. A pituitary functional deficit affecting all the anterior pituitary hormones (growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone, adrenocorticotropic hormone, and prolactin). MSH:C580003 SNOMEDCT_US:32390006 UMLS:C0242343 HP:0000871 Panhypopituitarism A pituitary functional deficit affecting all the anterior pituitary hormones (growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone, adrenocorticotropic hormone, and prolactin). PMID:12466332 Decreased inferosuperior length of the sternum. SNOMEDCT_US:298724002 UMLS:C0575497 UMLS:C4020883 Short sternum Hypoplastic sternum HP:0000879 Short sternum Decreased inferosuperior length of the sternum. Short sternum Underdeveloped scapula. HP:0000906 HP:0006616 UMLS:C1846434 Hypoplastic scapula Scapular hypoplasia Short scapulae Small scapula Small scapulae Small shoulder blade HP:0000882 Hypoplastic scapulae Underdeveloped scapula. Small shoulder blade Malformation of the rib cage. UMLS:C1838659 Deformed rib cage HP:0000886 Deformed rib cage Malformation of the rib cage. Deformed rib cage Any abnormality of the clavicles (collar bones). UMLS:C4021792 Abnormal clavicles Abnormal collarbone Abnormality of the clavicle HP:0000889 Abnormal clavicle morphology Any abnormality of the clavicles (collar bones). Abnormal collarbone Increased length of the clavicles. HP:0006592 SNOMEDCT_US:249687007 UMLS:C0426808 Elongated clavicles Long collarbone HP:0000890 Long clavicles Increased length of the clavicles. Long collarbone A bifid rib refers to cleavage of the sternal end of a rib, usually unilateral. Bifid ribs are usually asymptomatic, and are often discovered incidentally by chest x-ray. UMLS:C4721788 Cleft ribs Split ribs HP:0000892 Bifid ribs A bifid rib refers to cleavage of the sternal end of a rib, usually unilateral. Bifid ribs are usually asymptomatic, and are often discovered incidentally by chest x-ray. Cleft ribs Split ribs Reduced length of the clavicles. HP:0000898 HP:0005698 HP:0005902 SNOMEDCT_US:93250003 UMLS:C0426799 Clavicular hypoplasia Hypoplastic clavicles Short collarbone Underdeveloped clavicles HP:0000894 Short clavicles Reduced length of the clavicles. Short collarbone Abnormally flat configuration of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. UMLS:C1855177 HP:0000911 See PMID:15163819, figure 2, for the arthrographic appearance of a flat glenoid fossa. Flat glenoid fossa Abnormally flat configuration of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. PMID:15163819 A developmental anomaly with absence of one or more ribs. HP:0000881 HP:0006627 SNOMEDCT_US:249695006 UMLS:C0426816 Absent ribs Decreased rib number Missing ribs HP:0000921 Missing ribs A developmental anomaly with absence of one or more ribs. Absent ribs Decreased rib number Missing ribs An abnormality of the skeletal system. UMLS:C4021790 Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies HP:0000924 Abnormality of the skeletal system An abnormality of the skeletal system. Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies Any abnormality of the vertebral column. UMLS:C4020882 UMLS:C4021789 Abnormal spine Abnormal vertebral column Abnormality of the spine Abnormality of the vertebral column Abnormality of the backbone HP:0000925 Abnormality of the vertebral column Any abnormality of the vertebral column. Abnormal spine Abnormal vertebral column Abnormality of the spine Abnormality of the vertebral column Abnormality of the backbone A flattened vertebral body shape with reduced distance between the vertebral endplates. HP:0002940 HP:0003421 HP:0004595 HP:0004623 HP:0004627 HP:0005123 HP:0005644 HP:0008466 UMLS:C1844704 Flat vertebral bodies Flattened vertebrae Flattened vertebral bodies HP:0000926 Platyspondyly A flattened vertebral body shape with reduced distance between the vertebral endplates. Flattened vertebrae An abnormality of the skull, the bony framework of the head which is comprised of the neurocranium (with eight cranial bones) and the viscerocranium (facial skeleton) that comprises fourteen facial bones with the mandible as its largest bone. UMLS:C0235942 Abnormality of the skull Abnormality of the skull bones HP:0000929 Abnormal skull morphology An abnormality of the skull, the bony framework of the head which is comprised of the neurocranium (with eight cranial bones) and the viscerocranium (facial skeleton) that comprises fourteen facial bones with the mandible as its largest bone. Abnormality of the skull Abnormality of the skull bones Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5. HP:0002768 HP:0002799 HP:0002800 MSH:D001851 SNOMEDCT_US:312894000 SNOMEDCT_US:78441005 UMLS:C0029453 UMLS:C0747078 Generalised osteopenia Generalized osteopenia Osteopaenia HP:0000938 Osteopenia Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5. PMID:21234807 Generalised osteopenia Osteopaenia Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD). HP:0002774 MSH:D010024 SNOMEDCT_US:64859006 UMLS:C0029456 HP:0000939 Osteoporosis is a disease that is characterized by low bone mass, deterioration of bone tissue, and disruption of bone microarchitecture: it can lead to compromised bone strength and an increase in the risk of fractures. Osteoporosis Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD). PMID:28293453 An abnormality of the structure or form of the diaphysis, i.e., of the main or mid-section (shaft) of a long bone. HP:0006504 UMLS:C4021787 Abnormal shape of shaft of long bone Abnormality involving the diaphyses of the limbs Abnormality of shaft of long bone of the limbs Abnormality of the diaphyses Anomaly of the limb diaphyses Anomaly of the limb diaphyses morphology HP:0000940 Abnormal diaphysis morphology An abnormality of the structure or form of the diaphysis, i.e., of the main or mid-section (shaft) of a long bone. Abnormal shape of shaft of long bone Abnormality of shaft of long bone of the limbs UMLS:C4025815 Short shaft of long bone HP:0000941 Short diaphyses Short shaft of long bone An abnormality of one or more metaphysis, i.e., of the somewhat wider portion of a long bone that is adjacent to the epiphyseal growth plate and grows during childhood. HP:0006506 UMLS:C4025814 Abnormality of the wide portion of a long bone HP:0000944 Abnormal metaphysis morphology An abnormality of one or more metaphysis, i.e., of the somewhat wider portion of a long bone that is adjacent to the epiphyseal growth plate and grows during childhood. Abnormality of the wide portion of a long bone Underdevelopment of the ilium. HP:0003176 HP:0003178 Small wings of the pelvic girdle UMLS:C1861218 UMLS:C4280607 Short and small iliac bones Small iliac bones HP:0000946 Hypoplastic ilia Underdevelopment of the ilium. Small wings of the pelvic girdle An abnormality of the skin. HP:0001478 HP:0001479 HP:0005591 HP:0006736 HP:0007415 HP:0007580 MSH:D012868 MSH:D012871 SNOMEDCT_US:199879009 SNOMEDCT_US:95320005 UMLS:C0037268 UMLS:C0037274 Abnormality of the skin Dermatopathy Dermopathy Skin abnormality HP:0000951 Abnormality of the skin An abnormality of the skin. Abnormality of the skin Dermatopathy Dermopathy Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. HP:0001481 MSH:D004485 SNOMEDCT_US:281104002 SNOMEDCT_US:43116000 UMLS:C0013595 Eczema HP:0000964 Eczema has several forms including atopic dermatitis, contact dermatitis, dyshidrotic eczema, nummular eczema, seborrheic dermatitis, and stasis dermatitis. Eczema Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. Eczema Ectodermal dysplasia is a group of conditions in which there is abnormal development of the skin, hair, nails, teeth, or sweat glands. HP:0007615 MSH:D004476 SNOMEDCT_US:254154003 SNOMEDCT_US:8654005 UMLS:C0013575 HP:0000968 This term is kept in the HPO for now as 'ectodermal dysplasia' has been recorded as a phenotypic of other disorders such as DEAFNESS WITH ANHIDROTIC ECTODERMAL DYSPLASIA (MIM125050). Nevertheless it is preferable to use precise descriptions of the phenotypic abnormalities and this term should not be used for new annotations. It will be made obsolete in the future. Ectodermal dysplasia Ectodermal dysplasia is a group of conditions in which there is abnormal development of the skin, hair, nails, teeth, or sweat glands. Any structural abnormality of the sweat gland. MSH:D013543 SNOMEDCT_US:88232005 UMLS:C0038986 UMLS:C0262643 UMLS:C4020881 Abnormality of the sweat gland Abnormalities of sweating Sweat gland disease HP:0000971 Abnormal sweat gland morphology Any structural abnormality of the sweat gland. Abnormality of the sweat gland Abnormalities of sweating Sweat gland disease A condition in which the skin can be stretched beyond normal, and then returns to its initial position. HP:0007389 HP:0007493 HP:0007578 UMLS:C0241074 Hyperelastic skin Skin hyperelasticity Skin hyperextensibility Stretchable skin HP:0000974 Skin hyperelasticity is to be distinguished from cutis laxa, which refers to extra, redundant skin which tends to hang in folds. Hyperextensible skin A condition in which the skin can be stretched beyond normal, and then returns to its initial position. Hyperelastic skin Skin hyperelasticity Stretchable skin Hypertrichosis is increased hair growth that is abnormal in quantity or location. Excessive hair growth Increased hair growth on body MSH:D006983 SNOMEDCT_US:271607001 SNOMEDCT_US:29966009 UMLS:C0020555 HP:0000998 Hypertrichosis Hypertrichosis is increased hair growth that is abnormal in quantity or location. Excessive hair growth Increased hair growth on body UMLS:C4025813 Abnormality of fatty tissue below the skin HP:0001001 Abnormality of subcutaneous fat tissue Abnormality of fatty tissue below the skin Abnormally increased hair growth referring to a male pattern of body hair (androgenic hair). MSH:D006628 SNOMEDCT_US:399939002 UMLS:C0019572 Excessive hairiness HP:0001007 Hirsutism Abnormally increased hair growth referring to a male pattern of body hair (androgenic hair). Excessive hairiness An abnormality of the biliary tree. MSH:D001660 SNOMEDCT_US:105997008 UMLS:C0005424 UMLS:C0549613 Biliary tract disease HP:0001080 Biliary tract abnormality An abnormality of the biliary tree. Loss of iris tissue (atrophy) SNOMEDCT_US:95709007 UMLS:C0423319 Iris degeneration HP:0001089 Iris atrophy Loss of iris tissue (atrophy) Iris degeneration Diffusely large eye (with megalocornea) without glaucoma. HP:0200093 SNOMEDCT_US:246920008 UMLS:C0423221 UMLS:C1855852 UMLS:C4280603 Increased size of eyes Large eyes Megalophthalmos Increased size of palpebral fissures Large eyeballs Large of palpebral fissures HP:0001090 Note that Increased size of palpebral fissues is not a synonym of this term. Abnormally large globe Diffusely large eye (with megalocornea) without glaucoma. Increased size of eyes Large eyes Increased size of palpebral fissures Large eyeballs Large of palpebral fissures Any structural abnormality of the fundus of the eye. UMLS:C4025804 Abnormality of the fundus HP:0001098 Abnormal fundus morphology UMLS:C2673929 HP:0001099 Fundus atrophy Inflammation of the iris. MSH:D007500 SNOMEDCT_US:65074000 UMLS:C0022081 Inflammation of iris HP:0001101 Iritis Inflammation of the iris. Inflammation of iris Well-demarcated area(s) of partial or complete depigmentation in the fundus, reflecting atrophy of the retinal pigment epithelium with associated retinal photoreceptor loss. MSH:D012162 SNOMEDCT_US:405722004 SNOMEDCT_US:95695004 UMLS:C0035304 UMLS:C0521694 HP:0001105 Retinal atrophy Well-demarcated area(s) of partial or complete depigmentation in the fundus, reflecting atrophy of the retinal pigment epithelium with associated retinal photoreceptor loss. Any abnormality of the size or morphology of the cornea. UMLS:C4025802 HP:0001120 Abnormality of corneal size Any abnormality of the size or morphology of the cornea. The term corneal dystrophy embraces a heterogenous group of bilateral genetically determined non-inflammatory corneal diseases that are restricted to the cornea. HP:0007775 HP:0008005 SNOMEDCT_US:5587004 UMLS:C0010036 HP:0001131 Corneal dystrophy The term corneal dystrophy embraces a heterogenous group of bilateral genetically determined non-inflammatory corneal diseases that are restricted to the cornea. HP:0007712 HP:0007920 UMLS:C1857627 HP:0001135 Chorioretinal dystrophy An abnormality affecting one or both hands. HP:0005858 MSH:D006226 SNOMEDCT_US:299033004 UMLS:C0018564 Abnormal hands Abnormality of the hand Hand anomalies Hand deformities HP:0001155 Abnormality of the hand An abnormality affecting one or both hands. Abnormal hands Abnormality of the hand Hand anomalies Hand deformities Digits that appear disproportionately short compared to the hand/foot. The word brachydactyly is used here to describe a series distinct patterns of shortened digits (brachydactyly types A-E). This is the sense used here. HP:0001189 HP:0001201 HP:0005630 HP:0005657 HP:0005727 HP:0006017 HP:0006128 HP:0100667 MSH:D059327 SNOMEDCT_US:43476002 UMLS:C0221357 Brachydactyly syndrome Short fingers or toes HP:0001156 Brachydactyly Digits that appear disproportionately short compared to the hand/foot. The word brachydactyly is used here to describe a series distinct patterns of shortened digits (brachydactyly types A-E). This is the sense used here. Short fingers or toes A kind of polydactyly characterized by the presence of a supernumerary finger or fingers. MEDDRA:10036064 SNOMEDCT_US:81793007 UMLS:C0158733 Extra finger Finger polydactyly Polydactyly of the hand Supernumerary finger HP:0001161 Hand polydactyly A kind of polydactyly characterized by the presence of a supernumerary finger or fingers. MEDDRA:10036064 Polydactyly of fingers Extra finger Supernumerary finger Supernumerary digits located at the ulnar side of the hand (that is, on the side with the fifth finger). HP:0004698 HP:0005763 HP:0009984 SNOMEDCT_US:205131007 UMLS:C0431904 Extra little finger Extra pinkie finger Extra pinky finger Polydactyly affecting the 5th finger Postaxial polydactyly of fingers Postaxial polydactyly of hand Postaxial polydactyly of hands HP:0001162 Postaxial hand polydactyly Supernumerary digits located at the ulnar side of the hand (that is, on the side with the fifth finger). Extra little finger Extra pinkie finger Extra pinky finger An anomaly of a finger. HP:0003035 UMLS:C2674737 Abnormalities of the fingers Abnormality of finger HP:0001167 Abnormal finger morphology An anomaly of a finger. Abnormalities of the fingers Abnormality of finger An abnormal structure of the first digit of the hand. MSH:C536903 SNOMEDCT_US:299130003 UMLS:C0575897 Abnormality of the thumb Abnormality of the thumbs Thumb deformity HP:0001172 Abnormal thumb morphology Abnormality of the thumb Abnormality of the thumbs Thumb deformity HP:0002820 HP:0006044 HP:0006219 SNOMEDCT_US:249752003 UMLS:C0426870 Disproportionately large hands Large hands large hand HP:0001176 Large hands Large hands large hand Supernumerary digits located at the radial side of the hand. Polydactyly (supernumerary digits) involving the thumb occurs in many distinct forms of high variability and severity. Ranging from fleshy nubbins over varying degrees of partial duplication/splitting to completely duplicated or even triplicated thumbs or preaxial (on the radial side of the hand) supernumerary digits. HP:0005629 HP:0005634 HP:0006182 HP:0009604 MSH:C536332 SNOMEDCT_US:205135003 SNOMEDCT_US:445216006 UMLS:C1395852 Extra thumb Polydactyly affecting the thumb Preaxial polydactyly of hands Supernumerary thumb thumb polydactyly HP:0001177 Preaxial hand polydactyly Supernumerary digits located at the radial side of the hand. Polydactyly (supernumerary digits) involving the thumb occurs in many distinct forms of high variability and severity. Ranging from fleshy nubbins over varying degrees of partial duplication/splitting to completely duplicated or even triplicated thumbs or preaxial (on the radial side of the hand) supernumerary digits. Extra thumb Supernumerary thumb A developmental defect resulting in the presence of fewer than the normal number of fingers. SNOMEDCT_US:71358006 UMLS:C0728895 Hand has less than 5 fingers HP:0001180 Hand oligodactyly A developmental defect resulting in the presence of fewer than the normal number of fingers. Hand has less than 5 fingers An abnormality affecting the carpal bones of the wrist (scaphoid, lunate, triquetral, pisiform, trapezium, trapezoid, capitate, hamate). Abnormal wrist bones UMLS:C1840535 Abnormal carpal bones Abnormality of the carpal bones Anomalous carpal bones Carpal bone anomalies HP:0001191 Abnormal carpal morphology An abnormality affecting the carpal bones of the wrist (scaphoid, lunate, triquetral, pisiform, trapezium, trapezoid, capitate, hamate). Abnormal wrist bones UMLS:C4048199 HP:0001193 Ulnar deviation of the hand or of fingers of the hand An abnormality of the placenta (the organ that connects the developing fetus to the uterine wall) or of the umbilical cord (the cord that connects the fetus to the placenta). UMLS:C4025798 Abnormalities of placenta or umbilical cord HP:0001194 Abnormalities of placenta or umbilical cord An abnormality of the placenta (the organ that connects the developing fetus to the uterine wall) or of the umbilical cord (the cord that connects the fetus to the placenta). Abnormalities of placenta or umbilical cord Decreased length of the umbilical cord. SNOMEDCT_US:59795007 UMLS:C0266786 Short umbilical cord HP:0001196 Short umbilical cord Decreased length of the umbilical cord. Short umbilical cord An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. UMLS:C4025797 Abnormality of prenatal development or birth HP:0001197 Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality. Abnormality of prenatal development or birth An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. Abnormality of prenatal development or birth An abnormal structure of the tip (end) of a finger. UMLS:C4025796 Abnormality of the fingertips HP:0001211 Abnormal fingertip morphology Abnormality of the fingertips Ossification of carpal bones occurs later than age-adjusted norms. HP:0006069 UMLS:C1841684 UMLS:C4280599 Carpal delayed ossification Delayed carpal bone age Delayed carpal ossification Delayed maturation of carpal bones Delayed maturation of wrist bone HP:0001216 Delayed ossification of carpal bones Ossification of carpal bones occurs later than age-adjusted norms. Delayed maturation of wrist bone Chronic loss of joint motion in an interphalangeal joint of a finger due to structural changes in non-bony tissue. UMLS:C4021784 Interphalangeal joint flexion contractures HP:0001220 Interphalangeal joint contracture of finger Chronic loss of joint motion in an interphalangeal joint of a finger due to structural changes in non-bony tissue. A chronic loss of wrist joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the wrist. HP:0006049 HP:0006137 SNOMEDCT_US:202275008 UMLS:C0409345 Wrist contracture Wrist flexion deformity HP:0001239 Wrist flexion contracture A chronic loss of wrist joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the wrist. A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. HP:0001275 HP:0001303 HP:0002125 HP:0002182 HP:0002279 HP:0002306 HP:0002348 HP:0002391 HP:0002417 HP:0002430 HP:0002431 HP:0002432 HP:0002434 HP:0002437 HP:0002466 HP:0002479 HP:0002794 HP:0006997 HP:0010520 MSH:D004827 MSH:D012640 SNOMEDCT_US:128613002 SNOMEDCT_US:246545002 SNOMEDCT_US:313307000 SNOMEDCT_US:84757009 SNOMEDCT_US:91175000 UMLS:C0014544 UMLS:C0036572 Epileptic seizure Seizures Epilepsy HP:0001250 A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold. Seizure A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. PMID:15816939 Seizures Epilepsy Cerebellar ataxia refers to ataxia due to dysfunction of the cerebellum. This causes a variety of elementary neurological deficits including asynergy (lack of coordination between muscles, limbs and joints), dysmetria (lack of ability to judge distances that can lead to under- or overshoot in grasping movements), and dysdiadochokinesia (inability to perform rapid movements requiring antagonizing muscle groups to be switched on and off repeatedly). HP:0001253 HP:0002513 HP:0007050 HP:0007157 MSH:D002524 SNOMEDCT_US:85102008 UMLS:C0007758 Cerebellar ataxia HP:0001251 Ataxia can be differentiated into dyssynergy, asynergy, dysmetria (hypometria, hypermetria), dysdiadochokinesis, gait ataxia, truncal ataxia, limb ataxia, and dysarthria). Note: This term does not include sensory ataxia. Ataxia Cerebellar ataxia refers to ataxia due to dysfunction of the cerebellum. This causes a variety of elementary neurological deficits including asynergy (lack of coordination between muscles, limbs and joints), dysmetria (lack of ability to judge distances that can lead to under- or overshoot in grasping movements), and dysdiadochokinesia (inability to perform rapid movements requiring antagonizing muscle groups to be switched on and off repeatedly). Reduction of neurologic reflexes such as the knee-jerk reaction. HP:0002467 SNOMEDCT_US:405946002 UMLS:C0700078 Decreased reflex response Decreased reflexes HP:0001265 Hyporeflexia Reduction of neurologic reflexes such as the knee-jerk reaction. Decreased reflex response Decreased reflexes Cerebellar atrophy is defined as a cerebellum with initially normal structures, in a posterior fossa with normal size, which displays enlarged fissures (interfolial spaces) in comparison to the foliae secondary to loss of tissue. Cerebellar atrophy implies irreversible loss of tissue and result from an ongoing progressive disease until a final stage is reached or a single injury, e.g. an intoxication or infectious event. HP:0002364 HP:0006839 HP:0007072 HP:0007203 SNOMEDCT_US:95646004 UMLS:C0262404 UMLS:C0740279 UMLS:C4020873 Atrophic cerebellum Degeneration of cerebellum Infratentorial atrophy HP:0001272 Cerebellar atrophy can be diagnosed if the cerebellum is small with shrunken folia and large cerebellar fissures or if it has been shown to undergo progressive volume loss. Cerebellar atrophy Cerebellar atrophy is defined as a cerebellum with initially normal structures, in a posterior fossa with normal size, which displays enlarged fissures (interfolial spaces) in comparison to the foliae secondary to loss of tissue. Cerebellar atrophy implies irreversible loss of tissue and result from an ongoing progressive disease until a final stage is reached or a single injury, e.g. an intoxication or infectious event. PMID:12169461 PMID:26331051 Degeneration of cerebellum Absence of neurologic reflexes such as the knee-jerk reaction. HP:0001314 Absent reflexes MSH:D012021 SNOMEDCT_US:349006 SNOMEDCT_US:37280007 UMLS:C0234146 UMLS:C0241772 UMLS:C0278124 Absent deep tendon reflexes Absent tendon reflexes Deep tendon reflexes absent Loss of deep tendon reflexes HP:0001284 The strectch reflexes (also called deep tendon relfexes) include the knee-jerk reflex (patellar reflex, the biceps reflex, the triceps reflex, and the ankle jerk reflex or Achilles tendon reflex). Areflexia Absence of neurologic reflexes such as the knee-jerk reaction. Absent reflexes Absent tendon reflexes Inflammation of the meninges. MSH:D008581 SNOMEDCT_US:7180009 UMLS:C0025289 HP:0001287 Meningitis Inflammation of the meninges. Structural abnormality affecting one or more of the cranial nerves, which emerge directly from the brain stem. HP:0003480 UMLS:C1854510 UMLS:C4020872 Abnormality of cranial nerve Abnormality of the cranial nerves Cranial nerve disease Cranial nerve involvement Cranial nerve abnormality HP:0001291 Abnormal cranial nerve morphology Structural abnormality affecting one or more of the cranial nerves, which emerge directly from the brain stem. Abnormality of cranial nerve Diminution of tendon reflexes, which is an invariable sign of peripheral nerve disease. HP:0001316 UMLS:C1866934 Absent or decreased deep tendon reflexes Decreased deep tendon reflexes Decreased tendon reflexes Decreased to absent deep tendon reflexes Decreased/absent deep tendon reflexes Depressed tendon reflexes Diminished deep tendon reflexes Diminished or absent deep tendon reflexes Diminished or absent tendon reflexes Hypoactive to absent deep tendon reflexes Impaired tendon reflexes Reduced/absent deep tendon reflexes Weak or absent deep tendon reflexes HP:0001315 The deep tendon reflex is a monosynaptic reflex arc with sensory and motor nerve components, but the arc is much more vulnerable to sensory nerve damage. Ankle plantar flexion is retained in all but the most severe peripheral neuropathies, and thus loss of the Achilles tendon reflex in an objective indication of a substantial sensory nerve defect. Reduced tendon reflexes Diminution of tendon reflexes, which is an invariable sign of peripheral nerve disease. PMID:20941667 Any structural abnormality of the cerebellum. UMLS:C0742038 UMLS:C1866129 Abnormality of the cerebellum Cerebellar abnormalities Cerebellar abnormality Cerebellar anomaly Cerebellar signs HP:0001317 A malformed cerebellum may be abnormally small, dysplastic, or unusually large. The vermis and both hemispheres may be equally or disproportionately affected. Primary malformations of the pons, midbrain, and supratentorial structures are also seen in a substantial subset of patients. The wide range in morphological presentations results from the diversity of causes, including chromosomal abnormalities, specific genetic syndromes, and extrinsic factors. Abnormal cerebellum morphology Any structural abnormality of the cerebellum. PMID:27160001 Abnormality of the cerebellum Cerebellar abnormalities Cerebellar abnormality Cerebellar anomaly Cerebellar hypoplasia is a descriptive term implying a cerebellum with a reduced volume, but a normal shape and is stable over time. HP:0006806 HP:0006910 HP:0007038 HP:0007053 MSH:C562568 SNOMEDCT_US:16026008 UMLS:C0266470 Congenital cerebellar hypoplasia Hypoplasia of cerebellum Hypoplastic cerebellum Small cerebellum Underdeveloped cerebellum HP:0001321 By prenatal ultrasound, cerebellar hypoplasia is diagnosed if the cerebellum measures more than two standard deviations below the mean. In adults, cerebellar hypoplasia is typically diagnosed by computer tomography or magnetic resonance imaging. Cerebellar hypoplasia can be diagnosed if there is a small cerebellum with fissures of normal size compared with the folia (this is a distinguishing characteristic compared with cerebellar atrophy). Cerebellar hypoplasia (CH) refers to an underdevelopment of the cerebellum. This category of cerebellar malformation is distinct from Dandy Walker malformation in that it does not involve a concurrent enlargement of the posterior fossa, and almost all individuals exhibit cognitive and motor impairments. Cerebellar hypoplasia Cerebellar hypoplasia is a descriptive term implying a cerebellum with a reduced volume, but a normal shape and is stable over time. PMID:26331051 PMID:27160001 Small cerebellum Underdeveloped cerebellum Hyperreflexia is the presence of hyperactive stretch reflexes of the muscles. HP:0001282 HP:0006820 HP:0007184 HP:0007318 MSH:D012021 SNOMEDCT_US:86854008 UMLS:C0151889 Increased deep tendon reflexes Increased reflexes HP:0001347 Reflexes are graded according to the following scale: 0=absent; 1=present but diminished; 2=normoactive; 3=exaggerated; and 4=clonus. Clonus is always abnormal, and a grade 3 reflex may be abnormal if it is asymmetric or if it was previously grade 2 or less. Hyperreflexia Hyperreflexia is the presence of hyperactive stretch reflexes of the muscles. Increased reflexes A localized defect in the bone of the skull resulting from abnormal embryological development. The defect is covered by normal skin. In some cases, skull x-rays have shown underlying lytic bone lesions which have closed before the age of one year. UMLS:C4025787 UMLS:C4280595 UMLS:C4280596 Cranial defect Skull defect Calvarial defect HP:0001362 Calvarial skull defect A localized defect in the bone of the skull resulting from abnormal embryological development. The defect is covered by normal skin. In some cases, skull x-rays have shown underlying lytic bone lesions which have closed before the age of one year. Cranial defect Skull defect Calvarial defect An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. MSH:D007592 SNOMEDCT_US:399269003 UMLS:C0022408 UMLS:C0240083 Abnormal shape of joints Abnormality of the joints Anomaly of the joints Joint disease HP:0001367 Abnormal joint morphology An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. Abnormal shape of joints Abnormality of the joints Anomaly of the joints Joint disease Inflammation of a joint. MSH:D001168 SNOMEDCT_US:3723001 UMLS:C0003864 Arthritis Joint inflammation HP:0001369 Arthritis Inflammation of a joint. Arthritis Joint inflammation A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. HP:0001372 HP:0001381 HP:0005053 HP:0005189 HP:0005660 MSH:D003286 SNOMEDCT_US:203598005 SNOMEDCT_US:385522000 SNOMEDCT_US:55033002 SNOMEDCT_US:57048009 SNOMEDCT_US:7890003 SNOMEDCT_US:88565003 UMLS:C0009917 UMLS:C0009918 UMLS:C0333068 UMLS:C1850530 Flexed joint that cannot be straightened Flexion contractures Flexion contractures of joints HP:0001371 Flexion contracture A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. Flexed joint that cannot be straightened A reduction in the freedom of movement of one or more joints. HP:0003101 UMLS:C1857108 Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion HP:0001376 Limitation of joint mobility A reduction in the freedom of movement of one or more joints. Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion The capability that a joint (or a group of joints) has to move, passively and/or actively, beyond normal limits along physiological axes. HP:0001378 HP:0001380 HP:0001383 HP:0001388 HP:0002771 HP:0005034 HP:0005692 SNOMEDCT_US:298181000 UMLS:C1844820 Double-Jointed Extensible joints Flexible joints Hyperextensible joints Increased joint mobility Increased mobility of joints Joint hyperextensibility Joint hyperflexibility Joint hyperlaxity Joint laxity Joints move beyond expected range of motion Lax joints Loose-jointedness Joint instability Joint ligamentous laxity Ligamentous laxity HP:0001382 Synonyms of joint hypermobility (JH) include joint laxity and double-jointedness. In general terms, joint hyperlaxity is often considered a further synonym of JH. JH may be caused by a number of factors including intraarticular disease and injury or slacking of extraarticular structures such as joint capsules, ligaments, and muscles. Establishing whether a joint is hypermobile or not is a relatively easy task and it is carried out by (i) using professional tools, such as the orthopedic goniometer; (ii) following specific procedures; and (iii) comparing the measured range of motion (ROM) with normal parameters. When JH is observed at one or a few types of joints (usually fewer than five) it may be defined as localized joint hypermobility (LJH). Typically, LJH affects a single small or large joint and may be bilateral (e.g., bilateral genu recurvatum due to knee hyperextensibility). LJH may be inherited, but it may be an acquired trait related to, for example, past trauma, joint disease, surgery, or training (e.g., spine hypermobility). In individuals with JH at multiple sites (usually five or more), the term generalized joint hypermobility (GJH) is preferred. Joint hypermobility The capability that a joint (or a group of joints) has to move, passively and/or actively, beyond normal limits along physiological axes. PMID:28145606 Double-Jointed Flexible joints Increased mobility of joints Joints move beyond expected range of motion Lax joints Loose-jointedness An abnormality of the hip joint. UMLS:C4020870 Abnormality of the hip joint Abnormality of the hip joints HP:0001384 Abnormal hip joint morphology An abnormality of the hip joint. Abnormality of the hip joint Abnormality of the hip joints The presence of developmental dysplasia of the hip. HP:0008787 Abnormal formation of the hip MSH:D006618 SNOMEDCT_US:48334007 SNOMEDCT_US:52781008 UMLS:C0019555 Congenital hip dysplasia HP:0001385 Hip dysplasia The presence of developmental dysplasia of the hip. Abnormal formation of the hip An abnormality of the liver. MSH:D008107 SNOMEDCT_US:235856003 UMLS:C0023895 UMLS:C4021780 Abnormal liver Abnormality of the liver Liver abnormality Liver disease HP:0001392 Abnormality of the liver An abnormality of the liver. Abnormal liver Abnormality of the liver Liver abnormality Liver disease Increased pressure in the portal vein. MSH:D006975 SNOMEDCT_US:34742003 UMLS:C0020541 HP:0001409 Portal hypertension is defined as portal vein pressures exceeding 5 mm Hg or portal vein to hepatic vein gradient of greater than 10 mm Hg. Portal hypertension Increased pressure in the portal vein. Reduced ability of the liver to perform its functions. HP:0004393 HP:0005228 HP:0006570 MSH:D008107 SNOMEDCT_US:75183008 SNOMEDCT_US:77981007 UMLS:C0086565 UMLS:C0232744 UMLS:C3279149 Decreased liver function Liver dysfunction Hepatopathy Liver dysfunction, mild HP:0001410 Decreased liver function Reduced ability of the liver to perform its functions. Decreased liver function Liver dysfunction Liver dysfunction, mild 2008-04-07T10:59:00Z UMLS:C4025786 Abnormal hand muscles HP:0001421 Abnormality of the musculature of the hand Abnormal hand muscles 2008-04-07T10:18:00Z HP:0004300 UMLS:C4021779 Abnormal calf muscles Abnormality of calf musculature HP:0001430 Abnormal calf musculature morphology Abnormal calf muscles Simultaneous enlargement of the liver and spleen. 2008-02-20T10:51:00Z SNOMEDCT_US:36760000 UMLS:C0019214 Enlarged liver and spleen HP:0001433 Hepatosplenomegaly Simultaneous enlargement of the liver and spleen. Enlarged liver and spleen 2008-04-07T10:19:00Z HP:0004301 UMLS:C4021778 Abnormality of shoulder musculature HP:0001435 Abnormality of the shoulder girdle musculature Abnormality of shoulder musculature An anomaly of the musculature of foot. 2008-04-07T10:21:00Z UMLS:C4025785 Abnormal foot muscles HP:0001436 Abnormality of the foot musculature An anomaly of the musculature of foot. Abnormal foot muscles 2008-04-07T10:21:00Z UMLS:C4025784 HP:0001437 Abnormality of the musculature of the lower limbs A structural abnormality of the abdomen ('belly'), that is, the part of the body between the pelvis and the thorax. UMLS:C4020869 Abnormality of abdomen morphology Abnormality of abdomen structure Abnormality of the abdomen Abdomen abnormality HP:0001438 Abnormal abdomen morphology A structural abnormality of the abdomen ('belly'), that is, the part of the body between the pelvis and the thorax. Abnormality of abdomen structure Abdomen abnormality 2008-04-07T10:27:00Z UMLS:C4025783 Abnormal thigh muscles Abnormality of the musculature of the thigh HP:0001441 Abnormality thigh musculature morphology Abnormal thigh muscles 2008-04-07T10:31:00Z UMLS:C4025780 HP:0001445 Abnormality of the hip-girdle musculature 2008-04-07T10:40:00Z UMLS:C4025779 Abnormal upper limb muscles HP:0001446 Abnormality of the musculature of the upper limbs Abnormal upper limb muscles 2008-04-17T02:37:00Z UMLS:C4025778 Duplication of long bones of foot HP:0001449 Duplication of metatarsal bones Duplication of long bones of foot 2008-04-07T10:41:00Z UMLS:C4025776 HP:0001454 Abnormality of the upper arm 2008-04-07T10:42:00Z UMLS:C4025775 HP:0001457 Abnormality of the musculature of the upper arm Absence or underdevelopment of the musculature. 2008-04-07T10:46:00Z UMLS:C4025773 Absent/small skeletal muscles Absent/underdeveloped skeletal muscles HP:0001460 Aplasia/Hypoplasia involving the skeletal musculature Absence or underdevelopment of the musculature. Absent/small skeletal muscles Absent/underdeveloped skeletal muscles Absence or underdevelopment of the muscles of the shoulder. 2008-04-07T10:49:00Z UMLS:C4025772 Absent/small shoulder muscles Absent/underdeveloped shoulder muscles HP:0001464 Aplasia/Hypoplasia involving the shoulder musculature Absence or underdevelopment of the muscles of the shoulder. Absent/small shoulder muscles Absent/underdeveloped shoulder muscles 2008-04-07T10:50:00Z UMLS:C4025771 Shoulder muscle degeneration Wasting of shoulder muscles HP:0001465 Amyotrophy involving the shoulder musculature Shoulder muscle degeneration Wasting of shoulder muscles Absence or underdevelopment of the musculature of the upper limbs. 2008-04-07T10:51:00Z UMLS:C4025770 Absent/small upper limb muscles Absent/underdeveloped upper limb muscles HP:0001467 Aplasia/Hypoplasia involving the musculature of the upper limbs Absence or underdevelopment of the musculature of the upper limbs. Absent/small upper limb muscles Absent/underdeveloped upper limb muscles Absence or underdevelopment of the muscles of the upper arm. 2008-04-07T10:52:00Z UMLS:C4025769 Absent/small upper arm muscles Absent/underdeveloped upper arm muscles HP:0001468 Aplasia/Hypoplasia involving the musculature of the upper arm Absence or underdevelopment of the muscles of the upper arm. Absent/small upper arm muscles Absent/underdeveloped upper arm muscles 2008-04-07T10:55:00Z UMLS:C4025768 Abnormality of the musculature of the pelvis HP:0001469 Abnormal morphology of the pelvis musculature 2008-04-07T10:56:00Z UMLS:C4025766 Absent/small pelvis muscles Absent/underdeveloped pelvis muscles HP:0001471 Aplasia/Hypoplasia of the musculature of the pelvis Absent/small pelvis muscles Absent/underdeveloped pelvis muscles Increased density of the bony tissue of the scapula. UMLS:C1849263 HP:0001474 Sclerotic scapulae Increased density of the bony tissue of the scapula. Underdevelopment of one or more carpal bones. HP:0001209 HP:0006029 HP:0006072 HP:0006117 HP:0006130 HP:0006227 Small wrist bones UMLS:C1863749 UMLS:C4280594 Hypoplasia of carpal bones Hypoplastic carpal bones Small carpal bones Small carpals HP:0001498 Carpal bone hypoplasia Underdevelopment of one or more carpal bones. Small wrist bones Small carpal bones Small carpals HP:0008904 UMLS:C0262361 Abnormal growth Growth abnormality Growth issue HP:0001507 Growth abnormality Abnormal growth Growth abnormality Growth issue Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. HP:0001535 HP:0008853 HP:0008878 HP:0008916 Undergrowth SNOMEDCT_US:36440009 SNOMEDCT_US:432788009 UMLS:C0231246 UMLS:C2315100 Faltering weight Postnatal failure to thrive Weight faltering Poor weight gain HP:0001508 Although there is no clear consensus on the exact definition of FTT, it is usually diagnoses in a child growing below the 3rd percentile or in a child whose decreased growth has cross two major growth percentiles (for example, from above the 75th percentile to below the 25th percentile). Failure to thrive Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. Undergrowth Faltering weight Weight faltering Poor weight gain A deficiency or slowing down of growth pre- and postnatally. HP:0001434 HP:0001512 HP:0001514 HP:0001517 HP:0001532 HP:0008847 HP:0008870 HP:0008886 HP:0008893 HP:0008926 SNOMEDCT_US:276617005 SNOMEDCT_US:444896005 SNOMEDCT_US:59576002 UMLS:C0151686 UMLS:C0456070 UMLS:C0878787 UMLS:C1837385 UMLS:C3552463 Delayed growth Growth deficiency Growth delay Growth failure Growth retardation Poor growth Retarded growth Very poor growth HP:0001510 Poor or abnormally slow gains in weight or height in a child. Growth delay A deficiency or slowing down of growth pre- and postnatally. Delayed growth Growth deficiency Growth delay Growth failure Growth retardation Poor growth Retarded growth Very poor growth An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age. HP:0001515 HP:0008862 HP:0008892 HP:0008931 MSH:D005317 MSH:D007236 SNOMEDCT_US:199612005 SNOMEDCT_US:22033007 UMLS:C0015934 UMLS:C0021296 UMLS:C1386048 IUGR In utero growth retardation Intrauterine growth failure Intrauterine growth restriction Intrauterine growth retardation, IUGR Intrauterine retardation Prenatal growth deficiency Prenatal growth failure Prenatal growth retardation Prenatal onset growth retardation Prenatal-onset growth retardation Small for gestational age infant HP:0001511 Intrauterine growth restriction is a newer term that is preferred over Intrauterine growth retardation. The causes of IUGR include maternal abnormalities (chronic hypertension, cyanotic heart disease, smoking, drug abuse), placental or umbilical cord abnormalities (including placenta previa and cord anomalies), maternal medicationas, and genetic disorders of the fetus. Intrauterine growth retardation An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age. IUGR Prenatal growth deficiency Prenatal growth retardation Accumulation of substantial excess body fat. MSH:D009765 SNOMEDCT_US:414915002 SNOMEDCT_US:414916001 UMLS:C0028754 Having too much body fat Obesity HP:0001513 Obesity Having too much body fat Obesity Accumulation of fluid in the peritoneal cavity. MSH:D001201 SNOMEDCT_US:389026000 UMLS:C0003962 Accumulation of fluid in the abdomen HP:0001541 Ascites is commonly associated with liver disease that has resulted in portal hypertension and low serum albumin levels. Ascites Accumulation of fluid in the peritoneal cavity. Accumulation of fluid in the abdomen A morphological anomaly of the rib cage. UMLS:C4025763 Abnormality of the rib cage HP:0001547 Abnormal rib cage morphology A morphological anomaly of the rib cage. Abnormality of the rib cage Excessive postnatal growth which may comprise increased weight, increased length, and/or increased head circumference. UMLS:C1849265 UMLS:C1851731 UMLS:C3150281 General overgrowth Generalised overgrowth Generalized overgrowth HP:0001548 Overgrowth Excessive postnatal growth which may comprise increased weight, increased length, and/or increased head circumference. General overgrowth Generalised overgrowth Generalized overgrowth 2008-02-20T11:05:00Z UMLS:C4025762 Abnormality of the ileum HP:0001549 Abnormal ileum morphology Abnormality of the amniotic fluid, which is the fluid contained in the amniotic sac surrounding the developing fetus. SNOMEDCT_US:42170009 UMLS:C0266781 Abnormal amniotic fluid HP:0001560 Abnormality of the amniotic fluid Abnormality of the amniotic fluid, which is the fluid contained in the amniotic sac surrounding the developing fetus. The presence of excess amniotic fluid in the uterus during pregnancy. HP:0005098 MSH:D006831 SNOMEDCT_US:86203003 UMLS:C0020224 High levels of amniotic fluid Hydramnios Increased amniotic fluid index HP:0001561 Polyhydramnios is diagnosed if the deepest vertical pool of amniotic fluid is more than 8 cm or amniotic fluid index is more than 95th percentile for the corresponding gestational age. Polyhydramnios The presence of excess amniotic fluid in the uterus during pregnancy. High levels of amniotic fluid Increased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD above mean for age. Alternatively, an apparently increased maximum width of the tooth. Hyperplasia of tooth Hypertrophy of tooth SNOMEDCT_US:71485000 UMLS:C0266036 UMLS:C4280590 UMLS:C4280591 UMLS:C4280592 Increased size of tooth Increased width of tooth Large tooth Megalodontia Tooth mass excess HP:0001572 The standard reference has means and standard deviations by gender [Moyers et al, 1976]. Although it is easy to measure the width of teeth, and the definition is made with reference to the width of teeth, macrodontia actually means that the overall size of the tooth is increased. Macrodontia Increased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD above mean for age. Alternatively, an apparently increased maximum width of the tooth. PMID:19125428 Hyperplasia of tooth Hypertrophy of tooth Increased size of tooth Increased width of tooth Large tooth Tooth mass excess An abnormality of the integument, which consists of the skin and the superficial fascia. UMLS:C4025761 HP:0001574 Abnormality of skin, hair, or nails. Abnormality of the integument An abnormality of the integument, which consists of the skin and the superficial fascia. An abnormality of the hair. UMLS:C0157733 UMLS:C2677869 Abnormality of the hair Hair abnormality Abnormality of the hair shaft HP:0001595 Abnormal hair morphology An abnormality of the hair. Abnormality of the hair Hair abnormality Abnormality of the hair shaft An abnormality of the larynx. UMLS:C4021777 Laryngeal abnormalities Laryngeal anomalies HP:0001600 Abnormality of the larynx An abnormality of the larynx. Any abnormality of the cardiovascular system. HP:0003116 MSH:D002318 MSH:D018376 SNOMEDCT_US:49601007 UMLS:C0007222 UMLS:C0243050 Abnormality of the cardiovascular system Cardiovascular abnormality Cardiovascular disease HP:0001626 The cardiovascular system consists of the heart, vasculature, and the lymphatic system. Abnormality of the cardiovascular system Any abnormality of the cardiovascular system. Abnormality of the cardiovascular system Cardiovascular abnormality Cardiovascular disease Any structural anomaly of the heart. HP:3000001 MSH:D006330 SNOMEDCT_US:13213009 UMLS:C0018798 UMLS:C0152021 Abnormality of cardiac morphology Abnormality of the heart Abnormally shaped heart Cardiac abnormality Cardiac anomalies Cardiac anomaly Congenital heart defect Congenital heart defects Heart defect HP:0001627 Abnormal heart morphology Any structural anomaly of the heart. Abnormality of the heart Abnormally shaped heart Heart defect A hole between the two bottom chambers (ventricles) of the heart. The defect is centered around the most superior aspect of the ventricular septum. HP:0001652 Fyler:1300 MSH:D006345 SNOMEDCT_US:253549006 SNOMEDCT_US:30288003 UMLS:C0018818 Hole in heart wall separating two lower heart chambers VSD Ventricular septal defects Ventriculoseptal defect HP:0001629 Ventricular septal defect A hole between the two bottom chambers (ventricles) of the heart. The defect is centered around the most superior aspect of the ventricular septum. PMID:33327983 Hole in heart wall separating two lower heart chambers VSD Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum. HP:0001630 Fyler:2050 ICD-10:Q21.1 MSH:D006344 SNOMEDCT_US:253366007 SNOMEDCT_US:405752007 SNOMEDCT_US:70142008 UMLS:C0018817 ASD An opening in the wall separating the top two chambers of the heart Atria septal defect Atrial septum defect Atrioseptal defect Defect in the atrial septum Hole in heart wall separating two upper heart chambers HP:0001631 Atrial septal defect Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum. HPO_CONTRIBUTOR:DDD_dbrown ASD An opening in the wall separating the top two chambers of the heart Hole in heart wall separating two upper heart chambers Any structural anomaly of the mitral valve. HP:0031477 UMLS:C4025759 Abnormality of the mitral valve HP:0001633 Abnormal mitral valve morphology Any structural anomaly of the mitral valve. The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. HP:0006686 MSH:D006333 SNOMEDCT_US:42343007 SNOMEDCT_US:84114007 UMLS:C0018801 UMLS:C0018802 CHF Cardiac failure Cardiac failures Cardiac insufficiency Chronic heart failure Heart failure HP:0001635 Congestive heart failure The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. CHF Cardiac failure Cardiac failures Heart failure A structural anomaly of the muscle layer of the heart wall. UMLS:C4025758 Abnormality of the myocardium HP:0001637 Abnormal myocardium morphology A myocardial disorder in which the heart muscle is structurally and functionally abnormal, in the absence of coronary artery disease, hypertension, valvular disease and congenital heart disease sufficient to cause the observed myocardial abnormality. Fyler:1840 MSH:D009202 SNOMEDCT_US:57809008 SNOMEDCT_US:85898001 UMLS:C0878544 Disease of the heart muscle HP:0001638 Cardiomyopathy A myocardial disorder in which the heart muscle is structurally and functionally abnormal, in the absence of coronary artery disease, hypertension, valvular disease and congenital heart disease sufficient to cause the observed myocardial abnormality. PMID:17916581 Disease of the heart muscle Increased size of the heart, clinically defined as an increased transverse diameter of the cardiac silhouette that is greater than or equal to 50% of the transverse diameter of the chest (increased cardiothoracic ratio) on a posterior-anterior projection of a chest radiograph or a computed tomography. MSH:D006332 SNOMEDCT_US:8186001 UMLS:C0018800 Enlarged heart Increased heart size HP:0001640 Cardiomegaly Increased size of the heart, clinically defined as an increased transverse diameter of the cardiac silhouette that is greater than or equal to 50% of the transverse diameter of the chest (increased cardiothoracic ratio) on a posterior-anterior projection of a chest radiograph or a computed tomography. PMID:31194436 Enlarged heart Increased heart size Any structural abnormality of the pulmonary valve. Fyler:1600 Fyler:1602 SNOMEDCT_US:448643005 UMLS:C3164374 Abnormality of the pulmonary valve Anomaly of the pulmonary valve HP:0001641 Abnormal pulmonary valve morphology Any structural abnormality of the pulmonary valve. Any structural abnormality of a cardiac valve. HP:0001703 MSH:D006349 SNOMEDCT_US:368009 UMLS:C0018824 UMLS:C0241654 Abnormality of the heart valves Valvular abnormality Valvular heart disease HP:0001654 Abnormal heart valve morphology Any structural abnormality of a cardiac valve. In this case the right ventricle is more muscular than normal, causing a characteristic boot-shaped (coeur-en-sabot) appearance as seen on anterior- posterior chest x-rays. Right ventricular hypertrophy is commonly associated with any form of right ventricular outflow obstruction or pulmonary hypertension, which may in turn owe its origin to left-sided disease. The echocardiographic signs are thickening of the anterior right ventricular wall and the septum. Cavity size is usually normal, or slightly enlarged. In many cases there is associated volume overload present due to tricuspid regurgitation, in the absence of this, septal motion is normal. Fyler:3609 MSH:D017380 SNOMEDCT_US:89792004 UMLS:C0162770 Heart right ventricle hypertrophy HP:0001667 Right ventricular hypertrophy In this case the right ventricle is more muscular than normal, causing a characteristic boot-shaped (coeur-en-sabot) appearance as seen on anterior- posterior chest x-rays. Right ventricular hypertrophy is commonly associated with any form of right ventricular outflow obstruction or pulmonary hypertension, which may in turn owe its origin to left-sided disease. The echocardiographic signs are thickening of the anterior right ventricular wall and the septum. Cavity size is usually normal, or slightly enlarged. In many cases there is associated volume overload present due to tricuspid regurgitation, in the absence of this, septal motion is normal. Heart right ventricle hypertrophy An anomaly of the intra-atrial or intraventricular septum. HP:0001690 HP:0004760 MSH:D006343 SNOMEDCT_US:253273004 SNOMEDCT_US:396351009 SNOMEDCT_US:59494005 UMLS:C0018816 Abnormality of the cardiac septa Heart septal defect Septal defects HP:0001671 Abnormal cardiac septum morphology An anomaly of the intra-atrial or intraventricular septum. Septal defects Delayed or lack of conduction of atrial depolarizations through the atrioventricular node to the ventricles. HP:0001668 HP:0005142 HP:0006672 MSH:D054537 SNOMEDCT_US:233917008 UMLS:C0004245 UMLS:C1841659 Interruption of electrical communication between upper and lower chambers of heart Atrioventricular nodal disease HP:0001678 Atrioventricular block Delayed or lack of conduction of atrial depolarizations through the atrioventricular node to the ventricles. Interruption of electrical communication between upper and lower chambers of heart An abnormality of the aorta. HP:0030963 Fyler:1453 UMLS:C4025756 Abnormal aorta morphology Abnormality of the aorta HP:0001679 Abnormal aortic morphology An abnormality of the aorta. PMID:24910511 Abnormal aorta morphology An abnormality of the pericardium, i.e., of the fluid filled sac that surrounds the heart and the proximal ends of the aorta, vena cava, and the pulmonary artery. Fyler:1900 UMLS:C4025754 Abnormality of the pericardium HP:0001697 Abnormal pericardium morphology An abnormality of the pericardium, i.e., of the fluid filled sac that surrounds the heart and the proximal ends of the aorta, vena cava, and the pulmonary artery. Inflammation of the sac-like covering around the heart (pericardium). MSH:D010493 SNOMEDCT_US:3238004 UMLS:C0031046 Swelling or irritation of membrane around heart HP:0001701 Pericarditis Inflammation of the sac-like covering around the heart (pericardium). Swelling or irritation of membrane around heart Any structural anomaly of the tricuspid valve. HP:0031440 EPCC:06.01.00 UMLS:C4025753 Abnormality of the tricuspid valve HP:0001702 Abnormal tricuspid valve morphology Any structural anomaly of the tricuspid valve. An abnormality of the right ventricle of the heart. Fyler:1820 SNOMEDCT_US:253516002 UMLS:C0344887 Abnormality of the right ventricle Right ventricular abnormality HP:0001707 The function of the right ventricle is to receive blood from the right atrium and to eject blood into the pulmonary artery. Abnormal right ventricle morphology An abnormality of the right ventricle of the heart. Any structural abnormality of the left ventricle of the heart. Fyler:1810 SNOMEDCT_US:253535002 UMLS:C0344905 Abnormal heart left ventricle morphology Abnormality of the left ventricle Left ventricular abnormality HP:0001711 Abnormal left ventricle morphology Any structural abnormality of the left ventricle of the heart. Abnormal heart left ventricle morphology Enlargement or increased size of the heart left ventricle. HP:0005171 Fyler:3608 MSH:D017379 SNOMEDCT_US:55827005 UMLS:C0149721 Heart left ventricle hypertrophy Left ventricular wall hypertrophy HP:0001712 Left ventricular hypertrophy Enlargement or increased size of the heart left ventricle. MP:0002625 Heart left ventricle hypertrophy An abnormality of a cardiac ventricle. UMLS:C4025752 Abnormality of cardiac ventricle HP:0001713 Abnormal cardiac ventricle morphology An abnormality of a cardiac ventricle. Enlargement of the cardiac ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy. HP:0005167 SNOMEDCT_US:266249003 UMLS:C0340279 HP:0001714 Ventricular hypertrophy Enlargement of the cardiac ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy. An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in a coronary artery. SNOMEDCT_US:445512009 UMLS:C1611184 HP:0001717 Coronary artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in a coronary artery. A progressive form of hearing impairment. HP:0008590 UMLS:C1842138 Progressive hearing loss HP:0001730 Progressive hearing impairment A progressive form of hearing impairment. An abnormality of the pancreas. MSH:D010182 SNOMEDCT_US:3855007 UMLS:C0030286 UMLS:C4025751 Abnormality of the pancreas Pancreatic disease HP:0001732 Abnormality of the pancreas An abnormality of the pancreas. Abnormality of the pancreas Pancreatic disease The presence of inflammation in the pancreas. MSH:D010195 SNOMEDCT_US:75694006 UMLS:C0030305 Pancreatic inflammation HP:0001733 Pancreatitis The presence of inflammation in the pancreas. Pancreatic inflammation A structural anomaly of the nasopharynx. UMLS:C4025750 Abnormality of the nasopharynx HP:0001739 The nasopharynx (nasal part of the pharynx) lies behind the nose and above the level of the soft palate. Abnormal nasopharynx morphology An abnormality of the spleen. UMLS:C4025749 Abnormality of the spleen HP:0001743 The spleen is an abdominal organ that functions as a member of the hematopoietic system and of the immune system. Abnormality of the spleen An abnormality of the spleen. Abnormality of the spleen Abnormal increased size of the spleen. HP:0001745 HP:0006269 MSH:D013163 SNOMEDCT_US:16294009 UMLS:C0038002 Increased spleen size HP:0001744 Splenomegaly Abnormal increased size of the spleen. Increased spleen size Absence (aplasia) of the spleen. Fyler:4771 SNOMEDCT_US:702624008 SNOMEDCT_US:707147002 SNOMEDCT_US:93030006 UMLS:C0600031 Absent spleen HP:0001746 Asplenia Absence (aplasia) of the spleen. Absent spleen An abnormality of the functioning of the vestibular apparatus. HP:0006917 HP:0007921 UMLS:C1843865 Impaired vestibular function Interictal vestibular dysfunction Vestibular function defect HP:0001751 The vestibular apparatus is the nonauditory portion of the inner ear that mediates the subjective sensation of motion and spatial orientation of the head, adjusts muscular activity and body position to maintain posture, and stabilizes in space the fixation point of the eyes when the head moves, in order to provide a stable image upon the retina. The functioning of the vestibular system is often checked clinically by means of the caloric test, in which the head is tilted backward by about 60 degrees and either warm or cold water is introduced into the external auditory meatus on one side. The immediate results are usually vertigo, nausea, nystagmus, and twisting of the head and body. Abnormal vestibular function An abnormality of the functioning of the vestibular apparatus. A general descriptive term that describes impaired functioning of the vestibular apparatus that leads to manifestations such as dizziness or postural imbalance UMLS:C1848606 Vestibular deficiency Vestibular dysfunction Vestibular failure Vestibular hyporeflexia Vestibular loss Vestibulopathy HP:0001756 Vestibular hypofunction A general descriptive term that describes impaired functioning of the vestibular apparatus that leads to manifestations such as dizziness or postural imbalance PMID:32767115 An abnormality of the skeleton of foot. HP:0010216 HP:0010611 MSH:D005530 SNOMEDCT_US:229844004 UMLS:C0016506 Abnormal feet structure Abnormality of the feet Abnormality of the foot Foot deformities Foot deformity HP:0001760 A disorder of the foot that can either be congenital or acquired. Such deformities can include hammer toe, club foot deformity, flat feet, pes cavus, congenital vertical talus (rocker bottom foot), and many others. Abnormal foot morphology An abnormality of the skeleton of foot. Abnormal feet structure Abnormality of the feet Abnormality of the foot Foot deformities Foot deformity A measured foot length that is more than 2 SD below the mean for a newborn of 27 - 41 weeks gestation, or foot that is less than the 3rd centile for individuals from birth to 16 years of age (objective). Alternatively, a foot that appears disproportionately short (subjective). HP:0001764 HP:0001766 HP:0001778 HP:0008135 UMLS:C1848673 Hypoplastic feet Short feet Short foot Small feet HP:0001773 Short foot A measured foot length that is more than 2 SD below the mean for a newborn of 27 - 41 weeks gestation, or foot that is less than the 3rd centile for individuals from birth to 16 years of age (objective). Alternatively, a foot that appears disproportionately short (subjective). PMID:19125433 Short feet Short foot Small feet An anomaly of a toe. UMLS:C2674738 Abnormalities of the toes Abnormality of toe HP:0001780 Abnormal toe morphology An anomaly of a toe. Abnormalities of the toes Abnormality of toe Accumulation of fluid in the peritoneal cavity during the fetal period. SNOMEDCT_US:363125002 UMLS:C1285291 Foetal ascites HP:0001791 Fetal ascites Accumulation of fluid in the peritoneal cavity during the fetal period. Foetal ascites Lateral deviation of the great toe (i.e., in the direction of the little toe). HP:0004682 MSH:D000071378 MSH:D006215 SNOMEDCT_US:122480009 SNOMEDCT_US:415692008 UMLS:C0006386 UMLS:C0018536 Bunion Lateral deviation of great toe Lateral deviation of halluces HP:0001822 Hallux valgus Lateral deviation of the great toe (i.e., in the direction of the little toe). Bunion Reduction of total body weight. MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C1262477 Loss of weight HP:0001824 Weight loss Reduction of total body weight. A kind of polydactyly characterized by the presence of a supernumerary toe or toes. HP:0009135 SNOMEDCT_US:62218008 UMLS:C0158734 Duplication of bones of the toes Polydactyly of feet Polydactyly of the foot HP:0001829 Foot polydactyly A kind of polydactyly characterized by the presence of a supernumerary toe or toes. Duplication of bones of the toes Polydactyly of the foot most commonly refers to the presence of six toes on one foot. Postaxial polydactyly affects the lateral ray and the duplication may range from a well-formed articulated digit to a rudimentary digit. HP:0010346 UMLS:C2112129 UMLS:C4020865 Extra toe attached near the little toe Polydactyly affecting the 5th toe Postaxial polydactyly of feet Postaxial polydactyly of foot Posterior polydactyly of foot Fibular polydactyly HP:0001830 The modifier postaxial means that the supernumerary digit is not a hallux. Postaxial foot polydactyly Polydactyly of the foot most commonly refers to the presence of six toes on one foot. Postaxial polydactyly affects the lateral ray and the duplication may range from a well-formed articulated digit to a rudimentary digit. Extra toe attached near the little toe A toe that appears disproportionately short compared to the foot. HP:0001767 HP:0001781 HP:0001855 HP:0004701 HP:0005889 HP:0008099 UMLS:C1836195 Brachydactyly of the foot Hypoplasia of the toe Hypoplastic toes Short foot phalanges Short toe Short toes Stubby toes HP:0001831 This finding must be distinguished from digits that are of increased girth but of normal length and that of a long mid- and hind foot with normal digit lengths. The affected digits should be specified as described in the introductory comments. Note that we designate brachydactyly as a synonym, but this use of the term is distinct from the use of the same word in Bell's classification of brachdactyly. Short toe A toe that appears disproportionately short compared to the foot. Short toe Short toes Stubby toes Abnormalities of the metatarsal bones (i.e. of five tubular bones located between the tarsal bones of the hind- and mid-foot and the phalanges of the toes). UMLS:C4025745 Abnormality of the long bone of foot HP:0001832 Abnormal metatarsal morphology Abnormalities of the metatarsal bones (i.e. of five tubular bones located between the tarsal bones of the hind- and mid-foot and the phalanges of the toes). Abnormality of the long bone of foot Increased back to front length of the foot. HP:0008136 HP:0008143 SNOMEDCT_US:299462005 UMLS:C0576225 Disproportionately large feet Long foot large feet long feet HP:0001833 Long foot Increased back to front length of the foot. Disproportionately large feet Long foot large feet long feet Camptodactyly is a painless flexion contracture of the proximal interphalangeal (PIP) joint that is usually gradually progressive. This term refers to camptodactyly of one or more toes. UMLS:C4021774 Camptodactyly of feet HP:0001836 Camptodactyly of toe Camptodactyly is a painless flexion contracture of the proximal interphalangeal (PIP) joint that is usually gradually progressive. This term refers to camptodactyly of one or more toes. Duplication of all or part of the first ray. HP:0009607 HP:0010050 MSH:C566632 UMLS:C1866339 UMLS:C2112942 Partial/complete duplication of the phalanges of the big toe Polydactyly affecting the hallux Preaxial hallucal polydactyly Preaxial polydactyly of feet Preaxial polydactyly of foot Preaxial polydactyly of the feet Preaxial polydactyly, feet HP:0001841 This term applies for a wide variety of partial and/or complete duplications of the phalanges of the big toe (sometimes including the 1st metatarsal). A partial duplication can present itself on x-rays as a notched phalanx, bifid phalanx or a broadened phalanx. Polydactyly affecting the big toe is called preaxial or hallucal polydactyly of the feet. Preaxial foot polydactyly Duplication of all or part of the first ray. PMID:19125433 Partial/complete duplication of the phalanges of the big toe Preaxial polydactyly of the feet This term applies for all abnormalities of the big toe, also called hallux. UMLS:C4021773 Abnormalities of the hallux Abnormality of the big toe Abnormality of the hallux HP:0001844 Abnormal hallux morphology This term applies for all abnormalities of the big toe, also called hallux. Abnormality of the big toe Increased length of the big toe. HP:0001867 UMLS:C1864375 Increased length of the hallux Large halluces Long big toe Long halluces HP:0001847 Long hallux Increased length of the big toe. Long big toe A developmental defect resulting in the presence of fewer than the normal number of toes. HP:0001777 SNOMEDCT_US:249820005 UMLS:C0426934 Missing toes Oligodactyly of feet HP:0001849 Foot oligodactyly A developmental defect resulting in the presence of fewer than the normal number of toes. Missing toes An abnormality of the tarsus are the cluster of seven bones in the foot between the tibia and fibula and the metatarsus, including the calcaneus (heel) bone and the talus (ankle) bone. UMLS:C1862136 Abnormal ankle bones Abnormal tarsals HP:0001850 Abnormality of the tarsal bones An abnormality of the tarsus are the cluster of seven bones in the foot between the tibia and fibula and the metatarsus, including the calcaneus (heel) bone and the talus (ankle) bone. Abnormal ankle bones HP:0005615 UMLS:C4021772 Bifid distal phalanges of toes Bifid terminal phalanx of toe Notched outermost bones of toes HP:0001853 Bifid distal phalanx of toe Notched outermost bones of toes Short distance from the end of the toe to the most distal interphalangeal crease or distal interphalangeal joint flexion point, i.e., abnormally short distal phalanx of toe. UMLS:C4021771 Hypoplastic distal phalanges of feet Short outermost bone of toe HP:0001857 This term differs from Partial absence of the toe because in that term the phalanx must be missing, whereas here it may be small, but present. Relative shortening of the distal phalanges of the toes can be harder to assess than in the fingers, as they are normally quite short. Distal phalangeal lengths can be assessed subjectively by comparing that digit segment to the rest of the digit, to other normal digits in that patient, or to typical patients of that age or build. Short distal phalanx of toe Short distance from the end of the toe to the most distal interphalangeal crease or distal interphalangeal joint flexion point, i.e., abnormally short distal phalanx of toe. PMID:19125433 Short outermost bone of toe An abnormality of the hematopoietic system. HP:0003135 MSH:D006402 SNOMEDCT_US:191124002 SNOMEDCT_US:34093004 UMLS:C0018939 UMLS:C0850715 UMLS:C4020864 Abnormality of blood and blood-forming tissues Abnormality of the haematopoietic system Abnormality of the hematopoietic system Haematological abnormality Hematological abnormality Hematologic disease HP:0001871 The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes. Abnormality of blood and blood-forming tissues An abnormality of the hematopoietic system. Abnormality of blood and blood-forming tissues Abnormality of the haematopoietic system Haematological abnormality An abnormality of platelets. HP:0004807 HP:0005554 MSH:D013915 SNOMEDCT_US:127566005 SNOMEDCT_US:32942005 UMLS:C0040015 UMLS:C0151854 UMLS:C4020863 Platelet abnormalities Blood platelet disease Thrombasthenia HP:0001872 Platelets, also known as thrombocytes, are non-nucleated disk-shaped cells mainly involved in blood coagulation. Abnormality of thrombocytes An abnormality of platelets. Platelet abnormalities A reduction in the number of circulating thrombocytes. HP:0001906 HP:0004838 HP:0008175 HP:0008268 HP:0008302 MSH:D013921 SNOMEDCT_US:302215000 SNOMEDCT_US:415116008 UMLS:C0040034 UMLS:C0392386 Low platelet count HP:0001873 Thrombocytopenia can be divided into three major causes; 1) low production of platelets in the bone marrow; 2) intravascular breakdown of thrombocytes; and 3) increased turnover of platelets in spleen or liver (extravascular). Thrombocytopenia A reduction in the number of circulating thrombocytes. Low platelet count A neutrophil abnormality. SNOMEDCT_US:250274006 UMLS:C0427515 Abnormality of neutrophil Abnormality of neutrophils Abnormality of polymorphonuclear neutrophils HP:0001874 Neutrophils are the most abundant leukocytes in blood and are considered to be the first line of defense during inflammation and infections. They are myeloid granulocytes and their names is derived from the fact that their cytoplasm contains granules that stain with acidic dye as well as granules that stain with basic dye. Their nuclei consist of three to five lobes connected by slender threads of chromatin. Mature neutrophils live for approximately one day. Abnormality of neutrophils A neutrophil abnormality. PMID:21094463 PMID:26819959 Abnormality of neutrophils An abnormally low number of neutrophils in the peripheral blood. HP:0005515 HP:0005533 SNOMEDCT_US:165517008 UMLS:C0853697 Low blood neutrophil count Low neutrophil count Neutropoenia Peripheral neutropenia HP:0001875 Mild neutropenia is defined as an absolute neutrophil count of less than 1500 cells per microliter of blood, moderate less than 1000 cells per microliter of blood and, and severe is less than 500 cells per microliter of blood. Neutropenia An abnormally low number of neutrophils in the peripheral blood. PMID:25642312 Low blood neutrophil count Low neutrophil count Neutropoenia An abnormal reduction in numbers of all blood cell types (red blood cells, white blood cells, and platelets). MSH:D010198 SNOMEDCT_US:127034005 UMLS:C0030312 Low blood cell count Pancytopaenia HP:0001876 Pancytopenia An abnormal reduction in numbers of all blood cell types (red blood cells, white blood cells, and platelets). Low blood cell count Pancytopaenia Any structural abnormality of erythrocytes (red-blood cells). HP:0010973 SNOMEDCT_US:12222001 UMLS:C0391870 UMLS:C4020862 Abnormality of erythrocytes Abnormality of red blood cells Abnormality of erythroid lineage cell HP:0001877 Abnormal erythrocyte morphology Any structural abnormality of erythrocytes (red-blood cells). An abnormal count or structure of eosinophils. UMLS:C4025738 Abnormality of eosinophils HP:0001879 Eosinophils stain with acidophilic dyes including eosin red. They have a bilobed nucleus, are weakly phagocytic, and are involved in the immune defense against worms. Eosinophils are released into the peripheral blood in a phenotypically mature state, and are capable of undergoing activation and recruitment into tissues in response to appropriate stimuli, most notably cytokines interleukin-5 and the eotaxins. Eosinophils spend only a brief time in the peripheral blood (half-life of about 18 hours) before they migrate to the thymus or gastrointestinal tract, where they reside under homeostatic conditions. In response to inflammatory stimuli, eosinophils develop from committed bone marrow progenitors, after which they exit, migrate into the blood and subsequently accumulate in peripheral tissues where survival is prolonged. Abnormal eosinophil morphology An abnormal count or structure of eosinophils. PMID:23154224 Increased count of eosinophils in the blood. MSH:D004802 UMLS:C0014457 High blood eosinophil count HP:0001880 Eosinophilia Increased count of eosinophils in the blood. High blood eosinophil count An abnormality of leukocytes. SNOMEDCT_US:134199001 SNOMEDCT_US:24827003 UMLS:C0152009 Abnormality of leukocytes HP:0001881 Leukocytes are nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue. Abnormal leukocyte morphology An abnormality of leukocytes. An abnormal decreased number of leukocytes in the blood. MSH:D007970 SNOMEDCT_US:84828003 UMLS:C0023530 Decreased blood leukocyte number Low white blood cell count HP:0001882 Leukopenia An abnormal decreased number of leukocytes in the blood. Decreased blood leukocyte number Low white blood cell count A reduced number of lymphocytes in the blood. MSH:D008231 SNOMEDCT_US:48813009 UMLS:C0024312 Absolute lymphocyte count decrease Decreased blood lymphocyte number Low lymphocyte number Lymphocytopenia HP:0001888 Lymphopenia A reduced number of lymphocytes in the blood. Decreased blood lymphocyte number Low lymphocyte number An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. HP:0004830 HP:0004834 HP:0004849 HP:0004862 HP:0004865 HP:0008183 SNOMEDCT_US:248250000 SNOMEDCT_US:64779008 UMLS:C1458140 Bleeding diathesis Bleeding tendency Hemorrhagic diathesis HP:0001892 This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted. Abnormal bleeding An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. Bleeding tendency Increased numbers of platelets in the peripheral blood. MSH:D013922 SNOMEDCT_US:415115007 SNOMEDCT_US:6631009 UMLS:C0836924 UMLS:C0857460 Increased number of platelets in blood Increased platelet count Thrombocythaemia Thrombocythemia HP:0001894 Thrombocythemia and thrombocytosis are conditions with a higher than normal number of platelets. The term "thrombocythemia" is preferred when the cause of a high platelet count isn't known. The condition sometimes is called primary or essential thrombocythemia. Thrombocytosis Increased numbers of platelets in the peripheral blood. Increased number of platelets in blood A reduced number of reticulocytes in the peripheral blood. SNOMEDCT_US:124961001 UMLS:C0858867 HP:0001896 Reticulocytopenia A reduced number of reticulocytes in the peripheral blood. The presence of an increased mass of red blood cells in the circulation. UMLS:C1853288 Increased RBC mass HP:0001898 Increased red blood cell mass The presence of an increased mass of red blood cells in the circulation. Increased RBC mass SNOMEDCT_US:131141003 UMLS:C0549448 Increased Hb Increased haemoglobin HP:0001900 Increased hemoglobin Increased Hb Increased haemoglobin Polycythemia is diagnosed if the red blood cell count, the hemoglobin level, and the red blood cell volume all exceed the upper limits of normal. HP:0001893 MSH:D011086 SNOMEDCT_US:109992005 SNOMEDCT_US:127062003 UMLS:C0032461 UMLS:C1527405 Abnormally shaped erythrocytes Erythrocytosis Increased red blood cells Polyglobulia HP:0001901 Polycythemia Polycythemia is diagnosed if the red blood cell count, the hemoglobin level, and the red blood cell volume all exceed the upper limits of normal. Abnormally shaped erythrocytes Increased red blood cells A reduction in erythrocytes volume or hemoglobin concentration. HP:0001926 HP:0003136 HP:0005509 MSH:D000740 SNOMEDCT_US:165397008 SNOMEDCT_US:271737000 UMLS:C0002871 UMLS:C0162119 Anaemia Low number of red blood cells or haemoglobin Low number of red blood cells or hemoglobin Decreased haemoglobin Decreased hemoglobin HP:0001903 Anemia is not a specific entity but can result from many underlying pathologic processes. The three main causes of anemia are blood loss, decreased or faulty red blood cell production, and increased destruction of red blood cells. Various classifications are in clinical use including a classification according to the mean corpuscular volume (MCV) of the erythrocytes: microcytic, macrocytic, or normocytic. Anemias can also be classified according to variations in cell size and shape, as reflected by the red-cell distribution width (RDW). Additionally, anemias can be classified into those of inadequate production and hemolytic anemias. Anemia A reduction in erythrocytes volume or hemoglobin concentration. Low number of red blood cells or haemoglobin Low number of red blood cells or hemoglobin Decreased haemoglobin The formation of a blood clot inside a blood vessel that subsequently travels through the blood stream from the site where it formed to another location in the body, generally leading to vascular occlusion at the distant site. MSH:D013923 MSH:D016769 SNOMEDCT_US:13713005 SNOMEDCT_US:371039008 UMLS:C0040038 UMLS:C0085307 Blood clot in blood vessel Thromboembolic disease Thromboembolic events Embolism and thrombosis HP:0001907 Thromboembolism The formation of a blood clot inside a blood vessel that subsequently travels through the blood stream from the site where it formed to another location in the body, generally leading to vascular occlusion at the distant site. Blood clot in blood vessel Any structural abnormality or abnormal count of granulocytes. HP:0005438 SNOMEDCT_US:250274006 UMLS:C0427515 Abnormality of granulocytes HP:0001911 Abnormal granulocyte morphology Any structural abnormality or abnormal count of granulocytes. Any structural abnormality or abnormal count of basophils. UMLS:C4025736 Abnormality of basophils HP:0001912 Basophils are myeoloid granulocytes and part of the innate immune system. They represent the least abundant granulocyte population in mammals. They have a complex, almost C-shaped nucleus. Their granules stain blue with basic dye. They are not phagacytic. They are involved in the immune response to worms. Their cell surface has Fc receptors which may be attached to class E antibodies. Abnormal basophil morphology Any structural abnormality or abnormal count of basophils. PMID:24075190 An abnormally reduced number of granulocytes in the blood. MSH:D000380 SNOMEDCT_US:17182001 SNOMEDCT_US:417672002 UMLS:C0001824 HP:0001913 Granulocytopenia An abnormally reduced number of granulocytes in the blood. An elevation in the number of reticulocytes (immature erythrocytes) in the peripheral blood circulation. MSH:D045262 SNOMEDCT_US:46049004 UMLS:C0206160 Increased immature red blood cells Increased number of immature red blood cells Increased reticulocyte count Increased reticulocytes HP:0001923 Reticulocytosis An elevation in the number of reticulocytes (immature erythrocytes) in the peripheral blood circulation. Increased immature red blood cells Increased number of immature red blood cells An abnormality of the process of blood coagulation. That is, altered ability or inability of the blood to clot. MSH:D001778 MSH:D006474 SNOMEDCT_US:362970003 SNOMEDCT_US:64779008 UMLS:C0005779 UMLS:C0019087 UMLS:C1846821 Abnormal blood coagulation studies Coagulation abnormalities Coagulation abnormality Haemorrhagic disorders Blood coagulation disorder HP:0001928 Abnormality of coagulation An abnormality of the process of blood coagulation. That is, altered ability or inability of the blood to clot. Haemorrhagic disorders HP:0002146 HP:0004355 HP:0004367 UMLS:C4021768 Laboratory abnormality Metabolism abnormality HP:0001939 Abnormality of metabolism/homeostasis Laboratory abnormality Metabolism abnormality Abnormal acid accumulation or depletion of base. HP:0001940 MSH:D000138 SNOMEDCT_US:51387008 UMLS:C0001122 HP:0001941 When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Acidosis Abnormal acid accumulation or depletion of base. PMID:24381489 A decreased concentration of glucose in the blood. HP:0003356 MSH:D007003 SNOMEDCT_US:237630007 SNOMEDCT_US:271327008 SNOMEDCT_US:302866003 UMLS:C0020615 Hypoglycaemia Low blood sugar HP:0001943 Hypoglycemia A decreased concentration of glucose in the blood. Low blood sugar MSH:D003681 SNOMEDCT_US:34095006 UMLS:C0011175 Dehydration Exsiccosis HP:0001944 Dehydration Dehydration Body temperature elevated above the normal range. MSH:D005334 SNOMEDCT_US:386661006 SNOMEDCT_US:50177009 UMLS:C0015967 Fever Hyperthermia Pyrexia HP:0001945 Fever has been defined as a state of elevated core temperature, which is often, but not necessarily, part of the defensive responses of multicellular organisms (host) to the invasion of live (microorganisms) or inanimate matter recognized as pathogenic or alien by the host. The febrile response (of which fever is a component) is a complex physiologic reaction to disease, involving a cytokine-mediated rise in core temperature, generation of acute phase reactants, and activation of numerous physiologic, endocrinologic, and immunologic systems. The rise in temperature during fever is to be distinguished from that occurring during episodes of hyperthermia. Unlike fever, hyperthermia involves an unregulated rise in body temperature in which pyrogenic cytokines are not directly involved and against which standard antipyretics are ineffective. It represents a failure of thermoregulatory homeostasis, in which there is uncontrolled heat production, inadequate heat dissipation, or defective hypothalamic thermoregulation. Fever Body temperature elevated above the normal range. PMID:9759682 Fever Presence of elevated levels of ketone bodies in the body. HP:0003543 MSH:D007662 SNOMEDCT_US:213281004 SNOMEDCT_US:2538008 UMLS:C0022638 UMLS:C0235430 High levels of ketone bodies Hyperketosis HP:0001946 Ketone bodies are formed from acetyl-CoA in the liver by ketogenesis when the liver glycogen stores are depleted. Ketone bodies are acidic, and ketoacidosis ensues if the compensatory mechanisms are overloaded. The predominant ketones being acetoacetate, acetone, and beta-hydroxybutyrate. Ketosis Presence of elevated levels of ketone bodies in the body. PMID:28278308 High levels of ketone bodies Depletion of acid or accumulation base in the body fluids. MSH:D000471 SNOMEDCT_US:21420006 UMLS:C0002063 HP:0001948 When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Alkalosis Depletion of acid or accumulation base in the body fluids. PMID:24381489 Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). HP:0000833 Abnormal glucose tolerance UMLS:C0235401 Glucose intolerance HP:0001952 Glucose intolerance Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). PMID:29763085 Glucose intolerance Obesity located preferentially in the trunk of the body as opposed to the extremities. HP:0008885 MSH:D056128 SNOMEDCT_US:248311001 UMLS:C0311277 Centripetal obesity Truncal obesity HP:0001956 Truncal obesity Obesity located preferentially in the trunk of the body as opposed to the extremities. Truncal obesity UMLS:C3151525 Small heart Underdeveloped heart HP:0001961 Hypoplastic heart Small heart Underdeveloped heart Absence or underdevelopment of the metatarsal bones. UMLS:C1860182 Absent or hypoplastic metatarsal Absent/hypoplastic metacarpals Absent/hypoplastic metatarsals Absent/small long bone of foot Absent/underdeveloped long bone of foot Aplastic/hypoplastic metatarsals HP:0001964 Aplasia/Hypoplasia of metatarsal bones Absence or underdevelopment of the metatarsal bones. Absent/small long bone of foot Absent/underdeveloped long bone of foot An abnormal increase in the number of leukocytes in the blood. MSH:D007964 SNOMEDCT_US:111583006 UMLS:C0023518 Elevated white blood count High white blood count Increased blood leukocyte number HP:0001974 Leukocytosis An abnormal increase in the number of leukocytes in the blood. Elevated white blood count High white blood count Increased blood leukocyte number Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). UMLS:C4025731 Abnormal blood clot Abnormal blood clotting HP:0001977 Abnormal thrombosis Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). Abnormal blood clot An increased concentration of ammonia in the blood. HP:0008308 HP:0008334 MSH:D022124 SNOMEDCT_US:9360008 UMLS:C0220994 High blood ammonia levels HP:0001987 Hyperammonemia An increased concentration of ammonia in the blood. HPO_CONTRIBUTOR:gcarletti High blood ammonia levels Absence or hypoplasia of toes. UMLS:C3551148 Absent/small toe Absent/underdeveloped toe Aplastic/hypoplastic toe phalanges Absent/hypoplastic toes HP:0001991 Aplasia/Hypoplasia of toe Absence or hypoplasia of toes. Absent/small toe Absent/underdeveloped toe Absent/hypoplastic toes Excretion of non-amino organic acids in urine. UMLS:C0241775 HP:0001992 Organic aciduria Excretion of non-amino organic acids in urine. An abnormal morphology (form) of the face or its components. HP:0002004 HP:0002260 HP:0004643 HP:0004649 HP:0004652 HP:0004655 HP:0004675 HP:0005124 Deformity of face Malformation of face SNOMEDCT_US:248200007 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C0424503 UMLS:C1385263 UMLS:C4072832 UMLS:C4072833 Abnormal facial shape Abnormal morphology of the face Distinctive facies Dysmorphic facial features Dysmorphic facies Facial dysmorphism Unusual facial appearance Unusual facies Distortion of face Funny looking face HP:0001999 This term now covers many of the historical inexact descriptions such as Bird-like facies that probably should be avoided in modern genetics. This portion of the Ontology should be revised. Abnormal facial shape An abnormal morphology (form) of the face or its components. Deformity of face Malformation of face Abnormal facial shape Abnormal morphology of the face Dysmorphic facies Facial dysmorphism Unusual facial appearance Distortion of face Funny looking face UMLS:C1839783 UMLS:C4280583 UMLS:C4280584 Increased size of forehead Increased size of frontal region of face Large forehead Hyperplasia of forehead Hypertrophy of forehead HP:0002003 Large forehead Increased size of forehead Increased size of frontal region of face Large forehead Hyperplasia of forehead Hypertrophy of forehead A structural abnormality of the central nervous system. HP:0002405 HP:0002413 HP:0002481 HP:0007319 MSH:D002493 SNOMEDCT_US:23853001 UMLS:C0007682 UMLS:C4021765 Abnormality of the central nervous system Morphological abnormality of the CNS Morphological abnormality of the central nervous system Central nervous system disease HP:0002011 Morphological central nervous system abnormality A structural abnormality of the central nervous system. Morphological abnormality of the CNS An abnormality of the viscera of the abdomen. UMLS:C4021764 Abnormality of the abdominal organs Gastrointestinal tract defects HP:0002012 The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen. Abnormality of the abdominal organs An abnormality of the viscera of the abdomen. Abnormality of the abdominal organs Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day. MSH:D003967 SNOMEDCT_US:267060006 SNOMEDCT_US:62315008 UMLS:C0011991 Diarrhea Diarrhoea Watery stool HP:0002014 Diarrhea Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day. Diarrhea Diarrhoea Watery stool HP:0002014 PMID:28846339 Impaired ability to absorb one or more nutrients from the intestine. HP:0008270 UMLS:C3714745 Intestinal malabsorption Malabsorption HP:0002024 Malabsorption Impaired ability to absorb one or more nutrients from the intestine. Intestinal malabsorption Malabsorption A structural abnormality of the esophagus. SNOMEDCT_US:69771008 UMLS:C0266126 Abnormal oesophagus morphology Abnormality of esophagus structure Abnormality of oesophagus structure Anomaly of the esophagus Anomaly of the oesophagus HP:0002031 Abnormal esophagus morphology A structural abnormality of the esophagus. Abnormal oesophagus morphology Abnormality of esophagus structure Abnormality of oesophagus structure Anomaly of the oesophagus An abnormaltiy of the rectum, the final segment of the large intestine that stores solid waste until it passes through the anus. SNOMEDCT_US:86993003 UMLS:C0266210 Abnormality of the rectum Anomaly of the rectum HP:0002034 Abnormal rectum morphology An abnormaltiy of the rectum, the final segment of the large intestine that stores solid waste until it passes through the anus. Abnormality of the rectum Anomaly of the rectum Inflammation, or an inflammatory state in the large intestine. MSH:D015212 SNOMEDCT_US:24526004 SNOMEDCT_US:302168000 UMLS:C0021390 UMLS:C0578878 Inflammation of the large intestine Inflammatory bowel disease HP:0002037 Inflammation of the large intestine Inflammation of the large intestine Inflammatory bowel disease Atrophy of the cortex of the kidney. UMLS:C4025730 HP:0002048 Renal cortical atrophy Atrophy of the cortex of the kidney. Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum. HP:0002422 HP:0006890 SNOMEDCT_US:278849000 SNOMEDCT_US:418143002 SNOMEDCT_US:52522001 UMLS:C0154671 UMLS:C0235946 UMLS:C4020860 Degeneration of cerebrum Supratentorial atrophy HP:0002059 Atrophy may be progressive over time. Cerebral atrophy Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum. Degeneration of cerebrum Any structural abnormality of the telencephalon, which is also known as the cerebrum. UMLS:C4021762 Abnormality of the cerebrum Abnormality of the telencephalon Cerebral lesion HP:0002060 Abnormal cerebral morphology Any structural abnormality of the telencephalon, which is also known as the cerebrum. A kind of ataxia that affects movements of the extremities. MSH:D001259 UMLS:C0750937 Appendicular ataxia HP:0002070 Limb ataxia is generally caused by lesions of the cerebellar hemispheres and associated pathways. Limb ataxia A kind of ataxia that affects movements of the extremities. Truncal ataxia is a sign of ataxia characterized by instability of the trunk. It usually occurs during sitting. HP:0007014 MSH:D001259 SNOMEDCT_US:250067008 UMLS:C0427190 Instability or lack of coordination of central trunk muscles Trunk ataxia HP:0002078 Truncal ataxia is generally caused by midline damage to the cerebellar vermis and associated pathways. Patients with truncal ataxia may not be able to sit or stand without support. Truncal ataxia Truncal ataxia is a sign of ataxia characterized by instability of the trunk. It usually occurs during sitting. HPO_CONTRIBUTOR:UKT_rschuele Instability or lack of coordination of central trunk muscles An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. UMLS:C4018871 Respiratory abnormality HP:0002086 Abnormality of the respiratory system An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. An abnormality of the upper respiratory tract. UMLS:C4025727 Abnormality of the upper respiratory tract Upper respiratory tract issues HP:0002087 Abnormality of the upper respiratory tract An abnormality of the upper respiratory tract. Abnormality of the upper respiratory tract Upper respiratory tract issues Any structural anomaly of the lung. MSH:D008171 SNOMEDCT_US:19829001 UMLS:C0024115 UMLS:C4021760 Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusal lung shape Lung disease HP:0002088 Abnormal lung morphology Any structural anomaly of the lung. Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusal lung shape Lung disease SNOMEDCT_US:80825009 UMLS:C0265783 Hypoplastic lung Hypoplastic lungs Lung hypoplasia Poorly developed lungs Small lung Underdeveloped lung HP:0002089 Pulmonary hypoplasia Poorly developed lungs Small lung Underdeveloped lung Inflammation of any part of the lung parenchyma. MSH:D011014 SNOMEDCT_US:233604007 UMLS:C0032285 Pneumonia HP:0002090 Pneumonia Inflammation of any part of the lung parenchyma. Pneumonia Pulmonary hypertension is defined mean pulmonary artery pressure of 25mmHg or more and pulmonary capillary wedge pressure of 15mmHg or less when measured by right heart catheterisation at rest and in a supine position. HP:0006546 MSH:D006976 MSH:D065627 SNOMEDCT_US:11399002 SNOMEDCT_US:697898008 SNOMEDCT_US:70995007 UMLS:C0020542 UMLS:C2973725 UMLS:C3203102 Increased blood pressure in blood vessels of lungs Pulmonary artery hypertension Primary pulmonary hypertension HP:0002092 Pulmonary hypertension can be secondary to known cardiac, pulmonary, or hepatic disease. If no cause is identifiable, the term primary pulmonary hypertension is used. Pulmonary arterial hypertension Pulmonary hypertension is defined mean pulmonary artery pressure of 25mmHg or more and pulmonary capillary wedge pressure of 15mmHg or less when measured by right heart catheterisation at rest and in a supine position. Increased blood pressure in blood vessels of lungs Primary pulmonary hypertension HP:0006534 MSH:D011656 SNOMEDCT_US:87433001 UMLS:C0034067 Pulmonary emphysema HP:0002097 Emphysema An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. UMLS:C4025726 Abnormality of the pleura HP:0002103 Abnormal pleura morphology An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. Lack of breathing with no movement of the respiratory muscles and no exchange of air in the lungs. This term refers to a disposition to have recurrent episodes of apnea rather than to a single event. HP:0005936 HP:0005958 MSH:D001049 SNOMEDCT_US:1023001 SNOMEDCT_US:248583008 UMLS:C0003578 Absence of spontaneous respiration Apneic episodes Apnoea HP:0002104 Apnea Lack of breathing with no movement of the respiratory muscles and no exchange of air in the lungs. This term refers to a disposition to have recurrent episodes of apnea rather than to a single event. Any structural abnormality of the cerebral ventricles. UMLS:C4025724 Abnormality of the cerebral ventricles HP:0002118 Abnormal cerebral ventricle morphology Any structural abnormality of the cerebral ventricles. An increase in size of the ventricular system of the brain. HP:0002447 HP:0005691 HP:0007071 UMLS:C3278923 Cerebral ventricular dilatation Dilated cerebral ventricle Dilated cerebral ventricles Dilated ventricles Enlarged cerebral ventricles Enlarged ventricles Enlarged ventricular system Large cerebral ventricles and cisternae Ventricular dilatation HP:0002119 Ventriculomegaly An increase in size of the ventricular system of the brain. Atrophy of the cortex of the cerebrum. HP:0006823 HP:0006835 SNOMEDCT_US:278849000 UMLS:C0235946 Cerebral cortex atrophy Cortical atrophy Decrease in size of the outer layer of the brain due to loss of brain cells HP:0002120 Cortical atrophy is a finding that can be demonstrated by computer tomography or magnetic resonance imaging. Cerebral cortical atrophy Atrophy of the cortex of the cerebrum. Decrease in size of the outer layer of the brain due to loss of brain cells A structural abnormality of the spinal cord (myelon). MSH:D013118 SNOMEDCT_US:48522003 UMLS:C0037928 UMLS:C4025722 Abnormality of the spinal cord Spinal cord disease Spinal cord pathology HP:0002143 Abnormal spinal cord morphology A structural abnormality of the spinal cord (myelon). Abnormality of the spinal cord Spinal cord disease An abnormally decreased phosphate concentration in the blood. MSH:D017674 SNOMEDCT_US:4996001 UMLS:C0085682 Hypophosphataemia Low blood phosphate level HP:0002148 Hypophosphatemia An abnormally decreased phosphate concentration in the blood. HPO_CONTRIBUTOR:gcarletti Low blood phosphate level MSH:D053565 SNOMEDCT_US:71938000 UMLS:C0020438 Elevated urine calcium levels Hypercalcinuria HP:0002150 Hypercalciuria Elevated urine calcium levels An increased concentration of proteins in the blood. SNOMEDCT_US:37064009 UMLS:C0267988 HP:0002152 Hyperproteinemia An increased concentration of proteins in the blood. HPO_CONTRIBUTOR:gcarletti An abnormally increased potassium concentration in the blood. MSH:D006947 SNOMEDCT_US:14140009 SNOMEDCT_US:166689004 SNOMEDCT_US:238142003 UMLS:C0020461 Elevated serum potassium levels HP:0002153 Hyperkalemia An abnormally increased potassium concentration in the blood. Elevated serum potassium levels An elevated concentration of glycine in the blood. SNOMEDCT_US:64654004 UMLS:C0268559 Elevated blood glycine levels Hyperglycinaemia HP:0002154 Normal blood glycine levels are around 200-250 micromole per liter. Hyperglycinemia An elevated concentration of glycine in the blood. HPO_CONTRIBUTOR:gcarletti PMID:16902722 PMID:4696900 Elevated blood glycine levels An abnormal increase in the level of triglycerides in the blood. HP:0003082 HP:0008174 HP:0008332 UMLS:C1522137 Increased circulating Tg levels Increased plasma Tg levels Increased plasma triglycerides Increased serum triglycerides Increased triglycerides HP:0002155 Hypertriglyceridemia An abnormal increase in the level of triglycerides in the blood. Increased circulating Tg levels Increased plasma Tg levels Increased plasma triglycerides Increased serum triglycerides Increased triglycerides An increased concentration of nitrogen compounds in the blood. MSH:D053099 SNOMEDCT_US:445009001 UMLS:C0242528 Azotaemia HP:0002157 Abnormal levels of nitrogen-containing compounds, such as urea and creatinine. Azotemia An increased concentration of nitrogen compounds in the blood. HPO_CONTRIBUTOR:gcarletti An increased concentration of lysine in the blood. MSH:D020167 SNOMEDCT_US:58558003 UMLS:C0268553 Elevated blood lysine HP:0002161 Normal blood lysine levels are around 180-200 micromole per liter. Hyperlysinemia An increased concentration of lysine in the blood. HPO_CONTRIBUTOR:gcarletti PMID:4696900 Elevated blood lysine Progressive loss of neural cells and tissue. MSH:D009410 MSH:D019636 UMLS:C0027746 UMLS:C0524851 UMLS:C4020854 Ongoing loss of nerve cells Neuro-degenerative disease Neurodegenerative disease Progressive neurodegenerative disorder HP:0002180 Neurodegeneration Progressive loss of neural cells and tissue. Ongoing loss of nerve cells An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. MSH:D011655 SNOMEDCT_US:59282003 UMLS:C0034065 Blood clot in artery of lung HP:0002204 Pulmonary embolism Blood clot in artery of lung Excessive, increased hair growth located in the facial region. MSH:C565029 UMLS:C1851400 Increased facial hair growth HP:0002219 Facial hypertrichosis Increased facial hair growth Absence of axillary hair. HP:0004549 UMLS:C1859392 HP:0002221 Absent axillary hair Absence of axillary hair. Hemorrhage affecting the gastrointestinal tract. MSH:D006471 SNOMEDCT_US:74474003 UMLS:C0017181 GI haemorrhage GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage HP:0002239 Gastrointestinal hemorrhage Hemorrhage affecting the gastrointestinal tract. GI haemorrhage GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage Abnormally increased size of the liver. HP:0001393 HP:0001398 MSH:D006529 SNOMEDCT_US:80515008 UMLS:C0019209 Enlarged liver HP:0002240 Hepatomegaly Abnormally increased size of the liver. Enlarged liver An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. HP:0002628 MSH:D007410 SNOMEDCT_US:85919009 UMLS:C0021831 Abnormality of the intestine Enteropathy HP:0002242 Abnormal intestine morphology An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. Abnormality of the intestine A structural abnormality of the small intestine. UMLS:C4025717 Abnormality of the small intestine HP:0002244 Abnormal small intestine morphology A structural abnormality of the small intestine. Meckel's diverticulum is a congenital diverticulum located in the distal ileum. MEDDRA:10027055 MSH:D008467 SNOMEDCT_US:127962001 SNOMEDCT_US:37373007 UMLS:C0025037 HP:0002245 Meckel diverticulum Meckel's diverticulum is a congenital diverticulum located in the distal ileum. MEDDRA:10027055 Meckel's diverticulum An abnormality of the duodenum, i.e., the first section of the small intestine. UMLS:C4025716 Abnormality of the duodenum HP:0002246 Abnormal duodenum morphology An abnormality of the duodenum, i.e., the first section of the small intestine. The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. MSH:D008551 SNOMEDCT_US:249627005 SNOMEDCT_US:267055007 SNOMEDCT_US:269899009 SNOMEDCT_US:2901004 SNOMEDCT_US:35064005 UMLS:C0025222 UMLS:C0474585 Black faeces Black feces HP:0002249 Melena The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. Black faeces Black feces Any abnormality of the large intestine. UMLS:C4025715 Abnormality of the large intestine HP:0002250 The large intestine comprises the cecum and colon. Abnormal large intestine morphology Any abnormality of the large intestine. Abnormality of the large intestine An abnormality of the autonomic nervous system. UMLS:C4025714 HP:0002270 The autonomic nervous system is the part of the peripheral nervous system that controls visceral functions such as heart rate and digestion and functions largely below the level of consciousness. Abnormality of the autonomic nervous system An abnormality of the autonomic nervous system. HP:0004548 SNOMEDCT_US:297991008 UMLS:C0574763 Absent hair HP:0002298 Absent hair Absent hair Inability to initiate changes in activity or movement and to perform ordinary volitional movements rapidly and easily. SNOMEDCT_US:33994004 UMLS:C0085623 HP:0002304 Akinesia is a typical extrapyramidal abnormality. Akinesia Inability to initiate changes in activity or movement and to perform ordinary volitional movements rapidly and easily. An anomaly of the brainstem. UMLS:C1850601 Abnormal shape of brainstem Abnormality of brainstem morphology Abnormality of the brainstem HP:0002363 Abnormal brainstem morphology An anomaly of the brainstem. Abnormal shape of brainstem Underdevelopment of the brainstem. UMLS:C1842688 Brainstem hypoplasia Hypoplastic brain stem Hypoplastic brainstem Small brainstem Underdeveloped brainstem HP:0002365 This finding can be demonstrated by magnetic resonance imaging. Hypoplasia of the brainstem Underdevelopment of the brainstem. Small brainstem Underdeveloped brainstem UMLS:C4025710 Diminished movement HP:0002374 Diminished movement Diminished movement Abnormally diminished motor activity. In contrast to paralysis, hypokinesia is not characterized by a lack of motor strength, but rather by a poverty of movement. The typical habitual movements (e.g., folding the arms, crossing the legs) are reduced in frequency. HP:0002603 HP:0006795 MSH:D018476 SNOMEDCT_US:255385008 SNOMEDCT_US:43994002 UMLS:C0086439 Decreased muscle movement Decreased spontaneous movement Decreased spontaneous movements HP:0002375 Hypokinesia Abnormally diminished motor activity. In contrast to paralysis, hypokinesia is not characterized by a lack of motor strength, but rather by a poverty of movement. The typical habitual movements (e.g., folding the arms, crossing the legs) are reduced in frequency. Decreased muscle movement Decreased spontaneous movement Decreased spontaneous movements HP:0007245 HP:0007288 UMLS:C1836696 Brisk lower extremity reflexes Hyperreflexia in lower limbs Hyperreflexia in the lower limbs Increased deep tendon reflexes in the lower limbs Leg hyperreflexia Overactive lower leg reflex HP:0002395 Lower limb hyperreflexia Overactive lower leg reflex HP:0007136 HP:0008312 UMLS:C1843505 Anterior horn cell loss Degeneration of alpha-motor neurons in anterior horn cells of the spinal cord Degeneration of spinal cord anterior horn cells Loss of spinal cord anterior horn cells Progressive loss of anterior horn cells Spinal cord anterior horn cell degeneration HP:0002398 Degeneration of anterior horn cells An abnormality of the midbrain, which has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct. UMLS:C4021755 Abnormal shape of midbrain Abnormality of midbrain morphology Abnormality of the mesencephalon Abnormality of the midbrain HP:0002418 Abnormal midbrain morphology An abnormality of the midbrain, which has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct. Abnormal shape of midbrain Abnormality of the midbrain UMLS:C4025708 HP:0002438 Cerebellar malformation Any structural anomaly that affects the motor neuron. UMLS:C4025707 Abnormal shape of motor neuron HP:0002450 Abnormal motor neuron morphology Abnormal shape of motor neuron Reduced size of the cerebral cortex. HP:0006791 HP:0007151 UMLS:C1837503 Decreased volume of cerebral cortex HP:0002472 Small cerebral cortex Reduced size of the cerebral cortex. The presence of calcium deposition within brain structures. HP:0002502 HP:0005806 HP:0006848 SNOMEDCT_US:17944005 UMLS:C0270685 Abnormal deposits of calcium in the brain Brain calcification Intracerebral calcifications Intracranial calcification Intracranial calcifications HP:0002514 This finding can be demonstrated upon cerebral computer tomography, magnetic resonance imaging, or potentially by standard radiography of the skull. Cerebral calcification The presence of calcium deposition within brain structures. Abnormal deposits of calcium in the brain Inability to elicit tendon reflexes in the lower limbs. UMLS:C1856694 Absent lower limb tendon reflexes Areflexia in lower limbs Areflexia of the lower limbs Areflexia, lower limbs HP:0002522 Areflexia of lower limbs Inability to elicit tendon reflexes in the lower limbs. HP:0002400 UMLS:C1850496 Loss of brain cells Neuronal loss Neuronal loss in CNS HP:0002529 This finding can be demonstrated by neuropathology. Neuronal loss in central nervous system Loss of brain cells Neuronal loss in CNS Any structural abnormality of the cerebral cortex. UMLS:C4025701 Abnormality of the cerebral cortex HP:0002538 The cerebral cortex constitutes more than half the volume of the human brain and is presumed to be responsible for the neuronal computations underlying complex phenomena, such as perception, thought, language, attention, episodic memory and voluntary movement. Abnormal cerebral cortex morphology Any structural abnormality of the cerebral cortex. PMID:31373394 The presence of developmental dysplasia of the cerebral cortex. HP:0007139 MSH:D054220 SNOMEDCT_US:253153000 UMLS:C0431380 Neocortical dysplasia HP:0002539 Cortical dysplasia The presence of developmental dysplasia of the cerebral cortex. Absence of facial hair. UMLS:C1848192 Absent facial hair HP:0002550 Absent facial hair Absence of facial hair. Absent facial hair Developmental dysplasia of the hair. HP:0004515 UMLS:C4020850 UMLS:C4025700 Generalised trichodysplasia Generalized trichodysplasia HP:0002552 Trichodysplasia Developmental dysplasia of the hair. Generalised trichodysplasia Underdevelopment of the nipple. HP:0002560 HP:0003188 HP:0006652 SNOMEDCT_US:268290005 UMLS:C0432355 Nipple hypoplasia Small nipples HP:0002557 Hypoplastic nipples Underdevelopment of the nipple. Small nipples Presence of more than two nipples. HP:0002559 Fyler:4234 MSH:C562557 SNOMEDCT_US:50956007 UMLS:C0266011 Accessory nipple Increased nipple number accessory mamilla Accessory nipples Supernumerary nipples accessory mamillas HP:0002558 Supernumerary nipple Presence of more than two nipples. Accessory nipple Increased nipple number Accessory nipples Congenital failure to develop, and absence of, the nipple. SNOMEDCT_US:248820000 UMLS:C0425795 Absent nipple Absent nipples Athelia HP:0002561 This finding can be unilateral or bilateral. Absent nipple Absent nipple Absent nipples Placement of the nipples at a lower than normal location. UMLS:C1836933 Low-set nipples HP:0002562 Low-set nipples Placement of the nipples at a lower than normal location. Low-set nipples Greater than normal amounts of fat in the feces. This is a result of malabsorption of lipids in the small intestine and results in frothy foul-smelling fecal matter that floats. MSH:D045602 SNOMEDCT_US:27868004 SNOMEDCT_US:66187002 UMLS:C0038238 Fat in faeces Fat in feces Fatty stool Greasy stools HP:0002570 Steatorrhea Greater than normal amounts of fat in the feces. This is a result of malabsorption of lipids in the small intestine and results in frothy foul-smelling fecal matter that floats. Fat in faeces Fat in feces Greasy stools An abnormality of the stomach. UMLS:C4025699 Abnormality of the stomach HP:0002577 The stomach is the hollow, muscular organ of the gastrointestinal tract between the esophagus and the small intestine. Abnormal stomach morphology An abnormality of the stomach. Abnormal intestinal contractions, such as spasms and intestinal paralysis, related to the loss of the ability of the gut to coordinate muscular activity because of endogenous or exogenous causes. UMLS:C1836923 GI dysmotility HP:0002579 Gastrointestinal dysmotility Abnormal intestinal contractions, such as spasms and intestinal paralysis, related to the loss of the ability of the gut to coordinate muscular activity because of endogenous or exogenous causes. GI dysmotility Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. MSH:D003092 SNOMEDCT_US:64226004 UMLS:C0009319 HP:0002583 Colitis Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. An abnormality of the peritoneum. UMLS:C4025698 Abnormality of the peritoneum HP:0002585 The peritoneum is the thin tissue that lines the inner wall of the abdomen and covers most of the abdominal organs. Abnormal peritoneum morphology An abnormality of the peritoneum. Inflammation of the peritoneum. HP:0100591 MSH:D010538 SNOMEDCT_US:48661000 UMLS:C0031154 Inflammation of the peritoneum HP:0002586 Peritonitis Inflammation of the peritoneum. Hypoplasia of the pancreas. HP:0005221 SNOMEDCT_US:68591005 UMLS:C0266267 Hypoplastic pancreas Underdeveloped pancreas HP:0002594 Hypoplasia is defined in MPATH as resulting in a small organ or structure owing to failure to develop to normal size. Pancreatic hypoplasia Hypoplasia of the pancreas. Underdeveloped pancreas An abnormality of the vasculature. UMLS:C0241657 Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities HP:0002597 Abnormality of the vasculature An abnormality of the vasculature. Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities Reduced intensity of muscle tendon reflexes in the lower limbs. Reflexes are elicited by stretching the tendon of a muscle, e.g., by tapping. HP:0006861 UMLS:C1834696 Hyporeflexia in lower limbs Hyporeflexia of the lower limbs Hyporeflexia, lower limbs Hyporeflexia/areflexia in lower limbs HP:0002600 Reflexes are sensorimotor arcs that require some type of sensory (afferent) signal, and some motor response. While the simplest of reflexes involve direct synapse between the sensory fiber and the motor neuron (monosynaptic), many reflexes have several neurons interposed (polysynaptic reflexes). Hyporeflexia can result from a defect anywhere in this chain. Hyporeflexia of lower limbs Reduced intensity of muscle tendon reflexes in the lower limbs. Reflexes are elicited by stretching the tendon of a muscle, e.g., by tapping. Low Blood Pressure, vascular hypotension. HP:0005127 HP:0006701 MSH:D007022 SNOMEDCT_US:45007003 UMLS:C0020649 Arterial hypotension Low blood pressure HP:0002615 Hypotension Low Blood Pressure, vascular hypotension. Low blood pressure Abnormal outpouching or sac-like dilatation in the wall of an atery, vein or the heart. Fyler:2399 MSH:D000783 SNOMEDCT_US:432119003 SNOMEDCT_US:85659009 UMLS:C0002940 UMLS:C4020848 Aneurysmal dilatation Wider than typical opening or gap Aneurysm Aneurysms Aneurysmal disease HP:0002617 Aneurysm is considered a severe form of dilatation. Vascular dilatation Abnormal outpouching or sac-like dilatation in the wall of an atery, vein or the heart. PMID:30225143 Aneurysmal dilatation Wider than typical opening or gap Aneurysm Aneurysms Aneurysmal disease An anomaly of vein. UMLS:C0241665 Abnormal vein Venous abnormality HP:0002624 Abnormal venous morphology An anomaly of vein. Abnormal vein Abnormality of the absorption of fat from the gastrointestinal tract. SNOMEDCT_US:197494007 UMLS:C0554103 HP:0002630 Fat malabsorption Abnormality of the absorption of fat from the gastrointestinal tract. An abnormality of the bony pelvic girdle, which is a ring of bones connecting the vertebral column to the femurs. UMLS:C4020847 Abnormal shape of pelvic girdle bone Abnormality of pelvic girdle bone morphology Abnormality of the pelvic girdle HP:0002644 Abnormal pelvic girdle bone morphology An abnormality of the bony pelvic girdle, which is a ring of bones connecting the vertebral column to the femurs. Abnormal shape of pelvic girdle bone A general term describing features characterized by abnormal development of bones and connective tissues. HP:0005685 Abnormal skeletal development MSH:D010009 SNOMEDCT_US:105985007 SNOMEDCT_US:240190009 UMLS:C0029422 UMLS:C4280567 HP:0002652 The word skeletal dysplasia is most often used to describe a group of over 380 inherited conditions that involve abnormal development of bones and connective tissues. However, the word can also be used to describe the presence of congenital defects of bones or connective tissues that are found in one or more of the diseases, especially on prenatal ultrasound, i.e., a situation in which it is often not yet possible to make an exact etiological diagnosis. This is the sense of the phrase we use in the HPO. It is, however, preferable to annotate the observed abnormalities. Skeletal dysplasia A general term describing features characterized by abnormal development of bones and connective tissues. Abnormal skeletal development MSH:D010009 SNOMEDCT_US:59708000 UMLS:C0026760 HP:0002654 Multiple epiphyseal dysplasia Abnormal development of end part of bone SNOMEDCT_US:254080004 UMLS:C0392476 UMLS:C4280566 Abnormal development of the ends of long bones in arms and legs HP:0002656 Epiphyseal dysplasia Abnormal development of end part of bone Abnormal development of the ends of long bones in arms and legs HP:0005862 UMLS:C1865200 UMLS:C4280565 Delayed epiphyseal maturation Delayed opacification of the epiphyses Epiphyseal ossification delay Delayed maturation of end part of long bone HP:0002663 Delayed epiphyseal ossification Delayed maturation of end part of long bone An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor). HP:0003008 HP:0006741 Abnormal tissue mass MSH:D009369 NCIT:C3262 SNOMEDCT_US:108369006 SNOMEDCT_US:363346000 UMLS:C0006826 UMLS:C0027651 Neoplasia Oncological abnormality Tumor Tumour Cancer Oncology HP:0002664 The World Health Organization (WHO) classifies neoplasms into four main groups: (i) benign neoplasm, (ii) in situ neoplasm, (iii) malignant neoplasm, and (iv) neoplasm of uncertain or unknown behavior. A malignant neoplasm is also known as cancer. Neoplasm An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor). Abnormal tissue mass Cancer Oncology An abnormal narrowing of the foramen magnum. HP:0005468 SNOMEDCT_US:444879009 UMLS:C1535953 UMLS:C1861217 UMLS:C4072838 Foramen magnum stenosis Little foramen magnum Narrow foramen magnum Hypoplasia of foramen magnum Stenosis of foramen magnum HP:0002677 The foramen magnum is the aperture through which the medulla oblongata enters and exits the skull. Stenosis of the foramen magnum can represent a risk for compression to the spinal cord. Small foramen magnum An abnormal narrowing of the foramen magnum. Little foramen magnum Narrow foramen magnum Hypoplasia of foramen magnum Stenosis of foramen magnum Abnormality of the morphology (structure) of the calvaria (skullcap), that is, of that part of the skull that is made up of the superior portions of the frontal bone, occipital bone, and parietal bones and covers the cranial cavity that contains the brain. HP:0002648 Abnormality of cranium UMLS:C4025691 UMLS:C4280561 Abnormality of calvarium Abnormality of cranial vault Abnormality of the calvaria Abnormality of the shape of calvarium Abnormality of the skull cap Abnormality of the skullcap HP:0002683 The calvaria, or skull cap, is the upper part of the skull (cranium) and comprises the frontal, occipital and right and left parietal bones. Occasionally, calvaria is misspelled as 'calvarium' in the medical literature. Abnormal calvaria morphology Abnormality of the morphology (structure) of the calvaria (skullcap), that is, of that part of the skull that is made up of the superior portions of the frontal bone, occipital bone, and parietal bones and covers the cranial cavity that contains the brain. Abnormality of cranium Abnormality of calvarium Abnormality of cranial vault Abnormality of the skull cap Abnormality of the skullcap Hypoplasia of facial skeleton Small facial bones Small facial skeleton Underdevelopment of facial bones Underdevelopment of facial skeleton UMLS:C1846438 UMLS:C4229090 UMLS:C4280268 UMLS:C4280557 UMLS:C4280558 Decreased size of facial bones Decreased size of facial skeleton Flattening of facial bones Flattening of facial skeleton Hypotrophic facial bones Hypotrophic facial skeleton HP:0002692 Hypoplastic facial bones Hypoplasia of facial skeleton Small facial bones Small facial skeleton Underdevelopment of facial bones Underdevelopment of facial skeleton Decreased size of facial bones Decreased size of facial skeleton Flattening of facial bones Flattening of facial skeleton Hypotrophic facial bones Hypotrophic facial skeleton An abnormality of the base of the skull, which forms the floor of the cranial cavity and separates the brain from other facial structures. The skull base is made up of five bones: the ethmoid, sphenoid, occipital, paired frontal, and paired parietal bones, and is subdivided into 3 regions: the anterior, middle, and posterior cranial fossae. The petro-occipital fissure subdivides the middle cranial fossa into 1 central component and 2 lateral components. UMLS:C4025688 Abnormality of cranial base Abnormality of the skull base HP:0002693 Abnormal skull base morphology An abnormality of the base of the skull, which forms the floor of the cranial cavity and separates the brain from other facial structures. The skull base is made up of five bones: the ethmoid, sphenoid, occipital, paired frontal, and paired parietal bones, and is subdivided into 3 regions: the anterior, middle, and posterior cranial fossae. The petro-occipital fissure subdivides the middle cranial fossa into 1 central component and 2 lateral components. Abnormality of cranial base Abnormality of the skull base Increased bone density of the skull base without significant changes in bony contour. HP:0005757 UMLS:C1851714 UMLS:C4072847 UMLS:C4072848 Dense bone of skull base Hyperossification of skull base Hyperostosis of skull base Marked sclerosis of skull base Sclerosis of cranial base Sclerosis of the skull base Sclerotic skull base HyperCalcification of skull base HyperMineralization of skull base HP:0002694 Sclerosis of skull base Increased bone density of the skull base without significant changes in bony contour. Dense bone of skull base Hyperossification of skull base Hyperostosis of skull base Sclerosis of cranial base HyperCalcification of skull base HyperMineralization of skull base Any abnormality of the foramen magnum. UMLS:C4025687 Abnormality of the foramen magnum HP:0002699 The foramen magnum is the aperture through which the medulla oblongata enters and exits the skull. Abnormal foramen magnum morphology Any abnormality of the foramen magnum. An abnormal increase in the size of the foramen magnum. UMLS:C1844508 UMLS:C4073291 UMLS:C4280554 UMLS:C4280555 Big foramen magnum Dilation of foramen magnum Enlarged foramen magnum Wide foramen magnum Increased circumference of foramen magnum Increased diameter of foramen magnum HP:0002700 Large foramen magnum An abnormal increase in the size of the foramen magnum. Big foramen magnum Dilation of foramen magnum Wide foramen magnum Increased circumference of foramen magnum Increased diameter of foramen magnum An abnormality of the process of ossification of the skull. 2008-02-28T11:53:00Z Abnormality of skull bone formation UMLS:C4025686 UMLS:C4280550 UMLS:C4280551 UMLS:C4280552 UMLS:C4280553 Abnormality of ossification of calvarium Abnormality of ossification of cranium Abnormality of bone calcification of calvarium Abnormality of bone calcification of cranium Abnormality of bone calcification of skull Abnormality of bone formation of calvarium Abnormality of bone formation of cranium Abnormality of bone mineralization of calvarium Abnormality of bone mineralization of cranium Abnormality of bone mineralization of skull HP:0002703 The bones of the skull derive directly from mesenchyme cells by intramembranous ossification. Abnormality of skull ossification An abnormality of the process of ossification of the skull. Abnormality of skull bone formation Abnormality of ossification of calvarium Abnormality of ossification of cranium Abnormality of bone calcification of calvarium Abnormality of bone calcification of cranium Abnormality of bone calcification of skull Abnormality of bone formation of calvarium Abnormality of bone formation of cranium Abnormality of bone mineralization of calvarium Abnormality of bone mineralization of cranium Abnormality of bone mineralization of skull An abnormality of the immune system. HP:0003257 HP:0003346 HP:0010986 UMLS:C4021753 Abnormality of the immune system Immunological abnormality HP:0002715 The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages. Abnormality of the immune system An abnormality of the immune system. Abnormality of the immune system Immunological abnormality 2008-02-25T10:41:00Z UMLS:C4025685 HP:0002717 Cortisol is the main member of the glucocorticoid family in humans and together with aldosterone is one of the main secretions of the adrenal cortex. Adrenal overactivity Increased susceptibility to infections. HP:0002957 HP:0002964 HP:0005405 UMLS:C0239998 Frequent infections Frequent, severe infections Increased frequency of infection Predisposition to infections Recurrent infections Susceptibility to infection infections, recurrent HP:0002719 Recurrent infections Increased susceptibility to infections. Frequent infections Frequent, severe infections Increased frequency of infection Predisposition to infections Recurrent infections Susceptibility to infection infections, recurrent Failure of the immune system to protect the body adequately from infection, due to the absence or insufficiency of some component process or substance. HP:0005362 HP:0005371 MSH:D007153 SNOMEDCT_US:234532001 UMLS:C0021051 Decreased immune function Immune deficiency HP:0002721 Immunodeficiency Failure of the immune system to protect the body adequately from infection, due to the absence or insufficiency of some component process or substance. PMID:20042227 Decreased immune function Underdevelopment of the lymph nodes. UMLS:C1865377 UMLS:C4025683 Small lymph nodes HP:0002732 Lymph node hypoplasia Underdevelopment of the lymph nodes. Small lymph nodes A structural lymph node abnormality. HP:0008149 UMLS:C0149727 Abnormal lymph node histology Abnormality of the lymph nodes HP:0002733 Abnormal lymph node morphology A structural lymph node abnormality. Abnormal lymph node histology Abnormality of the lymph nodes Osteomyelitis is an inflammatory process accompanied by bone destruction and caused by an infecting microorganism. HP:0002755 HP:0005901 MSH:D010019 SNOMEDCT_US:111253001 SNOMEDCT_US:60168000 UMLS:C0029443 UMLS:C2242472 Bone infection HP:0002754 Osteomyelitis can be acute or chronic and can be caused by a variety of microbial agents. Osteomyelitis Osteomyelitis is an inflammatory process accompanied by bone destruction and caused by an infecting microorganism. PMID:15276398 Bone infection Any morphological abnormality of cartilage. HP:0410007 UMLS:C4025680 Abnormal shape of cartilage Abnormality of cartilage morphology HP:0002763 Abnormal cartilage morphology Any morphological abnormality of cartilage. Abnormal shape of cartilage UMLS:C3277114 Relatively short spine HP:0002766 Relatively short spine Relatively short spine A structural anomaly of the trachea. MSH:D014133 SNOMEDCT_US:47125007 UMLS:C0040580 UMLS:C4025678 Abnormal trachea morphology Abnormality of the trachea Tracheal disease HP:0002778 Abnormal tracheal morphology A structural anomaly of the trachea. Calcification (abnormal deposits of calcium) in the tracheal tissues. SNOMEDCT_US:81089005 UMLS:C0264324 Calcification of the trachea Tracheal calcifications Tracheal ectopic calcification HP:0002787 Tracheal calcification Calcification (abnormal deposits of calcium) in the tracheal tissues. PMID:18663210 Tracheal calcifications An anomaly of the rhythm or depth of breathing. UMLS:C1837388 Abnormal pattern of respiration Abnormal respiratory patterns Unusual breathing patterns HP:0002793 Abnormal pattern of respiration An anomaly of the rhythm or depth of breathing. Abnormal pattern of respiration Abnormal respiratory patterns Unusual breathing patterns HP:0005952 Fyler:4200 UMLS:C4025677 Abnormal respiration Functional respiratory abnormality Impaired pulmonary function Respiratory problem HP:0002795 Abnormal respiratory system physiology Abnormal respiration Functional respiratory abnormality Respiratory problem Any abnormality of bones of the arms or legs. UMLS:C4082761 Abnormal shape of limb bone Abnormality of limb bone morphology Arm and/or leg bone differences Limb abnormality HP:0002813 Abnormal limb bone morphology Any abnormality of bones of the arms or legs. Abnormal shape of limb bone Arm and/or leg bone differences Limb abnormality An abnormality of the leg. SNOMEDCT_US:449715001 UMLS:C1096086 Abnormality of the leg Abnormality of the lower limb Lower limb deformities HP:0002814 Abnormality of the lower limb An abnormality of the leg. Abnormality of the lower limb Lower limb deformities An abnormality of the knee joint or surrounding structures. UMLS:C4025676 Abnormality of the knee HP:0002815 Abnormality of the knee An abnormality of the knee joint or surrounding structures. Abnormality of the knee An abnormality of the arm. HP:0003838 UMLS:C4020900 Abnormality of the arm Abnormality of the upper limb HP:0002817 Abnormality of the upper limb An abnormality of the arm. Abnormality of the upper limb Any anomaly of the structure of the femur. HP:0001439 UMLS:C4021750 Abnormality of femur morphology Abnormality of the femora Abnormality of the thighbone HP:0002823 The femur (plural: femora) is the thigh bone. Abnormal femur morphology Any anomaly of the structure of the femur. Abnormality of the thighbone UMLS:C3277116 Long tailbone HP:0002831 Long coccyx Long tailbone Inflammation of a lymph node. MSH:D008199 SNOMEDCT_US:19471005 UMLS:C0024205 Inflammation of the lymph nodes HP:0002840 Lymphadenitis Inflammation of a lymph node. Inflammation of the lymph nodes An abnormality of T cells. HP:0002734 HP:0030332 UMLS:C1855752 Abnormal T cells Abnormality of T cells Cellular immune defect Defective cellular immunity HP:0002843 T-cells are lymphocytes whose principle function in the adaptive immune system is to mediate cell-mediated immunity. Abnormal T cell morphology An abnormality of T cells. Abnormal T cells A structural abnormality of B cells. UMLS:C4021748 Abnormal B cells Abnormality of B cells HP:0002846 B cells are bursal or bone marrow-derived lymphocytes whose principle function in the adaptive immune system is to make antibodies against antigens. A simple definition of B lymphocytes is a population of cells that express clonally diverse cell surface immunoglobulin (Ig) receptors recognizing specific antigenic epitopes. Over 10 B cell-specific cell surface molecules have been identified by monoclonal antibodies, including CD19, which is considered a pan-B cell and possibly follicular dendritic cell marker, and CD20, which is considered to be a marker for mature B cells. Abnormal B cell morphology A structural abnormality of B cells. PMID:18725575 Abnormal B cells An abnormality of the ilium, the largest and uppermost bone of the pelvis. UMLS:C4021746 Abnormality of the ilium Iliac abnormalities HP:0002867 Abnormal ilium morphology An abnormality of the ilium, the largest and uppermost bone of the pelvis. A kind of neoplasm of the liver that originates from immature liver precursor cells and macroscopically is composed of tissue resembling fetal or mature liver cells or bile ducts. MSH:D018197 NCIT:C3728 SNOMEDCT_US:109843000 SNOMEDCT_US:45024009 UMLS:C0206624 HP:0002884 Hepatoblastoma occurs nearly exclusively in infants and children. Hepatoblastoma A kind of neoplasm of the liver that originates from immature liver precursor cells and macroscopically is composed of tissue resembling fetal or mature liver cells or bile ducts. eMedicine:986802 A tumor (abnormal growth of tissue) of the liver. MSH:D008113 NCIT:C3262 SNOMEDCT_US:126851005 SNOMEDCT_US:93870000 UMLS:C0023903 UMLS:C0345904 Liver cancer Liver tumor Liver tumour HP:0002896 Neoplasm of the liver A tumor (abnormal growth of tissue) of the liver. Liver cancer Liver tumor Liver tumour MSH:D009373 UMLS:C0027654 Embryonal neoplasia Embryonal tumors Embryonal tumours HP:0002898 Embryonal neoplasm Embryonal tumours An abnormally decreased potassium concentration in the blood. MSH:D007008 SNOMEDCT_US:166690008 SNOMEDCT_US:43339004 UMLS:C0020621 Low blood potassium levels HP:0002900 Hypokalemia An abnormally decreased potassium concentration in the blood. Low blood potassium levels An abnormally decreased calcium concentration in the blood. MSH:D006996 SNOMEDCT_US:5291005 UMLS:C0020598 Hypocalcaemia Low blood calcium levels HP:0002901 Hypocalcemia An abnormally decreased calcium concentration in the blood. Low blood calcium levels An abnormally decreased sodium concentration in the blood. MSH:D007010 SNOMEDCT_US:89627008 UMLS:C0020625 Low blood sodium levels HP:0002902 Hyponatremia An abnormally decreased sodium concentration in the blood. Low blood sodium levels An increased amount of bilirubin in the blood. SNOMEDCT_US:26165005 UMLS:C0311468 High blood bilirubin levels HP:0002904 Hyperbilirubinemia An increased amount of bilirubin in the blood. High blood bilirubin levels An abnormally increased phosphate concentration in the blood. MSH:D054559 SNOMEDCT_US:20165001 UMLS:C0085681 UMLS:C0553706 High blood phosphate levels HP:0002905 Hyperphosphatemia An abnormally increased phosphate concentration in the blood. HPO_CONTRIBUTOR:gcarletti High blood phosphate levels An abnormality of chromosome segregation. UMLS:C4025670 HP:0002916 Abnormality of chromosome segregation An abnormality of chromosome segregation. An abnormally decreased magnesium concentration in the blood. HP:0003284 SNOMEDCT_US:190855004 UMLS:C0151723 Low blood Mg levels Low blood magnesium levels HP:0002917 Hypomagnesemia An abnormally decreased magnesium concentration in the blood. Low blood Mg levels Low blood magnesium levels An abnormally increased magnesium concentration in the blood. SNOMEDCT_US:66978005 UMLS:C0151714 High blood Mg levels High blood magnesium levels HP:0002918 Hypermagnesemia An abnormally increased magnesium concentration in the blood. High blood Mg levels High blood magnesium levels High levels of ketone bodies (acetoacetic acid, beta-hydroxybutyric acid, and acetone) in the urine. Ketone bodies are insignificant in the blood and urine of normal individuals in the postprandial or overnight-fasted state. MSH:D007662 SNOMEDCT_US:274783007 SNOMEDCT_US:36815008 UMLS:C0162275 Ketonaciduria Ketone bodies in urine Acetonuria Ketoaciduria HP:0002919 Acetone is the main component of the ketone bodies. Ketonuria High levels of ketone bodies (acetoacetic acid, beta-hydroxybutyric acid, and acetone) in the urine. Ketone bodies are insignificant in the blood and urine of normal individuals in the postprandial or overnight-fasted state. PMID:11344564 Ketone bodies in urine Ketoaciduria An abnormality of the cerebrospinal fluid (CSF). UMLS:C0151583 Abnormal CSF findings Abnormality of the CSF Abnormality of the cerebrospinal fluid HP:0002921 The cerebrospinal fluid (CSF) is secreted by the choroid plexus, and flows uninterrupted throughout the central nervous system (the central cerebrospinal canal of the spinal cord and through the four interconnected cerebral ventricles in the brain). Abnormal cerebrospinal fluid morphology An abnormality of the cerebrospinal fluid (CSF). Abnormal CSF findings Abnormality of the CSF Increased concentration of protein in the cerebrospinal fluid. UMLS:C1806780 Cerebrospinal fluid protein increased Cerebrospinal fluid with increased protein Elevated cerebrospinal fluid protein Elevated csf protein Hyperproteinorrhachia Increased CSF protein Increased protein in csf Spinal fluid protein elevated HP:0002922 Increased CSF protein concentration Increased concentration of protein in the cerebrospinal fluid. HPO_CONTRIBUTOR:KI_phemming PMID:29114301 An abnormal functionality of the thyroid gland. UMLS:C0857576 Abnormal thyroid function HP:0002926 Abnormality of thyroid physiology An abnormal functionality of the thyroid gland. Abnormal thyroid function Decreased height of the intervertebral disk. SNOMEDCT_US:11301007 UMLS:C0263870 Narrow intervertebral disc spaces Narrow intervertebral spaces HP:0002945 A decrease in the height of the intervertebral disks is usually observed as a narrowing of the space between the vertebrae on X-ray examination. Intervertebral space narrowing Decreased height of the intervertebral disk. SNOMEDCT_US:87294007 UMLS:C0265681 HP:0002946 Supernumerary vertebrae An abnormality of the lower arm. UMLS:C4025666 Abnormality of the forearm HP:0002973 Abnormal forearm morphology An abnormality of the lower arm. Abnormality of the forearm Absence or underdevelopment of tissue in the central nervous system. 2008-03-31T05:13:00Z HP:0001323 UMLS:C4025665 Absent/underdeveloped central nervous system tissue Aplasia/Hypoplasia involving the CNS HP:0002977 Aplasia/Hypoplasia involving the central nervous system Absence or underdevelopment of tissue in the central nervous system. Absent/underdeveloped central nervous system tissue Aplasia/Hypoplasia involving the CNS An abnormality of the calf, i.e. of the posterior part of the lower leg. UMLS:C4021832 Abnormality of the calf HP:0002981 Abnormality of the calf An abnormality of the calf, i.e. of the posterior part of the lower leg. Abnormality of the calf The presence of abnormally small extremities. HP:0003030 HP:0005753 MEDDRA:10027546 SNOMEDCT_US:74370006 UMLS:C0025995 Smaller or shorter than typical limbs HP:0002983 Micromelia The presence of abnormally small extremities. MEDDRA:10027546 Micromelia Smaller or shorter than typical limbs An elbow contracture that limits the ability of the elbow joint to be extended (straightened), meaning that the elbow is fixed in an flexed (bent) position. HP:0003937 HP:0004984 HP:0005654 SNOMEDCT_US:202271004 UMLS:C0409338 Elbow flexion contractures Elbow flexion deformity Fixed flexion at the elbow joint HP:0002987 Elbow flexion contracture An elbow contracture that limits the ability of the elbow joint to be extended (straightened), meaning that the elbow is fixed in an flexed (bent) position. Absence of the fibula. HP:0006373 MEDDRA:10054882 UMLS:C1836186 Absent calf bone Absent fibulae Absent-hypoplastic fibulae HP:0002990 Fibular aplasia Absence of the fibula. MEDDRA:10054882 Fibula agenesis Absent calf bone An anomaly of the calf bone (fibula), one of the two bones of the calf. UMLS:C4025664 Abnormality of fibula morphology Abnormality of the calf bone HP:0002991 Abnormal fibula morphology An anomaly of the calf bone (fibula), one of the two bones of the calf. Abnormality of the calf bone Abnormality of the tibia (shinbone). UMLS:C4025663 Abnormality of the shankbone Abnormality of the shinbone Abnormality of tibia morphology HP:0002992 Abnormal tibia morphology Abnormality of the tibia (shinbone). Abnormality of the shankbone Abnormality of the shinbone HP:0006395 UMLS:C1849955 Decreased elbow mobility Limited elbow mobility Limited elbow movement Restricted elbow motion HP:0002996 Limited elbow movement Decreased elbow mobility Limited elbow mobility Limited elbow movement Restricted elbow motion Abnormality originating in one or more muscles, i.e., of the set of muscles of body. HP:0003197 HP:0003708 HP:0040290 UMLS:C4021745 Muscular abnormality HP:0003011 Abnormality of the musculature Abnormality originating in one or more muscles, i.e., of the set of muscles of body. Muscular abnormality Abnormality of the wrist, the structure connecting the hand and the forearm. HP:0001224 UMLS:C4021744 Abnormalities of the wrists Abnormality of the wrist HP:0003019 Abnormality of the wrist Abnormality of the wrist, the structure connecting the hand and the forearm. Abnormalities of the wrists Abnormality of the wrist One or more abnormally short long bone. HP:0000949 HP:0004983 HP:0004988 HP:0005000 HP:0005029 HP:0005044 HP:0005052 HP:0005077 HP:0005083 HP:0005647 HP:0005822 HP:0006382 HP:0006457 HP:0006472 UMLS:C1854912 Long bone shortening Short long bone Short tubular bones shortened long tubular bones HP:0003026 Long bones are also known as tubular bones. Short long bone One or more abnormally short long bone. Long bone shortening Short long bone An anomaly of the joint that connects the foot with the leg. UMLS:C4025660 Abnormality of the ankles HP:0003028 Abnormality of the ankle Abnormality of the ankles UMLS:C1838664 Enlargement of the ankles HP:0003029 Enlargement of the ankles Enlargement of the ankles An elevation in bone density in one or more diaphyses. Sclerosis is normally detected on a radiograph as an area of increased opacity. HP:0005611 MSH:D003966 SNOMEDCT_US:318761000119105 SNOMEDCT_US:34643004 UMLS:C0011989 Craniodiaphyseal osteosclerosis Diaphyseal osteosclerosis Increased bone density in shaft of long bone HP:0003034 Diaphyseal sclerosis An elevation in bone density in one or more diaphyses. Sclerosis is normally detected on a radiograph as an area of increased opacity. Increased bone density in shaft of long bone Increase in size of one or more joints. UMLS:C1859111 Enlarged joints Prominent joints HP:0003037 Enlarged joints Increase in size of one or more joints. Enlarged joints Underdevelopment of the fibula. HP:0002985 HP:0005887 HP:0006401 UMLS:C1832119 Hypoplastic fibula Short calf bone Short fibula Short fibulae HP:0003038 Fibular hypoplasia Underdevelopment of the fibula. Short calf bone An abnormality of the shoulder, which is defined as the structures surrounding the shoulder joint where the humerus attaches to the scapula. UMLS:C4025659 Abnormality of the shoulder HP:0003043 Abnormal shoulder morphology An abnormality of the shoulder, which is defined as the structures surrounding the shoulder joint where the humerus attaches to the scapula. Abnormality of the shoulder Chronic reduction in active and passive mobility of the shoulder joint due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. SNOMEDCT_US:202265005 UMLS:C0409336 HP:0003044 Shoulder flexion contracture Chronic reduction in active and passive mobility of the shoulder joint due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. Abnormality of the patella (knee cap). UMLS:C4021743 Abnormal kneecap Abnormality of the patella Patellar abnormality HP:0003045 Abnormal patella morphology Abnormality of the patella (knee cap). Abnormal kneecap SNOMEDCT_US:43689004 UMLS:C0231678 Ulnar deviation of wrists HP:0003049 Ulnar deviation of the wrist Abnormal increase in size of one or more metaphyses. HP:0005018 UMLS:C1855544 Enlarged wide portion of a long bone HP:0003051 Enlarged metaphyses Abnormal increase in size of one or more metaphyses. Enlarged wide portion of a long bone An abnormality of the humerus (i.e., upper arm bone). HP:0002988 UMLS:C4021742 Abnormality of the humeri HP:0003063 Abnormality of the humerus An abnormality of the humerus (i.e., upper arm bone). Underdevelopment of the patella. HP:0005020 UMLS:C1840068 Hypoplastic patellae Small kneecap Small patella Small patellae Underdeveloped kneecap HP:0003065 Patellar hypoplasia Underdevelopment of the patella. Small kneecap Underdeveloped kneecap Abnormal flatness (decreased height) of epiphyses. HP:0004982 HP:0005051 HP:0005076 HP:0005080 UMLS:C1857527 Flat end part of bone Flat epiphyses HP:0003071 Flattened epiphysis Abnormal flatness (decreased height) of epiphyses. Flat end part of bone An abnormally increased calcium concentration in the blood. HP:0008250 MSH:D006934 SNOMEDCT_US:166702002 SNOMEDCT_US:66931009 UMLS:C0020437 High blood calcium levels Hypercalcaemia Increased calcium in blood HP:0003072 Hypercalcemia An abnormally increased calcium concentration in the blood. High blood calcium levels Increased calcium in blood Reduction in the concentration of albumin in the blood. Low albumin MSH:D034141 SNOMEDCT_US:119247004 UMLS:C0239981 Hypoalbuminaemia Low blood albumin HP:0003073 Hypoalbuminemia Reduction in the concentration of albumin in the blood. Low albumin Low blood albumin An increased concentration of glucose in the blood. MSH:D006943 SNOMEDCT_US:237598005 SNOMEDCT_US:80394007 UMLS:C0020456 High blood glucose High blood sugar HP:0003074 Hyperglycemia An increased concentration of glucose in the blood. High blood glucose High blood sugar A decreased concentration of protein in the blood. MSH:D007019 SNOMEDCT_US:8900005 UMLS:C0020639 Decreased protein levels in blood HP:0003075 Hypoproteinemia A decreased concentration of protein in the blood. HPO_CONTRIBUTOR:gcarletti Decreased protein levels in blood An increased concentration of glucose in the urine. HP:0003122 HP:0011016 MSH:D006029 SNOMEDCT_US:45154002 UMLS:C0017979 Glucose in urine Glucosuria HP:0003076 Glycosuria, the excretion of abnormal amounts of glucose in the urine, generally results in osmotic diuresis. Glycosuria An increased concentration of glucose in the urine. HPO_CONTRIBUTOR:gcarletti Glucose in urine An elevated lipid concentration in the blood. HP:0008159 HP:0008356 MSH:D006949 SNOMEDCT_US:55822004 UMLS:C0020473 Elevated lipids in blood HP:0003077 Hyperlipidemia is an elevation of the blood levels of lipids including primarily cholesterol, phospholipids and triglycerides and cholesterol esters. The lipids are transported on lipoproteins some of which are commonly used for clinical measurements, including chylomicrons, very-low density lipoproteins (VLDL), intermediate-density lipoproteins (IDL), low-density lipoproteins, and high-density lipoproteins (HDL). Hyperlipidemia An elevated lipid concentration in the blood. Elevated lipids in blood An increased concentration of potassium(1+) in the urine. UMLS:C1846351 Hyperkaliuresis Increased urinary K Increased urinary potassium HP:0003081 Increased urinary potassium An increased concentration of potassium(1+) in the urine. Increased urinary K Increased urinary potassium Disproportionately long fibulae. UMLS:C1848109 Disproportionately long fibula Long calf bone Long fibula HP:0003085 Long fibula Disproportionately long fibulae. Long calf bone Long fibula Underdevelopment of the proximal epiphysis of the femur. HP:0003374 HP:0008791 HP:0008792 UMLS:C1839254 Small capital femoral epiphyses Small femoral capital epiphyses Small innermost thighbone end part Small proximal femoral epiphyses Underdevelopment of the innermost thighbone end part HP:0003090 Hypoplasia of the capital femoral epiphysis Underdevelopment of the proximal epiphysis of the femur. Small innermost thighbone end part Underdevelopment of the innermost thighbone end part An abnormal shortening of the femur. HP:0009749 SNOMEDCT_US:93255008 UMLS:C0345375 Femoral hypoplasia Hypoplasia of the femora Short femurs Short thighbone HP:0003097 Short femur An abnormal shortening of the femur. Short thighbone Relatively increased growth of the fibula compared to that of the tibia. UMLS:C1864298 Overgrowth of calf bone HP:0003099 Fibular overgrowth Relatively increased growth of the fibula compared to that of the tibia. PMID:17259417 Overgrowth of calf bone Any deviation from the normal concentration of cholesterol in the blood circulation. 2008-03-17T01:02:00Z HP:0003464 UMLS:C4025656 Abnormal cholesterol homeostasis Abnormality of cholesterol metabolism HP:0003107 Abnormal circulating cholesterol concentration Abnormality of cholesterol metabolism An increased concentration of glycine in the urine. HP:0002931 MSH:C563009 SNOMEDCT_US:236477004 UMLS:C0341706 UMLS:C0543541 Glycinuria High urine glycine levels HP:0003108 Normal urinary glycine total (free and combined form) excretion is around 450 mg per 24 hours. Hyperglycinuria An increased concentration of glycine in the urine. HPO_CONTRIBUTOR:gcarletti PMID:18901181 PMID:20240447 High urine glycine levels An increased excretion of phosphates in the urine. HP:0003266 SNOMEDCT_US:22450000 UMLS:C0268079 UMLS:C0948023 High urine phosphate levels Phosphaturia HP:0003109 Hyperphosphaturia An increased excretion of phosphates in the urine. High urine phosphate levels An abnormality of the composition of urine or the levels of its components. HP:0011865 HP:0011866 UMLS:C4025655 Pee issues Urine issues HP:0003110 Abnormality of urine homeostasis An abnormality of the composition of urine or the levels of its components. Pee issues Urine issues Abnormality of the homeostasis (concentration) of a monoatomic ion. HP:0003253 SNOMEDCT_US:237840007 UMLS:C1704431 UMLS:C4025654 Abnormality of ion homeostasis Electrolyte disorders Electrolyte disturbance HP:0003111 Abnormal blood ion concentration Abnormality of the homeostasis (concentration) of a monoatomic ion. Electrolyte disorders The presence of an abnormal decrease or increase of one or more amino acids in the blood circulation. UMLS:C4025653 Abnormality of serum amino acid level Abnormality of serum amino acid levels HP:0003112 Abnormal circulating amino acid concentration The presence of an abnormal decrease or increase of one or more amino acids in the blood circulation. Abnormality of serum amino acid levels Concentration of a hormone in the blood circulation outside of normal limits. UMLS:C4025652 Abnormal circulating hormone level Abnormality of circulating hormone level HP:0003117 Abnormal circulating hormone concentration Concentration of a hormone in the blood circulation outside of normal limits. Abnormality of circulating hormone level Any deviation from the normal concentration of a lipid in the blood circulation. HP:0003611 MSH:D050171 SNOMEDCT_US:370992007 UMLS:C0242339 UMLS:C4025650 Dyslipidaemia Dyslipidemia HP:0003119 According to CHEBI:18059 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. Abnormal circulating lipid concentration Any deviation from the normal concentration of a lipid in the blood circulation. Dyslipidaemia A contracture (chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin) that prevent normal movement of one or more joints of the limbs. HP:0005631 HP:0005839 UMLS:C1969879 Limb contractures HP:0003121 Limb joint contracture A contracture (chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin) that prevent normal movement of one or more joints of the limbs. Limb contractures An increased concentration of cholesterol in the blood. HP:0008154 HP:0008173 HP:0008359 High cholesterol MSH:D006937 SNOMEDCT_US:13644009 SNOMEDCT_US:166830008 UMLS:C0020443 UMLS:C0595929 Elevated serum cholesterol Elevated total cholesterol Increased total cholesterol HP:0003124 Hypercholesterolemia An increased concentration of cholesterol in the blood. HPO_CONTRIBUTOR:gcarletti High cholesterol Elevated serum cholesterol Elevated total cholesterol Increased total cholesterol An abnormally decreased calcium concentration in the urine. SNOMEDCT_US:86353007 UMLS:C0020599 Low urine calcium levels HP:0003127 Hypocalciuria An abnormally decreased calcium concentration in the urine. Low urine calcium levels An increased amount of nitrogen in the form of urea in the blood. UMLS:C0151539 Increased BUN Increased blood urea nitrogen HP:0003138 Increased blood urea nitrogen An increased amount of nitrogen in the form of urea in the blood. HPO_CONTRIBUTOR:gcarletti Increased BUN Increased blood urea nitrogen An decreased concentration of cholesterol in the blood. SNOMEDCT_US:61336008 UMLS:C0151718 Decreased circulating cholesterol level HP:0003146 Hypocholesterolemia An decreased concentration of cholesterol in the blood. HPO_CONTRIBUTOR:gcarletti Decreased circulating cholesterol level Increased excretion of oxalates in the urine. MSH:D006959 SNOMEDCT_US:367621000119107 UMLS:C0020500 High urine oxalate levels Increased level of oxalate in urine HP:0003159 Hyperoxaluria Increased excretion of oxalates in the urine. High urine oxalate levels Increased level of oxalate in urine PMID:11135054 An abnormality of the acetabulum, i.e., the Acetabular part of hip bone, which together with the head of the femur forms the hip joint. UMLS:C4021739 Abnormality of the acetabulum Abnormality of the hipbone socket Acetabular abnormality HP:0003170 Abnormal acetabulum morphology An abnormality of the acetabulum, i.e., the Acetabular part of hip bone, which together with the head of the femur forms the hip joint. Abnormality of the hipbone socket An anomaly of the the pubic bone, i.e., of the ventral and anterior of the three principal components (pubis, ilium, ischium) of the hip bone. UMLS:C4021738 Abnormality of the pubic bone Abnormality of the pubic bones Abnormality of the pubis HP:0003172 Abnormal pubic bone morphology An anomaly of the the pubic bone, i.e., of the ventral and anterior of the three principal components (pubis, ilium, ischium) of the hip bone. Abnormality of the pubic bone Abnormality of the pubic bones Abnormality of the pubis Underdevelopment of the pubis, which together with the ilium and the ischium, is one of the three bones that make up the hip bone. UMLS:C1865030 Hypoplastic pubic bones Hypoplastic pubis HP:0003173 Hypoplastic pubic bone Underdevelopment of the pubis, which together with the ilium and the ischium, is one of the three bones that make up the hip bone. Hypoplastic pubic bones An anomaly of the ischium, which forms the lower and back part of the hip bone. SNOMEDCT_US:93008005 UMLS:C0685661 Abnormality of the ischial bones Abnormality of the ischium Anomaly of the ischium HP:0003174 The ischium, together with the ilium and the pubis, forms the hip bone (os coxae). Abnormal ischium morphology An anomaly of the ischium, which forms the lower and back part of the hip bone. Underdevelopment of the ischium, which forms the lower and back part of the hip bone. UMLS:C1859447 Hypoplastic ischial bones Hypoplastic ischii Hypoplastic ischium HP:0003175 Hypoplastic ischia Underdevelopment of the ischium, which forms the lower and back part of the hip bone. Underdevelopment of the breast. HP:0000784 SNOMEDCT_US:8915006 UMLS:C0266013 Underdeveloped breasts HP:0003187 Breast hypoplasia Underdevelopment of the breast. Underdeveloped breasts Distance from nasion to subnasale more than two standard deviations above the mean, or alternatively, an apparently increased length from the nasal root to the nasal base. HP:0005283 HP:0200142 UMLS:C1839798 Elongated nose Increased height of nose Increased length of nose Increased nasal height Increased nasal length Long nose Nasal elongation HP:0003189 Long nose Distance from nasion to subnasale more than two standard deviations above the mean, or alternatively, an apparently increased length from the nasal root to the nasal base. PMID:19152422 Elongated nose Increased height of nose Increased length of nose Increased nasal height Increased nasal length Long nose Nasal elongation Distance from nasion to subnasale more than two standard deviations below the mean, or alternatively, an apparently decreased length from the nasal root to the nasal tip. HP:0000440 HP:0000449 HP:0000450 HP:0003192 HP:0003195 HP:0005270 HP:0200092 SNOMEDCT_US:249310005 UMLS:C0426414 UMLS:C1854114 Decreased length of nose Hypoplastic nose Nasal hypoplasia Short nose Shortened nose Small nose HP:0003196 Note: a small nose has both decreased height and a decreased width. These should be coded separately. Short nose Distance from nasion to subnasale more than two standard deviations below the mean, or alternatively, an apparently decreased length from the nasal root to the nasal tip. PMID:19152422 Decreased length of nose Short nose Shortened nose Small nose HP:0003732 UMLS:C1837108 Decreased muscle mass HP:0003199 Decreased muscle mass Decreased muscle mass The presence of skeletal muscular atrophy (which is also known as amyotrophy). HP:0001299 HP:0003545 HP:0003671 HP:0003702 HP:0003746 HP:0006995 HP:0007171 HP:0007356 HP:0009010 HP:0009048 HP:0100868 MSH:D009133 SNOMEDCT_US:74035001 UMLS:C0234958 UMLS:C0270948 UMLS:C0541794 UMLS:C1843479 Amyotrophy Amyotrophy involving the extremities Muscle atrophy Muscle atrophy, neurogenic Muscle degeneration Muscle hypotrophy Muscle wasting Muscular atrophy Neurogenic muscle atrophy Neurogenic muscle atrophy, especially in the lower limbs Neurogenic muscular atrophy HP:0003202 Skeletal muscle atrophy The presence of skeletal muscular atrophy (which is also known as amyotrophy). Muscle degeneration Muscle wasting Pathological deposition of calcium salts in one or more arteries. 2008-03-26T04:05:00Z HP:0012455 UMLS:C1168153 HP:0003207 Most individuals aged over 60 years have progressively enlarging deposits of calcium mineral in their major arteries. This vascular calcification reduces aortic and arterial elastance, which impairs cardiovascular hemodynamics, resulting in substantial morbidity and mortality in the form of hypertension, aortic stenosis, cardiac hypertrophy, myocardial and lower-limb ischemia, congestive heart failure, and compromised structural integrity.The severity and extent of mineralization reflect atherosclerotic plaque burden and strongly and independently predict cardiovascular morbidity and mortality. (From PMID:18519861). Arterial calcification Pathological deposition of calcium salts in one or more arteries. PMID:18519861 An increased concentration of dicarboxylic acid in the urine. HP:0033455 UMLS:C1856432 Elevated urinary dicarboxylic acid level HP:0003215 A dicarboxylic acid is an oxoacid containing two carboxy groups. Dicarboxylic aciduria occurs during increased mobilization or inhibited beta-oxidation of fatty acids, where a number of 3-hydroxydicarboxylic acids are excreted in the urine. Dicarboxylic aciduria An increased concentration of dicarboxylic acid in the urine. HPO_CONTRIBUTOR:gcarletti Decreased concentration of methylcobalamin. Methylcobalamin is a form of vitamin B12. HP:0008287 UMLS:C4021736 Methylcobalamin deficiency HP:0003223 Decreased methylcobalamin Decreased concentration of methylcobalamin. Methylcobalamin is a form of vitamin B12. An abnormally increased sodium concentration in the blood. MSH:D006955 SNOMEDCT_US:286926003 SNOMEDCT_US:39355002 UMLS:C0020488 High blood sodium levels HP:0003228 Hypernatremia An abnormally increased sodium concentration in the blood. High blood sodium levels An increased concentration of tyrosine in the blood. SNOMEDCT_US:56595005 UMLS:C1879362 Increased tyrosine in blood Tyrosinemia HP:0003231 Defect in fumarylacetoacetase. Hypertyrosinemia An increased concentration of tyrosine in the blood. Increased tyrosine in blood Concentration of carnitine in the blood circulation below the lower limit of normal. SNOMEDCT_US:421784001 UMLS:C1142132 Decreased plasma carnitine Carnitine deficiency HP:0003234 Carnitine is responsible for the transport of fatty acids from the cytosol into the mitochondria. Decreased circulating carnitine concentration Concentration of carnitine in the blood circulation below the lower limit of normal. HPO_CONTRIBUTOR:gcarletti Decreased plasma carnitine Carnitine deficiency An increased concentration of methionine in the blood. MSH:C564683 SNOMEDCT_US:124283007 SNOMEDCT_US:43123004 SNOMEDCT_US:57835009 UMLS:C0268621 Increased methionine in blood Methioninemia HP:0003235 Elevated blood methionine levels in the range of 500-2000 micromolar. Hypermethioninemia An increased concentration of methionine in the blood. HPO_CONTRIBUTOR:gcarletti Increased methionine in blood Underdevelopment of part or all of the external reproductive organs. HP:0000788 HP:0003245 UMLS:C1855333 Hypogenitalism Small genitalia Underdevelopment of external reproductive organs HP:0003241 Partial or complete failure of the genitalia to develop, often as a consequence of hypogonadism. External genital hypoplasia Underdevelopment of part or all of the external reproductive organs. Underdevelopment of external reproductive organs UMLS:C1851722 Overgrowth of external genitalia HP:0003247 Overgrowth of external genitalia Overgrowth of external genitalia Aplasia of the vagina. HP:0008709 MSH:C536523 SNOMEDCT_US:248871003 SNOMEDCT_US:87380008 UMLS:C0220763 UMLS:C1321884 UMLS:C1841990 Absent vagina Congenital absence of the vagina HP:0003250 Aplasia of the vagina Aplasia of the vagina. Absent vagina A increased concentration of arginine in the urine. UMLS:C4025635 High urine arginine levels HP:0003268 Normal urinary arginine total (free and combined form) excretion is around 30 mg per 24 hours. Argininuria A increased concentration of arginine in the urine. PMID:18901181 PMID:20240447 High urine arginine levels Abnormal increased size of the viscera of the abdomen. SNOMEDCT_US:28543008 UMLS:C0042782 HP:0003271 Visceromegaly is enlargement of the internal organs in the abdomen, including liver, spleen, stomach, kidneys, or pancreas. Visceromegaly Abnormal increased size of the viscera of the abdomen. An abnormality of the hip bone. UMLS:C4021735 Abnormality of the hip bone Abnormality of the hips HP:0003272 The hip region comprises the vasculature of hip, skin of hip, superficial fascia of hip, the hip bone, hip joint, and musculature of hip. The hip is part of the pelvic girdle. Abnormal hip bone morphology An abnormality of the hip bone. Abnormality of the hip bone Abnormality of the hips Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the hip joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. SNOMEDCT_US:202283002 UMLS:C0409354 Flexion contracture of hips Flexion contractures of hips Hip contractures Hip flexion contractures HP:0003273 Hip contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the hip joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. PMID:16214063 PMID:24975760 PMID:31282072 Underdeveloped acetabulae. UMLS:C1846442 Acetabular hypoplasia Hypoplastic acetabula HP:0003274 Hypoplastic acetabulae Underdeveloped acetabulae. A functional anomaly of mitochondria. UMLS:C4021734 Mitochondrial dysfunction HP:0003287 Abnormality of mitochondrial metabolism A functional anomaly of mitochondria. An increased concentration of lysine in the urine. HP:0002158 UMLS:C4021733 High urine lysine levels Lysinuria HP:0003297 Normal urinary lysine total (free and combined form) excretion is around 80 mg per 24 hours. Hyperlysinuria An increased concentration of lysine in the urine. PMID:18901181 PMID:20240447 High urine lysine levels Abnormal morphology of vertebral body. UMLS:C1839326 Abnormal vertebral bodies Abnormally shaped vertebrae HP:0003312 Abnormal form of the vertebral bodies SNOMEDCT_US:298186005 UMLS:C0574967 Cervical spine joint hypermobility HP:0003318 Cervical spine hypermobility Any abnormality of the cervical vertebral column. HP:0004587 UMLS:C1852464 Abnormal cervical spine Abnormality of cervical vertebra Abnormality of the cervical vertebrae Cervical spine abnormalities Cervical vertebral abnormalities Disorder of cervical vertebra Cervical vertebral anomalies HP:0003319 Abnormality of the cervical spine Any abnormality of the cervical vertebral column. Abnormal cervical spine Abnormality of cervical vertebra Abnormality of the cervical vertebrae Cervical vertebral anomalies HP:0005782 UMLS:C1833753 HP:0003321 Biconcave flattened vertebrae Any anomaly in the composite material or the layered arrangement of the bony skeleton. UMLS:C4025630 HP:0003330 Abnormal bone structure Any anomaly in the composite material or the layered arrangement of the bony skeleton. An abnormality of the process of endochondral ossification, which is a type of replacement ossification in which bone tissue replaces cartilage. HP:0003331 UMLS:C4025628 HP:0003336 This term is intended to describe histological abnormalities of enchondral ossification observed upon bone biopsy. Abnormal enchondral ossification An abnormality of the process of endochondral ossification, which is a type of replacement ossification in which bone tissue replaces cartilage. An increased concentration of an amino acid in the urine. HP:0002903 HP:0008335 HP:0200014 SNOMEDCT_US:35912001 UMLS:C0238621 UMLS:C4020843 High urine amino acid levels Hyperaminoaciduria Increased levels of animo acids in urine Abnormal urinary amino-acid findings HP:0003355 Aminoaciduria An increased concentration of an amino acid in the urine. High urine amino acid levels Increased levels of animo acids in urine Abnormal urinary amino-acid findings Decreased concentration of sulfate in the urine. UMLS:C1848958 Decreased urinary sulfate Decreased urinary sulphate HP:0003359 Decreased urinary sulfate Decreased concentration of sulfate in the urine. Decreased urinary sulfate Decreased urinary sulphate UMLS:C4025622 Abnormal neck or head of thigh bone Abnormality of the femoral neck or head region HP:0003366 Abnormal femoral neck/head morphology Abnormal neck or head of thigh bone An abnormality of the femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). UMLS:C4025621 Abnormal neck of thigh bone Abnormality of the femoral neck HP:0003367 Abnormal femoral neck morphology An abnormality of the femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). Abnormal neck of thigh bone An abnormality of the femoral head. UMLS:C4025620 Abnormal head of thigh bone Abnormality of the femoral head HP:0003368 Abnormal femoral head morphology An abnormality of the femoral head. Abnormal head of thigh bone An abnormal flattening of the proximal epiphysis of the femur. HP:0006393 UMLS:C1842155 Flat capital femoral epiphyses Flat end part of innermost thighbone Flat femoral capital epiphyses Flat proximal femoral epiphyses Flattened proximal femoral epiphyses HP:0003370 Flat capital femoral epiphysis An abnormal flattening of the proximal epiphysis of the femur. Flat end part of innermost thighbone An abnormal enlargement of the proximal epiphysis of the femur. UMLS:C1859697 Enlarged capital femoral epiphyses Enlarged end part of innermost thighbone HP:0003371 Enlargement of the proximal femoral epiphysis An abnormal enlargement of the proximal epiphysis of the femur. Enlarged end part of innermost thighbone An anomaly of the atlantoaxial joint, i.e., of the joint between the first (atlas) and second (axis) cervical vertebrae. UMLS:C4025617 HP:0003413 Atlantoaxial abnormality An anomaly of the atlantoaxial joint, i.e., of the joint between the first (atlas) and second (axis) cervical vertebrae. An abnormality related to a defect of vertebral separation during development. HP:0005705 SNOMEDCT_US:205455005 UMLS:C0432163 Abnormal spinal segmentation HP:0003422 The vertebral column derives from somites, transient paired segments of mesoderm that surround the neural tube in the early embryo. The formation of the vertebrar involves many processes including resegmentation of the rostral and caudal regions of adjacent somites that then fuse to form vertebral elements. Disruption of these processes can a cause of severe segmentation defects of the vetebrae. The frequency of segmentation defects of the vetebra has been estimated at 0.5 of 1000 births. The range of segmentation defects includes left-right uneven formation of somites that results in hemivertebrae or wedge vertebrae. Incomplete segmentation can result in fused segments such as block vertebrae. A failure of the process of resegmentation and migration of the sclerotomal compartment can result in a failure of midline fusion, such as butterlfy vertebrae. Vertebral segmentation defect An abnormality related to a defect of vertebral separation during development. PMID:23653580 PMID:23801490 SNOMEDCT_US:165624002 UMLS:C0151900 HP:0003452 Increased serum iron Increased concentration of long-chain fatty acids in the blood circulation. HP:0008333 HP:0045016 UMLS:C1859241 Elevated long chain fatty acids Elevated serum long-chain fatty acids Increased serum long-chain fatty acids HP:0003455 This feature can be measured in plasma, as well as in cultured fibroblasts of amniocytes. Elevated circulating long chain fatty acid concentration Increased concentration of long-chain fatty acids in the blood circulation. An abnormality of one or more of the vertebrae. HP:0005719 Fyler:4108 SNOMEDCT_US:205043005 SNOMEDCT_US:74877002 UMLS:C0158775 UMLS:C4020839 UMLS:C4020840 Abnormal vertebrae Abnormality of the vertebrae Vertebral anomalies Multiple vertebral anomalies HP:0003468 A vertebra is one of 33 bony segments that form the spinal column of humans. There are 7 cervical, 12 thoracic, 5 lumbar, 5 sacral and 4 coccygeal vertebrae (the coccygeal vertebrae are fused into one coccyx bone). Abnormal vertebral morphology An abnormality of one or more of the vertebrae. Multiple vertebral anomalies A kind of short stature in which different regions of the body are shortened to differing extents. HP:0008895 HP:0008900 UMLS:C0878659 UMLS:C1846797 Short stature, disproportionate Short stature, severe disproportionate HP:0003498 Disproportionate short stature A kind of short stature in which different regions of the body are shortened to differing extents. Short stature, severe disproportionate A type of disproportionate short stature characterized by a short trunk but a average-sized limbs. HP:0001524 HP:0003500 HP:0008923 UMLS:C1846435 Disproportionate short-trunked dwarfism Disproportionate short-trunked short stature Short-trunked dwarfism HP:0003521 Disproportionate short-trunk short stature A type of disproportionate short stature characterized by a short trunk but a average-sized limbs. Disproportionate short-trunked dwarfism Disproportionate short-trunked short stature Short-trunked dwarfism A reduction in methionine synthase activity. UMLS:C1848580 Decreased activity of methionine synthase Methionine synthase activity decreased Methionine synthase deficiency Reduced methionine synthase activity HP:0003524 Cobalamin-dependent methionine synthase catalyzes the transfer of a methyl group from N5-methyltetrahydrofolate to homocysteine, producing tetrahydrofolate and methionine, i.e., (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine. Decreased methionine synthase activity A reduction in methionine synthase activity. Concentration of calcitonin, a 32-amino acid polypeptide hormone that is produced primarily by the parafollicular cells of the thyroid, in the blood circulation above the upper limit of normal. UMLS:C1868394 Elevated calcitonin HP:0003528 Calcitonin is a 32-amino acid polypeptide hormone that is produced primarily by the parafollicular cells of the thyroid. It acts to reduce blood calcium (Ca2+), opposing the effects of parathyroid hormone. Elevated circulating calcitonin concentration Elevated calcitonin Level of ornithine in the urine above the upper limit of normal. UMLS:C4025602 Ornithine high in urine HP:0003532 Ornithinuria Level of ornithine in the urine above the upper limit of normal. Excretion of glycosaminoglycan in the urine. Glycosaminoglycans are long unbranched polysaccharides consisting of a repeating disaccharide unit. UMLS:C4025598 HP:0003541 Urinary glycosaminoglycan excretion Excretion of glycosaminoglycan in the urine. Glycosaminoglycans are long unbranched polysaccharides consisting of a repeating disaccharide unit. An increased concentration of pyruvate in the blood. UMLS:C1849488 Increased serum pyruvic acid HP:0003542 An abnormal increase in the concentration of pyruvate in the blood. Pyruvate is involved in energy metabolism, forming part of glycolysis and the citric acid cycle. Increased serum pyruvate An increased concentration of pyruvate in the blood. HPO_CONTRIBUTOR:gcarletti Any abnormality of the soft tissues, including both connective tissue (tendons, ligaments, fascia, fibrous tissues, and fat). UMLS:C4025596 HP:0003549 Abnormality of connective tissue Any abnormality of the soft tissues, including both connective tissue (tendons, ligaments, fascia, fibrous tissues, and fat). The term dystrophy means abnormal growth. However, muscular dystrophy is used to describe primary myopathies with a genetic basis and a progressive course characterized by progressive skeletal muscle weakness and wasting, defects in muscle proteins, and histological features of muscle fiber degeneration (necrosis) and regeneration. If possible, it is preferred to use other HPO terms to describe the precise phenotypic abnormalities. HP:0003544 HP:0003806 MSH:D009136 SNOMEDCT_US:193225000 SNOMEDCT_US:73297009 UMLS:C0026850 UMLS:C1864711 Muscle biopsy shows dystrophic changes HP:0003560 Muscular dystrophy can be demonstrated by muscle biopsy. Muscular dystrophy The term dystrophy means abnormal growth. However, muscular dystrophy is used to describe primary myopathies with a genetic basis and a progressive course characterized by progressive skeletal muscle weakness and wasting, defects in muscle proteins, and histological features of muscle fiber degeneration (necrosis) and regeneration. If possible, it is preferred to use other HPO terms to describe the precise phenotypic abnormalities. Muscle biopsy shows dystrophic changes A decreased concentration of citrulline in the blood. UMLS:C1839532 HP:0003572 Low plasma citrulline A decreased concentration of citrulline in the blood. HPO_CONTRIBUTOR:gcarletti An abnormally increased sodium concentration in the cytosol. UMLS:C4025593 High intracellular Na Increased intracellular Na+ levels HP:0003575 Increased intracellular sodium An abnormally increased sodium concentration in the cytosol. HPO_CONTRIBUTOR:gcarletti Increased concentration of trimethylamine in the urine. MSH:C536561 SNOMEDCT_US:237959005 UMLS:C0342739 High urine trimethylamine levels HP:0003614 Increased concentration of trimethylamine, an organic amino compound with an oder characterized as that of rotting fish, in the urine. Trimethylaminuria is generally caused by impaired oxidation of trimethylamine into the odorless compound trimethylamine N-oxide. Trimethylaminuria Increased concentration of trimethylamine in the urine. High urine trimethylamine levels Loss (disappearance) of previously present subcutaneous fat tissue in arm or leg. HP:0003757 UMLS:C1837764 Loss of fat tissue below the skin in limbs Loss of subcutaneous adipose tissue from extremities HP:0003635 Loss of subcutaneous adipose tissue in limbs Loss (disappearance) of previously present subcutaneous fat tissue in arm or leg. Loss of fat tissue below the skin in limbs The presence of free hemoglobin in the urine. MSH:D006456 SNOMEDCT_US:68600005 UMLS:C0019048 Haemoglobin in urine Hemoglobin in urine HP:0003641 If, following hemolysis, haptoglobins (hemoglobin-binding proteins) are saturated, then free hemoglobin appears in the urine. Hemoglobinuria The presence of free hemoglobin in the urine. Haemoglobin in urine Hemoglobin in urine Abnormally increased concentration of hydrogencarbonate in the urine. UMLS:C1839865 Increased urine HCO3 concentration Increased urine bicarbonate concentration HP:0003646 Bicarbonaturia Abnormally increased concentration of hydrogencarbonate in the urine. Increased urine bicarbonate concentration A decreased concentration of methionine in the blood. UMLS:C1848555 Decreased plasma methionine Decreased serum methionine HP:0003658 Normal methionine blood levels are around 30 micromole per liter. Hypomethioninemia A decreased concentration of methionine in the blood. HPO_CONTRIBUTOR:gcarletti Decreased plasma methionine Decreased serum methionine Muscular atrophy affecting the muscles of the pelvis. 2008-04-07T10:57:00Z UMLS:C4025581 HP:0003665 Amyotrophy of the musculature of the pelvis Muscular atrophy affecting the muscles of the pelvis. Muscular atrophy affecting muscles in the distal portions of the extremities. HP:0002484 HP:0002934 HP:0003486 HP:0003699 HP:0006786 HP:0006864 HP:0008937 HP:0008958 HP:0009015 HP:0009040 HP:0009065 UMLS:C1848736 Amyotrophy of distal limb muscles Distal amyotrophy, especially of the hands and feet Distal limb muscle atrophy Distal muscle atrophy Distal muscle atrophy, upper and lower limbs Distal muscle degeneration Distal muscle wasting Distal muscular atrophy Muscle atrophy, distal HP:0003693 Most polyneuropathies affect distal lower extremity miuscles early on. Polyneuropathies are roughly symmeetric in distribution and tend to affect nerves in a length-dependent manner, with the longest nerves first (stocking-glove distribution). Distal amyotrophy Muscular atrophy affecting muscles in the distal portions of the extremities. Distal muscle degeneration Distal muscle wasting Absence of the epiphysis located at the proximal end of the distal phalanx of the 5th finger. 2008-12-22T01:37:43Z UMLS:C4025577 Absent end part of the outermost bone of the little finger Absent end part of the outermost bone of the pinkie finger Absent end part of the outermost bone of the pinky finger HP:0003696 Absent epiphysis of the distal phalanx of the 5th finger Absence of the epiphysis located at the proximal end of the distal phalanx of the 5th finger. Absent end part of the outermost bone of the little finger Absent end part of the outermost bone of the pinkie finger Absent end part of the outermost bone of the pinky finger Abnormal increase in muscle size and mass not due to training. HP:0009042 UMLS:C2265792 Hypertrophic muscles Increased skeletal muscle cells Muscle hypertrophy Muscular hypertrophy HP:0003712 Increased muscle bulk based on clinical observation. Myofiber hyperplasia and hypertrophy may contribute but this is not easily tested clinically. Skeletal muscle hypertrophy Abnormal increase in muscle size and mass not due to training. Increased skeletal muscle cells UMLS:C1859442 Minimal fat below the skin HP:0003717 Minimal subcutaneous fat Minimal fat below the skin Amyotrophy affecting the muscles of the shoulder girdle. UMLS:C1847766 Shoulder girdle atrophy Shoulder girdle muscle wasting Shoulder-girdle muscle atrophy HP:0003724 Shoulder girdle muscle atrophy Amyotrophy affecting the muscles of the shoulder girdle. Shoulder girdle muscle wasting Shoulder-girdle muscle atrophy Muscle hypertrophy affecting the thighs. UMLS:C1846674 Increased thigh size HP:0003733 Proximal lower limb hypertrophy Thigh hypertrophy Muscle hypertrophy affecting the thighs. Increased thigh size A reduced amount of fat tissue in the lowest layer of the integument. This feature can be appreciated by a reduced skinfold thickness. HP:0001002 HP:0007409 SNOMEDCT_US:248316006 UMLS:C0424631 UMLS:C1857657 Decreased subcutaneous adipose tissue Decreased subcutaneous fat Reduced fat tissue below the skin Reduced subcutaneous fat Scanty adipose tissue HP:0003758 Reduced subcutaneous adipose tissue Reduced fat tissue below the skin Congenital underdevelopment of lymph vessels. UMLS:C4025570 Underdeveloped lymphatic vessels HP:0003759 This feature can be demonstrated by lymphography. Hypoplasia of lymphatic vessels Congenital underdevelopment of lymph vessels. Underdeveloped lymphatic vessels Pulp calcifications may appear as punctate calcifications, irregular, roughly spherical mineralized masses in any part of the pulp. It may occur isolated or associated to calcifications elsewhere such as the carotid arteries and kidneys. The diagnosis pulp calcifications can be established using radiological studies. MSH:D003784 SNOMEDCT_US:57602001 UMLS:C1527284 UMLS:C4280259 UMLS:C4280546 Pulp calcifications Pulp denticles Pulp stones Pulpoliths False denticles False pulp stones True denticles True pulp stones HP:0003771 Pulp calcification Pulp calcifications may appear as punctate calcifications, irregular, roughly spherical mineralized masses in any part of the pulp. It may occur isolated or associated to calcifications elsewhere such as the carotid arteries and kidneys. The diagnosis pulp calcifications can be established using radiological studies. PMID:31468724 Pulp calcifications Pulp denticles Pulp stones False denticles False pulp stones True denticles True pulp stones Developmental hypoplasia (shortening) of middle phalanx of toe. UMLS:C4021723 Short middle bones (feet) Short middle phalanges of toes HP:0003795 Short middle phalanx of toe Developmental hypoplasia (shortening) of middle phalanx of toe. Short middle bones (feet) Muscular atrophy affecting the muscles of the limb girdle. Limb-girdle myopathy UMLS:C1404521 UMLS:C1842552 Wasting of limb-girdle muscle HP:0003797 Limb-girdle muscle atrophy Muscular atrophy affecting the muscles of the limb girdle. Wasting of limb-girdle muscle HP:0003845 UMLS:C4021722 Abnormal shape of end part of upper limb long bones Abnormality involving the epiphyses of the upper limbs Abnormality of upper limb epiphysis morphology Epihyseal plate abnormality of the upper limbs HP:0003839 Abnormal upper limb epiphysis morphology Abnormal shape of end part of upper limb long bones A delay in the process of formation and maturation of the epiphysis of one or more long bones of the upper limbs. UMLS:C4025560 UMLS:C4280544 Delayed maturation fo the end part of the upper limb bone HP:0003840 Delayed upper limb epiphyseal ossification A delay in the process of formation and maturation of the epiphysis of one or more long bones of the upper limbs. Delayed maturation fo the end part of the upper limb bone UMLS:C4025557 Round end part of upper limb bones HP:0003843 Round epiphyses of the upper limbs Round end part of upper limb bones UMLS:C4025556 Small end part of upper limb bones HP:0003844 Small epiphyses of the upper limbs Small end part of upper limb bones An elevation in bone density in one or more diaphyses of the arms. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4025547 Increased bone density in central part of long bone of upper limbs HP:0003860 Diaphyseal sclerosis of the upper limbs An elevation in bone density in one or more diaphyses of the arms. Sclerosis is normally detected on a radiograph as an area of increased opacity. Increased bone density in central part of long bone of upper limbs Clefting affecting the humerus. UMLS:C4025545 Notched long bone in upper arm HP:0003864 Bifid humerus Clefting affecting the humerus. Notched long bone in upper arm UMLS:C4025539 Deformed long bone in upper arm HP:0003871 Deformed humerus Deformed long bone in upper arm UMLS:C4025535 HP:0003876 Osteoporotic humerus UMLS:C4025527 Abnormality of the deltoid tuberosities HP:0003889 Abnormal deltoid tuberosity morphology An anomaly of the humeral epiphysis. UMLS:C4021714 Abnormality of end part of the long bone of the upper arm Abnormality of the humeral epiphyses HP:0003891 Abnormality of the humeral epiphysis An anomaly of the humeral epiphysis. Abnormality of end part of the long bone of the upper arm Lack of formation of bone in the epiphysis of the humerus. UMLS:C4021713 Absent maturation of end part of long bone in upper arm Absent ossification of the humeral epiphyses HP:0003892 Normally, the proximal humeral epiphysis can be visualized at about 40 weeks of gestation. Absent humeral epiphyseal ossification Lack of formation of bone in the epiphysis of the humerus. Absent maturation of end part of long bone in upper arm A delay in the process of formation and maturation of the humeral epiphysis. UMLS:C4021712 UMLS:C4280543 Delayed maturation/delayed ossification of the humeral epiphyses Delayed maturation of the end part of the long bone in upper arm HP:0003894 Delayed humeral epiphyseal ossification A delay in the process of formation and maturation of the humeral epiphysis. Delayed maturation of the end part of the long bone in upper arm UMLS:C4025525 Flattened end part of long bone in upper arm HP:0003895 Flattened humeral epiphyses Flattened end part of long bone in upper arm UMLS:C4025523 UMLS:C4280542 Irregular maturation of the end part of the long bone in upper arm HP:0003897 Irregular ossification of the humeral epiphyses Irregular maturation of the end part of the long bone in upper arm UMLS:C4025522 Large end part of long bone in upper arm HP:0003898 Large humeral epiphyses Large end part of long bone in upper arm UMLS:C4025521 Round end part of long bone in upper arm HP:0003899 Round humeral epiphyses Round end part of long bone in upper arm UMLS:C4025520 Small end part of long bone in upper arm HP:0003900 Small humeral epiphyses Small end part of long bone in upper arm UMLS:C4025517 Abnormality of the humeral metaphyses Abnormality of the wide portion of the long bone in upper arm HP:0003907 Abnormal humeral metaphysis morphology Abnormality of the wide portion of the long bone in upper arm UMLS:C4025513 Irregular bone maturation of the wide portion of the long bone in upper arm HP:0003914 Irregular ossification of humeral metaphyses Irregular bone maturation of the wide portion of the long bone in upper arm UMLS:C4025509 Hardening of wide portion of long bone of upper arm Stiffening of wide portion of long bone of upper arm HP:0003918 Sclerotic humeral metaphysis Hardening of wide portion of long bone of upper arm Stiffening of wide portion of long bone of upper arm An anomaly of the humeral diaphysis. UMLS:C4025502 Abnormality of shaft of long bone in upper arm Abnormality of the humeral diaphysis HP:0003926 Abnormal humeral diaphysis morphology An anomaly of the humeral diaphysis. Abnormality of shaft of long bone in upper arm UMLS:C4025496 Increased bone density in shaft of long bone in upper arm HP:0003933 Sclerosis of humeral diaphysis Increased bone density in shaft of long bone in upper arm UMLS:C4025491 Abnormality of the joint spaces of the elbow HP:0003943 Abnormality of the joint spaces of the elbow Abnormality of the joint spaces of the elbow UMLS:C4025488 Abnormality of end part of the elbow bone HP:0003946 Abnormality of the epiphyses of the elbow Abnormality of end part of the elbow bone A delay in the process of formation and maturation of the epiphysis of one or more long bones that are part of the elbow. UMLS:C4025487 Delayed maturation of the end part of the elbow bone HP:0003947 Delayed elbow epiphyseal ossification A delay in the process of formation and maturation of the epiphysis of one or more long bones that are part of the elbow. Delayed maturation of the end part of the elbow bone UMLS:C4025485 Abnormal wide portion of elbow bone HP:0003949 Abnormal elbow metaphysis morphology Abnormal wide portion of elbow bone Absence of one or more forearm bones associated with congenital failure of development. UMLS:C4021701 Absent forearm bone Aplasia of the forearm bones HP:0003953 Absent forearm bone Absence of one or more forearm bones associated with congenital failure of development. Absent forearm bone UMLS:C4025479 Deformed forearm bones HP:0003959 Deformed forearm bones Deformed forearm bones UMLS:C4025475 HP:0003964 Osteoporotic forearm bones The total absence of the hand, with no bony elements distal to the radius or ulna. SNOMEDCT_US:371199008 UMLS:C0265594 Absent hand Acheiria HP:0004050 Absent hand The total absence of the hand, with no bony elements distal to the radius or ulna. PMID:19125433 Absent hand Ossification of hand bones is less advanced than would be expected according to age-adjusted norms. UMLS:C4020833 UMLS:C4021686 Delay maturation/delayed ossification of the hand Delayed maturation of the hand bones HP:0004052 Delayed ossification of the hand bones Ossification of hand bones is less advanced than would be expected according to age-adjusted norms. Delayed maturation of the hand bones Deviated fingers is a term that should be used if one or more fingers of the hand are deviated from their normal position, either to the radial or ulnar side. A deviation of a finger can be caused by an abnormal form of one or more of the phalanges of the affected finger, or by a deviation or displacement of one or more phalanges. HP:0006229 SNOMEDCT_US:203556007 SNOMEDCT_US:26517000 UMLS:C0410740 Atypical position of finger Deviated fingers Finger pointing in a different direction than usual HP:0004097 Deviation of finger Deviated fingers is a term that should be used if one or more fingers of the hand are deviated from their normal position, either to the radial or ulnar side. A deviation of a finger can be caused by an abnormal form of one or more of the phalanges of the affected finger, or by a deviation or displacement of one or more phalanges. Atypical position of finger Finger pointing in a different direction than usual Significant increase in the length and girth of most or all of a digit compared to its contralateral digit (if unaffected) or compared to what would be expected for age/body build. The increased girth is accompanied by an increase in the dorso-ventral dimension AND the lateral dimension of the digit. MEDDRA:10025386 MSH:C562546 SNOMEDCT_US:48449000 UMLS:C0265552 Finger overgrowth Megalodactyly HP:0004099 There are no recognized standards for the girth of digits and this finding can vary substantially in the population. This assessment relies on the judgment of the examiner to recognize when the difference between the expected and the observed is significant. The affected digits should be specified. The definition does not mandate the component of the increased size (bone, connective tissue, etc.), but should exclude edema. The requirement that the girth is most, or all, of the digit is intended to distinguish this from broad fingertips. This should be distinguished from Broad fingers or Broad fingertips as the girth is circumferential in macrodactyly, which is not the case for broad fingers or broad fingertips, which are increased only (or predominantly) in their lateral (A/P) width. Macrodactyly Significant increase in the length and girth of most or all of a digit compared to its contralateral digit (if unaffected) or compared to what would be expected for age/body build. The increased girth is accompanied by an increase in the dorso-ventral dimension AND the lateral dimension of the digit. PMID:19125433 MEDDRA:10025386 Macrodactyly Finger overgrowth This term groups together three conditions that presumably represent different degrees of severity of a midline defect of the nose or nasal tip. 2009-01-21T04:59:54Z HP:0003190 UMLS:C4025411 UMLS:C4280539 Central defect of nose Central nasal defect Midline defect of the nose Midline nasal defect Central cleft of nose Midline cleft of nose HP:0004122 Midline defect of the nose This term groups together three conditions that presumably represent different degrees of severity of a midline defect of the nose or nasal tip. Central defect of nose Central nasal defect Midline defect of the nose Midline nasal defect Central cleft of nose Midline cleft of nose An abnormality affecting one or both 5th fingers. UMLS:C4021678 Abnormality of the 5th finger Abnormality of the little finger Abnormality of the pinkie finger Abnormality of the pinky finger HP:0004207 Abnormal 5th finger morphology An abnormality affecting one or both 5th fingers. Abnormality of the little finger Abnormality of the pinkie finger Abnormality of the pinky finger Abnormality of the phalanges of the 5th (little) finger. UMLS:C4025408 Abnormality of the little finger bone Abnormality of the phalanges of the 5th finger Abnormality of the pinkie finger bone Abnormality of the pinky finger bone HP:0004213 Abnormal 5th finger phalanx morphology Abnormality of the phalanges of the 5th (little) finger. Abnormality of the little finger bone Abnormality of the pinkie finger bone Abnormality of the pinky finger bone UMLS:C4025406 Abnormality of the middle bone of little finger Abnormality of the middle bone of pinkie finger Abnormality of the middle bone of pinky finger HP:0004219 Abnormality of the middle phalanx of the 5th finger Abnormality of the middle bone of little finger Abnormality of the middle bone of pinkie finger Abnormality of the middle bone of pinky finger Hypoplastic/small middle phalanx of the fifth finger. HP:0001243 HP:0003069 HP:0004221 HP:0005649 HP:0005706 HP:0005734 HP:0005813 UMLS:C1834060 5th finger middle phalangeal hypoplasia Brachymesophalangism V Brachymesophalangy V (finger) Fifth finger mid-phalanx hypoplasia Hypoplastic fifth finger middle phalanx Hypoplastic middle phalanx of the 5th finger Hypoplastic/small middle phalanx of the 5th finger Hypoplastic/small middle phalanx of the little finger Short middle bone of the little finger Short middle bone of the pinkie finger Short middle bone of the pinky finger Short middle phalanx of the little finger Type A3 brachydactyly HP:0004220 Brachymesophalangia-V, a short and broad middle phalanx of the fifth digit, is the most common of all skeletal anomalies of the hand. When this feature appears alone, it is clinically known as brachydactyly type A3 (BDA3). Short middle phalanx of the 5th finger Hypoplastic/small middle phalanx of the fifth finger. PMID:18494372 Short middle bone of the little finger Short middle bone of the pinkie finger Short middle bone of the pinky finger Abnormality of the epiphysis of the middle phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. UMLS:C4025405 Abnormality of the end part of middle little finger bone Abnormality of the end part of middle pinkie finger bone Abnormality of the end part of middle pinky finger bone HP:0004224 Abnormality of the epiphysis of the middle phalanx of the 5th finger Abnormality of the epiphysis of the middle phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. Abnormality of the end part of middle little finger bone Abnormality of the end part of middle pinkie finger bone Abnormality of the end part of middle pinky finger bone Abnormality of the distal phalanx of the 5th (little) finger. UMLS:C4021673 Abnormality of the distal phalanx of the little finger Abnormality of the outermost little finger bone Abnormality of the outermost pinkie finger bone Abnormality of the outermost pinky finger bone Abnormality of the terminal phalanx of the little finger HP:0004225 Abnormality of the distal phalanx of the 5th finger Abnormality of the distal phalanx of the 5th (little) finger. Abnormality of the outermost little finger bone Abnormality of the outermost pinkie finger bone Abnormality of the outermost pinky finger bone Hypoplastic/small distal phalanx of the fifth finger. HP:0006171 UMLS:C1836674 Brachytelophalangism V Fifth digit distal phalangeal hypoplasia Hypoplastic/small terminal phalanx of the little finger Short distal phalanx of the fifth finger Short outermost little finger bone Short outermost pinkie finger bone Short outermost pinky finger bone HP:0004227 Short distal phalanx of the 5th finger Hypoplastic/small distal phalanx of the fifth finger. Short outermost little finger bone Short outermost pinkie finger bone Short outermost pinky finger bone The presence of more than the normal number of carpal bones. Extra wrist bones SNOMEDCT_US:20136007 SNOMEDCT_US:9181003 UMLS:C0265609 Supernumerary carpal bones HP:0004232 Accessory carpal bones The presence of more than the normal number of carpal bones. Extra wrist bones Increased size of carpal bones. Large wrist bones UMLS:C4021671 Large carpals HP:0004237 Large carpal bones Increased size of carpal bones. Large wrist bones UMLS:C4025376 UMLS:C4280534 Deficient maturation of hand bones HP:0004274 Deficient ossification of hand bones Deficient maturation of hand bones UMLS:C3276746 Duplication of hand bones HP:0004275 Duplication of hand bones Duplication of hand bones UMLS:C4025374 Irregular maturation of hand bones HP:0004280 Irregular ossification of hand bones Irregular maturation of hand bones UMLS:C4025368 HP:0004288 Pseudoepiphyses of hand bones An abnormality of the gastric mucous membrane. 2008-02-20T11:12:00Z UMLS:C4025362 Abnormality of the gastric mucosa Abnormality of the mucous membrane layer of stomach HP:0004295 Abnormal gastric mucosa morphology An abnormality of the gastric mucous membrane. Abnormality of the mucous membrane layer of stomach 2008-02-20T11:24:00Z UMLS:C4025361 Abnormality of GI blood vessels Abnormality of GI vasculature Abnormality of gastrointestinal vasculature HP:0004296 Abnormal gastrointestinal vascular morphology Abnormality of GI blood vessels Abnormality of GI vasculature An abnormality of the biliary system. 2008-02-20T11:34:00Z UMLS:C0940767 HP:0004297 Abnormality of the biliary system An abnormality of the biliary system. The presence of any abnormality affecting the abdominal wall. 2008-02-20T11:40:00Z HP:0001462 UMLS:C4021664 Abnormality of external features of the abdomen Abnormality of the abdominal wall HP:0004298 Abnormality of the abdominal wall The presence of any abnormality affecting the abdominal wall. Abnormality of the abdominal wall Any abnormality of the skeletal muscle cell. Muscle fibers are subdivided into two types. Type I fibers are fatigue-resistant and rich in oxidative enzymes (they stain light with the myosin ATPase reaction), and type II fibers are fast-contracting, fatigue-prone, and rich in glycolytic enzymes (these fibers stain darkly). Normal muscle tissue has a random distribution of type I and type II fibers. 2008-02-20T12:04:00Z HP:0003706 HP:0011806 UMLS:C4021663 Abnormal muscle fibre morphology Abnormal skeletal muscle fiber morphology Abnormal skeletal muscle fibre morphology Abnormality of muscle fibers Abnormality of muscle fibres HP:0004303 Normal human muscle is composed of many individual muscle fibers bundled together by layers of connective tissue that are arranged in a nesting-doll like fashion. The inner most structure, the single muscle fiber, is covered by a thin layer of primarily reticular fibers called the endomysium. The endomysium is quite inconspicuous and muscle fibers appear to be in direct contact with each other. The finest capillaries, nerve twigs and lymphatic capillaries are found within the endomysium. Groups of muscle fibers are bound together by the thicker perimysium, forming structures called fascicles. Capillaries, nerve fibers and lymphatic vessels also track in the perimyseum. Bundles of fascicles are encased within the dense irregular connective tissue of the epimysium. These connective tissue layers provide mechanical protection for the muscle fibers and increase the tensile strength of the muscle. The layers are continuous with the tendon, which provides attachment to bone. Individual muscle fibers are syncytia, formed by embryonic fusion of many myoblasts or later, myosatellite cells. Each muscle fiber contains many nuclei, peripherally positioned immediately adjacent to the sarcolemmal membrane. In healthy muscle only 3-5 percent of fibers contain nuclei that are located internally, within the cell, but many disease processes lead to internal nuclei. Each nucleus provides a segment of the cell with needed translated protein products. Abnormal muscle fiber morphology Any abnormality of the skeletal muscle cell. Muscle fibers are subdivided into two types. Type I fibers are fatigue-resistant and rich in oxidative enzymes (they stain light with the myosin ATPase reaction), and type II fibers are fast-contracting, fatigue-prone, and rich in glycolytic enzymes (these fibers stain darkly). Normal muscle tissue has a random distribution of type I and type II fibers. PMID:22938878 Abnormal muscle fibre morphology Abnormal skeletal muscle fibre morphology Abnormality of muscle fibres An abnormality of the endocardium. 2008-02-20T01:23:00Z HP:0005260 UMLS:C4021662 Abnormality of the endocardium Abnormality of the endomycoardium HP:0004306 Abnormal endocardium morphology An abnormality of the endocardium. Developmental defect characterized by an anomalous anatomic location of the heart. 2008-02-20T01:23:00Z UMLS:C4025359 HP:0004307 Abnormal anatomic location of the heart An abnormality of macrophages. 2008-02-20T03:14:00Z HP:0004310 UMLS:C4021661 Abnormality of histiocytes Abnormality of macrophages HP:0004311 Abnormal macrophage morphology An abnormality of macrophages. A reticulocyte abnormality. 2008-02-20T03:19:00Z UMLS:C4025358 Abnormality of reticulocytes HP:0004312 Reticulocytes are immature erythrocytes that show a basophilic reticulum under vital staining. Abnormal reticulocyte morphology A reticulocyte abnormality. An abnormally decreased level of immunoglobulin in blood. 2008-02-20T03:34:00Z HP:0010703 MSH:D000361 SNOMEDCT_US:119250001 UMLS:C0086438 UMLS:C4048270 Decreased antibody level in blood Decreased immunoglobulin level Decreased serum immunoglobulin Hypogammaglobulinemia Immunoglobulin deficiency Reduced immunoglobulin levels HP:0004313 In humans, immunoglobulins comprise the five antibody isotypes IgA, IgD, IgE, IgG and IgM. Decreased circulating antibody level An abnormally decreased level of immunoglobulin in blood. A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms). 2008-02-27T03:19:00Z HP:0001509 HP:0003501 HP:0003507 HP:0003512 HP:0003518 HP:0003519 HP:0008871 HP:0008882 HP:0008888 HP:0008913 SNOMEDCT_US:237836003 UMLS:C0349588 Decreased body height Height less than 3rd percentile Short stature Small stature Stature below 3rd percentile HP:0004322 Short stature A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms). Decreased body height Short stature Small stature An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. 2008-02-27T03:21:00Z HP:0010718 UMLS:C0878621 UMLS:C4025357 Abnormality of body weight Abnormality of habitus HP:0004323 Abnormality of body weight An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. Abnormality of body weight Abnormally increased body weight. 2008-02-27T03:21:00Z HP:0045083 MSH:D015430 SNOMEDCT_US:161831008 SNOMEDCT_US:262286000 SNOMEDCT_US:8943002 UMLS:C0043094 Increased body weight Weight gain HP:0004324 Increased body weight Increased body weight Weight gain Abnormally low body weight. 2008-02-27T03:22:00Z HP:0001823 HP:0001826 MSH:D013851 MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:248342006 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C0041667 UMLS:C1262477 UMLS:C1844806 Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile HP:0004325 Decreased body weight Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile Severe weight loss, wasting of muscle, loss of appetite, and general debility related to a chronic disease. 2008-02-27T03:23:00Z MSH:D002100 SNOMEDCT_US:238108007 SNOMEDCT_US:285384003 UMLS:C0006625 Wasting syndrome HP:0004326 Cachexia Severe weight loss, wasting of muscle, loss of appetite, and general debility related to a chronic disease. Wasting syndrome Any structural anomaly of the vitreous body. 2008-02-27T04:20:00Z UMLS:C4025356 Abnormal vitreous humour morphology HP:0004327 The vitreous humor is the clear gel that fills the space between the lens and the retina. Abnormal vitreous humor morphology Any structural anomaly of the vitreous body. Abnormal vitreous humour morphology An abnormality of the anterior segment of the eyeball (which comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens). 2008-02-27T04:23:00Z UMLS:C4025355 Abnormal anterior segment morphology Abnormality of the anterior segment of the eye Abnormality of the anterior segment of the eyeball Abnormality of the anterior segment of the globe HP:0004328 The anterior segment comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens. Abnormal anterior eye segment morphology An abnormality of the anterior segment of the eyeball (which comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens). 2008-02-27T04:25:00Z UMLS:C4025354 Abnormal morphology of the posterior segment of the globe Abnormality of the posterior segment of the eye Abnormality of the posterior segment of the eyeball Abnormality of the posterior segment of the globe HP:0004329 The posterior segment comprises the anterior hyaloid membrane and all of the optical structures behind it: the vitreous humor, retina, choroid, and optic nerve. Abnormal posterior eye segment morphology An increase in the magnitude or amount of ossification of the skull. 2008-02-28T11:54:00Z SNOMEDCT_US:17401000119104 UMLS:C0020496 UMLS:C4072850 UMLS:C4072851 Hyperossification of skull Hyperostosis of skull Sclerosis of bones of skull Sclerosis of skull Increased Mineralization of skull Increased calcification of skull HP:0004330 Increased skull ossification An increase in the magnitude or amount of ossification of the skull. Hyperossification of skull Hyperostosis of skull Sclerosis of bones of skull Sclerosis of skull Increased Mineralization of skull Increased calcification of skull A reduction in the magnitude or amount of ossification of the skull. 2008-02-28T11:54:00Z HP:0003780 SNOMEDCT_US:253980008 UMLS:C0432073 UMLS:C4280533 Decreased bone formation of skull Deficient skull ossification Hypoossification of skull Ossification defect of skull Poorly mineralized skull Poorly ossified skull Poorly ossified skull bones Decreased calcification of skull Decreased mineralization of skull HP:0004331 Decreased skull ossification A reduction in the magnitude or amount of ossification of the skull. Decreased bone formation of skull Hypoossification of skull Ossification defect of skull Poorly ossified skull Decreased calcification of skull Decreased mineralization of skull An abnormality of lymphocytes. 2008-02-28T06:46:00Z HP:0001887 HP:0012140 SNOMEDCT_US:250284007 UMLS:C0427546 Abnormal lymphocytes Abnormality of cells of the lymphoid lineage HP:0004332 A lymphocyte refers to a cell of the B cell, T cell, or natural killer cell lineage. Abnormal lymphocyte morphology An abnormality of lymphocytes. Partial or complete wasting (atrophy) of the skin. 2008-03-04T06:24:00Z HP:0000985 HP:0001077 MEDDRA:10040799 SNOMEDCT_US:399979006 SNOMEDCT_US:400190005 UMLS:C0151514 Atrophic skin Skin atrophy Skin degeneration HP:0004334 Dermal atrophy Partial or complete wasting (atrophy) of the skin. MEDDRA:10040799 Skin atrophy Skin degeneration Abnormality of an amino acid metabolic process. 2008-03-08T07:53:00Z UMLS:C1328440 Amino acid levels abnormal HP:0004337 Abnormality of amino acid metabolism Abnormality of an amino acid metabolic process. Any deviation from the normal concentration of a aromatic amino acid in the blood circulation. 2008-03-08T07:55:00Z UMLS:C4025352 Abnormality of aromatic amino acid family metabolism HP:0004338 Abnormal circulating aromatic amino acid concentration Any deviation from the normal concentration of a aromatic amino acid in the blood circulation. Any deviation from the normal concentration of a sulfur amino acid in the blood circulation. 2008-03-08T08:01:00Z UMLS:C4021660 Abnormal circulating sulphur amino acid concentration Abnormality of sulfur-containing amino acids HP:0004339 Cysteine and methionine contain a sulfur atom. Abnormal circulating sulfur amino acid concentration Any deviation from the normal concentration of a sulfur amino acid in the blood circulation. HPO_CONTRIBUTOR:gcarletti Abnormal circulating sulphur amino acid concentration 2008-03-08T08:08:00Z UMLS:C4021659 Abnormality of B-vitamin metabolism HP:0004340 Abnormality of vitamin B metabolism 2008-03-08T08:09:00Z UMLS:C4021658 Abnormality of the vitamin B12 metabolism HP:0004341 Abnormality of vitamin B12 metabolism This term applies to all changes in bone mineral density which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. Changes may affect all bones of the organism, just certain bones or only parts of bones and include decreased mineralisation as may be seen in osteoporosis or increased mineralisation and or ossification as in osteopetrosis, exostoses or any kind of atopic calicfications of different origin and distribution. The overall amount of mineralization of the bone-organ can be measured as the amount of matter per cubic centimeter of bones, usually measured by densitometry of the lumbar spine or hip. The measurements are usually reported as g/cm3 or as a Z-score (the number of standard deviations above or below the mean for the patient's age and sex). Note that measurement with this method does not reflect local changes in other bones, and as such might not be correct with regard the hole bone-organ. 2008-03-11T08:10:00Z UMLS:C4021657 Abnormality of bone mineralisation and ossification HP:0004348 Abnormality of bone mineral density This term applies to all changes in bone mineral density which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. Changes may affect all bones of the organism, just certain bones or only parts of bones and include decreased mineralisation as may be seen in osteoporosis or increased mineralisation and or ossification as in osteopetrosis, exostoses or any kind of atopic calicfications of different origin and distribution. The overall amount of mineralization of the bone-organ can be measured as the amount of matter per cubic centimeter of bones, usually measured by densitometry of the lumbar spine or hip. The measurements are usually reported as g/cm3 or as a Z-score (the number of standard deviations above or below the mean for the patient's age and sex). Note that measurement with this method does not reflect local changes in other bones, and as such might not be correct with regard the hole bone-organ. A reduction of bone mineral density, that is, of the amount of matter per cubic centimeter of bones. 2008-03-11T08:10:00Z UMLS:C2674432 Decreased bone mineral density Decreased bone mineral density Z score Low solidness and mass of the bones HP:0004349 Reduced bone mineral density A reduction of bone mineral density, that is, of the amount of matter per cubic centimeter of bones. Decreased bone mineral density Low solidness and mass of the bones Any deviation from the normal concentration of a purine in the blood circulation. 2008-03-17T01:04:00Z UMLS:C4025346 Abnormal circulating purine level HP:0004352 Purines are nitrogenous bases including the two nucleotide bases deoxyadenosine and deoxyguanosine. Abnormal circulating purine concentration Any deviation from the normal concentration of a carboxylic acid in the blood circulation. 2008-03-17T01:11:00Z UMLS:C4025344 HP:0004354 Carboxylic acid refers to an organic compound that contains a carboxyl group (-COOH). Abnormal circulating carboxylic acid concentration Any deviation from the normal concentration of a carboxylic acid in the blood circulation. HPO_CONTRIBUTOR:gcarletti 2008-03-17T02:40:00Z UMLS:C4025342 HP:0004356 A major lysosomal function is the breakdown and recycling of macromolecules and organelles into basic precursors. Abnormality of lysosomal metabolism Any deviation from the normal circulation of leucine in the blood circulation. 2008-03-17T03:02:00Z UMLS:C4025341 HP:0004357 Abnormal circulating leucine concentration Any deviation from the normal circulation of leucine in the blood circulation. A deviation from the normal concentration of a fatty acid in the blood circulation. 2008-03-17T03:28:00Z UMLS:C4020830 UMLS:C4021656 Abnormality of fatty acid metabolism Fatty acids abnormal HP:0004359 A fatty acid is an aliphatic monocarboxylic acid derived from or contained in esterified form. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. R-COOH. Fatty acids are usually derived from triglycerides or phospholipids. Abnormal circulating fatty-acid concentration A deviation from the normal concentration of a fatty acid in the blood circulation. An abnormality of the balance or maintenance of the balance of acids and bases in bodily fluids, resulting in an abnormal pH. 2008-03-17T03:35:00Z MSH:D000137 UMLS:C0001118 Acid base imbalance HP:0004360 Abnormality of acid-base homeostasis An abnormality of the balance or maintenance of the balance of acids and bases in bodily fluids, resulting in an abnormal pH. Any deviation from the normal concentration of calcium in the blood circulation. 2008-03-17T04:15:00Z HP:0040077 Abnormal blood calcium concentration Abnormal blood calcium levels Abnormal circulating Ca concentration Abnormal circulating Ca2+ concentration HP:0004363 Abnormal circulating calcium concentration Any deviation from the normal concentration of calcium in the blood circulation. Abnormal blood calcium concentration Abnormal blood calcium levels Abnormal circulating Ca concentration Abnormal circulating Ca2+ concentration Any deviation from the normal concentration of a nitrogen compound in the blood circulation. 2008-03-17T04:51:00Z UMLS:C4025336 HP:0004364 Ammonia (NH3), one of the most clinically important nitrogen compounds in human metabolism, is a substance containing nitrogen resulting from the catabolism of protein. It is converted to the less toxic substance urea prior to excretion in urine. Abnormal circulating nitrogen compound concentration Any deviation from the normal concentration of a nitrogen compound in the blood circulation. HPO_CONTRIBUTOR:gcarletti An abnormality of glycolysis. 2008-03-17T05:00:00Z UMLS:C4025334 HP:0004366 Abnormality of glycolysis An abnormality of glycolysis. Abnormally elevated concentration of a purine compound. Purine compounds are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring. 2008-03-18T06:31:00Z UMLS:C4025332 Increased purine level Increased purine levels HP:0004368 Increased circulating purine concentration Increased purine levels Abnormally reduced concentration of a purine compound. Purine compounds are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring. 2008-03-18T06:32:00Z UMLS:C4025331 Decreased purine level Decreased purine levels HP:0004369 Decreased circulating purine concentration Decreased purine levels An abnormality of temperature homeostasis. 2008-03-18T06:34:00Z MSH:D001832 UMLS:C0005904 UMLS:C1832160 Abnormality of temperature regulation Poor temperature regulation Body temperature changes HP:0004370 Abnormality of temperature regulation An abnormality of temperature homeostasis. Abnormality of temperature regulation Poor temperature regulation Body temperature changes Abnormality of glycosaminoglycan metabolism. 2008-03-18T06:36:00Z UMLS:C4025330 HP:0004371 A glycosaminoglycan is any polysaccharide containing a substantial proportion of aminomonosaccharide residues. Glycosaminoglycan (GAG) are long unbranched polysaccharides consisting of a repeating disaccharide unit. Among the most common GAGs are chondroitin sulfate, dermatan sulfate, chondroitin sulfate, keratan sulfate, heparan sulfate, and hyaluronan. Abnormality of glycosaminoglycan metabolism Abnormality of glycosaminoglycan metabolism. Abnormality of the anal canal. 2008-03-18T08:11:00Z UMLS:C4025329 Abnormality of the anus HP:0004378 The anal canal is continuous proximally with the rectum and distally terminates with the anus. Abnormality of the anus Abnormality of the anal canal. Abnormality of the anus Abnormal calcification of the mitral valve. 2008-03-18T08:55:00Z HP:0005149 HP:0200129 SNOMEDCT_US:473372009 UMLS:C0919718 HP:0004382 Mitral valve calcification Abnormal calcification of the mitral valve. Underdevelopment of the left side of the heart. May include atresia of the aortic or mitral orifice and hypoplasia of the ascending aorta. 2008-03-18T08:56:00Z MSH:D018636 SNOMEDCT_US:62067003 UMLS:C0152101 Heart left ventricle hypoplasia Left ventricular hypoplasia Underdeveloped left heart HP:0004383 Hypoplastic left heart syndrome is an unsatisfactory term describing lethal underdevelopment of the left ventricle (LV). It represents the more severe end of a spectrum of LV hypoplasia, mandating single-ventricle palliation or cardiac transplantation. Less severe borderline ventricular hypoplasia may instead allow various biventricular therapeutic strategies and better long-term outcomes. Hypoplastic left heart Underdevelopment of the left side of the heart. May include atresia of the aortic or mitral orifice and hypoplasia of the ascending aorta. PMID:22192721 Underdeveloped left heart Inflammation of the alimentary part of the gastrointestinal system. 2008-03-18T09:01:00Z UMLS:C1535950 GI inflammation Gastrointestinal inflammation HP:0004386 Gastrointestinal inflammation GI inflammation Gastrointestinal inflammation A colon of abnormally small caliber. 2008-03-18T09:02:00Z MSH:C562563 SNOMEDCT_US:18389004 UMLS:C0266200 UMLS:C3553395 Microcolon on contrast enema HP:0004388 Microcolon A colon of abnormally small caliber. PMID:3484569 Microcolon on contrast enema 2008-03-18T09:11:00Z MSH:C562464 SNOMEDCT_US:78809005 SNOMEDCT_US:87252009 UMLS:C0236048 HP:0004394 Multiple gastric polyps An abnormality of the pylorus. 2008-03-18T09:15:00Z UMLS:C4025326 HP:0004400 Abnormality of the pylorus An abnormality of the pylorus. An abnormality of the nipple. 2008-03-18T09:18:00Z SNOMEDCT_US:700153004 UMLS:C3839073 Abnormality of the nipple HP:0004404 Abnormal nipple morphology An abnormality of the nipple. Abnormality of the nipple An anomaly in the ability to perceive and distinguish scents (odors). 2008-03-18T09:21:00Z HP:0004410 UMLS:C4021655 Abnormal sense of smell Abnormality of olfaction Abnormality of the sense of smell Smell defect HP:0004408 Abnormality of the sense of smell Abnormal sense of smell Abnormality of the sense of smell Smell defect An abnormality of the pulmonary artery. 2008-03-18T09:28:00Z SNOMEDCT_US:128588008 SNOMEDCT_US:198914002 SNOMEDCT_US:36110001 UMLS:C0009681 Abnormality of lung artery HP:0004414 Abnormality of the pulmonary artery An abnormality of the pulmonary artery. Abnormality of lung artery The formation of a blood clot inside an artery. 2008-03-18T09:32:00Z SNOMEDCT_US:65198009 UMLS:C0151942 Blood clot in artery HP:0004420 Arterial thrombosis The formation of a blood clot inside an artery. Blood clot in artery A forehead with abnormal flatness. 2008-03-18T09:41:00Z HP:0004659 UMLS:C1857485 Flat forehead Flattened forehead Frontal flattening HP:0004425 Flat forehead A forehead with abnormal flatness. Flat forehead Flattened forehead Frontal flattening An abnormality of the cheek- one of two bilateral soft tissue facial structures in the region of the face inferior to the eyes and between the nose and the ear. "Buccal" means relating to the cheek. The cheek is part of the midface 2008-03-18T09:42:00Z UMLS:C4025324 Abnormality of the cheek Abnormality of the cheeks Anomaly of the cheeks Deformity of the cheeks Malformation of the cheeks HP:0004426 Abnormal cheek morphology Abnormality of the cheek Abnormality of the cheeks Anomaly of the cheeks Deformity of the cheeks Malformation of the cheeks Excessive growth of the bones of cranium, i.e., of the skull. 2008-03-18T09:57:00Z HP:0002698 Enlargement of skull bones Excessive growth of skull bones Hypertrophy of cranial bones Overgrowth of skull bones Thick skull bones UMLS:C1832451 UMLS:C4280528 UMLS:C4280529 UMLS:C4280530 UMLS:C4280531 Hyperostosis of cranial bones Hyperostosis of cranial vault Increased ossification of cranial bones HP:0004437 Cranial hyperostosis Excessive growth of the bones of cranium, i.e., of the skull. Enlargement of skull bones Excessive growth of skull bones Hypertrophy of cranial bones Overgrowth of skull bones Thick skull bones Hyperostosis of cranial bones Increased ossification of cranial bones The presence of abnormally shaped erythrocytes. 2008-03-18T10:06:00Z SNOMEDCT_US:165479004 UMLS:C0221281 HP:0004447 General description for abnormally shaped erythrocytes. Poikilocytosis The presence of abnormally shaped erythrocytes. An abnormality of the middle-ear ossicles (three small bones called malleus, incus, and stapes) that are contained within the middle ear and serve to transmit sounds from the air to the fluid-filled labyrinth (cochlea). HP:0001759 UMLS:C1836678 Malformed ossicles Ossicular malformation HP:0004452 Abnormality of the middle ear ossicles An abnormality of the middle-ear ossicles (three small bones called malleus, incus, and stapes) that are contained within the middle ear and serve to transmit sounds from the air to the fluid-filled labyrinth (cochlea). The progressive development of an abnormally large skull. HP:0000261 UMLS:C1859896 Macrocephaly, progressive Progressively abnormally enlarging cranium Progressively abnormally enlarging skull HP:0004481 Progressive macrocephaly The progressive development of an abnormally large skull. Progressively abnormally enlarging cranium Progressively abnormally enlarging skull Excessive growth of the calvaria. Enlargement of calvarial bones Excessive growth of calvarial bones Hypertrophy of calvarial bones Overgrowth of calvarial bones Thick calvarial bones MSH:C537963 UMLS:C1863351 UMLS:C4280519 UMLS:C4280520 Hyperostosis of calvarial bones Increased ossification of calvarial bones Overgrowth of skullcap HP:0004490 The calvaria (skull cap) is made up of the frontal, occipital, right and left parietal, right and left temporal, sphenoid, and ethmoid bones, and thus comprises the upper dome-like part of the skull and does not include the lower jaw. Calvarial hyperostosis Excessive growth of the calvaria. Enlargement of calvarial bones Excessive growth of calvarial bones Hypertrophy of calvarial bones Overgrowth of calvarial bones Thick calvarial bones Hyperostosis of calvarial bones Increased ossification of calvarial bones Overgrowth of skullcap Excessive growth of the craniofacial bones. Enlargement of craniofacial bones Excessive growth of craniofacial bones Hypertrophy of craniofacial bones Overgrowth of craniofacial bones Thick craniofacial bones UMLS:C1868085 UMLS:C4280516 UMLS:C4280517 UMLS:C4280518 Excessive bone growth of the skull and face Hyperostosis of craniofacial bones Increased ossification of craniofacial bones HP:0004493 Craniofacial hyperostosis Excessive growth of the craniofacial bones. Enlargement of craniofacial bones Excessive growth of craniofacial bones Hypertrophy of craniofacial bones Overgrowth of craniofacial bones Thick craniofacial bones Excessive bone growth of the skull and face Hyperostosis of craniofacial bones Increased ossification of craniofacial bones Hyperplasia of the islets of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. HP:0001736 HP:0006275 UMLS:C0597167 Hyperplastic islets of langerhans Hypertrophic pancreatic islets Islet of Langerhans hyperplasia Islets of langerhans hypertrophy Pancreatic islet-cell hypertrophy HP:0004510 The islets of Langerhans contain the alpha cells (producing glucagon), beta cells (insulin and amylin), delta cells (somatostatin),PP cells (pancreatic polypeptide), and the epsilon cells (ghrelin). Pancreatic islet-cell hyperplasia Hyperplasia of the islets of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. A flattened vertebral body shape with reduced distance between the vertebral endplates affecting the cervical spine. HP:0005641 UMLS:C1856641 Flattened cervical vertebral bodies HP:0004558 Cervical platyspondyly A flattened vertebral body shape with reduced distance between the vertebral endplates affecting the cervical spine. Increased bone density affecting the bones of the spine (vertebral column). UMLS:C4020828 UMLS:C4280254 UMLS:C4280513 UMLS:C4280514 UMLS:C4280515 Increased density of spinal bone Ivory spinal bone Compact spinal bone Concrete spinal bone Dense spinal bone Eburnation of spinal bone Increased spinal bone density Z-score Sclerosis of spinal bone HP:0004563 Increased spinal bone density Increased bone density affecting the bones of the spine (vertebral column). Increased density of spinal bone Ivory spinal bone Compact spinal bone Concrete spinal bone Dense spinal bone Eburnation of spinal bone Sclerosis of spinal bone Increased top to bottom height of vertebral bodies. HP:0005693 UMLS:C1864853 Tall vertebral bodies HP:0004570 Increased vertebral height Increased top to bottom height of vertebral bodies. UMLS:C4025311 HP:0004582 Irregularity of vertebral bodies Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward. HP:0002952 HP:0004561 HP:0004620 UMLS:C1856087 Biconcave 'codfish' vertebrae Biconcave vertebrae Codfish vertebrae Fish vertebrae Scalloping of vertebral bodies HP:0004586 This finding has been called fish or codfish vertebra because of the characteristic biconcave form of fish vertebral bodies. Biconcave vertebral bodies Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward. UMLS:C4025310 HP:0004589 Dysplasia of second lumbar vertebra UMLS:C1970816 Small sacrum HP:0004590 Hypoplastic sacrum Small sacrum UMLS:C1835444 HP:0004591 Disc-like vertebral bodies A flattened vertebral body shape with reduced distance beween the vertebral endplates affecting the thoracic spine. UMLS:C1862428 HP:0004592 Thoracic platyspondyly A flattened vertebral body shape with reduced distance beween the vertebral endplates affecting the thoracic spine. UMLS:C1832983 HP:0004599 Absent or minimally ossified vertebral bodies A lack of ossification of the vertebral bodies. HP:0008427 UMLS:C1860202 HP:0004606 Unossified vertebral bodies A lack of ossification of the vertebral bodies. Reduced size of cervical vertebrae. HP:0008429 UMLS:C1851130 Small cervical vertebrae HP:0004629 Small cervical vertebral bodies Reduced size of cervical vertebrae. Underdevelopment of one or more muscles innervated by the facial nerve (the seventh cranial nerve). Small facial muscles UMLS:C1834042 UMLS:C4280509 UMLS:C4280510 UMLS:C4280511 Decreased size of facial muscles Deficiency of facial musculature Underdevelopment of facial muscles Atrophy of facial musculature Hypotrophic facial musculature HP:0004660 Hypoplasia of facial musculature Underdevelopment of one or more muscles innervated by the facial nerve (the seventh cranial nerve). Small facial muscles Decreased size of facial muscles Deficiency of facial musculature Underdevelopment of facial muscles Atrophy of facial musculature Hypotrophic facial musculature UMLS:C1859116 Large ankle bones HP:0004679 Large tarsal bones Large ankle bones Decrease in mass and density of the metatarsal bones. UMLS:C1836873 HP:0004699 Osteoporotic metatarsal Decrease in mass and density of the metatarsal bones. Short (hypoplastic) fifth metatarsal bone. HP:0004702 HP:0010671 UMLS:C4021649 Hypoplasia of the fifth metatarsal bone Short 5th long bone of foot HP:0004704 Short fifth metatarsal Short (hypoplastic) fifth metatarsal bone. Short 5th long bone of foot An abnormality of the renal collecting system. HP:0004731 UMLS:C1851303 Abnormal collecting system Abnormality of the renal collecting system Renal collecting system anomalies HP:0004742 Abnormal renal collecting system morphology An abnormality of the renal collecting system. Underdevelopment or reduced size of the heart right ventricle, often due to a reduced number of cells. HP:0004951 Fyler:1821 UMLS:C4082954 Heart right ventricle hypoplasia Small right heart chamber Underdeveloped right heart chamber HP:0004762 Hypoplasia of right ventricle Underdevelopment or reduced size of the heart right ventricle, often due to a reduced number of cells. MP:0010422 Heart right ventricle hypoplasia Small right heart chamber Underdeveloped right heart chamber Underdevelopment of the small intestine. UMLS:C4025291 Underdeveloped small intestine HP:0004790 Hypoplasia of the small intestine Underdevelopment of the small intestine. Underdeveloped small intestine A type of poikilocytosis characterized by the presence in the blood of erythrocytes of varying sizes and abnormal shapes. UMLS:C2675920 HP:0004823 Anisopoikilocytosis A type of poikilocytosis characterized by the presence in the blood of erythrocytes of varying sizes and abnormal shapes. An abnormally elevated blood pressure in the circulation of the pulmonary artery. HP:0004958 UMLS:C3805917 Elevated lung artery pressure increased pulmonary artery pressure HP:0004890 Elevated pulmonary artery pressure An abnormally elevated blood pressure in the circulation of the pulmonary artery. increased pulmonary artery pressure Concentration of vitamin A below the lower limit of normal in the blood circulation. MSH:D014802 SNOMEDCT_US:72000004 UMLS:C0042842 Low levels of vitamin A Vitamin A deficiency HP:0004905 Reduced circulating vitamin A concentration Vitamin A deficiency An abnormality of magnesium ion homeostasis. HP:0008274 UMLS:C4020826 UMLS:C4025274 Abnormal Mg concentration Abnormality of magnesium homeostasis Abnormal magnesium metabolism HP:0004921 Abnormal magnesium concentration An abnormality of magnesium ion homeostasis. Abnormal Mg concentration An increased concentration of L-phenylalanine in the blood. MSH:D010661 SNOMEDCT_US:68528007 UMLS:C0751435 HP:0004923 Hyperphenylalaninemia An increased concentration of L-phenylalanine in the blood. 2008-03-26T04:07:00Z UMLS:C4025271 Abnormality of the lung blood vessels HP:0004930 Abnormality of the pulmonary vasculature Abnormality of the lung blood vessels Abnormal calcification of the vasculature. MSH:D061205 SNOMEDCT_US:237897009 UMLS:C0342649 HP:0004934 Vascular calcification Abnormal calcification of the vasculature. Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. MSH:D020246 SNOMEDCT_US:111293003 UMLS:C0042487 Blood clot in vein HP:0004936 Venous thrombosis Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. Blood clot in vein Calcification, that is, pathological deposition of calcium salts, affecting arteries distributed throughout the body. HP:0004967 UMLS:C4025269 Generalised arterial calcification HP:0004940 Generalized arterial calcification Calcification, that is, pathological deposition of calcium salts, affecting arteries distributed throughout the body. Generalised arterial calcification A congenital defect with aplasia (absence) of one of the right or left pulmonary artery. SNOMEDCT_US:86252004 UMLS:C0265905 Absent lung artery Missing pulmonary artery HP:0004960 This is a rare feature that has been observed in recessive lethal osteogenesis imperfecta with mutation in CRTAP. Absent pulmonary artery A congenital defect with aplasia (absence) of one of the right or left pulmonary artery. PMID:17192541 Absent lung artery Missing pulmonary artery An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the thoracic aorta. UMLS:C1969292 HP:0004962 Thoracic aorta calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the thoracic aorta. Calcification, that is, pathological deposition of calcium salts in the aorta. UMLS:C1096249 HP:0004963 Note that the phrase "aortic calcification" is mainly used to describe calcification of the aortic valve rather than of the aorta itself. Calcification of the aorta Calcification, that is, pathological deposition of calcium salts in the aorta. Underdevelopment of the pulmonary artery. Fyler:2966 SNOMEDCT_US:54682008 UMLS:C0265910 Underdeveloped lung artery Underdeveloped pulmonary artery HP:0004971 Pulmonary artery hypoplasia Underdevelopment of the pulmonary artery. Underdeveloped lung artery Underdeveloped pulmonary artery Abnormally increased density of metaphyseal bone. UMLS:C3552526 Increased bone density in wide portion of long bone Sclerotic metaphyses HP:0004979 Metaphyseal sclerosis Abnormally increased density of metaphyseal bone. Increased bone density in wide portion of long bone UMLS:C1857192 HP:0004997 Multicentric ossification of proximal humeral epiphyses Absence or underdevelopment of the proximal epiphysis of the femur. UMLS:C4025261 Absent/small end part of innermost thighbone Absent/underdeveloped end part of innermost thighbone HP:0005003 Aplasia/Hypoplasia of the capital femoral epiphysis Absence or underdevelopment of the proximal epiphysis of the femur. Absent/small end part of innermost thighbone Absent/underdeveloped end part of innermost thighbone Developmental hypoplasia (shortening) of all phalanges of the foot. UMLS:C4025257 Short toe bones HP:0005035 Shortening of all phalanges of the toes Developmental hypoplasia (shortening) of all phalanges of the foot. Short toe bones Overgrowth of the proximal part of the fibula. UMLS:C2673395 Overgrowth of innermost part of calf bone HP:0005067 Proximal fibular overgrowth Overgrowth of the proximal part of the fibula. Overgrowth of innermost part of calf bone Deterioration or loss of the tissues of the cochlea. 2008-03-25T05:06:00Z HP:0008156 UMLS:C1849095 Progressive cochlear degeneration HP:0005102 Cochlear degeneration Deterioration or loss of the tissues of the cochlea. Ossification affecting the external ear cartilage. 2008-03-25T05:09:00Z HP:0008549 UMLS:C1408806 Cartilaginous ossification of pinnae Ossification of pinnae Petrified ear Ear cartilage calcification HP:0005103 Calcification of the auricular cartilage Ossification affecting the external ear cartilage. PMID:15523361 PMID:23259082 Underdevelopment of the nasal septum. 2008-03-25T05:15:00Z UMLS:C1861328 Decreased size of nasal septum Decreased size of septum of nose Hypoplasia of septum of nose Small nasal septum Small septum of nose HP:0005104 Hypoplastic nasal septum Underdevelopment of the nasal septum. Decreased size of nasal septum Decreased size of septum of nose Hypoplasia of septum of nose Small nasal septum Small septum of nose 2008-03-25T05:21:00Z Fyler:4870 UMLS:C4025252 Abnormal nose morphology Abnormal of morphology of nose Abnormal of nasal shape Abnormal of shape of nose HP:0005105 This is a category for overall abnormal morphology that may be replaced later with more exact descriptions. Abnormal nasal morphology Abnormal nose morphology Abnormal of morphology of nose Abnormal of nasal shape Abnormal of shape of nose An abnormality of the sacral bone. 2008-03-25T06:03:00Z UMLS:C4025250 Abnormality of the sacrum HP:0005107 The sacrum is the large, roughly triangular bone at the base of the verterbal column that is formed by fusion of the five sacral vertebrae S1 to S5. Abnormal sacrum morphology An abnormality of the sacral bone. Any structural abnormality of the intervertebral disk. 2008-03-25T06:05:00Z UMLS:C4025249 Abnormality of the intervertebral disc Abnormality of the intervertebral disk HP:0005108 Any abnormality of the fibrocartilaginous structures that are located between adjacent vertebral bodies. Abnormal intervertebral disk morphology Any structural abnormality of the intervertebral disk. Abnormality of the intervertebral disc Any structural abnormality of a cardiac atrium. 2008-03-26T04:12:00Z UMLS:C4025246 Abnormality of cardiac atrium morphology Abnormality of heart atrium HP:0005120 Abnormal cardiac atrium morphology Any structural abnormality of a cardiac atrium. Abnormality of heart atrium Refers to the specific combination of defects with a severely dysplastic pulmonary valve and massively dilated branch pulmonary arteries. HP:0005131 SNOMEDCT_US:6996004 UMLS:C0265831 Absent pulmonary valve HP:0005134 The distinctive feature of APVS is the airway obstruction caused by tracheobronchial compression that results from massive dilatation of the main pulmonary artery (PA) and its first- and second-order branches. Consequential tracheomalacia and bronchomalacia determine the timing and severity of respiratory compromise, as well as the morbidity and mortality of these patients. Absence of the pulmonary valve Refers to the specific combination of defects with a severely dysplastic pulmonary valve and massively dilated branch pulmonary arteries. HPO_CONTRIBUTOR:DDD_dbrown Mitral annular calcification (MAC) results from progressive calcium deposition along and beneath the mitral valve annulus. UMLS:C1835130 Premature calcification of mitral annulus HP:0005136 MAC is a common degenerative process involving the fibrous annulus of the mitral valve, and is generally an incidental finding associated with aging. This term applies if MAC occurs at a substantially younger age than usual. Mitral annular calcification Mitral annular calcification (MAC) results from progressive calcium deposition along and beneath the mitral valve annulus. PMID:23587525 Abnormal calcification of a cardiac valve. UMLS:C1856483 Calcifications of the cardiac valves HP:0005146 Cardiac valve calcification Abnormal calcification of a cardiac valve. An impairment of the electrical continuity between the atria and ventricles. UMLS:C4025244 HP:0005150 Abnormal atrioventricular conduction An impairment of the electrical continuity between the atria and ventricles. PMID:15372490 A type of cardiomyopathy characterized pathologically by hamartomatous lesions of cardiac Purkinje cells. MSH:C535584 UMLS:C1708371 Arachnocytosis of the myocardium Foamy myocardial transformation Focal lipid cardiomyopathy Infantile cardiomyopathy with histiocytoid changes Infantile xanthomatous cardiomyopathy Isolated cardiac lipidosis Myocardial or conduction system hamartoma Oncocytic cardiomyopathy HP:0005152 This HPO term intends to refer to the histological changes that characterize histiocytoid cardiomyopthy. The disease entity Histiocytoid cardiomyopathy is a rare arrhythmogenic disorder characterized by incessant ventricular tachycardia, cardiomegaly, and often sudden death by age 2 years. Histiocytoid cardiomyopathy A type of cardiomyopathy characterized pathologically by hamartomatous lesions of cardiac Purkinje cells. PMID:21585276 PMID:28050600 Underdeveloped, small left heart atrium Fyler:3040 UMLS:C1970625 Left atrium hypoplasia Underdeveloped left heart atrium HP:0005156 Hypoplastic left atrium A congenital malformation of the pulmonary valve characterized by leaflet deformation. UMLS:C1866206 Dysplasia of pulmonary valve Pulmonary valve dysplasia HP:0005164 Dysplastic pulmonary valve A congenital malformation of the pulmonary valve characterized by leaflet deformation. PMID:7704986 Synovial hyperplasia involves proliferation of mesenchymal stromal/stem cells and leads to synovial thickening, which can be observed radiographically. MSH:D013585 SNOMEDCT_US:240206002 UMLS:C0410574 Synovial hyperplasia Synovial hypertrophy HP:0005186 Synovial hyperplasia is a frequent clinical finding in patients with joint injury and other joint disorders. Synovial lining hyperplasia Synovial hyperplasia involves proliferation of mesenchymal stromal/stem cells and leads to synovial thickening, which can be observed radiographically. PMID:27412524 PMID:30618151 Absence of the abdominal musculature. UMLS:C3149223 Absent abdominal musculature HP:0005199 Aplasia of the abdominal wall musculature Absence of the abdominal musculature. Hypertrophy of the stomach. Increased stomach size UMLS:C1834341 UMLS:C4280502 HP:0005207 Gastric hypertrophy Hypertrophy of the stomach. Increased stomach size Underdevelopment of the colon. UMLS:C1392839 Hypoplasia of the colon Underdeveloped colon HP:0005210 Hypoplastic colon Underdevelopment of the colon. Underdeveloped colon The presence of abnormal calcium deposition lesions in the pancreas. UMLS:C1842406 Pancreatic calcifications HP:0005213 Pancreatic calcification The presence of abnormal calcium deposition lesions in the pancreas. Pancreatic calcifications UMLS:C1850328 HP:0005223 Duplicated colon The presence of developmental dysplasia of the pancreas. UMLS:C4019084 HP:0005232 Dysplasia is defined in MPATH as a distortion or deficiency of the tissue or cellular architecture. Pancreatic dysplasia The presence of developmental dysplasia of the pancreas. The presence of a hypoplastic gallbladder. SNOMEDCT_US:93259002 UMLS:C0345282 Hypoplastic gallbladder HP:0005233 Hypoplasia of the gallbladder The presence of a hypoplastic gallbladder. The presence of degenerative changes of the liver. UMLS:C4025230 HP:0005237 Degenerative liver disease The presence of degenerative changes of the liver. Developmental hypoplasia of the intestine. UMLS:C4021640 Hypoplastic intestines Underdeveloped instestine HP:0005245 Intestinal hypoplasia Developmental hypoplasia of the intestine. Underdeveloped instestine Underdevelopment of the abdominal musculature. UMLS:C3279407 Abdominal muscular hypoplasia HP:0005247 Hypoplasia of the abdominal wall musculature Underdevelopment of the abdominal musculature. HP:0001590 UMLS:C1837482 Small chest Small thorax HP:0005257 Thoracic hypoplasia Small chest Small thorax Any structural anomaly of the synovium, which is a membrane that lines the cavity of synovial joints and consists of a lining layer of macrophage-like synoviocytes and fibroblast-like synoviocytes, as well as a sublining of connective tissue. Synovial cells are thought to contribute to joint homeostasis by secreting various factors such as hyaluronic acid and lubricin important for joint lubrication and function, as well as disposing of the waste products. 2008-03-26T04:27:00Z UMLS:C4025225 HP:0005262 Abnormal synovial membrane morphology Any structural anomaly of the synovium, which is a membrane that lines the cavity of synovial joints and consists of a lining layer of macrophage-like synoviocytes and fibroblast-like synoviocytes, as well as a sublining of connective tissue. Synovial cells are thought to contribute to joint homeostasis by secreting various factors such as hyaluronic acid and lubricin important for joint lubrication and function, as well as disposing of the waste products. PMID:27412524 The presence of inflammation of the gastric mucous membrane. 2008-03-26T04:32:00Z MEDDRA:10017853 MSH:D005756 SNOMEDCT_US:4556007 UMLS:C0017152 Stomach inflammation HP:0005263 Gastritis The presence of inflammation of the gastric mucous membrane. MEDDRA:10017853 Gastritis Stomach inflammation An abnormality of the gallbladder. 2008-03-26T04:40:00Z SNOMEDCT_US:253803008 SNOMEDCT_US:49714001 UMLS:C0266249 Abnormality of the gallbladder Anomaly of the gallbladder HP:0005264 Abnormality of the gallbladder An abnormality of the gallbladder. Abnormality of the gallbladder An abnormality of the jejunum, i.e., of the middle section of the small intestine. 2008-03-26T04:44:00Z UMLS:C4025224 Abnormality of the jejunum HP:0005265 Abnormal jejunum morphology An abnormality of the jejunum, i.e., of the middle section of the small intestine. A discrete abnormal tissue mass that protrudes into the lumen of the intestine and is attached to the intestinal wall either by a stalk, pedunculus, or a broad base. 2008-03-26T04:46:00Z MSH:D007417 SNOMEDCT_US:254588001 UMLS:C0021846 Intestinal polyps HP:0005266 Intestinal polyp A discrete abnormal tissue mass that protrudes into the lumen of the intestine and is attached to the intestinal wall either by a stalk, pedunculus, or a broad base. Lack of the cartilage of the nasal septum. UMLS:C4021638 UMLS:C4280501 Absent nasal septal cartilage Absent nasal septum Ageneis of nasal septal cartilage Failure of development of nasal septal cartilage HP:0005273 Absent nasal septal cartilage Lack of the cartilage of the nasal septum. Absent nasal septal cartilage Absent nasal septum Ageneis of nasal septal cartilage Failure of development of nasal septal cartilage UMLS:C1855616 Cartilaginous nasal ossification HP:0005275 Cartilaginous ossification of nose Cartilaginous nasal ossification UMLS:C1844731 UMLS:C4280496 UMLS:C4280497 Decreased size of nasal tip Decreased size of tip of nose Hypoplasia of tip of nose Small nasal tip Small tip of nose Underdevelopment of nasal tip Underdevelopment of tip of nose Aplasia of nasal tip Deficient nasal tip Hypotrophic nasal tip Hypotrophic tip of nose HP:0005278 Hypoplastic nasal tip Decreased size of nasal tip Decreased size of tip of nose Hypoplasia of tip of nose Small nasal tip Small tip of nose Underdevelopment of nasal tip Underdevelopment of tip of nose Aplasia of nasal tip Deficient nasal tip Hypotrophic nasal tip Hypotrophic tip of nose Abnormality of the nostril. 2008-03-26T06:04:00Z UMLS:C4021637 Abnormal naris morphology Abnormality of the nares Abnormality of the nostrils Anomaly of the nares Deformity of the nares Deformity of the nostrils Malformation of the nares Malformation of the nostrils HP:0005288 Abnormal nostril morphology Abnormality of the nostril. Abnormality of the nostrils Anomaly of the nares Deformity of the nares Deformity of the nostrils Malformation of the nares Malformation of the nostrils UMLS:C1855736 UMLS:C4280491 UMLS:C4280492 UMLS:C4280493 Decreased size of internal carotid artery Small internal carotid artery Aplasia of internal carotid artery Deficiency of internal carotid artery Hypotrophic internal carotid artery HP:0005290 Internal carotid artery hypoplasia Decreased size of internal carotid artery Small internal carotid artery Aplasia of internal carotid artery Deficiency of internal carotid artery Hypotrophic internal carotid artery Calcification, that is, pathological deposition of calcium salts in the arch of aorta. UMLS:C1969291 HP:0005303 Aortic arch calcification Calcification, that is, pathological deposition of calcium salts in the arch of aorta. UMLS:C1970501 Underdeveloped lung veins HP:0005304 Hypoplastic pulmonary veins Underdeveloped lung veins Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow. SNOMEDCT_US:95455008 UMLS:C0151945 Blood clot in cerebral vein Cerebral thrombosis Cerebral vein thrombosis HP:0005305 Cerebral venous thrombosis Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow. Blood clot in cerebral vein A developmental defect characterized by the lack of formation of the pulmonary blood vessels. UMLS:C1970630 Absent lung vessels HP:0005311 Agenesis of pulmonary vessels Absent lung vessels UMLS:C3277426 Lack of facial fat below the skin HP:0005320 Lack of facial subcutaneous fat Lack of facial fat below the skin Underdevelopment of the urinary bladder. HP:0005342 UMLS:C1855335 Hypoplastic bladder Underdeveloped bladder HP:0005343 Hypoplasia of the bladder Underdevelopment of the urinary bladder. Underdeveloped bladder Any structural abnormality of the carotid arteries, including the common carotid artery and its' arterial branches. 2008-03-26T06:37:00Z UMLS:C4025211 Abnormality of the carotid arteries HP:0005344 Abnormal carotid artery morphology An abnormality of the structure of the veins that return deoxygenated blood from the body into the heart, i.e., the superior vena cava and the inferior vena cava. 2008-03-26T06:40:00Z HP:0030971 UMLS:C4025210 Abnormality of the vena cava HP:0005345 Abnormal vena cava morphology A severe form of B lymphocytopenia in which the count of B cells is very low or absent. HP:0002856 UMLS:C1863715 UMLS:C4020824 Absent B cells Absence of B cells HP:0005365 Severe B lymphocytopenia A severe form of B lymphocytopenia in which the count of B cells is very low or absent. An abnormality of the humoral immune system, which comprises antibodies produced by B cells as well as the complement system. UMLS:C3150510 Defective humoral immunity HP:0005368 Abnormality of humoral immunity An abnormality of the humoral immune system, which comprises antibodies produced by B cells as well as the complement system. An abnormality of the physiological functioning of B cells. HP:0005398 UMLS:C1849242 Abnormality of B cell physiology Reduced B cell function HP:0005372 This term refers to any abnormality of the B cells, which play a role in the humoral immune response. The main functions of B cells are to produce antibodies, to perform the role of antigen presenting cells, and to develop into memory cells. Abnormality of B cell physiology An abnormality of the physiological functioning of B cells. Abnormality of B cell physiology Reduced B cell function An immunodeficiency characterized by defective cell-mediated immunity or humoral immunity. HP:0005375 UMLS:C1855204 HP:0005374 Cellular immunodeficiency An immunodeficiency characterized by defective cell-mediated immunity or humoral immunity. http://www.dictionary.com/browse/cellular-immunodeficiency An abnormally low count of T cells. HP:0005412 HP:0045071 MSH:C536783 UMLS:C2931322 Decrease in T cell count Decrease in T cell number Decreased numbers of circulating T cells Low T cell count Reduced number of T cells HP:0005403 T lymphocytopenia An abnormally low count of T cells. Decrease in T cell count Low T cell count Reduced number of T cells An abnormal increase from the normal count of B cells. UMLS:C1858972 Increase in B cell count Increase in B cell number Increased number of B cells HP:0005404 Increased B cell count An abnormal increase from the normal count of B cells. Decreased or impaired activation of T cells in response to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. HP:0005370 HP:0005436 UMLS:C1846550 Decreased T lymphocyte activation Decreased T-cell activation Decreased T-lymphocyte activation Defective T cell activation Profound depletion of T4+ lymphocytes HP:0005419 Decreased T cell activation Decreased or impaired activation of T cells in response to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. ISBN:0781735149 Abnormally reduced ability of T cells to perform their functions in cell-mediated immunity. HP:0002844 HP:0005373 HP:0005383 HP:0005409 UMLS:C1860127 Impaired T cell function T-cell dysfunction HP:0005435 Impaired T cell function Abnormally reduced ability of T cells to perform their functions in cell-mediated immunity. Impaired T cell function T-cell dysfunction An increased density in the cranial sutures following obliteration. UMLS:C4025195 HP:0005441 Sclerotic cranial sutures An increased density in the cranial sutures following obliteration. UMLS:C1835442 HP:0005451 Decreased cranial base ossification Normally, the posterior and lateral fontanelles are obliterated by about six months after birth, the anterior fontanelle closes by about the middle of the second year. This term refers to the situation in which the fontanelles close at an inappropriately early time point. Early closure of the cranial sutures Premature closure of the cranial sutures MSH:D003398 SNOMEDCT_US:1667003 SNOMEDCT_US:57219006 UMLS:C0010278 UMLS:C0277827 UMLS:C4072853 Early closure of the fontanelles Obliterated fontanelles Early closure of the bregma sutures Premature closure of the bregma sutures HP:0005458 Premature closure of fontanelles Normally, the posterior and lateral fontanelles are obliterated by about six months after birth, the anterior fontanelle closes by about the middle of the second year. This term refers to the situation in which the fontanelles close at an inappropriately early time point. Early closure of the cranial sutures Premature closure of the cranial sutures Early closure of the fontanelles Early closure of the bregma sutures Premature closure of the bregma sutures Underdevelopment of the frontal bone. HP:0005493 UMLS:C1845147 UMLS:C4280483 UMLS:C4280484 Decreased size of bone of forehead Hypoplastic frontal bones Small bone of forehead Underdevelopment of bone of forehead Hypotrophic frontal bone Hypotrophic frontal bones Thin bone of forehead HP:0005466 Hypoplasia of the frontal bone Underdevelopment of the frontal bone. Decreased size of bone of forehead Small bone of forehead Underdevelopment of bone of forehead Hypotrophic frontal bone Hypotrophic frontal bones Thin bone of forehead Reduced convexity of the occiput (posterior part of skull). HP:0000247 HP:0000249 Flat back of skull Flat back of the head Flat back of the skull Flat posterior head UMLS:C1837402 UMLS:C4280482 Flat posterior cranium Posterior flattening of the skull HP:0005469 Reduced convexity of the occiput gives an appearance of flattening. There are no objective measures for convexity of the occiput, and evaluation depends heavily on the experience of the observer. This finding may or may not be accompanied by Brachycephaly (which should be coded separately), and may be observed more frequently when an infant is placed to sleep on his/her back. Occipital plagiocephaly can result from fusion or sclerosis of the lambdoid suture. If unilateral, this is accompanied by unilateral occipital flattening and bulging of the ispilateral frontal bone. Flat occiput Reduced convexity of the occiput (posterior part of skull). PMID:19125436 Flat back of skull Flat back of the head Flat back of the skull Flat posterior head Flat posterior cranium Abnormal reduction in ossification of the calvaria (roof of the skull consisting of the frontal bone, parietal bones, temporal bones, and occipital bone). HP:0002701 HP:0002702 HP:0005454 HP:0005471 UMLS:C1833762 Poorly ossified calvaria Poorly ossified calvarium Soft calvaria Soft skullcap Undermineralized calvarium Skull soft on palpation HP:0005474 A hypomineralised skull castes little or no acoustic shadow on prenatal ultrasound. This makes visualisation of the intracranial anatomy clearer than normal. In conditions associated with profound hypomineralisation, the skull shape can be distorted by pressure from the ultrasound transducer later in pregnancy. Decreased calvarial ossification Abnormal reduction in ossification of the calvaria (roof of the skull consisting of the frontal bone, parietal bones, temporal bones, and occipital bone). PMID:31173381 Soft skullcap Head circumference which falls below 2 standard deviations below the mean for age and gender because of insufficient head growth after birth. HP:0000241 HP:0000259 HP:0005499 Development of small head that was not present at birth UMLS:C1847514 Acquired microcephaly Deceleration of head growth Microcephaly, acquired Microcephaly, postnatal Postnatal deceleration of head circumference Postnatal microcephaly HP:0005484 Secondary microcephaly Head circumference which falls below 2 standard deviations below the mean for age and gender because of insufficient head growth after birth. Development of small head that was not present at birth Acquired microcephaly A fontanelle that is small for age. Little cranial sutures Small cranial sutures SNOMEDCT_US:276710001 UMLS:C0456133 UMLS:C4072854 UMLS:C4072855 Little fontanelle Microfontanelle Small soft spot Small bregma sutures HP:0005486 Small fontanelle A fontanelle that is small for age. PMID:12825844 Little cranial sutures Small cranial sutures Little fontanelle Microfontanelle Small soft spot Small bregma sutures A transient reduction in the number of erythroblasts in the circulation. UMLS:C4082199 Transient decrease in blood erythrocyte number HP:0005510 An erythroblast, the immediate precursor of a normal erythrocyte which, still retains a cell nucleus. Transient erythroblastopenia A transient reduction in the number of erythroblasts in the circulation. Transient decrease in blood erythrocyte number Increased megakaryocyte number, i.e., of platelet precursor cells, present in the bone marrow. UMLS:C4025187 HP:0005513 Increased megakaryocyte count Increased megakaryocyte number, i.e., of platelet precursor cells, present in the bone marrow. Average platelet volume below the lower limit of the normal reference interval. HP:0001938 UMLS:C1096368 UMLS:C1833182 Small platelet size Small platelets Small platelets size HP:0005537 Mean platelet volume (MPV) is a measure of the average size of platelets, with a typical reference range of 7.5 to 11.5 femtoliters (fL). Decreased mean platelet volume Average platelet volume below the lower limit of the normal reference interval. Small platelet size Small platelets Small platelets size A reduced count of megakaryocytes. UMLS:C1858312 Megakaryocytes decreased im bone marrow HP:0005548 Megakaryocytes are giant cells in the bone marrow. Mature blood platelets are released from the cytoplasm of megakaryocytes. Megakaryocytopenia A reduced count of megakaryocytes. The frontal suture divides the two halves of the frontal bone of the skull in infants and children and generally undergoes fusion by the age of six. A persistent frontal suture is referred to as a "metopic suture". 2008-03-27T10:04:00Z UMLS:C4025180 HP:0005556 Abnormality of the metopic suture The frontal suture divides the two halves of the frontal bone of the skull in infants and children and generally undergoes fusion by the age of six. A persistent frontal suture is referred to as a "metopic suture". An anomaly of the form or number of cells in the bone marrow. 2008-03-27T10:46:00Z MSH:D001855 SNOMEDCT_US:127035006 UMLS:C0005956 UMLS:C4021634 Abnormality of bone marrow cell morphology Anomaly of the bone marrow cells Bone marrow disease HP:0005561 Abnormal bone marrow cell morphology An anomaly of the form or number of cells in the bone marrow. Bone marrow disease A reduction in the count of nephrons per kidney. UMLS:C1841994 UMLS:C2673888 Oligonephronia Decreased numbers of glomeruli HP:0005563 Decreased numbers of nephrons A reduction in the count of nephrons per kidney. HPO_CONTRIBUTOR:Eurenomics_ewuehl A duplication of the renal pelvis. UMLS:C1839269 HP:0005580 Duplication of renal pelvis A duplication of the renal pelvis. 2008-03-28T09:03:00Z HP:0005940 Fyler:4232 UMLS:C4021631 Tracheobronchial anomalies HP:0005607 Abnormal tracheobronchial morphology SNOMEDCT_US:51047007 UMLS:C0232769 Gallbladder dysfunction HP:0005609 Gallbladder dysfunction Gallbladder dysfunction Absence or underdevelopment of the femur. HP:0006396 HP:0006425 UMLS:C1851310 Absent/small thighbone Absent/underdeveloped thighbone Hypoplastic to absent femora Hypoplastic/aplastic femora HP:0005613 Aplasia/hypoplasia of the femur Absence or underdevelopment of the femur. Absent/small thighbone Absent/underdeveloped thighbone The ability of the interphalangeal joints to move beyond their normal range of motion. UMLS:C4025172 Increased mobility of hinge joints HP:0005620 Hypermobility of interphalangeal joints The ability of the interphalangeal joints to move beyond their normal range of motion. Increased mobility of hinge joints Absent ossification of the calvaria (vault of the skull). UMLS:C4021629 Absent bone maturation of skullcap Absent ossification of skull vault HP:0005623 Absent ossification of calvaria Absent ossification of the calvaria (vault of the skull). Absent bone maturation of skullcap Osteoporosis affecting predominantly the vertebrae. UMLS:C4025170 HP:0005625 Osteoporosis of vertebrae Osteoporosis affecting predominantly the vertebrae. UMLS:C1408532 Absent forearm Absent forearms HP:0005632 Absent forearm Absent forearm Absent forearms The presence of abnormal calcium deposition of the intervertebral disk. SNOMEDCT_US:240211000 UMLS:C0410607 Intervertebral disc calcification Multiple intervertebral disc calcifications Multiple intervertebral disk calcifications HP:0005645 Intervertebral disk calcification The presence of abnormal calcium deposition of the intervertebral disk. Intervertebral disc calcification Multiple intervertebral disc calcifications UMLS:C4025150 Flattened end part of knee bone HP:0005715 Flattened knee epiphyses Flattened end part of knee bone Underdevelopment (reduced size) of the tibia. HP:0002993 HP:0006436 HP:0006445 UMLS:C1850259 UMLS:C1855277 Hypoplasia of the tibia Hypoplastic tibia Short shinbone Short skankbone Short tibiae Shortening of the shankbone Shortening of the shinbone Shortening of the tibia HP:0005736 Short tibia Underdevelopment (reduced size) of the tibia. Short shinbone Short skankbone A limitation in the passive range of motion of a joint of the lower limb resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin. UMLS:C1859523 Contractures of the joints of the lower limbs Contractures, lower limbs HP:0005750 Lower-limb joint contracture Absence or underdevelopment of the tibia. UMLS:C1969181 Absent/hypoplastic tibia Absent/small shankbone Absent/small shinbone Absent/underdeveloped shankbone Absent/underdeveloped shinbone Aplastic/hypoplastic tibia HP:0005772 Aplasia/Hypoplasia of the tibia Absence or underdevelopment of the tibia. Absent/small shankbone Absent/small shinbone Absent/underdeveloped shankbone Absent/underdeveloped shinbone Underdevelopment of both forearm bones, the ulna and the radius, resulting in a shortened forearm. UMLS:C1855299 Short forearm HP:0005773 Short forearm Underdevelopment of both forearm bones, the ulna and the radius, resulting in a shortened forearm. Short forearm A flattened vertebral body shape with reduced distance beween the vertebral endplates affecting the lumbar spine. HP:0004588 UMLS:C4025136 HP:0005787 Lumbar platyspondyly A flattened vertebral body shape with reduced distance beween the vertebral endplates affecting the lumbar spine. Underdevelopment of the humerus. HP:0002989 HP:0003014 HP:0003064 HP:0006419 HP:0006464 HP:0006468 UMLS:C1832117 Humeral hypoplasia Humeral shortening Hypoplastic humerus Short humeri Short humerus Short long bone of upper arm Short upper arms HP:0005792 Short humerus Underdevelopment of the humerus. Short humerus Short long bone of upper arm Short upper arms Aplasia (absence) of the distal phalanges. UMLS:C1861339 Absent outermost digital bones HP:0005807 Absent distal phalanges Aplasia (absence) of the distal phalanges. Absent outermost digital bones The presence of more than 12 rib pairs. HP:0000901 SNOMEDCT_US:205460009 UMLS:C0345397 Extra ribs HP:0005815 Supernumerary ribs The presence of more than 12 rib pairs. Extra ribs Short (hypoplastic) middle phalanx of finger, affecting one or more fingers. HP:0001208 HP:0006068 HP:0006081 HP:0010240 UMLS:C1846950 Brachymesophalangy Disproportionately short middle phalanges Hypoplasia of the middle phalanges of the hand Hypoplastic middle phalanges Hypoplastic middle phalanx Midphalangeal hypoplasia Short middle bone of finger Short middle phalanges Shortened middle finger bones HP:0005819 Short middle phalanx of finger Short (hypoplastic) middle phalanx of finger, affecting one or more fingers. Short middle bone of finger UMLS:C4025128 HP:0005825 Mixed sclerosis of humeral metaphyses One or more bent (flexed) toe joints that cannot be straightened actively or passively. HP:0001860 HP:0008128 HP:0008367 HP:0200027 UMLS:C1406835 Contractures involving the toes Contractures of the toes Toe contractures HP:0005830 Flexion contracture of toe One or more bent (flexed) toe joints that cannot be straightened actively or passively. An abnormally round shape of the middle phalanx of the finger. UMLS:C4025126 Rounded middle bone of finger HP:0005844 Rounded middle phalanx of finger An abnormally round shape of the middle phalanx of the finger. Rounded middle bone of finger A lack of bone mineralization of one or more body of cervical vertebra. UMLS:C4025115 HP:0005885 Absent ossification of cervical vertebral bodies A lack of bone mineralization of one or more body of cervical vertebra. The presence of an abnormal curvature of the cervical vertebral column. UMLS:C3151523 Abnormal neck curve HP:0005905 Abnormal cervical curvature The presence of an abnormal curvature of the cervical vertebral column. Abnormal neck curve 2008-03-27T02:13:00Z UMLS:C4025110 Abnormality of end part of long bone of hand Abnormality of metacarpal epiphyses HP:0005913 Abnormal metacarpal epiphysis morphology Abnormality of end part of long bone of hand Aplasia or Hypoplasia affecting the metacarpal bones. 2008-03-27T02:14:00Z HP:0006007 UMLS:C1836192 Absent or hypoplastic metacarpals Absent/small long bones of hand Absent/underdeveloped long bones of hand Aplastic/hypoplastic metacarpals Hypoplastic metacarpals Hypoplastic/absent metacarpal bones Hypoplastic/absent metacarpals Metacarpal aplasia/hypoplasia HP:0005914 Aplasia/Hypoplasia involving the metacarpal bones Aplasia or Hypoplasia affecting the metacarpal bones. Absent/small long bones of hand Absent/underdeveloped long bones of hand Any abnormal shape or structure of the metacarpal bones. 2008-03-27T02:17:00Z HP:0001163 HP:0010556 UMLS:C4021615 Abnormal shape of long bones of hand Abnormal shape of metacarpal bones HP:0005916 Abnormal metacarpal morphology Any abnormal shape or structure of the metacarpal bones. Abnormal shape of long bones of hand The presence of more than the normal number of metacarpal bones. 2008-03-27T02:18:00Z SNOMEDCT_US:91846008 UMLS:C0545617 Extra long bones of hand HP:0005917 Supernumerary metacarpal bones The presence of more than the normal number of metacarpal bones. Extra long bones of hand Abnormalities affecting the phalanx of finger. 2008-03-27T02:19:00Z HP:0005786 HP:0006259 UMLS:C4021614 Abnormal form of phalanges of the hand Abnormality of phalanx of finger Abnormality of the finger bones Abnormality of the phalanges Abnormality of the phalanges of the hand HP:0005918 This category is a supercategory for abnormalties affect phalanges of the hand. Abnormal finger phalanx morphology Abnormalities affecting the phalanx of finger. Abnormality of the finger bones Abnormality of one or all of the epiphyses of the phalanges of the hand. Note that this includes the epiphysis of the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). 2008-03-27T02:21:00Z HP:0009151 UMLS:C4021613 HP:0005920 Abnormal epiphysis morphology of the phalanges of the hand Abnormality of one or all of the epiphyses of the phalanges of the hand. Note that this includes the epiphysis of the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). Any structural anomaly of the hand. 2008-03-27T02:25:00Z HP:0003098 UMLS:C4025109 Abnormal shape of hand HP:0005922 This is a category to be used for general descriptions of hand dysmorphology. In time, it should be replaced by more accurate descriptions. Abnormal hand morphology Any structural anomaly of the hand. Abnormal shape of hand 2008-03-27T02:27:00Z UMLS:C4025108 Abnormalities of the metaphyses of the hand Abnormality of the wide portion of the hand bone HP:0005923 Abnormal hand metaphysis morphology Abnormality of the wide portion of the hand bone Any abnormality of the epiphyses of the phalanges or metacarpal bones. 2008-03-27T02:28:00Z UMLS:C4025107 Abnormality of the end part of the hand bone Abnormality of the end part of the hand bones Abnormality of the epiphyses of the fingers Abnormality of the epiphyses of the hand Abnormality of the epiphyses of the phalanges of the hand HP:0005924 Abnormal hand epiphysis morphology Any abnormality of the epiphyses of the phalanges or metacarpal bones. Abnormality of the end part of the hand bone 2008-03-27T02:28:00Z UMLS:C4025106 Abnormalities of shaft of long bone of the hand Abnormalities of the diaphyses of the hand HP:0005925 Abnormal hand diaphysis morphology Abnormalities of shaft of long bone of the hand Absence (due to failure to form) or underdevelopment of the bones of the hand. 2008-03-27T02:29:00Z UMLS:C4021612 Absent/small hand bones Absent/underdeveloped hand bones Hypoplasia/absence of hand bones HP:0005927 Aplasia/hypoplasia involving bones of the hand Absence (due to failure to form) or underdevelopment of the bones of the hand. Absent/small hand bones Absent/underdeveloped hand bones An anomaly of epiphysis, which is the expanded articular end of a long bone that developes from a secondary ossification center, and which during the period of growth is either entirely cartilaginous or is separated from the shaft by a cartilaginous disk. 2008-03-27T03:00:00Z HP:0000936 UMLS:C4021611 Abnormal shape of end part of bone Abnormality of epiphysis morphology Abnormality of the epiphyses Anomaly of the epiphyses Epiphyseal abnormality HP:0005930 Abnormal epiphysis morphology An anomaly of epiphysis, which is the expanded articular end of a long bone that developes from a secondary ossification center, and which during the period of growth is either entirely cartilaginous or is separated from the shaft by a cartilaginous disk. Abnormal shape of end part of bone A decreased concentration of arginine in the blood. UMLS:C1859735 UMLS:C4025095 Low blood arginine levels Arginine deficiency HP:0005961 Hypoargininemia A decreased concentration of arginine in the blood. HPO_CONTRIBUTOR:gcarletti Low blood arginine levels Developmental hypoplasia of the thyroid gland. MSH:D050033 SNOMEDCT_US:367524008 UMLS:C0151516 Hypoplastic thyroid Small thyroid gland HP:0005990 Thyroid hypoplasia Developmental hypoplasia of the thyroid gland. Small thyroid gland Reduced amount of adipose tissue in the region of the neck. UMLS:C1837763 Loss of adipose tissue around the neck Loss of fat around neck HP:0005995 Decreased adipose tissue around neck Reduced amount of adipose tissue in the region of the neck. Loss of fat around neck UMLS:C1860111 Abnormally shaped wrist bones HP:0006014 Abnormally shaped carpal bones Abnormally shaped wrist bones Delay in the process of formation and maturation of the epiphysis of one or more phalanx. UMLS:C4021609 Delayed phalangeal epiphyseal bone maturation Delayed bone maturation of end part of digital bone HP:0006016 Delayed phalangeal epiphyseal ossification Delay in the process of formation and maturation of the epiphysis of one or more phalanx. Delayed bone maturation of end part of digital bone UMLS:C1850632 Rounded end part of bone HP:0006026 Rounded epiphyses Rounded end part of bone A delay in the process of formation and maturation of the epiphysis of one or more long bones. UMLS:C1835573 Multiple carpal ossification centres HP:0006067 Multiple carpal ossification centers A delay in the process of formation and maturation of the epiphysis of one or more long bones. Multiple carpal ossification centres SNOMEDCT_US:298193009 UMLS:C0574974 Increased mobility in finger joint HP:0006094 Finger joint hypermobility Increased mobility in finger joint Increased length of the proximal phalanx of finger. UMLS:C4025090 Long innermost finger bone HP:0006127 Long proximal phalanx of finger Increased length of the proximal phalanx of finger. Long innermost finger bone Abnormally large size of one or more growth plates (epiphyses) of the metacarpal bones (i.e., the tubular bones of the hand between the carpus and the phalanges). UMLS:C1865035 Enlarged end part of long bone of hand HP:0006134 Enlarged metacarpal epiphyses Abnormally large size of one or more growth plates (epiphyses) of the metacarpal bones (i.e., the tubular bones of the hand between the carpus and the phalanges). Enlarged end part of long bone of hand Increased length of multiple or a single phalanx of finger. UMLS:C4025087 Long finger bone HP:0006155 Long phalanx of finger Increased length of multiple or a single phalanx of finger. Long finger bone Bending or curvature of a thumb towards the ulnar side (towards the ring finger). Curved thumb deviated towards palm SNOMEDCT_US:299137000 UMLS:C0575904 UMLS:C4280465 Ulnar deviation of the 1st finger HP:0006156 Ulnar deviation of thumb Bending or curvature of a thumb towards the ulnar side (towards the ring finger). PMID:10955488 Curved thumb deviated towards palm UMLS:C1859700 HP:0006163 Enlarged metacarpophalangeal joints UMLS:C1859369 Cylindrical shaped long bones of hand HP:0006166 Tubular metacarpal bones Cylindrical shaped long bones of hand UMLS:C1839285 Two carpal ossification centres present at birth HP:0006176 Two carpal ossification centers present at birth Two carpal ossification centres present at birth UMLS:C1861350 Enlarged innermost hinge joint HP:0006185 Enlarged proximal interphalangeal joints Enlarged innermost hinge joint UMLS:C1851811 Increased mobility of outermost hinge joint HP:0006201 Hypermobility of distal interphalangeal joints Increased mobility of outermost hinge joint UMLS:C1859701 Enlarged hinge joints HP:0006247 Enlarged interphalangeal joints Enlarged hinge joints Concentration of alpha-fetoprotein in the blood circulation above the upper limit of normal. 2008-03-28T09:17:00Z UMLS:C0235971 UMLS:C0476489 Increased levels of alpha fetoprotein Increased serum alpha-fetoprotein Serum alpha-fetoprotein increased Alpha fetoprotein abnormal HP:0006254 An elevation of alpha-feto protein, which is produced by the fetal liver and the yolk sac and may be increased in the serum of pregnant women with a fetus with some types of developmental anomaly such as open neural tube defects and omphalocele. Elevated circulating alpha-fetoprotein concentration Concentration of alpha-fetoprotein in the blood circulation above the upper limit of normal. HPO_CONTRIBUTOR:gcarletti 2008-03-28T10:14:00Z UMLS:C4025076 Abnormality of hand joint mobility HP:0006256 Abnormality of hand joint mobility Abnormality of hand joint mobility 2008-03-28T02:29:00Z UMLS:C4025075 Abnormal wrist bone maturation HP:0006257 Abnormality of carpal bone ossification Abnormal wrist bone maturation 2008-03-28T02:55:00Z HP:0004266 UMLS:C4021604 Abnormality of phalangeal joints of the hand Abnormality of the small joints of the hand HP:0006261 Abnormal phalangeal joint morphology of the hand Abnormality of the small joints of the hand A small/hypoplastic or absent/aplastic 5th finger. 2008-03-28T02:59:00Z UMLS:C4025074 Absent/small little finger Absent/small pinkie finger Absent/small pinky finger Absent/underdeveloped little finger Absent/underdeveloped pinkie finger Absent/underdeveloped pinky finger HP:0006262 Aplasia/Hypoplasia of the 5th finger A small/hypoplastic or absent/aplastic 5th finger. Absent/small little finger Absent/small pinkie finger Absent/small pinky finger Absent/underdeveloped little finger Absent/underdeveloped pinkie finger Absent/underdeveloped pinky finger Small/hypoplastic or absent/aplastic fingers. 2008-03-28T03:09:00Z UMLS:C4025071 Absent/small fingers Absent/underdeveloped fingers HP:0006265 Aplasia/Hypoplasia of fingers Small/hypoplastic or absent/aplastic fingers. Absent/small fingers Absent/underdeveloped fingers Reduced size of the placenta. SNOMEDCT_US:289264006 UMLS:C0566694 Small placenta HP:0006266 Small placenta Reduced size of the placenta. Small placenta Increased size of the placenta. SNOMEDCT_US:289263000 UMLS:C0566693 Large placenta Placental enlargement HP:0006267 Large placenta Increased size of the placenta. Large placenta Underdevelopment of the spleen. UMLS:C1970617 Underdeveloped spleen HP:0006270 Hypoplastic spleen Underdevelopment of the spleen. Underdeveloped spleen Reduced number of beta cells in the pancreatic islets of Langerhans. UMLS:C1856904 HP:0006274 The beta cells are responsible for producing insulin and amylin. Reduced pancreatic beta cells Reduced number of beta cells in the pancreatic islets of Langerhans. UMLS:C1969875 HP:0006279 Beta-cell dysfunction Developmental hypoplasia of the dental enamel. HP:0000671 HP:0001565 HP:0003770 Defective enamel matrix Thin dental enamel Thin tooth enamel MSH:D003744 SNOMEDCT_US:26597004 SNOMEDCT_US:699382004 SNOMEDCT_US:699421005 UMLS:C0011351 UMLS:C1851854 UMLS:C4280456 UMLS:C4280457 Dental enamel hypoplasia Enamel hypotrophy Enamel, underdeveloped Hypoplasia of dental enamel Hypoplasia of tooth enamel Underdeveloped teeth enamel Dysplasia of tooth enamel Enamel dysplasia HP:0006297 Enamel hypoplasia can be caused by genetic or environmental factors. It may occur in both deciduous and permanent dentitions, although more often in the permanent dentition. Enamel hypoplasia may concern a single tooth, several teeth, or the complete dentition and may affect part or the complete surface of the tooth. Enamel hypoplasia regroups different clinical aspects: localized hypoplasia, generalized hypoplasia, enamel pits, enamel striae, and grooves defects. The term should be used to describe a quantitative defect of enamel. Enamel hypotrophy cannot be used as hypotrophy indicates loss of cells, whereas enamel is an acellular structure and thus not a tissue. Enamel hypoplasia Developmental hypoplasia of the dental enamel. PMID:18499550 PMID:31468724 Defective enamel matrix Thin dental enamel Thin tooth enamel Hypoplasia of tooth enamel Underdeveloped teeth enamel Dysplasia of tooth enamel Dagger-shaped calcifications in the dental pulp. UMLS:C4025067 Dagger shaped pulp denticles Dagger shaped pulp stones HP:0006302 Dagger-shaped pulp calcifications Dagger-shaped calcifications in the dental pulp. Dagger shaped pulp denticles Dagger shaped pulp stones UMLS:C1855642 UMLS:C4280454 UMLS:C4280455 Atrophy of alveolar margins Atrophy of alveolar processes of jaw Resorption of alveolar margins Resorption of alveolar processes of jaw Resorption of alveolar ridges Shrinking of alveolar ridges Shrinking of gum ridges Alveolar bone loss Flattening of alveolar margin Flattening of alveolar processes of jaw Flattening of alveolar ridges Flattening of gum ridges HP:0006308 Atrophy of alveolar ridges Atrophy of alveolar margins Atrophy of alveolar processes of jaw Resorption of alveolar margins Resorption of alveolar processes of jaw Resorption of alveolar ridges Shrinking of alveolar ridges Shrinking of gum ridges Flattening of alveolar margin Flattening of alveolar processes of jaw Flattening of alveolar ridges Flattening of gum ridges Tooth root length more than 2 SD below mean, or subjectively apparently decreased tooth root length. Underdeveloped tooth roots UMLS:C2678330 Decreased length of dental roots Decreased length of tooth roots Dental root hypoplasia Dental root hypotrophy Rhizomicry Root dwarfism Short dental roots Short tooth roots Underdeveloped dental roots HP:0006336 Short dental root Tooth root length more than 2 SD below mean, or subjectively apparently decreased tooth root length. PMID:31468724 Underdeveloped tooth roots Decreased length of dental roots Decreased length of tooth roots Short dental roots Short tooth roots Underdeveloped dental roots An alteration of the normally relatively smooth margins of the kneecap in radiographic images leading to an irregular contour. HP:0006458 UMLS:C1836870 Irregular patellar contour Irregular patellar margins HP:0006369 Irregular patellae An alteration of the normally relatively smooth margins of the kneecap in radiographic images leading to an irregular contour. A type of knee joint contracture in which the knee is in a fixed bent (flexed) configuration such that it cannot be straightened actively or passively. HP:0002978 Inability to straighten knee SNOMEDCT_US:202289003 UMLS:C0409355 Flexion contracture of knees Flexion contractures at both knees Flexion contractures of knees Flexion deformity of the knee Knee flexion contractures Knee flexion deformity HP:0006380 Knee flexion contracture A type of knee joint contracture in which the knee is in a fixed bent (flexed) configuration such that it cannot be straightened actively or passively. PMID:31282072 Inability to straighten knee Flexion contractures at both knees Shortening of the legs related to developmental hypoplasia of the bones of the leg. HP:0003054 SNOMEDCT_US:249786007 UMLS:C0426901 Short legs Short lower limbs HP:0006385 Short lower limbs Shortening of the legs related to developmental hypoplasia of the bones of the leg. Short legs Short lower limbs An abnormal increase in the bone density of the long bones. UMLS:C1849307 Increased density of long bones HP:0006392 Increased density of long bones An abnormal increase in the bone density of the long bones. Increased density of long bones UMLS:C1859462 Absent knee end part HP:0006400 Absent knee epiphyses Absent knee end part UMLS:C1840307 Short outer part of limbs HP:0006402 Distal shortening of limbs Short outer part of limbs UMLS:C1968943 HP:0006426 Rudimentary to absent tibiae UMLS:C1844516 Increased density of shaft of long bone HP:0006440 Increased density of long bone diaphyses Increased density of shaft of long bone Underdevelopment or shortening of the end of the fibula (calf bone) nearest the knee. UMLS:C1859478 Small innermost upper end of calf bone Underdeveloped innermost upper end of calf bone HP:0006442 Hypoplasia of proximal fibula Underdevelopment or shortening of the end of the fibula (calf bone) nearest the knee. PMID:880750 Small innermost upper end of calf bone Underdeveloped innermost upper end of calf bone Absence of the patella. HP:0003046 HP:0006475 UMLS:C1868578 Absent kneecap Absent patella Absent patellae Absent patellas Aplastic patellae HP:0006443 Patellar aplasia Absence of the patella. Absent kneecap UMLS:C1849580 HP:0006446 Dysplastic patella UMLS:C1857193 HP:0006450 Multicentric ossification of proximal femoral epiphyses Formation of bone in the patella later than normal. UMLS:C4021597 UMLS:C4280446 Delayed patellae ossification Delayed bone maturation of the knee cap HP:0006454 The patella initially ossifies at between three and five years, commencing as multiple foci that rapidly coalesce. As the patellar ossification center enlarges the expanding margins may be irregular and associated with accessory ossification centers. These are most common superolaterally and may lead to the development of a bipartite patella. The bipartite patella has cartilaginous continuity despite the appearance of osseous discontinuity. The patella expands to all cartilaginous contours during late adolescence when the epiphyseal ossification centers around the knee are also in the final stages of maturation. The only cartilage not replaced is that occupying the superior two-thirds of the articular surface (the lower one-third is covered by the fat pad). The subchondral plate does not assume the actual articular contours until the late stages of osseous maturation (after ten to twelve years). Accordingly, typical measurements such as medial and lateral angulation cannot be accurately done prior to the final stages of patellar ossification expansion and maturation (PMID:6729496). Delayed patellar ossification Formation of bone in the patella later than normal. PMID:6729496 Delayed bone maturation of the knee cap HP:0004985 HP:0006403 UMLS:C1837407 HP:0006466 Ankle flexion contracture An abnormality of the islet of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. These are the alpha cells, which produce glucagon, the beta cells, which produce insulin and amylin, the delta cells, which produce somatostatin, the PP cells, which produce pancreatic polypeptide, and the epsilon cells, which produce ghrelin. 2008-03-28T04:41:00Z HP:0100567 UMLS:C4025043 HP:0006476 Abnormality of the pancreatic islet cells An abnormality of the islet of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. These are the alpha cells, which produce glucagon, the beta cells, which produce insulin and amylin, the delta cells, which produce somatostatin, the PP cells, which produce pancreatic polypeptide, and the epsilon cells, which produce ghrelin. Any abnormality of the alveolar ridges (on the upper or lower jaws). The alveolar ridges contain the sockets (alveoli) of the teeth. 2008-03-28T04:44:00Z Abnormality of the alveolar ridges SNOMEDCT_US:235013007 UMLS:C0341007 UMLS:C4280445 Abnormality of alveolar margin Abnormality of dentoalveolar ridges Abnormality of gum ridge Defect in alveolar ridge Abnormality of alveolar processes of jaw HP:0006477 Abnormal alveolar ridge morphology Any abnormality of the alveolar ridges (on the upper or lower jaws). The alveolar ridges contain the sockets (alveoli) of the teeth. Abnormality of alveolar margin Abnormality of dentoalveolar ridges Abnormality of gum ridge Abnormality of alveolar processes of jaw An abnormality of the dental pulp. 2008-03-28T04:46:00Z UMLS:C4025042 Abnormality of the dental pulp Abnormality of tooth pulp Endodontic abnormality HP:0006479 Abnormal dental pulp morphology An abnormality of the dental pulp. Abnormality of tooth pulp Endodontic abnormality An abnormality of the morphology of the tooth. 2008-03-28T05:41:00Z HP:0000697 MSH:D014071 SNOMEDCT_US:422775003 UMLS:C0040427 UMLS:C0262444 Abnormality of dental morphology Abnormality of dental shape Abnormality of shape of tooth Abnormally shaped teeth Deformity of teeth Dental deformity Dental malformations Malformation of teeth Malformed teeth Misshapen teeth Misshapened teeth HP:0006482 Abnormal dental morphology An abnormality of the morphology of the tooth. Abnormality of dental shape Abnormality of shape of tooth Abnormally shaped teeth Deformity of teeth Dental deformity Dental malformations Malformation of teeth Malformed teeth Misshapen teeth Misshapened teeth The presence of an altered number of of teeth. 2008-03-28T05:44:00Z SNOMEDCT_US:335443002 UMLS:C1290508 Abnormal complement of teeth Abnormal number of teeth Abnormal tooth count HP:0006483 Humans usually have 20 primary teeth (also called deciduous teeth) and 32 permanent teeth. This term comprises anomalies with too many or too few teeth. Abnormal number of teeth The presence of an altered number of of teeth. Abnormal complement of teeth Abnormal number of teeth Abnormal tooth count An abnormality of the dental root. 2008-03-28T05:52:00Z UMLS:C4025041 Abnormality of the dental root Abnormality of tooth root Dental root anomaly HP:0006486 Abnormal dental root morphology An abnormality of the dental root. Abnormality of the dental root Abnormality of tooth root An anomaly of the femoral metaphysis. 2008-03-28T06:02:00Z Abnormality of the wide portion of the femoral bone UMLS:C4025040 UMLS:C4280444 Abnormality of the femoral metaphysis HP:0006489 Abnormal femoral metaphysis morphology An anomaly of the femoral metaphysis. Abnormality of the wide portion of the femoral bone 2008-03-28T06:02:00Z UMLS:C4025039 Abnormality of lower-limb metaphyses Abnormality of the wide portion of the lower-limb bone HP:0006490 Abnormal lower-limb metaphysis morphology Abnormality of the wide portion of the lower-limb bone 2008-03-28T06:03:00Z Abnormality of the wide portion of shankbone Abnormality of the wide portion of shinbone UMLS:C4025038 Abnormality of the tibial metaphysis HP:0006491 Abnormal tibial metaphysis morphology Abnormality of the wide portion of shankbone Abnormality of the wide portion of shinbone Absence or underdevelopment of the fibula. 2008-03-28T06:03:00Z HP:0005672 HP:0006421 UMLS:C1856732 Absent/small calf bone Absent/underdeveloped calf bone Fibular aplasia/hypoplasia Hypoplastic/aplastic fibulae HP:0006492 Aplasia/Hypoplasia of the fibula Absence or underdevelopment of the fibula. Absent/small calf bone Absent/underdeveloped calf bone Absence (due to failure to form) or underdevelopment of the bones of the lower limbs. 2008-03-28T06:04:00Z UMLS:C4025037 Absent/small lower limb bones Absent/underdeveloped lower limb bones HP:0006493 Aplasia/hypoplasia involving bones of the lower limbs Absence (due to failure to form) or underdevelopment of the bones of the lower limbs. Absent/small lower limb bones Absent/underdeveloped lower limb bones 2008-03-28T06:08:00Z UMLS:C4025036 Absent/small foot bones Absent/underdeveloped foot bones HP:0006494 Aplasia/Hypoplasia involving bones of the feet Absent/small foot bones Absent/underdeveloped foot bones Absence (due to failure to form) or underdevelopment of the bones of the upper limbs. 2008-03-28T06:16:00Z UMLS:C4025035 Absent/small bones of the upper limbs Absent/underdeveloped bones of the upper limbs HP:0006496 Aplasia/hypoplasia involving bones of the upper limbs Absence (due to failure to form) or underdevelopment of the bones of the upper limbs. Absent/small bones of the upper limbs Absent/underdeveloped bones of the upper limbs Absence or underdevelopment of the patella. 2008-03-28T06:25:00Z HP:0005006 HP:0005027 HP:0005702 HP:0005729 HP:0006374 MSH:C535568 UMLS:C1868577 Absent or hypoplastic patellae Absent/hypoplastic patella Absent/small kneecap Absent/underdeveloped kneecap Aplastic or hypoplastic patellae Hypoplastic or absent patella Patellar aplasia/hypoplasia Small to absent patellae HP:0006498 Aplasia/Hypoplasia of the patella Absence or underdevelopment of the patella. Absent/small kneecap Absent/underdeveloped kneecap An anomaly of a growth plate of a femur. 2008-03-28T06:28:00Z HP:0006412 HP:0008811 UMLS:C4025034 Abnormality of femoral epiphysis Abnormality of thighbone end part HP:0006499 Abnormal femoral epiphysis morphology An anomaly of a growth plate of a femur. Abnormality of thighbone end part An anomaly of one or more epiphyses of one or both legs. 2008-03-28T06:31:00Z UMLS:C4021595 Abnormal shape of end part of lower limb end bone Abnormality involving the epiphyses of the lower limbs Abnormality of lower limb epiphysis morphology HP:0006500 Abnormal lower limb epiphysis morphology Abnormal shape of end part of lower limb end bone Absence or underdevelopment of the carpal bones. 2008-03-28T06:35:00Z UMLS:C4025033 Absent/small wrist bones Absent/underdeveloped wrist bones HP:0006502 Aplasia/Hypoplasia involving the carpal bones Absence or underdevelopment of the carpal bones. Absent/small wrist bones Absent/underdeveloped wrist bones Absence (due to failure to form) or underdevelopment of one or more forearm bones. 2008-03-28T06:45:00Z UMLS:C4025032 Absent/small forearm bones Absent/underdeveloped forearm bones HP:0006503 Aplasia/hypoplasia involving forearm bones Absence (due to failure to form) or underdevelopment of one or more forearm bones. Absent/small forearm bones Absent/underdeveloped forearm bones An anomaly of one or more epiphyses of a limb. 2008-03-28T06:48:00Z UMLS:C4021593 Abnormal shape of end part of limb bones Abnormality involving the epiphyses of the limbs Abnormality of limb epiphysis morphology HP:0006505 An epiphysis is the expanded articular end of a long bone that developes from a secondary ossification center, and which during the period of growth is either entirely cartilaginous or is separated from the shaft by a cartilaginous disk. Abnormal limb epiphysis morphology Abnormal shape of end part of limb bones Absence (due to failure to form) or underdevelopment of the humerus. 2008-03-29T09:15:00Z UMLS:C4025031 Absent/small long bone in upper arm Absent/underdeveloped long bone in upper arm HP:0006507 Aplasia/hypoplasia of the humerus Absence (due to failure to form) or underdevelopment of the humerus. Absent/small long bone in upper arm Absent/underdeveloped long bone in upper arm 2008-03-29T09:19:00Z UMLS:C4025030 Abnormality of end part of shinbone HP:0006508 Abnormality of tibial epiphyses Abnormality of end part of shinbone An abnormality of the pulmonary lymphatic chain. UMLS:C4025026 HP:0006529 Abnormal pulmonary lymphatics An abnormality of the pulmonary lymphatic chain. UMLS:C4025025 HP:0006533 Bronchodysplasia UMLS:C4025024 Underdevelopment of the bronical cartilage HP:0006539 Bronchial cartilage hypoplasia Underdevelopment of the bronical cartilage The presence of abnormal calcium deposition in the liver. UMLS:C1696466 Liver calcifications HP:0006559 Hepatic calcification The presence of abnormal calcium deposition in the liver. UMLS:C1837257 HP:0006561 Lipid accumulation in hepatocytes The presence of reduced numbers of intrahepatic bile duct than normal. UMLS:C1861621 UMLS:C4021591 Hepatic ductopenia Intrahepatic duct deficiency HP:0006571 Reduced number of intrahepatic bile ducts The presence of reduced numbers of intrahepatic bile duct than normal. HP:0006629 UMLS:C1861226 Small abnormally formed scapula Small abnormally formed shoulder blade HP:0006584 Small abnormally formed scapulae Small abnormally formed shoulder blade Lack of development of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. UMLS:C4021589 Aplasia of the glenoid fossa HP:0006591 Absent glenoid fossa Lack of development of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. A less than normal number of sternal ossification centers. The sternum is initially formed from bilateral sternal plates that chondrify and begin to fuse with ribs at 10 weeks gestational age. Ossification starts in the manubrium and upper part of the sternal body at the 6th month, in the middle of the sternal body at the 7th month, in the lower part of the body during the 1st postnatal year and in the xiphoid process between years 5 and 18. The number of ossification centers vary up to six, and it is the ossification centers that are visualized by prenatal ultrasound. This term describes a reduction in the number of ossification centers compared with age-related norms. UMLS:C1856223 Decreased number of sternal ossification centres HP:0006611 Decreased number of sternal ossification centers A less than normal number of sternal ossification centers. The sternum is initially formed from bilateral sternal plates that chondrify and begin to fuse with ribs at 10 weeks gestational age. Ossification starts in the manubrium and upper part of the sternal body at the 6th month, in the middle of the sternal body at the 7th month, in the lower part of the body during the 1st postnatal year and in the xiphoid process between years 5 and 18. The number of ossification centers vary up to six, and it is the ossification centers that are visualized by prenatal ultrasound. This term describes a reduction in the number of ossification centers compared with age-related norms. PMID:10204210 Decreased number of sternal ossification centres Lack of formation of mineralized bony tissue of the sternum. HP:0006654 HP:0006666 UMLS:C1857074 UMLS:C4280443 Absent sternal mineralization Lack of sternal ossification Absent bone maturation in sternum HP:0006628 Absent sternal ossification Lack of formation of mineralized bony tissue of the sternum. Absent bone maturation in sternum Underdevelopment of the glenoid fossa, which is the cavity in the lateral part of the scapula which articulates with the head of the humerus. HP:0006632 UMLS:C1834384 Glenoid hypoplasia Hypoplastic glenoid fossa HP:0006633 Glenoid fossa hypoplasia Underdevelopment of the glenoid fossa, which is the cavity in the lateral part of the scapula which articulates with the head of the humerus. UMLS:C1865241 Large sternal ossification centres HP:0006642 Large sternal ossification centers Large sternal ossification centres UMLS:C1406921 HP:0006644 Thoracic dysplasia UMLS:C4025006 HP:0006681 Absent atrioventricular node Calcium deposition in the myocardium. Fyler:1889 UMLS:C1096561 Calcified myocardium HP:0006690 Calcification affecting the muscle layer of the heart. Myocardial calcification Calcium deposition in the myocardium. Abnormally short chordae tendineae of the tricuspid valve. UMLS:C4025001 HP:0006692 The chordae tendineae connect the papillary muscles to the tricuspid valve and the mitral valve. Short chordae tendineae of the tricuspid valve Abnormally short chordae tendineae of the tricuspid valve. A localized outpouching of ventricular cavity that is generally associated with dyskinesia and paradoxical expansion during systole. SNOMEDCT_US:90539001 UMLS:C0392464 Ventricular aneurysm HP:0006698 Aneurysm is considered a severe form of dilatation. Ventricular aneurysms may have rim of calcium in the affected regions of the ventricular wall (which can become fibrotic). Thromboembolism is a potential complication. Ventricular aneurysms can be diagnosed by ventriculography. Dilatation of the ventricular cavity A localized outpouching of ventricular cavity that is generally associated with dyskinesia and paradoxical expansion during systole. 2008-03-29T03:17:00Z UMLS:C4024996 Absent/small lungs Absent/underdeveloped lungs HP:0006703 Aplasia/Hypoplasia of the lungs Absent/small lungs Absent/underdeveloped lungs Any structural abnormality of the coronary arteries. 2008-03-29T03:33:00Z Fyler:3100 SNOMEDCT_US:28574005 UMLS:C0158623 HP:0006704 Abnormal coronary artery morphology Any structural abnormality of the coronary arteries. An abnormality of an atrioventricular valve. 2008-03-29T03:34:00Z HP:0006675 UMLS:C4024995 Abnormality of the atrioventricular valves HP:0006705 Abnormal atrioventricular valve morphology An abnormality of an atrioventricular valve. An abnormality of the hepatic vasculature. 2008-03-29T03:41:00Z UMLS:C4024994 Abnormality of liver blood vessels Abnormality of the liver vasculature HP:0006707 Abnormality of the hepatic vasculature An abnormality of the hepatic vasculature. Abnormality of liver blood vessels 2008-03-29T03:51:00Z HP:0006602 HP:0006669 UMLS:C3150086 Absent/rudimentary nipples Absent/small nipples Absent/underdeveloped nipples Nipples absent or rudimentary HP:0006709 Aplasia/Hypoplasia of the nipples Absent/small nipples Absent/underdeveloped nipples Absence or underdevelopment of the clavicles (collar bones). 2008-03-29T03:53:00Z UMLS:C4024993 Absent/small collarbone Absent/underdeveloped collarbone HP:0006710 Aplasia/Hypoplasia of the clavicles Absence or underdevelopment of the clavicles (collar bones). Absent/small collarbone Absent/underdeveloped collarbone 2008-03-29T03:53:00Z UMLS:C4024992 Absent/small outermost thorax bone Absent/underdeveloped thorax bone HP:0006711 Aplasia/Hypoplasia involving bones of the thorax Absent/small outermost thorax bone Absent/underdeveloped thorax bone 2008-03-29T03:54:00Z HP:0006636 UMLS:C1847363 Absent/small ribs Absent/underdeveloped ribs Hypoplastic or missing ribs HP:0006712 Aplasia/Hypoplasia of the ribs Absent/small ribs Absent/underdeveloped ribs 2008-03-29T03:58:00Z UMLS:C4024991 Absent/small shoulder blade Absent/underdeveloped shoulder blade HP:0006713 Aplasia/Hypoplasia of the scapulae Absent/small shoulder blade Absent/underdeveloped shoulder blade 2008-03-29T04:01:00Z UMLS:C4024990 Absent/small sternum Absent/underdeveloped sternum HP:0006714 Aplasia/Hypoplasia of the sternum Absent/small sternum Absent/underdeveloped sternum A tumor (abnormal growth of tissue) of the stomach. MSH:D013274 NCIT:C3262 SNOMEDCT_US:126824007 UMLS:C0038356 UMLS:C4020813 Stomach tumor Stomach tumour Neoplasia of the stomach HP:0006753 Neoplasm of the stomach A tumor (abnormal growth of tissue) of the stomach. Stomach tumor Stomach tumour Any anomaly of the anterior horn cell. Abnormality of the anterior horn cell MSH:D016472 SNOMEDCT_US:85672005 UMLS:C0154681 UMLS:C4020812 Abnormality of the anterior horn cells Anomaly of the anterior horn cells Anterior horn cell disease HP:0006802 Anterior horn cells are efferent neurons that passes from the central nervous system or a ganglion toward or to a muscle. They conduct nerve impulses that lead to movement of muscles. Abnormal anterior horn cell morphology Any anomaly of the anterior horn cell. Underdevelopment of the cerebrum. HP:0001322 UMLS:C1855330 Small cerebrum Underdeveloped cerebrum HP:0006872 Cerebral hypoplasia Underdevelopment of the cerebrum. Small cerebrum Underdeveloped cerebrum The presence of developmental dysplasia of the cortex of frontal lobe and the cortex of parietal lobe. UMLS:C4024959 HP:0006930 Frontoparietal cortical dysplasia The presence of developmental dysplasia of the cortex of frontal lobe and the cortex of parietal lobe. Proximal spinal muscular atrophy, i.e., muscular weakness and atrophy related to loss of the motor neurons of the spinal cord and brainstem. UMLS:C4024957 HP:0006959 Proximal spinal muscular atrophy Proximal spinal muscular atrophy, i.e., muscular weakness and atrophy related to loss of the motor neurons of the spinal cord and brainstem. The presence of calcium deposition in the choroid plexus. UMLS:C1863184 Calcified choroid plexus HP:0006960 Choroid plexus calcification The presence of calcium deposition in the choroid plexus. UMLS:C3277687 CNS degeneration HP:0007009 Central nervous system degeneration CNS degeneration A morphological abnormality of the metencephalon. UMLS:C4024951 HP:0007027 The metencephalon comprises the pons and the cerebellum; contains a portion of the fourth ventricle; and the trigeminal nerve, abducens nerve, facial nerve, and a portion of the vestibulocochlear nerve. The metencephalon is part of the hindbrain. Poorly formed metencephalon A morphological abnormality of the metencephalon. Cerebellar dysplasia (abnormal growth or development) is defined by abnormal cerebellar foliation, white matter arborization, and gray-white matter junction. Cerebellar dysplasia is a neuroimaging finding that describes abnormalities of both the cerebellar cortex and white matter and is associated with variable neurodevelopmental outcome. Dysplasia may globally involve the cerebellum or affect only one cerebellar hemisphere. In addition, cerebellar dysplasia may be associated with cortical/subcortical cysts. HP:0006893 UMLS:C3278322 HP:0007033 Any part of the cerebellum can be dysplastic, from small focal regions within one hemisphere to abnormal foliation throughout the cerebellum. Hypoplastic cerebella are frequently also dysmorphic, as observed in tubulinopathies and cobblestone malformations. Cerebellar dysplasia Cerebellar dysplasia (abnormal growth or development) is defined by abnormal cerebellar foliation, white matter arborization, and gray-white matter junction. Cerebellar dysplasia is a neuroimaging finding that describes abnormalities of both the cerebellar cortex and white matter and is associated with variable neurodevelopmental outcome. Dysplasia may globally involve the cerebellum or affect only one cerebellar hemisphere. In addition, cerebellar dysplasia may be associated with cortical/subcortical cysts. PMID:25105227 PMID:27160001 Hyperactive stretch reflexes of muscles that move proximal joints (elbow, knee). UMLS:C1836012 Hyperreflexia proximally HP:0007054 Proximal hyperreflexia UMLS:C0240116 Hyperreflexia in knees Overactive knee reflex Brisk knee jerk HP:0007083 Hyperactive patellar reflex Overactive knee reflex Brisk knee jerk Amyotrophy (muscular atrophy) affecting the proximal musculature. HP:0006792 HP:0006966 HP:0008943 HP:0008980 HP:0009041 UMLS:C1850794 Muscle atrophy, proximal Proximal muscle atrophy Proximal muscle wasting Symmetric proximal muscular atrophy Symmetrical, proximal limb muscle atrophy Wasting of muscles near the body HP:0007126 Proximal amyotrophy usually has a roughly symmetric distribution. Proximal amyotrophy Amyotrophy (muscular atrophy) affecting the proximal musculature. Wasting of muscles near the body Muscular atrophy of distal arm muscles. UMLS:C4021581 Distal upper limb muscle atrophy HP:0007149 Distal upper limb amyotrophy Muscular atrophy of distal arm muscles. UMLS:C1849485 HP:0007190 Neuronal loss in the cerebral cortex Muscular atrophy affecting the lower limb. UMLS:C4024921 HP:0007210 Lower limb amyotrophy Muscular atrophy affecting the lower limb. Agenesis of the midbrain. UMLS:C4024913 HP:0007265 Midbrain and mesencephalon are synonymous. Absent mesencephalon Agenesis of the midbrain. HPO_CONTRIBUTOR:KI_phemming Muscular weakness and atrophy related to loss of the motor neurons of the spinal cord and brainstem. MSH:D009134 SNOMEDCT_US:5262007 UMLS:C0026847 Spinal muscle degeneration Spinal muscle wasting HP:0007269 Spinal muscular atrophy Muscular weakness and atrophy related to loss of the motor neurons of the spinal cord and brainstem. Spinal muscle degeneration Spinal muscle wasting HP:0006874 SNOMEDCT_US:418143002 SNOMEDCT_US:52522001 UMLS:C0154671 Neuroaxonal degeneration in the brain HP:0007313 Cerebral degeneration Underdevelopment of the frontal lobe of the cerebrum. HP:0002424 UMLS:C1849172 Frontal lobe hypoplasia Hypoplastic frontal lobes Underdeveloped frontal lobe HP:0007333 Hypoplasia of the frontal lobes Underdevelopment of the frontal lobe of the cerebrum. Underdeveloped frontal lobe Any structural anomaly of the limbic system, a set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. UMLS:C1863392 Limbic malformation HP:0007343 Abnormal morphology of the limbic system UMLS:C1843858 Atrophic and degenerative changes in the spinal cord HP:0007344 Atrophy/Degeneration involving the spinal cord UMLS:C1843175 HP:0007350 Hyperreflexia in upper limbs UMLS:C1851431 HP:0007352 Cerebellar calcifications 2008-03-31T05:30:00Z HP:0006857 HP:0007368 UMLS:C3279222 Absent/small cerebellum Absent/underdeveloped cerebellum Atrophy/Degeneration affecting the cerebellum Atrophy/Hypoplasia of the cerebellum Cerebellar hypoplasia/atrophy HP:0007360 Aplasia/Hypoplasia of the cerebellum Absent/small cerebellum Absent/underdeveloped cerebellum A structural abnormality of the pons. 2008-03-31T05:32:00Z UMLS:C4024905 Abnormality of the pons HP:0007361 The pons is the portion of the brainstem superior to the medulla oblongata. Abnormal pons morphology A structural abnormality of the pons. 2008-03-31T05:33:00Z UMLS:C4024904 Absent/small brainstem Absent/underdeveloped brainstem HP:0007362 Aplasia/Hypoplasia of the brainstem Absent/small brainstem Absent/underdeveloped brainstem 2008-03-31T05:43:00Z UMLS:C4024902 Absent/small cerebrum Absent/underdeveloped cerebrum HP:0007364 Aplasia/Hypoplasia of the cerebrum Absent/small cerebrum Absent/underdeveloped cerebrum 2008-04-01T10:22:00Z UMLS:C4024900 Brainstem atrophy HP:0007366 Atrophy/Degeneration affecting the brainstem 2008-04-01T10:23:00Z UMLS:C4024899 Atrophy/Degeneration affecting the CNS HP:0007367 Atrophy/Degeneration affecting the central nervous system Atrophy/Degeneration affecting the CNS The presence of atrophy (wasting) of the cerebrum, also known as the telencephalon, the largest and most highly developed part of the human brain. 2008-04-01T10:28:00Z UMLS:C4024898 HP:0007369 Atrophy/Degeneration affecting the cerebrum The presence of atrophy (wasting) of the cerebrum, also known as the telencephalon, the largest and most highly developed part of the human brain. Wasting involving the motor neuron. 2008-04-01T10:39:00Z UMLS:C4024896 Motor neuron degeneration HP:0007373 Motor neuron atrophy Wasting involving the motor neuron. Motor neuron degeneration An abnormality of the choroid plexus, which is the area in the cerebral ventricles in which cerebrospinal fluid is produced by modified ependymal cells. 2008-04-01T10:52:00Z UMLS:C4024893 HP:0007376 The choroid plexus is a structure in the ventricles of the brain where cerebrospinal fluid (CSF) is produced. Abnormal choroid plexus morphology An abnormality of the choroid plexus, which is the area in the cerebral ventricles in which cerebrospinal fluid is produced by modified ependymal cells. A tumor (abnormal growth of tissue) of the gastrointestinal tract. 2008-04-01T11:55:00Z MSH:D005770 NCIT:C3262 SNOMEDCT_US:126768004 UMLS:C0017185 GI tract tumor GI tract tumour Gastrointestinal tract neoplasia Gastrointestinal tract neoplasm Gastrointestinal tract tumor Gastrointestinal tract tumour Neoplasm of the GI tract HP:0007378 Neoplasm of the gastrointestinal tract A tumor (abnormal growth of tissue) of the gastrointestinal tract. GI tract tumor GI tract tumour Gastrointestinal tract tumor Gastrointestinal tract tumour Neoplasm of the GI tract A tumor (abnormal growth of tissue) of the genitourinary system. 2008-04-01T12:00:00Z MSH:D014565 NCIT:C3262 UMLS:C0042065 UMLS:C4020809 Genitourinary tract neoplasm Genitourinary tract tumors Genitourinary tract tumours Neoplasm of the GU tract Genitourinary tract neoplasia HP:0007379 Neoplasm of the genitourinary tract A tumor (abnormal growth of tissue) of the genitourinary system. Genitourinary tract tumors Genitourinary tract tumours Neoplasm of the GU tract Underdevelopment of the sweat glands. UMLS:C1832455 Underdeveloped sweat glands HP:0007387 Hypoplastic sweat glands Underdevelopment of the sweat glands. Underdeveloped sweat glands Lack of subcutaneous adipose tissue. HP:0007519 UMLS:C0241267 UMLS:C4024855 Absent fat below the skin General absence of subcutaneous fat Lack of fatty tissue below the skin HP:0007485 Absence of subcutaneous fat Lack of subcutaneous adipose tissue. Absent fat below the skin Lack of fatty tissue below the skin The presence of fewer than normal sweat glands. HP:0007555 HP:0007594 UMLS:C4021574 Decreased sweat glands Decreased sweat pores HP:0007500 Decreased number of sweat glands The presence of fewer than normal sweat glands. Decreased sweat glands Decreased sweat pores UMLS:C1832454 HP:0007515 Hypoplastic pilosebaceous units HP:0001091 HP:0007693 HP:0007739 HP:0007969 HP:0008008 SNOMEDCT_US:13164000 UMLS:C0234632 Decreased central vision Decreased clarity of vision Decreased visual acuity Poor visual acuity HP:0007663 Reduced visual acuity Decreased clarity of vision Congenital underdevelopment of the iris. HP:0000638 HP:0007724 HP:0007998 SNOMEDCT_US:95714006 UMLS:C0344539 Hypoplastic iris Iris hypoplasia Underdeveloped iris HP:0007676 Hypoplasia of the iris Congenital underdevelopment of the iris. Underdeveloped iris Abnormal development (dysgenesis) of the anterior segment of the eye globe. These structures are mainly of mesenchymal origin. HP:0007696 HP:0007699 HP:0008040 SNOMEDCT_US:65075004 UMLS:C0266525 Anterior chamber cleavage defect Anterior chamber cleavage disorder Anterior chamber malformation Anterior chamber mesodermal anomalies Anterior segment developmental abnormality Anterior segment dysgenesis Anterior segment mesencyhmal dysgenesis Anterior segment ocular dysgenesis HP:0007700 In anterior segment mesenchymal ocular dysgenesis (ASMOD), multiple tissues are affected, including the iris, cornea, and lens as well as the Schlemm's canal and trabecular meshwork drainage structures located at the anterior segment angle where the iris and cornea meet. These abnormalities may result from a primary defect in the migration and/or differentiation of the mesenchymal cells that contribute to development of the cornea, iris, and drainage structures. Ocular anterior segment dysgenesis Abnormal development (dysgenesis) of the anterior segment of the eye globe. These structures are mainly of mesenchymal origin. HPO_CONTRIBUTOR:DDD_ncarter SNOMEDCT_US:111521006 UMLS:C0155118 HP:0007705 Corneal degeneration Cornea plana is an abnormally flat shape of the cornea such that the normal protrusion of the cornea from the sclera is missing. The reduced corneal curvature can lead to hyperopia, and a hazy corneal limbus and arcus lipoides may develop at an early age. SNOMEDCT_US:204145006 UMLS:C0344529 Cornea plana HP:0007720 Flat cornea Cornea plana is an abnormally flat shape of the cornea such that the normal protrusion of the cornea from the sclera is missing. The reduced corneal curvature can lead to hyperopia, and a hazy corneal limbus and arcus lipoides may develop at an early age. Abnormal development of the choroid and retina. UMLS:C4024809 HP:0007731 Chorioretinal dysplasia Abnormal development of the choroid and retina. Underdevelopment of the lacrimal gland. UMLS:C1863200 Hypoplastic lacrimal gland Underdeveloped tear gland HP:0007732 Lacrimal gland hypoplasia Underdevelopment of the lacrimal gland. Underdeveloped tear gland Abnormally big lacrimal glands. UMLS:C1867030 Enlarged tear gland HP:0007734 Enlarged lacrimal glands Abnormally big lacrimal glands. Enlarged tear gland Reduced transparency of the stroma of cornea. HP:0000515 HP:0007662 HP:0007896 HP:0007966 SNOMEDCT_US:246957002 UMLS:C0423250 UMLS:C1856661 Cloudy cornea Corneal stromal opacity Cloudy corneas HP:0007759 Opacification of the corneal stroma Reduced transparency of the stroma of cornea. Cloudy corneas UMLS:C1854685 Retinal hypoplasia Underdeveloped retina HP:0007770 Hypoplasia of the retina Underdeveloped retina Underdevelopment of the ciliary body. UMLS:C1836890 HP:0007774 Hypoplasia of the ciliary body Underdevelopment of the ciliary body. A kind of cataract that progresses with age. HP:0007828 UMLS:C4021566 Cataract, progressive HP:0007834 Progressive cataract A kind of cataract that progresses with age. MSH:D015861 SNOMEDCT_US:61267008 UMLS:C0035320 HP:0007850 Retinal vascular proliferation Deposition of calcium salts in the retina. UMLS:C1867289 HP:0007862 Retinal calcification Deposition of calcium salts in the retina. Underdevelopment of the lacrimal puncta. UMLS:C4021564 Hypoplasia of the lacrimal puncta Hypoplastic lacrimal puncta HP:0007892 Hypoplasia of the lacrimal punctum Underdevelopment of the lacrimal puncta. Hypoplasia of the lacrimal puncta Hypoplastic lacrimal puncta UMLS:C1968574 Underdeveloped tear duct HP:0007900 Hypoplastic lacrimal duct Underdeveloped tear duct UMLS:C3275963 Abnormality of iris blood vessels HP:0007905 Abnormal iris vasculature Abnormality of iris blood vessels A reduction of corneal clarity. HP:0007844 HP:0007883 HP:0008502 MSH:D003318 SNOMEDCT_US:413921009 SNOMEDCT_US:64634000 SNOMEDCT_US:95735008 UMLS:C0010038 UMLS:C0521719 Corneal clouding Corneal opacities Reduction of corneal clarity Scarring or clouding of the cornea of the eye HP:0007957 Corneal opacity A reduction of corneal clarity. The presence of developmental dysplasia of the retina. HP:0007901 HP:0008022 MSH:D015792 SNOMEDCT_US:95494009 UMLS:C0035313 Retinal dysgenesis HP:0007973 This feature is a congenital developmental anomaly of the retina characterized by abnormal growth and differentiation. The retina contains numerous tubular structures and rosettes. Retinal dysplasia (synonym: retinal dysgenesis) is often accompanied by retinal detachment and micropthalmos, but the latter features should be coded separately. Retinal dysplasia The presence of developmental dysplasia of the retina. Underdevelopment of the stroma of iris. HP:0007991 HP:0008027 UMLS:C1860344 Hypoplastic iris stoma Iris stromal hypoplasia Underdeveloped iris stroma HP:0007990 Hypoplastic iris stroma Underdevelopment of the stroma of iris. Underdeveloped iris stroma Congenital malformation of the lacrimal duct associated with incomplete development of the bony nasolacrimal canal or craniofacial anomalies. UMLS:C4024757 Malformed tear ducts HP:0007993 Malformed lacrimal duct Congenital malformation of the lacrimal duct associated with incomplete development of the bony nasolacrimal canal or craniofacial anomalies. Malformed tear ducts An abnormally reduced response to stimulation of the cornea (by touch, foreign body, blowing air). The corneal reflex (also known as the blink reflex, normally results in an involuntary blinking of the eyelids. MSH:D012021 SNOMEDCT_US:103254005 UMLS:C0151572 Decreased blink reflex Reduced corneal reflex HP:0008000 Decreased corneal reflex An abnormally reduced response to stimulation of the cornea (by touch, foreign body, blowing air). The corneal reflex (also known as the blink reflex, normally results in an involuntary blinking of the eyelids. Absence or underdevelopment of the lacrimal gland. UMLS:C1835602 Absent/underdeveloped lacrimal glands Absent/underdeveloped tear glands HP:0008038 Aplastic/hypoplastic lacrimal glands Absence or underdevelopment of the lacrimal gland. Absent/underdeveloped lacrimal glands Absent/underdeveloped tear glands A structural abnormality of retinal vasculature. 2008-04-02T12:09:00Z UMLS:C4024753 Abnormality of retina blood vessels Abnormality of the retinal vasculature HP:0008046 Abnormal retinal vascular morphology A structural abnormality of retinal vasculature. Abnormality of retina blood vessels 2008-04-02T12:10:00Z UMLS:C4024752 Abnormality of eye blood vessels HP:0008047 Abnormality of the vasculature of the eye Abnormality of eye blood vessels Absence or underdevelopment of the iris. 2008-04-02T01:50:00Z UMLS:C4024748 Absent/small iris Absent/underdeveloped iris HP:0008053 Aplasia/Hypoplasia of the iris Absence or underdevelopment of the iris. Absent/small iris Absent/underdeveloped iris Absence or underdevelopment of the uvea, the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid. 2008-04-02T03:24:00Z UMLS:C4024746 Absent/underdeveloped uvea HP:0008055 Aplasia/Hypoplasia affecting the uvea Absence or underdevelopment of the uvea, the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid. Absent/underdeveloped uvea 2008-04-02T03:25:00Z UMLS:C4024745 Absent/small eye Absent/underdeveloped eye HP:0008056 Aplasia/Hypoplasia affecting the eye Absent/small eye Absent/underdeveloped eye 2008-04-02T03:27:00Z UMLS:C4024744 Absent/small fundus HP:0008057 Aplasia/Hypoplasia affecting the fundus Absent/small fundus https://en.wikipedia.org/wiki/febrile_seizure 2008-04-02T03:30:00Z UMLS:C4024740 Absent/small retina Absent/underdeveloped retina HP:0008061 Aplasia/Hypoplasia of the retina Absent/small retina Absent/underdeveloped retina Absence or underdevelopment of the anterior segment of the eye. 2008-04-02T03:33:00Z UMLS:C4024739 HP:0008062 Aplasia/Hypoplasia affecting the anterior segment of the eye Absence or underdevelopment of the anterior segment of the eye. Absence or underdevelopment of the lens. 2008-04-02T03:33:00Z UMLS:C4024738 Absent/small lens Absent/underdeveloped lens HP:0008063 Aplasia/Hypoplasia of the lens Absence or underdevelopment of the lens. Absent/small lens Absent/underdeveloped lens 2008-04-02T03:44:00Z UMLS:C4024737 Absent/small skin Absent/underdeveloped skin HP:0008065 Aplasia/Hypoplasia of the skin Absent/small skin Absent/underdeveloped skin 2008-04-02T03:56:00Z UMLS:C4024736 Abnormally loose or hyperelastic skin Abnormally loose or stretchable skin HP:0008067 Abnormally lax or hyperextensible skin Abnormally loose or hyperelastic skin Abnormally loose or stretchable skin Reduction in bone mineral density affecting any or all of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. UMLS:C1836872 HP:0008076 Osteoporotic tarsals Reduction in bone mineral density affecting any or all of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. The presence of a fifth metatarsal bone that has not undergone ossification at an age when ossification is usually visible. UMLS:C1844712 HP:0008087 Nonossified fifth metatarsal The presence of a fifth metatarsal bone that has not undergone ossification at an age when ossification is usually visible. An anomaly of the fifth metatarsal bone. UMLS:C4024733 Abnormality of the 5th long bone of foot HP:0008089 Abnormality of the fifth metatarsal bone An anomaly of the fifth metatarsal bone. Abnormality of the 5th long bone of foot Delayed maturation and calcification of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. HP:0008145 UMLS:C1846853 UMLS:C4280418 Tarsal delayed ossification Delayed ankle bone maturation HP:0008103 Delayed tarsal ossification Delayed maturation and calcification of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. Delayed ankle bone maturation UMLS:C1856746 Deformed ankle bones HP:0008119 Deformed tarsal bones Deformed ankle bones Excessive amounts of mucopolysaccharide in the urine. HP:0003567 UMLS:C4024726 HP:0008155 This finding is suggestive of the diagnosis of a mucopolysaccharidosis. Mucopolysacchariduria Excessive amounts of mucopolysaccharide in the urine. UMLS:C4024719 Small adrenal cortex HP:0008182 Adrenocortical hypoplasia Small adrenal cortex MSH:D050033 UMLS:C1563716 Thyroid dysplasia HP:0008188 Thyroid dysgenesis The congenital absence of the thyroid gland. MSH:D050033 UMLS:C0749420 UMLS:C4020805 Athyroidal hypothyroidism HP:0008191 Thyroid agenesis The congenital absence of the thyroid gland. PMID:2918525 Abnormal development of the adrenal gland. UMLS:C1856017 Adrenal gland dysplasia Dysplastic adrenal glands HP:0008216 Adrenal gland dysgenesis Abnormal development of the adrenal gland. Enlargement of the adrenal gland. SNOMEDCT_US:419920004 UMLS:C1621895 Enlarged adrenal glands HP:0008221 Adrenal hyperplasia Enlargement of the adrenal gland. Enlarged adrenal glands Developmental hypoplasia of the adrenal medulla. UMLS:C4024717 Small adrenal medulla HP:0008239 Adrenal medullary hypoplasia Developmental hypoplasia of the adrenal medulla. Small adrenal medulla An abnormality of zinc ion homeostasis. UMLS:C4020802 UMLS:C4024711 Abnormality of zinc homeostasis Abnormal zinc metabolism HP:0008277 Abnormal blood zinc concentration An abnormality of zinc ion homeostasis. Atrophy (wasting) of the cerebellar cortex. UMLS:C4024710 Cerebellar cortex degeneration HP:0008278 Cerebellar cortical atrophy may be associated with vacuolated or binucleated Purkinje cells. Cerebellar cortical atrophy Atrophy (wasting) of the cerebellar cortex. Cerebellar cortex degeneration UMLS:C3151556 HP:0008306 Abnormal iron deposition in mitochondria An abnormality of the mitochondria in muscle tissue. UMLS:C4021546 Abnormal mitochondria in muscle HP:0008316 This finding is typically demonstrated by muscle biopsy. Abnormal mitochondria in muscle tissue An abnormality of the mitochondria in muscle tissue. Any structural anomaly of the mitochondria. UMLS:C4014650 Abnormal mitochondrion morphology HP:0008322 This feature may be assessed by means of electron microscopy. Abnormal mitochondrial morphology Any structural anomaly of the mitochondria. An increased urine level of any amino acid carrying two amino groups (Asparagine, glutamine and lysine, cystine, ornithine). UMLS:C4024698 HP:0008339 Diaminoaciduria Concentration of a branched chain amino acid in the blood above the upper limit of normal. UMLS:C4024697 HP:0008344 Elevated circulating branched chain amino acid concentration Concentration of a branched chain amino acid in the blood above the upper limit of normal. HPO_CONTRIBUTOR:gcarletti Absence or underdevelopment of the big toe. 2008-04-04T11:33:00Z HP:0004694 HP:0008118 HP:0008126 UMLS:C1836213 Absent/small big toe Absent/underdeveloped big toe Aplastic/hypoplastic halluces HP:0008362 Aplasia/Hypoplasia of the hallux Absence or underdevelopment of the big toe. Absent/small big toe Absent/underdeveloped big toe Absence or underdevelopment of the tarsal bones. 2008-04-04T11:35:00Z HP:0008109 UMLS:C1848671 Absent/small ankle bone Absent/underdeveloped ankle bone Aplastic/hypoplastic tarsals HP:0008363 Aplasia/Hypoplasia of the tarsal bones Absence or underdevelopment of the tarsal bones. Absent/small ankle bone Absent/underdeveloped ankle bone Contractures of one or more joints of the feet meaning chronic loss of joint motion due to structural changes in non-bony tissue. 2008-04-04T11:44:00Z HP:0100492 SNOMEDCT_US:239742004 UMLS:C0343149 Contractures involving the joints of the feet Contractures of the foot joints Joint contractures involving the joints of the feet HP:0008366 Foot joint contracture Contractures of the foot joints An abnormality of the formation and mineralization of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. 2008-04-04T11:53:00Z UMLS:C4021544 UMLS:C4025075 Abnormal ossification of tarsal bones Hardening of ankle bones Abnormal maturation of ankle bones HP:0008369 Abnormal tarsal ossification An abnormality of the formation and mineralization of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. Hardening of ankle bones Abnormal maturation of ankle bones Any abnormal process of ossification of the metatarsal bones, which normally are each ossified from two centers: one for the body, and one for the head (metatarsal II,III,IV, and V) and one for the body and one for the base (metatarsal I). The ossification process begins in the center of the body about the ninth week, and extends toward either extremity. The center for the base of the first metatarsal appears about the third year, and the centers for the heads of the other bones between the fifth and eighth years. They join the bodies between the eighteenth and twentieth years. 2008-04-04T11:59:00Z UMLS:C4021543 Abnormal ossification involving metatarsal bones Abnormal maturation of long bone of foot HP:0008371 Abnormal metatarsal ossification Any abnormal process of ossification of the metatarsal bones, which normally are each ossified from two centers: one for the body, and one for the head (metatarsal II,III,IV, and V) and one for the body and one for the base (metatarsal I). The ossification process begins in the center of the body about the ninth week, and extends toward either extremity. The center for the base of the first metatarsal appears about the third year, and the centers for the heads of the other bones between the fifth and eighth years. They join the bodies between the eighteenth and twentieth years. Abnormal maturation of long bone of foot Concentration of vitamin A in the blood circulation outside limits of normal. 2008-04-04T12:29:00Z UMLS:C4024686 HP:0008372 Abnormal circulating vitamin A concentration 2008-04-04T12:35:00Z HP:0000827 UMLS:C4024685 Puberty and gonadal disorders HP:0008373 Puberty and gonadal disorders Puberty and gonadal disorders Small, underdeveloped vertebral bodies. HP:0008431 SNOMEDCT_US:205456006 UMLS:C0345394 Underdeveloped vertebrae HP:0008417 Vertebral hypoplasia Small, underdeveloped vertebral bodies. Underdeveloped vertebrae The presence of degenerative changes of intervertebral disk. MSH:D055959 SNOMEDCT_US:77547008 UMLS:C0158266 Degeneration of intervertebral discs Degeneration of intervertebral disks Degenerative disc disease Degenerative intervertebral disc Degenerative intervertebral disk HP:0008419 Intervertebral disc degeneration The presence of degenerative changes of intervertebral disk. Degeneration of intervertebral discs Degenerative disc disease Degenerative intervertebral disc UMLS:C1863313 HP:0008421 Tall lumbar vertebral bodies The presence of developmental dysplasia of the vertebral column. UMLS:C4021853 HP:0008423 Spinal dysplasia The presence of developmental dysplasia of the vertebral column. UMLS:C1859366 Underdeveloped 5th lumbar vertebrae HP:0008424 Hypoplastic 5th lumbar vertebrae Underdeveloped 5th lumbar vertebrae HP:0008415 UMLS:C1835570 Cervical vertebrae hypoplasia Underdeveloped cervical vertebrae HP:0008434 Hypoplastic cervical vertebrae Underdeveloped cervical vertebrae UMLS:C1856644 Absent/small tailbone Absent/underdeveloped tailbone HP:0008436 Absent/hypoplastic coccyx Absent/small tailbone Absent/underdeveloped tailbone UMLS:C2751478 HP:0008437 Bifid thoracic vertebrae A morphological abnormality of the vertebral arch, i.e., of the posterior part of a vertebra. UMLS:C1835764 Vertebral arch abnormalities HP:0008438 A vertebral arch is the posterior part of a vertebra and forms the canal through which the spinal cord passes. A vertebral arch consists of (i) a pair of vertebral pedicles, which are short thick processes that extend from the vertebral body to connect the body to the vertebral arch; (ii) a pari of vertebral laminae (broad plates that extending dorsally and medially from the pedicles fusing with one another to complete the roof of the vertebral arch); (iii) the spinous process (a process that is directed backward and downward from the junction of the laminae and to which muscles and ligaments attach); (iv) two superior articular processes and two inferior articular processes that articulate between two adjacent vertebrae); and (v) two transverse processes that extend at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes and allow the attachment of muscles and ligaments. Vertebral arch anomaly A morphological abnormality of the vertebral arch, i.e., of the posterior part of a vertebra. Any abnormality of the atlas and the axis. UMLS:C4024675 HP:0008440 The atlas is the first cervical vertebral body and the axis is the second vertebral body. C1-C2 vertebral abnormality Any abnormality of the atlas and the axis. Excessive growth of the bones of the vertebral bodies. UMLS:C1834057 HP:0008442 Vertebral hyperostosis Excessive growth of the bones of the vertebral bodies. A progressive disorder of vertebral joint degeneration that occurs in the setting of any condition characterized by decreased afferent innervation, involving loss of deep pain and proprioceptive sensation in the vertebral column. Patients most commonly present with symptoms of lower back pain, sitting imbalance, progressive spinal deformity (usually kyphosis), and an audible clicking sound on changing postures. SNOMEDCT_US:298380006 UMLS:C0575157 Charcot spinal arthropathy Spinal deformities Spinal neuroarthropathy HP:0008443 Neuropathic spinal arthropathy presents almost exclusively in patients who have suffered traumatic spinal cord injury or less commonly, secondary to syringomyelia, meningocele, myelomeningocele, diabetes mellitus, peripheral neuropathies, anesthetic leprosy, congenital analgesia, Parkinson's disease, arachnoiditis, transverse myelitis, and others. Neuropathic spinal arthropathy A progressive disorder of vertebral joint degeneration that occurs in the setting of any condition characterized by decreased afferent innervation, involving loss of deep pain and proprioceptive sensation in the vertebral column. Patients most commonly present with symptoms of lower back pain, sitting imbalance, progressive spinal deformity (usually kyphosis), and an audible clicking sound on changing postures. PMID:29755231 UMLS:C2751480 HP:0008447 Hypoplastic coccygeal vertebrae A developmental defect of the sacrum characterized by partial or disordered development of the sacrum in which portions of the sacrum, which normally is formed by fusion of five sacral vertebrae S1-S5, fail to form or fail to form normally. UMLS:C1851305 Absence of some of the sacral and coccygeal bones Partial sacral agenesis Sacral dysgenesis HP:0008455 Dysplastic sacrum Absence of some of the sacral and coccygeal bones UMLS:C4024674 Underdeveloped spinal processes HP:0008460 Hypoplastic spinal processes Underdeveloped spinal processes UMLS:C4024671 HP:0008464 Absent spinous processes of lower thoracic and lumbar vertebrae A developmental defect characterized by agenesis of one or more vertebral bodies. SNOMEDCT_US:15843004 UMLS:C0158776 Absent vertebrae HP:0008465 Absent vertebra A developmental defect characterized by agenesis of one or more vertebral bodies. PMID:26167231 Absent vertebrae Dysplasia of the cervical vertebral column. MSH:C566140 UMLS:C1861693 HP:0008469 Cervical vertebral dysplasia Dysplasia of the cervical vertebral column. UMLS:C2751479 HP:0008475 Hypoplastic sacral vertebrae Decreased ossification of the cervical vertebral bodies, i.e., of the Cervical vertebrae set. UMLS:C4024670 HP:0008477 Poorly ossified cervical vertebrae Decreased ossification of the cervical vertebral bodies, i.e., of the Cervical vertebrae set. HP:0002773 UMLS:C1863353 Small vertebrae Small vertebral bodies Underdeveloped back bones HP:0008479 Hypoplastic vertebral bodies Underdeveloped back bones UMLS:C1850329 HP:0008490 Sacral segmentation defect 2008-04-04T02:30:00Z UMLS:C4024662 Absent/small vertebrae Absent/underdeveloped vertebrae HP:0008515 Aplasia/Hypoplasia of the vertebrae Absent/small vertebrae Absent/underdeveloped vertebrae 2008-04-04T02:31:00Z UMLS:C4024661 HP:0008516 Abnormality of the vertebral spinous processes Aplasia or developmental hypoplasia of the sacral bone. 2008-04-04T02:32:00Z UMLS:C4024660 Absent/small sacrum Absent/underdeveloped sacrum HP:0008517 Aplasia/Hypoplasia of the sacrum Aplasia or developmental hypoplasia of the sacral bone. Absent/small sacrum Absent/underdeveloped sacrum 2008-04-04T02:33:00Z UMLS:C4024659 Absent/small backbone Absent/small spine Absent/small vertebral column Absent/underdeveloped backbone Absent/underdeveloped spine Absent/underdeveloped vertebral column HP:0008518 Aplasia/Hypoplasia involving the vertebral column Absent/small backbone Absent/small spine Absent/small vertebral column Absent/underdeveloped backbone Absent/underdeveloped spine Absent/underdeveloped vertebral column Any structural abnormality of the coccyx. 2008-04-04T02:41:00Z HP:0002830 UMLS:C4024658 Abnormal tailbone Abnormality of the coccyx HP:0008519 Abnormal coccyx morphology Any structural abnormality of the coccyx. Abnormal tailbone Underdevelopment of the external ear. HP:0000393 HP:0000409 HP:0008550 HP:0008618 HP:0008621 MSH:D065817 SNOMEDCT_US:35045004 UMLS:C0152423 Bilateral microtia Hypoplasia of the external ear Hypoplastic ears Hypoplastic pinna Small ears Small pinnae Underdeveloped ears HP:0008551 The definitions of microtia follow a widely used, surgically based, classification of ear anomalies outlined by Weerda 1988. As microtia indicates at least both decreased length and width, and in more severe forms it includes abnormal shape of structures, all forms are acknowledged to be bundled terms, but are retained here because they are well established. Microtia Underdevelopment of the external ear. PMID:19152421 PMID:3270622 Small ears Underdeveloped ears The presence of a malformed cochlea. UMLS:C1862050 HP:0008554 A cochlear malformation may include a membranous abnormality, a bony abnormality, or a combination of the two. Cochlear malformation The presence of a malformed cochlea. A malformation of the auricle of the ear. HP:0008594 UMLS:C1846460 External ear malformation HP:0008572 External ear malformation A malformation of the auricle of the ear. External ear malformation Developmental hypoplasia of the cochlea. UMLS:C2676974 Hypoplastic cochlea Underdeveloped cochlea HP:0008586 Hypoplasia of the cochlea Developmental hypoplasia of the cochlea. Underdeveloped cochlea A progressive type of conductive deafness. UMLS:C1861325 Progressive conductive deafness HP:0008607 Progressive conductive hearing impairment A progressive type of conductive deafness. UMLS:C1857263 HP:0008608 Hypertrophic auricular cartilage An abnormality of the morphology or structure of the middle ear. UMLS:C1857456 Middle ear malformation Morphological abnormality of the middle ear HP:0008609 Abnormal middle ear morphology An abnormality of the morphology or structure of the middle ear. HPO_CONTRIBUTOR:DDD_mbitner-glidicz Middle ear malformation Morphological abnormality of the middle ear Absence of sex glands (gonads are the organs that produce gametes; testis in males and ovary in females). UMLS:C4024652 Absent gonadal tissue Gonadal agenesis HP:0008633 Gonadal agenesis refers to the lack of development of gonads during fetal development; it may not be possible clinically to determine if gonal tissue was present at any point of development. For this reason, we regard agonadism and gonadal agenesis as synonymous. Agonadism Abnormal enlargement of the urinary bladder. UMLS:C4021531 Hypertrophic urinary bladder HP:0008635 Hypertrophy of the urinary bladder Abnormal enlargement of the urinary bladder. UMLS:C0239761 Underdeveloped gonad HP:0008639 Gonadal hypoplasia Underdeveloped gonad Aplasia or developmental hypoplasia of the fallopian tube. UMLS:C4020791 UMLS:C4024646 Absent/small fallopian tube Absent/underdeveloped fallopian tube Absent or rudimentary fallopian tubes HP:0008655 Aplasia/Hypoplasia of the fallopian tube Aplasia or developmental hypoplasia of the fallopian tube. Absent/small fallopian tube Absent/underdeveloped fallopian tube Hypertrophy of the clitoris. HP:0000057 HP:0008728 SNOMEDCT_US:80212005 UMLS:C0156394 Clitoral enlargement Clitoromegaly Enlarged clitoris Hypertrophic clitoris Prominent clitoris HP:0008665 Increased size of the clitoris. Clitoral hypertrophy Hypertrophy of the clitoris. Enlarged clitoris Incomplete maturation or aberrant formation of the male gametes. SNOMEDCT_US:4529005 UMLS:C0520933 UMLS:C4020789 Impaired spermatogenesis Abnormal sperm development HP:0008669 Abnormal spermatogenesis Incomplete maturation or aberrant formation of the male gametes. MP:0001156 Abnormal sperm development Absence or underdevelopment of the kidney. HP:0004744 HP:0008701 UMLS:C1857453 Absent/small kidney Absent/underdeveloped kidney Renal agenesis/hypoplasia Renal aplasia/hypoplasia HP:0008678 Renal hypoplasia/aplasia Absence or underdevelopment of the kidney. Absent/small kidney Absent/underdeveloped kidney Absence or developmental hypoplasia of the uterus. UMLS:C4024640 Absent/small uterus Absent/underdeveloped uterus HP:0008684 Aplasia/hypoplasia of the uterus Absence or developmental hypoplasia of the uterus. Absent/small uterus Absent/underdeveloped uterus UMLS:C1844923 Hypoplastic prostate Underdeveloped prostate HP:0008687 Hypoplasia of the prostate Underdeveloped prostate Developmental hypoplasia of the fallopian tube. UMLS:C1968706 Rudimentary fallopian tubes Underdeveloped fallopian tube HP:0008697 Hypoplasia of the fallopian tube Developmental hypoplasia of the fallopian tube. Underdeveloped fallopian tube UMLS:C4024637 HP:0008702 Absent internal genitalia Deposition of calcium salts in gonadal tissue. UMLS:C4024636 HP:0008703 Gonadal calcification Deposition of calcium salts in gonadal tissue. SNOMEDCT_US:253847002 UMLS:C0302885 HP:0008715 Testicular dysgenesis The presence of a diverticulum (sac or pouch) in the wall of the urethra. SNOMEDCT_US:90531003 UMLS:C0152443 HP:0008722 Urethral diverticulum The presence of a diverticulum (sac or pouch) in the wall of the urethra. Developmental hypoplasia of the ovary. SNOMEDCT_US:93279005 UMLS:C0685840 UMLS:C1835452 Hypoplastic ovary Underdeveloped ovary HP:0008724 Hypoplasia of the ovary Developmental hypoplasia of the ovary. Underdeveloped ovary Developmental hypoplasia of the vagina. HP:0011938 SNOMEDCT_US:253836009 UMLS:C0345309 UMLS:C1442988 Hypoplastic vagina Rudimentary vagina Underdeveloped vagina HP:0008726 Hypoplasia of the vagina Developmental hypoplasia of the vagina. Underdeveloped vagina Reduced volume of the testicle (the male gonad). HP:0000043 SNOMEDCT_US:276411001 UMLS:C0241355 Decreased testicular size Hypoplastic testes Small testes Small testis Testicular hypoplasia HP:0008734 Decreased testicular size Reduced volume of the testicle (the male gonad). Decreased testicular size Small testes Small testis HP:0008632 SNOMEDCT_US:34911001 UMLS:C0266435 Underdeveloped penis HP:0008736 Hypoplasia of penis Underdeveloped penis Ossification affecting the set of cartilages of larynx. UMLS:C1855622 HP:0008747 This term describes abnormal ossification affecting one or more of the cartilages of the larnyx (cricoid cartilage, thyroid cartilage, epiglottic cartilage, arytenoid cartilage, corniculate cartilage, cuneiform cartilage, triticeal cartilage, and sesamoid cartilage). Cartilaginous ossification of larynx Ossification affecting the set of cartilages of larynx. Underdevelopment of the larynx. HP:0005935 SNOMEDCT_US:253736003 UMLS:C0431527 Hypoplastic larynx HP:0008749 Laryngeal hypoplasia Underdevelopment of the larynx. Presence of a gap in the posterior laryngotracheal wall with a continuity between the larynx and the esophagus. MSH:C537875 SNOMEDCT_US:232461002 UMLS:C1840311 Laryngotracheal cleft Laryngotracheoesophageal cleft i HP:0008751 Embryologically, the trachea and esophagus share a common lumen until they are separated by the development of the tracheoesophageal septum. Failure of this fusion and incomplete development of the tracheoesophageal septum may lead to congenital abnormalities such as isolatedlaryngeal cleft, tracheoesophageal fistula, and esophageal atresia, depending on the severity of the abnormality. Patients with laryngeal cleft may present with feeding difficulty, chronic cough, stridor, pneumonia or respiratory distress, depending on the size of the cleft. Laryngeal cleft Presence of a gap in the posterior laryngotracheal wall with a continuity between the larynx and the esophagus. PMID:17178945 A malformation of the laryngeal cartilage. HP:0008375 UMLS:C4021530 Vocal impairment, severe, due to laryngeal cartilage abnormalities HP:0008752 Laryngeal cartilage malformation A malformation of the laryngeal cartilage. Calcification (abnormal deposits of calcium) in the laryngeal tissues. HP:0008748 UMLS:C1859158 Laryngeal calcifications HP:0008754 Laryngeal calcification Calcification (abnormal deposits of calcium) in the laryngeal tissues. Laryngeal calcifications Lack of intentional participation in interactions with another person. UMLS:C1849683 No social interaction HP:0008763 No social interaction No social interaction The presence of aplasia or developmental hypoplasia of the ear. 2008-04-04T05:44:00Z UMLS:C4024627 Absent/small ear Absent/underdeveloped ear HP:0008771 Aplasia/Hypoplasia of the ear The presence of aplasia or developmental hypoplasia of the ear. Absent/small ear Absent/underdeveloped ear The presence of aplasia or developmental hypoplasia of all or part of the external ear. 2008-04-04T05:45:00Z UMLS:C4024626 Absent/small external ear Absent/underdeveloped external ear HP:0008772 Aplasia/Hypoplasia of the external ear The presence of aplasia or developmental hypoplasia of all or part of the external ear. Absent/small external ear Absent/underdeveloped external ear Aplasia or developmental hypoplasia of all or part of the middle ear. 2008-04-04T05:47:00Z HP:0008533 HP:0008548 UMLS:C4021529 Absent/small middle ear Absent/underdeveloped middle ear Hypoplastic/aplastic middle ear structures Middle ear hypoplasia/aplasia HP:0008773 Aplasia/Hypoplasia of the middle ear Aplasia or developmental hypoplasia of all or part of the middle ear. Absent/small middle ear Absent/underdeveloped middle ear Aplasia or developmental hypoplasia of the inner ear. 2008-04-04T05:48:00Z UMLS:C4024625 Absent/small inner ear Absent/underdeveloped inner ear HP:0008774 Aplasia/Hypoplasia of the inner ear Aplasia or developmental hypoplasia of the inner ear. Absent/small inner ear Absent/underdeveloped inner ear An abnormality of the prostate. 2008-04-04T06:01:00Z UMLS:C0747987 Abnormality of the prostate HP:0008775 Abnormal prostate morphology An abnormality of the prostate. Abnormality of the prostate Any structural abnormality of the renal artery. 2008-04-04T06:13:00Z UMLS:C4024624 Abnormal kidney artery Abnormality of the renal artery HP:0008776 Abnormal renal artery morphology Any structural abnormality of the renal artery. Abnormal kidney artery Delayed maturation and calcification of the pubic bone. HP:0008795 HP:0008827 UMLS:C1861528 UMLS:C1866710 UMLS:C4280411 Absent pubic ossification in infancy Delayed maturation fo pubic bone Delayed mineralization of pubic bone HP:0008788 Delayed pubic bone ossification Delayed maturation and calcification of the pubic bone. Delayed maturation fo pubic bone Delayed mineralization of pubic bone Underdevelopment of the femoral head. HP:0008831 UMLS:C1856920 Hypoplastic femoral head Small femoral heads Small head of thigh bone HP:0008802 Hypoplasia of the femoral head Underdevelopment of the femoral head. Small head of thigh bone A smaller than normal acetabulum that has insufficient femoral head coverage leading to abnormal hip joint contact pressures, instability and pain. HP:0008799 MSH:D006617 UMLS:C1328407 Dysplastic acetabulae HP:0008807 Acetabular dysplasia can lead to hip pain and early-onset hip osteoarthritis. Acetabular dysplasia A smaller than normal acetabulum that has insufficient femoral head coverage leading to abnormal hip joint contact pressures, instability and pain. PMID:23764788 PMID:34377520 An abnormally flattened femoral head. UMLS:C1860601 Flat head of thigh bone Flattened femoral heads HP:0008812 Flattened femoral head An abnormally flattened femoral head. Flat head of thigh bone Flattened femoral heads Lack of ossification of the proximal epiphysis of the femur. UMLS:C1968686 Absent ossification of femoral capital epiphyses HP:0008820 The ossification center of the capital femoral epiphysis appears at the end of the first year after birth. Absent ossification of capital femoral epiphysis Lack of ossification of the proximal epiphysis of the femur. Developmental delay of ossification of the proximal epiphysis of the femur. UMLS:C1855222 Delayed ossification of the proximal femoral epiphysis Delayed ossification proximal femoral epiphyses HP:0008828 The proximal femoral epiphyseal ossification center normally appears at about age 6 months. Delayed proximal femoral epiphyseal ossification Developmental delay of ossification of the proximal epiphysis of the femur. Delayed ossification of the femoral head. UMLS:C1846446 UMLS:C4280410 Delayed maturation of the head of the thigh bone HP:0008829 Delayed femoral head ossification Delayed ossification of the femoral head. Delayed maturation of the head of the thigh bone There is normally one ossification center in the head of the femur. This term applies if there are multiple such centers. UMLS:C1846447 HP:0008835 Additionally, the ossification center of the capital femoral epiphysis appears at the end of the first year after birth. This is not what this term refers to. Multicentric femoral head ossification There is normally one ossification center in the head of the femur. This term applies if there are multiple such centers. Underdevelopment of the bony pelvis. HP:0003373 HP:0008816 UMLS:C3536734 Hypoplastic pelvic bones Small pelvis HP:0008839 Hypoplastic pelvis Underdevelopment of the bony pelvis. A type of disproportionate short stature characterized by a short limbs but an average-sized trunk. HP:0001523 HP:0003505 HP:0003509 HP:0008858 HP:0008869 HP:0008875 HP:0008880 HP:0008881 HP:0008889 HP:0008912 HP:0008914 HP:0008928 UMLS:C1849937 Brachymelic dwarfism Disproportionate short limb dwarfism Dwarfism, short-limbed Micromelic dwarfism Short limb dwarfism, disproportionate Short stature, disproportionate short limb Short stature, disproportionate short-limb Short-limb dwarfism Short-limbed dwarfism Short limb dwarfism HP:0008873 A type of dwarfism (marked short stature with adult height below 147 cm) in which the limbs are disproportionatley affected. Note that brachymelia is a general term refering to shortening of the limbs. Micromelia refers to the shortening of entire limbs (in contrast to rhizomelia, mesomelia, and acromelia, which refer to shortening of the proximal, middle, or distal portions of the limbs). Disproportionate short-limb short stature A type of disproportionate short stature characterized by a short limbs but an average-sized trunk. Short limb dwarfism, disproportionate Short-limbed dwarfism Short limb dwarfism A loss of adipose tissue. HP:0008938 UMLS:C4024615 Loss of fat tissue HP:0008887 Adipose tissue loss A loss of adipose tissue. Loss of fat tissue Muscular atrophy affecting proximally located muscles of the arms. HP:0008995 UMLS:C1866013 Proximal muscle atrophy in upper limbs Proximal upper limb muscle atrophy HP:0008948 Proximal upper limb amyotrophy Muscular atrophy affecting proximally located muscles of the arms. Underdevelopment of muscles of the shoulder. UMLS:C1969001 Underdeveloped shoulder muscle HP:0008952 Shoulder muscle hypoplasia Underdevelopment of muscles of the shoulder. Underdeveloped shoulder muscle Muscular atrophy affecting proximally located muscles of the legs, i.e., of the thigh. HP:0003748 HP:0008974 UMLS:C1836767 Amyotrophy involving the thigh Amyotrophy of the thigh musculature Proximal lower limb muscle atrophy Thigh muscle atrophy Wasting of thigh muscle HP:0008956 Proximal lower limb amyotrophy Muscular atrophy affecting proximally located muscles of the legs, i.e., of the thigh. Wasting of thigh muscle Underdevelopment of the muscuklature of the calf. UMLS:C3805450 Hypoplastic calf muscles Underdeveloped calf muscles HP:0008962 Calf muscle hypoplasia Underdevelopment of the muscuklature of the calf. Underdeveloped calf muscles Muscle hypertrophy primarily affecting the legs. UMLS:C1850663 HP:0008968 Muscle hypertrophy of the lower extremities Muscle hypertrophy primarily affecting the legs. Muscle hypertrophy affecting the calf muscles. HP:0003703 HP:0009024 UMLS:C1843057 Calf hypertrophy Increased size of calf muscles Muscular hypertrophy of the calf muscles HP:0008981 Distal lower limb hypertrophy Calf muscle hypertrophy Muscle hypertrophy affecting the calf muscles. Increased size of calf muscles Underdevelopment of muscles of the neck. UMLS:C1969000 UMLS:C4280408 UMLS:C4280409 Decreased size of neck muscle Small neck muscle Underdevelopment of neck muscle Deficiency of neck muscle Hypotrophic neck muscle HP:0008984 Neck muscle hypoplasia Underdevelopment of muscles of the neck. Decreased size of neck muscle Small neck muscle Underdevelopment of neck muscle Deficiency of neck muscle Hypotrophic neck muscle An abnormal increase in the amount of intramuscular fat tissue. UMLS:C1835389 Increased IM fat Increased intramuscular fat HP:0008985 Increased intramuscular fat An abnormal increase in the amount of intramuscular fat tissue. Increased IM fat Increased intramuscular fat Congenital lack, i.e., aplasia of the diaphragm. SNOMEDCT_US:702613006 SNOMEDCT_US:72424001 UMLS:C0221360 Absent diaphragm Agenesis of diaphragm HP:0008986 An extremely large diaphragmatic defect, or apparent absence of the hemidiaphragm, is called agenesis of the diaphragm; this defect probably represents the severe end of the Bochdalek hernia spectrum rather than a distinct entity. Agenesis of the diaphragm Congenital lack, i.e., aplasia of the diaphragm. Absent diaphragm Muscular atrophy affecting the muscles that attach to the pelvic girdle (the gluteal muscles, the lateral rotators, adductor magnus, adductor brevis, adductor longus, pectineus, and gracilis muscles). HP:0008992 UMLS:C0240679 Pelvic girdle muscle wasting HP:0008988 Pelvic girdle muscle atrophy Muscular atrophy affecting the muscles that attach to the pelvic girdle (the gluteal muscles, the lateral rotators, adductor magnus, adductor brevis, adductor longus, pectineus, and gracilis muscles). An abnormal increase in the amount of intraabdominal fat tissue. UMLS:C1835390 HP:0008993 Increased intraabdominal fat An abnormal increase in the amount of intraabdominal fat tissue. Loss (reduction of previously present) of subcutaneous adipose tissue in the region of the trunk. HP:0008989 UMLS:C1835384 Loss of fat tissue in trunk Loss of subcutaneous truncal adipose tissue Loss of truncal adipose tissue HP:0009002 Loss of truncal subcutaneous adipose tissue Loss (reduction of previously present) of subcutaneous adipose tissue in the region of the trunk. Loss of fat tissue in trunk The presence of an abnormally increased amount of subcutaneous adipose tissue in the trunk of the body. UMLS:C1837781 Increased fat below the skin in trunk HP:0009003 Increased subcutaneous truncal adipose tissue The presence of an abnormally increased amount of subcutaneous adipose tissue in the trunk of the body. Increased fat below the skin in trunk Underdevelopment of the musculature. HP:0009034 SNOMEDCT_US:205530002 UMLS:C0240414 Muscle hypoplasia Poorly developed skeletal musculature Underdeveloped muscle Underdeveloped muscles HP:0009004 Hypoplasia of the musculature Underdevelopment of the musculature. Poorly developed skeletal musculature Underdeveloped muscle Underdevelopment of the serratus anterior muscle, which is involved in abduction, upward Rotation, and elevation of the scapula. UMLS:C1868167 HP:0009011 Hypoplasia of serratus anterior muscle Underdevelopment of the serratus anterior muscle, which is involved in abduction, upward Rotation, and elevation of the scapula. Underdevelopment of muscles of the arm. UMLS:C1846478 Underdevelopment of upper limb muscles HP:0009016 Upper limb muscle hypoplasia Underdevelopment of muscles of the arm. Underdevelopment of upper limb muscles The presence of an abnormally increased amount of connective tissue. UMLS:C1866021 HP:0009025 Increased connective tissue The presence of an abnormally increased amount of connective tissue. Underdevelopment of the latissimus dorsi muscle, which is involved in adduction, extension, internal rotation, and transverse extension of the shoulder and assists in movement of the scapula. UMLS:C3805860 HP:0009026 Hypoplasia of latissimus dorsi muscle Underdevelopment of the latissimus dorsi muscle, which is involved in adduction, extension, internal rotation, and transverse extension of the shoulder and assists in movement of the scapula. UMLS:C4024602 Loss of fat tissue below the skin from upper limbs HP:0009056 Loss of subcutaneous adipose tissue from upper limbs Loss of fat tissue below the skin from upper limbs An abnormal accumulation of lipids in skeletal muscle. HP:0100949 UMLS:C1837262 Fat accumulation in muscle fibers Fat accumulation in muscle fibres Fat deposits in muscle fibers Fat deposits in muscle fibres Increased muscle lipid content Lipid accumulation in skeletal muscle Muscle lipidosis Skeletal muscle lipid accumulation HP:0009058 Increased neutral lipid content may be observed on muscle biopsies specimen with the specific staining of Sudan black or oil red O techniques by optic microscopy. Increased muscle lipid content An abnormal accumulation of lipids in skeletal muscle. PMID:20691590 Fat accumulation in muscle fibers Fat accumulation in muscle fibres Fat deposits in muscle fibers Fat deposits in muscle fibres Increased muscle lipid content Lipid accumulation in skeletal muscle Skeletal muscle lipid accumulation Progressive spinal muscular atrophy, i.e., muscular weakness and atrophy related to loss of the motor neurons of the spinal cord and brainstem. UMLS:C4082951 Progressive spinal muscle degeneration Progressive spinal muscle wasting HP:0009067 Progressive spinal muscular atrophy Progressive spinal muscular atrophy, i.e., muscular weakness and atrophy related to loss of the motor neurons of the spinal cord and brainstem. Progressive spinal muscle degeneration Progressive spinal muscle wasting UMLS:C1854934 UMLS:C4280407 Increasing size of gum ridge Progressive hypertrophy of alveolar process of jaw Increasing overgrowth of gum ridge HP:0009092 Progressive alveolar ridge hypertropy Increasing size of gum ridge Progressive hypertrophy of alveolar process of jaw Increasing overgrowth of gum ridge 2008-04-04T08:40:00Z UMLS:C4024597 Absent/small pelvis Absent/underdeveloped pelvis HP:0009103 Aplasia/Hypoplasia involving the pelvis Absent/small pelvis Absent/underdeveloped pelvis Absence or underdevelopment of the pubic bone. 2008-04-04T08:41:00Z HP:0008841 UMLS:C1849305 Absent/small pubic bones Absent/underdeveloped pubic bones Hypoplastic/aplastic pubic bones HP:0009104 Aplasia/Hypoplasia of the pubic bone Absence or underdevelopment of the pubic bone. Absent/small pubic bones Absent/underdeveloped pubic bones Hypoplastic/aplastic pubic bones Abnormal ossification (bone tissue formation) affecting the pubic bone, also known as the pubis. 2008-04-04T08:41:00Z UMLS:C4024596 UMLS:C4280403 Abnormal maturation of the pubic bone HP:0009105 Abnormal ossification of the pubic bone Abnormal ossification (bone tissue formation) affecting the pubic bone, also known as the pubis. Abnormal maturation of the pubic bone An abnormality of the formation and mineralization of any bone of the bony pelvis. 2008-04-04T08:42:00Z UMLS:C4021525 UMLS:C4280402 Abnormal ossification involving the bones of the pelvis Abnormal maturation of the pelvis bone HP:0009106 Abnormal pelvis bone ossification An abnormality of the formation and mineralization of any bone of the bony pelvis. Abnormal maturation of the pelvis bone 2008-04-04T08:42:00Z UMLS:C4024595 Abnormal maturation of thigh bone head and neck HP:0009107 Abnormal ossification involving the femoral head and neck Abnormal maturation of thigh bone head and neck 2008-04-04T08:44:00Z UMLS:C4024594 Absent/small head and neck of thighbone Absent/underdeveloped head and neck of thighbone HP:0009108 Aplasia/Hypoplasia involving the femoral head and neck Absent/small head and neck of thighbone Absent/underdeveloped head and neck of thighbone Absence (due to failure to form) or underdevelopment of one or more components of the skeleton. 2008-04-05T10:53:00Z UMLS:C4024592 Absent/small skeleton Absent/underdeveloped skeleton HP:0009115 Aplasia/hypoplasia involving the skeleton Absence (due to failure to form) or underdevelopment of one or more components of the skeleton. Absent/small skeleton Absent/underdeveloped skeleton 2008-04-05T10:53:00Z UMLS:C4024591 HP:0009116 Aplasia/Hypoplasia involving bones of the skull An abnormality of the axial skeleton, which comprises the skull, the vertebral column, the ribs and the sternum. 2008-04-05T11:16:00Z UMLS:C4020785 UMLS:C4024586 Abnormality of the axial skeleton HP:0009121 Abnormal axial skeleton morphology An abnormality of the axial skeleton, which comprises the skull, the vertebral column, the ribs and the sternum. Absence (due to failure to form) or underdevelopment of bones of the axial skeleton. 2008-04-05T11:29:00Z UMLS:C4024585 HP:0009122 Aplasia/hypoplasia affecting bones of the axial skeleton Absence (due to failure to form) or underdevelopment of bones of the axial skeleton. An abnormality of adipose tissue, which is loose connective tissue composed of adipocytes. 2008-04-05T11:40:00Z UMLS:C4021524 Abnormality of adipose tissue Abnormality of fat tissue Abnormality of fatty tissue HP:0009124 Abnormal adipose tissue morphology An abnormality of adipose tissue, which is loose connective tissue composed of adipocytes. Abnormality of adipose tissue Abnormality of fat tissue Abnormality of fatty tissue An increase in adipose tissue mass by hyperplastic growth (increase in the number of adipocytes) or by hypertrophic growth (increase in the size of adipocytes occurring primarily by lipid accumulation within the cell). 2008-04-05T11:43:00Z UMLS:C4024583 Increased adipose tissue Increased fat tissue HP:0009126 Increased adipose tissue An increase in adipose tissue mass by hyperplastic growth (increase in the number of adipocytes) or by hypertrophic growth (increase in the size of adipocytes occurring primarily by lipid accumulation within the cell). Increased adipose tissue Increased fat tissue 2008-04-07T02:00:00Z UMLS:C4024582 Abnormal limb muscles Muscle issues in the arms and/or legs HP:0009127 Abnormality of the musculature of the limbs Abnormal limb muscles Muscle issues in the arms and/or legs 2008-04-07T02:01:00Z UMLS:C4024581 Absent/small muscles of extremities Absent/underdeveloped muscles of extremities HP:0009128 Aplasia/Hypoplasia involving the musculature of the extremities Absent/small muscles of extremities Absent/underdeveloped muscles of extremities Muscular atrophy involving the muscles of the upper limbs. 2008-04-07T05:01:00Z HP:0003471 UMLS:C4021523 Amyotrophy involving the upper limbs HP:0009129 Upper limb amyotrophy Muscular atrophy involving the muscles of the upper limbs. Muscular atrophy involving the muscles of the hand. 2008-04-07T05:01:00Z HP:0006967 HP:0008934 HP:0008951 HP:0009038 UMLS:C0239830 Amyotrophy involving the musculature of the hand Amyotrophy of hand muscles Hand muscle degeneration Hand muscle wasting Hand muscle wasting, bilateral HP:0009130 This term can be used to described bilateral amyotrophy of the musculature of the hand. Hand muscle atrophy Muscular atrophy involving the muscles of the hand. Hand muscle degeneration A disease or lesion affecting the muscles of the thorax. 2008-04-07T05:06:00Z UMLS:C4024580 HP:0009131 Abnormality of the musculature of the thorax A disease or lesion affecting the muscles of the thorax. This term applies to all changes in bone mineral density of the tarsal bones, which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. 2008-04-17T02:39:00Z UMLS:C4021522 Abnormality of bone mineral density involving tarsal bones HP:0009132 Abnormal tarsal bone mineral density This term applies to all changes in bone mineral density of the tarsal bones, which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. 2008-04-17T02:45:00Z UMLS:C4024578 Duplication involving bones of the feet HP:0009136 Duplication involving bones of the feet Duplication involving bones of the feet 2008-05-02T01:23:00Z UMLS:C4024574 Duplication of bones involving the upper extremities HP:0009142 Duplication of bones involving the upper extremities Duplication of bones involving the upper extremities 2008-05-02T01:29:00Z UMLS:C4024573 HP:0009144 Supernumerary bones of the axial skeleton Any structural anomaly of a cerebral artery. The cerebral arteries comprise three main pairs of arteries and their branches, which supply the cerebrum of the brain. These are the anterior cerebral artery, the middle cerebral artery, and the posterior cerebral artery. 2008-05-02T01:39:00Z UMLS:C4021520 Abnormality of cerebral artery Abnormality of the cerebral arteries HP:0009145 Abnormal cerebral artery morphology Any structural anomaly of a cerebral artery. The cerebral arteries comprise three main pairs of arteries and their branches, which supply the cerebrum of the brain. These are the anterior cerebral artery, the middle cerebral artery, and the posterior cerebral artery. Abnormality of cerebral artery Abnormality of the cerebral arteries Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. 2008-12-22T01:39:32Z UMLS:C4024572 Enlarged end part of the outermost bone of little finger Enlarged end part of the outermost bone of pinkie finger Enlarged end part of the outermost bone of pinky finger HP:0009147 Enlarged epiphysis of the distal phalanx of the 5th finger Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. Enlarged end part of the outermost bone of little finger Enlarged end part of the outermost bone of pinkie finger Enlarged end part of the outermost bone of pinky finger Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. 2008-12-22T01:40:08Z UMLS:C4024571 Small end part of the outermost bone of little finger Small end part of the outermost bone of pinkie finger Small end part of the outermost bone of pinky finger HP:0009148 Small epiphysis of the distal phalanx of the 5th finger Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. Small end part of the outermost bone of little finger Small end part of the outermost bone of pinkie finger Small end part of the outermost bone of pinky finger Abnormality of the proximal phalanx of the little (5th) finger. 2008-12-22T02:00:20Z UMLS:C4024570 Abnormality of the innermost bone little finger Abnormality of the innermost bone pinkie finger Abnormality of the innermost bone pinky finger HP:0009150 Abnormality of the proximal phalanx of the 5th finger Abnormality of the proximal phalanx of the little (5th) finger. Abnormality of the innermost bone little finger Abnormality of the innermost bone pinkie finger Abnormality of the innermost bone pinky finger Abnormality of one or all of the epiphyses of the proximal, middle, and distal phalanges of the 5th finger. 2008-12-22T02:07:27Z UMLS:C4024569 Abnormality of end part of little finger bone Abnormality of end part of pinkie finger bone Abnormality of end part of pinky finger bone HP:0009152 Abnormality of the epiphyses of the 5th finger Abnormality of one or all of the epiphyses of the proximal, middle, and distal phalanges of the 5th finger. Abnormality of end part of little finger bone Abnormality of end part of pinkie finger bone Abnormality of end part of pinky finger bone Abnormality of the epiphysis of the proximal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. 2008-12-22T05:47:42Z UMLS:C4024568 Abnormality of end part of the innermost bone of little finger Abnormality of end part of the innermost bone of pinkie finger Abnormality of end part of the innermost bone of pinky finger HP:0009153 Abnormality of the epiphysis of the proximal phalanx of the 5th finger Abnormality of the epiphysis of the proximal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. Abnormality of end part of the innermost bone of little finger Abnormality of end part of the innermost bone of pinkie finger Abnormality of end part of the innermost bone of pinky finger Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. 2008-12-22T05:50:39Z UMLS:C4024566 Enlarged end part of the innermost bone of little finger Enlarged end part of the innermost bone of pinkie finger Enlarged end part of the innermost bone of pinky finger HP:0009158 Enlarged epiphysis of the proximal phalanx of the 5th finger Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. Enlarged end part of the innermost bone of little finger Enlarged end part of the innermost bone of pinkie finger Enlarged end part of the innermost bone of pinky finger Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. 2008-12-22T05:50:39Z UMLS:C4024565 Small end part of the innermost bone of little finger Small end part of the innermost bone of pinkie finger Small end part of the innermost bone of pinky finger HP:0009159 Small epiphysis of the proximal phalanx of the 5th finger Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. Small end part of the innermost bone of little finger Small end part of the innermost bone of pinkie finger Small end part of the innermost bone of pinky finger Absence of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger. 2008-12-22T05:50:39Z UMLS:C4024564 Absent end part of the innermost bone of little finger Absent end part of the innermost bone of pinkie finger Absent end part of the innermost bone of pinky finger HP:0009160 Absent epiphysis of the proximal phalanx of the 5th finger Absence of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger. Absent end part of the innermost bone of little finger Absent end part of the innermost bone of pinkie finger Absent end part of the innermost bone of pinky finger Absence or underdevelopment (hypoplasia) of the middle phalanx of the little (5th) finger. 2008-12-22T05:55:56Z HP:0006242 UMLS:C1834034 Absent/hypoplastic middle phalanx of 5th finger Absent/small middle bone of pinky finger Absent/underdeveloped middle bone of little finger Absent/underdeveloped middle bone of pinkie finger Absent/underdeveloped middle bone of pinky finger HP:0009161 Aplasia/Hypoplasia of the middle phalanx of the 5th finger Absence or underdevelopment (hypoplasia) of the middle phalanx of the little (5th) finger. Absent/small middle bone of pinky finger Absent/underdeveloped middle bone of little finger Absent/underdeveloped middle bone of pinkie finger Absent/underdeveloped middle bone of pinky finger 2008-12-22T06:53:39Z HP:0006154 UMLS:C1968592 Abnormal calcification of the wrist bones Carpal calcifications HP:0009164 Abnormal calcification of the carpal bones Abnormal calcification of the wrist bones Displacement of the 5th finger from its normal position. 2008-12-29T03:29:20Z HP:0006036 UMLS:C4021515 Displaced little finger Displaced pinkie finger Displaced pinky finger Laterally displaced fifth finger HP:0009179 Deviation of the 5th finger Displacement of the 5th finger from its normal position. Displaced little finger Displaced pinkie finger Displaced pinky finger Displacement of the 5th finger towards the ulnar side. 2008-12-29T03:30:05Z UMLS:C4024553 HP:0009180 Ulnar deviation of the 5th finger Displacement of the 5th finger towards the ulnar side. Chronic loss of joint motion in the 5th finger due to structural changes in non-bony tissue. The term camptodactyly of the 5th finger is used if the distal and/or proximal interphalangeal joints are affected. 2008-12-29T04:11:30Z HP:0001184 UMLS:C1865702 5th finger camptodactyly Fifth finger camptodactyly HP:0009183 Joint contracture of the 5th finger Chronic loss of joint motion in the 5th finger due to structural changes in non-bony tissue. The term camptodactyly of the 5th finger is used if the distal and/or proximal interphalangeal joints are affected. Chronic loss of joint motion of the distal interphalangeal joint of the 5th finger due to structural changes in non-bony tissue. 2008-12-29T04:16:15Z UMLS:C4024551 HP:0009184 Contracture of the distal interphalangeal joint of the 5th finger Chronic loss of joint motion of the distal interphalangeal joint of the 5th finger due to structural changes in non-bony tissue. Proximal interphalangeal (PIP) flexion deformity of the little finger. That is, the PIP joint of a little finger is bent (flexed) and cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. 2008-12-29T04:16:58Z HP:0005047 HP:0006062 UMLS:C3554612 HP:0009185 Contracture of the proximal interphalangeal joint of the 5th finger Proximal interphalangeal (PIP) flexion deformity of the little finger. That is, the PIP joint of a little finger is bent (flexed) and cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. Chronic loss of joint motion of the metacarpophalangeal joint of the 5th finger due to structural changes in non-bony tissue. 2008-12-29T04:18:00Z UMLS:C4024550 HP:0009186 Contracture of the metacarpophalangeal joint of the 5th finger Chronic loss of joint motion of the metacarpophalangeal joint of the 5th finger due to structural changes in non-bony tissue. A secondary ossification center in the distal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2008-12-30T12:28:19Z UMLS:C4024548 HP:0009188 Pseudoepiphysis of the distal phalanx of the 5th finger A secondary ossification center in the distal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. Absence or underdevelopment (hypoplasia) of the proximal phalanx of the little (5th) finger. 2009-01-05T05:57:28Z UMLS:C4024544 Absent/small innermost little finger bone Absent/small innermost pinkie finger bone Absent/small innermost pinky finger bone Absent/underdeveloped innermost pinky finger bone HP:0009192 Aplasia/Hypoplasia of the proximal phalanx of the 5th finger Absence or underdevelopment (hypoplasia) of the proximal phalanx of the little (5th) finger. Absent/small innermost little finger bone Absent/small innermost pinkie finger bone Absent/small innermost pinky finger bone Absent/underdeveloped innermost pinky finger bone A pseudoepiphysis is a secondary ossification center distinct from the normal epiphysis. The normal metacarpal epiphyses are located at the distal ends of the metacarpal bones. Accessory epiphyses (which are also known as pseudoepiphyses) can also occasionally be observed at the proximal ends of the metacarpals, usually involving the 2nd metacarpal bone. 2008-12-30T02:03:34Z HP:0006091 HP:0006164 UMLS:C1860253 Accessory proximal metacarpal ossification centers Accessory proximal metacarpal ossification centres Metacarpal pseudoepiphyses HP:0009193 Pseudoepiphyses of the metacarpals A pseudoepiphysis is a secondary ossification center distinct from the normal epiphysis. The normal metacarpal epiphyses are located at the distal ends of the metacarpal bones. Accessory epiphyses (which are also known as pseudoepiphyses) can also occasionally be observed at the proximal ends of the metacarpals, usually involving the 2nd metacarpal bone. Accessory proximal metacarpal ossification centres Abnormally small size of the epiphyses located at the distal end of the metacarpals in respect to age-dependent norms. 2008-12-30T02:03:34Z UMLS:C4024543 Small end part of the long bone of hand HP:0009194 Small epiphyses of the metacarpals Abnormally small size of the epiphyses located at the distal end of the metacarpals in respect to age-dependent norms. Small end part of the long bone of hand Absence of the epiphyses of the metacarpal bones, which are normally located at the distal ends of the metacarpals. 2008-12-30T02:03:34Z HP:0006013 UMLS:C4021513 Absent end part of the long bone of hand Absent metacarpal ossification center Absent metacarpal ossification centre HP:0009196 Absent metacarpal epiphyses Absence of the epiphyses of the metacarpal bones, which are normally located at the distal ends of the metacarpals. Absent end part of the long bone of hand Absent metacarpal ossification centre Abnormality of the epiphysis of the distal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. 2009-01-05T04:41:32Z HP:0004228 UMLS:C4021512 Abnormality of end part of the outermost bone of the little finger Abnormality of end part of the outermost bone of the pinkie finger Abnormality of end part of the outermost bone of the pinky finger Abnormality of the epiphysis of the terminal phalanx of the little finger HP:0009198 Abnormality of the epiphysis of the distal phalanx of the 5th finger Abnormality of the epiphysis of the distal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. Abnormality of end part of the outermost bone of the little finger Abnormality of end part of the outermost bone of the pinkie finger Abnormality of end part of the outermost bone of the pinky finger A secondary ossification center in the proximal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-01-05T05:10:13Z UMLS:C4024540 HP:0009200 Pseudoepiphysis of the proximal phalanx of the 5th finger A secondary ossification center in the proximal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. Absence of the epiphysis located at the proximal end of the middle phalanx of the 5th finger. 2009-01-05T05:22:18Z UMLS:C4024537 Absent end part of the middle bone of the little finger Absent end part of the middle bone of the pinkie finger Absent end part of the middle bone of the pinky finger HP:0009203 Absent epiphysis of the middle phalanx of the 5th finger Absence of the epiphysis located at the proximal end of the middle phalanx of the 5th finger. Absent end part of the middle bone of the little finger Absent end part of the middle bone of the pinkie finger Absent end part of the middle bone of the pinky finger Abnormally large size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. 2009-01-05T05:22:18Z UMLS:C4024534 Enlarged end part of the middle bone of the little finger Enlarged end part of the middle bone of the pinkie finger Enlarged end part of the middle bone of the pinky finger HP:0009206 Enlarged epiphysis of the middle phalanx of the 5th finger Abnormally large size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. Enlarged end part of the middle bone of the little finger Enlarged end part of the middle bone of the pinkie finger Enlarged end part of the middle bone of the pinky finger A secondary ossification center in the middle phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-01-05T05:22:18Z UMLS:C4024530 HP:0009210 Pseudoepiphysis of the middle phalanx of the 5th finger A secondary ossification center in the middle phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. Abnormally small size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. 2009-01-05T05:22:18Z UMLS:C4024529 Small end part of the middle bone of the little finger Small end part of the middle bone of the pinkie finger Small end part of the middle bone of the pinky finger HP:0009211 Small epiphysis of the middle phalanx of the 5th finger Abnormally small size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. Small end part of the middle bone of the little finger Small end part of the middle bone of the pinkie finger Small end part of the middle bone of the pinky finger Hypoplastic/small proximal phalanx of the fifth finger. 2009-01-05T06:01:34Z UMLS:C4021509 Hypoplastic/small proximal phalanx of the 5th finger Short innermost little finger bone Short innermost pinkie finger bone Short innermost pinky finger bone Short proximal phalanx of the fifth finger HP:0009226 Short proximal phalanx of the 5th finger Hypoplastic/small proximal phalanx of the fifth finger. Short innermost little finger bone Short innermost pinkie finger bone Short innermost pinky finger bone Short proximal phalanx of the fifth finger Hypoplasia (congenital reduction in size) of the fifth finger, also known as the little finger. 2009-01-05T06:54:07Z HP:0001205 HP:0004208 HP:0004210 HP:0004211 HP:0004215 HP:0004217 HP:0005804 HP:0005888 UMLS:C1842878 Fifth finger brachydactyly Hypoplastic phalanges of the little finger Hypoplastic/small 5th finger Hypoplastic/small little finger Short 5th finger Short fifth finger Short fifth fingers Short little finger Short phalanges of the little finger Short pinkie finger Short pinky finger HP:0009237 Short 5th finger Hypoplasia (congenital reduction in size) of the fifth finger, also known as the little finger. Short 5th finger Short fifth finger Short fifth fingers Short little finger Short pinkie finger Short pinky finger 2009-01-05T07:25:50Z UMLS:C4024507 Absent/small outermost bone of little finger Absent/small outermost bone of pinkie finger Absent/small outermost bone of pinky finger Absent/underdeveloped outermost bone of pinky finger HP:0009239 Aplasia/Hypoplasia of the distal phalanx of the 5th finger Absent/small outermost bone of little finger Absent/small outermost bone of pinkie finger Absent/small outermost bone of pinky finger Absent/underdeveloped outermost bone of pinky finger 2009-01-13T10:50:19Z UMLS:C4024413 HP:0009370 Type A brachydactyly Aplasia/Hypoplasia of the phalanges of the 5th finger. 2009-01-13T11:58:25Z UMLS:C4024410 Absent/small little finger bones Absent/small pinkie finger bones Absent/small pinky finger bones Absent/underdeveloped pinky finger bones HP:0009376 Aplasia/Hypoplasia of the phalanges of the 5th finger Aplasia/Hypoplasia of the phalanges of the 5th finger. Absent/small little finger bones Absent/small pinkie finger bones Absent/small pinky finger bones Absent/underdeveloped pinky finger bones Aplasia of one or more fingers. 2009-01-13T01:05:32Z HP:0004093 SNOMEDCT_US:71358006 UMLS:C0728895 Absent fingers HP:0009380 Aplasia of the fingers Aplasia of one or more fingers. Absent fingers Abnormally short finger associated with developmental hypoplasia. 2009-01-13T01:07:38Z HP:0004098 HP:0006015 SNOMEDCT_US:249765007 UMLS:C0239594 UMLS:C1844548 Hypoplastic digits Hypoplastic fingers Hypoplastic/small fingers Short finger Stubby finger Stubby fingers HP:0009381 Short finger Abnormally short finger associated with developmental hypoplasia. Short finger Stubby finger Stubby fingers Absence of one or more epiphyses of the 5th finger. 2009-01-13T01:19:03Z UMLS:C4024407 Absent end part of little finger bone Absent end part of pinkie finger bone Absent end part of pinky finger bone HP:0009382 Absent epiphyses of the 5th finger Absence of one or more epiphyses of the 5th finger. Absent end part of little finger bone Absent end part of pinkie finger bone Absent end part of pinky finger bone Abnormally large size of the epiphyses of the 5th finger with respect to age-dependent norms. 2009-01-13T01:19:03Z UMLS:C4024404 Enlarged end part of the little finger bones Enlarged end part of the pinkie finger bones Enlarged end part of the pinky finger bones HP:0009385 Enlarged epiphyses of the 5th finger Abnormally large size of the epiphyses of the 5th finger with respect to age-dependent norms. Enlarged end part of the little finger bones Enlarged end part of the pinkie finger bones Enlarged end part of the pinky finger bones A secondary ossification center in the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-01-13T01:19:03Z UMLS:C4024400 HP:0009389 Pseudoepiphyses of the 5th finger A secondary ossification center in the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. Abnormally small size of the epiphyses of the 5th finger with respect to age-dependent norms. 2009-01-13T01:19:03Z UMLS:C4024399 Small end part of little finger bone Small end part of pinkie finger bone Small end part of pinky finger bone HP:0009390 Small epiphyses of the 5th finger Abnormally small size of the epiphyses of the 5th finger with respect to age-dependent norms. Small end part of little finger bone Small end part of pinkie finger bone Small end part of pinky finger bone Bending or curvature of a finger toward the ulnar side (i.e., away from the thumb). The deviation is at the metacarpal-phalangeal joint, and this finding is distinct from clinodactyly. 2009-01-15T09:39:43Z HP:0001200 HP:0004096 SNOMEDCT_US:276662009 SNOMEDCT_US:367510009 UMLS:C0231679 Finger bends toward pinky Ulnar Drift HP:0009465 Ulnar deviation of finger Bending or curvature of a finger toward the ulnar side (i.e., away from the thumb). The deviation is at the metacarpal-phalangeal joint, and this finding is distinct from clinodactyly. PMID:19125433 Finger bends toward pinky Contractures of one ore more joints of the hands meaning chronic loss of joint motion due to structural changes in non-bony tissue. 2009-01-15T09:59:59Z HP:0001160 HP:0001237 HP:0004094 HP:0005814 HP:0006096 HP:0006173 HP:0006215 HP:0006238 HP:0006255 HP:0009409 HP:0009472 HP:0010563 MEDDRA:10010821 SNOMEDCT_US:86414002 UMLS:C0158113 Contractures involving the hands Contractures of the hands HP:0009473 Joint contracture of the hand Contractures of one ore more joints of the hands meaning chronic loss of joint motion due to structural changes in non-bony tissue. MEDDRA:10010821 Contracture of hand joint Displacement of the hand or of fingers of the hand from their normal position. 2009-01-15T10:45:01Z UMLS:C4024338 Displaced hand or fingers of the hand HP:0009484 Deviation of the hand or of fingers of the hand Displacement of the hand or of fingers of the hand from their normal position. Displaced hand or fingers of the hand Divergence of the longitudinal axis of the hand at the wrist in a posterior (ulnar) direction (i.e., towards the little finger). 2009-01-15T10:51:52Z SNOMEDCT_US:249757009 UMLS:C0241521 Ulnar deviation of hands Ulnar deviation of the hands HP:0009487 Ulnar deviation of the hand Divergence of the longitudinal axis of the hand at the wrist in a posterior (ulnar) direction (i.e., towards the little finger). PMID:19125433 Ulnar deviation of hands Ulnar deviation of the hands Underdevelopment of the pharynx. 2009-01-21T05:24:16Z Small pharynx UMLS:C4024295 UMLS:C4280396 UMLS:C4280397 UMLS:C4280398 UMLS:C4280399 UMLS:C4280400 Decreased size of pharynx Underdevelopment of pharynx Decreased diameter of pharynx Decreased length of pharynx Decreased volume of pharynx Decreased width of pharynx Hypotrophic pharynx HP:0009555 Hypoplasia of the pharynx Underdevelopment of the pharynx. Small pharynx Decreased size of pharynx Underdevelopment of pharynx Decreased diameter of pharynx Decreased length of pharynx Decreased volume of pharynx Decreased width of pharynx Hypotrophic pharynx Abnormality of one or all of the epiphyses of the proximal, and distal phalanges of the thumb and/or the 1st metacarpal. 2009-01-29T11:46:15Z HP:0004074 UMLS:C4021429 Abnormality of end part of thumb long bone Abnormality of the epiphyses of the thumb Abnormality of thumb epiphyses HP:0009599 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). Abnormality of thumb epiphysis Abnormality of one or all of the epiphyses of the proximal, and distal phalanges of the thumb and/or the 1st metacarpal. Abnormality of end part of thumb long bone Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the thumb joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. The term camptodactyly is used if the distal and/or proximal interphalangeal joints are affected. 2009-01-29T01:06:31Z HP:0004061 HP:0006043 SNOMEDCT_US:239736003 UMLS:C0409346 Contracture of thumb Flexion deformities of thumbs Joint contractures of the thumb Thumb joint contracture HP:0009600 Thumb contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the thumb joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. The term camptodactyly is used if the distal and/or proximal interphalangeal joints are affected. PMID:16214063 PMID:24975760 PMID:31282072 Hypoplastic/small or absent thumb. 2009-01-29T01:08:24Z HP:0002950 HP:0006225 MSH:C536903 UMLS:C3179508 Absent or hypoplastic thumbs Absent/hypoplastic thumb Absent/hypoplastic thumbs Absent/small thumb Absent/underdeveloped thumb Aplasia/hypoplasia of thumbs Aplastic/hypoplastic thumbs Hypoplastic to aplastic thumbs Hypoplastic/absent thumb Thumb aplasia/hypoplasia HP:0009601 Aplasia/Hypoplasia of the thumb Hypoplastic/small or absent thumb. Absent/small thumb Absent/underdeveloped thumb A structural anomaly of one or more phalanges of the thumb. 2009-01-29T01:10:39Z HP:0004063 HP:0004064 UMLS:C4021428 Abnormality of the thumb bones Abnormality of thumb phalanges HP:0009602 Abnormality of thumb phalanx A structural anomaly of one or more phalanges of the thumb. Abnormality of the thumb bones Displacement of the thumb from its normal position. 2009-01-29T01:49:57Z HP:0004062 UMLS:C3552414 Abnormal thumb placement Deviated thumb Displacement of the thumb HP:0009603 Deviation of the thumb Displacement of the thumb from its normal position. Abnormal thumb placement Complete duplication of the distal phalanx of the thumb. On x-ray two separate bones appear side to side. 2009-01-29T03:28:16Z HP:0004084 HP:0005784 UMLS:C4021427 Complete duplication of outermost bone of the thumb HP:0009606 Complete duplication of distal phalanx of the thumb Complete duplication of the distal phalanx of the thumb. On x-ray two separate bones appear side to side. Complete duplication of outermost bone of the thumb Complete duplication of the proximal phalanx of the thumb. On x-ray two separate bones appear side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-29T03:32:28Z HP:0004078 UMLS:C4024273 Complete duplication of the innermost bone of the thumb HP:0009608 Complete duplication of proximal phalanx of the thumb Complete duplication of the proximal phalanx of the thumb. On x-ray two separate bones appear side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Complete duplication of the innermost bone of the thumb Partail or complete duplication of the first metacarpal bone. 2009-01-29T03:33:31Z UMLS:C4021426 Partial/complete duplication of the 1st long bone of hand Partial/complete duplication of the 1st metacarpal HP:0009609 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin. This term applies if the first metacarpal is completely or partially duplicated. Depending on the severity, the appearance on x-ray can vary from a notched metacarpal (the duplicated bone is almost completely fused with the metacarpal), a partially fused appearance of the two bones (in most cases the fused bone resembles a Y-shape), or two separate metacarpal bones appearing side to side. Duplication of the 1st metacarpal Partail or complete duplication of the first metacarpal bone. Partial/complete duplication of the 1st long bone of hand Partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. 2009-01-29T03:48:49Z HP:0004086 HP:0005703 HP:0005827 HP:0005848 HP:0006090 UMLS:C1860162 Bifid distal phalanx of thumb Bifid terminal phalanges of thumbs Bifid thumb distal phalanx Incipient distal thumb phalanx duplication Notched outermost bone of the thumb Notched outermost bone of thumb Notched terminal thumb phalanx HP:0009611 Note that with bifid distal phalanx, the terminal phalanx of the thumb is clefted but is still one bone. With duplication of the terminal phalanx of the thumb, the distal phalanx is split into two bones that are located side by side. With triphalangeal thumb, the thumb has three phalanxes located one after the other. Bifid distal phalanx of the thumb Partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. Notched outermost bone of the thumb Complete or partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. 2009-01-29T03:51:43Z UMLS:C4021425 Double thumb distal phalanges Duplicated terminal phalanx of thumb Duplication of distal thumb phalanx Duplication of terminal thumb phalanx Duplication of the outermost bone of the thumb Partial/complete duplication of the distal phalanx of the thumb HP:0009612 Duplication of the distal phalanx of the thumb Complete or partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. Duplication of the outermost bone of the thumb Complete or partial duplication of the proximal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-29T03:59:56Z UMLS:C4021424 Notched innermost bone of thumb Partial/complete duplication of the proximal phalanx of the thumb HP:0009613 Duplication of the proximal phalanx of the thumb Complete or partial duplication of the proximal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Notched innermost bone of thumb This term applies if the proximal phalanx of the thumb is partially duplicated. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-29T04:01:27Z UMLS:C4024272 Notched thumb bone HP:0009614 Bifid proximal phalanx of the thumb This term applies if the proximal phalanx of the thumb is partially duplicated. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Notched thumb bone Complete duplication of the first metacarpal bone. 2009-01-29T04:06:17Z UMLS:C4024271 Complete duplication of the first long bone of hand HP:0009615 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin, equivalent to the proximal phalanges of the other digits. This term applies if the first metacarpal is completely duplicated. On x-ray two separate metacarpal bones appear side to side. This term applies if the first metacarpal is completely duplicated. Complete duplication of the first metacarpal Complete duplication of the first metacarpal bone. Complete duplication of the first long bone of hand Partial duplication of the first metacarpal bone. 2009-01-29T04:06:17Z UMLS:C4021423 Notched first long bone of hand partial duplication of the first metacarpal HP:0009616 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin (equivalent to the proximal phalanges of the other digits). This term applies if the first metacarpal is partially duplicated. Depending on the severity the appearance on x-ray can vary from a notched metacarpal (the duplicated bone is almost completely fused with the metacarpal) to a partially fused appearance of the two bones. In most cases the fused bone resembles a Y-shape. Bifid first metacarpal Partial duplication of the first metacarpal bone. Notched first long bone of hand Any anomaly of the distal phalanx of thumb. 2009-01-29T04:13:47Z HP:0004081 UMLS:C4021422 Abnormality of terminal thumb phalanx Abnormality of the outermost bone of the thumb HP:0009617 Abnormality of the distal phalanx of the thumb Any anomaly of the distal phalanx of thumb. Abnormality of the outermost bone of the thumb An anomaly of the shape or form of the proximal phalanx of the thumb. 2009-01-29T04:13:47Z HP:0004076 UMLS:C4021421 Abnormal innermost thumb bone Abnormality of proximal thumb phalanx HP:0009618 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Abnormality of the proximal phalanx of the thumb An anomaly of the shape or form of the proximal phalanx of the thumb. Abnormal innermost thumb bone In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Chronic loss of joint motion of the carpometacarpal joint of the thumb due to structural changes in non-bony tissue. This joint is formed by the first metacarpal and the trapezial bone and is also called Articulatio carpometacarpalis pollicis, carpometacarpal articulation of thumb, carpometacarpal joint of thumb or first carpometacarpal articulation. Seldom referred to as thumb saddle joint. 2009-01-29T04:52:18Z UMLS:C4024269 Contracture of the carpometacarpal joint of the thumb HP:0009624 Carpometacarpal thumb joint contracture Chronic loss of joint motion of the carpometacarpal joint of the thumb due to structural changes in non-bony tissue. This joint is formed by the first metacarpal and the trapezial bone and is also called Articulatio carpometacarpalis pollicis, carpometacarpal articulation of thumb, carpometacarpal joint of thumb or first carpometacarpal articulation. Seldom referred to as thumb saddle joint. Chronic loss of joint motion of the metacarpophalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio metacarpophalangealis pollicis. 2009-01-29T04:52:18Z UMLS:C2108151 Contracture of the metacarpophalangeal joint of the thumb HP:0009625 Metacarpophalangeal thumb joint contracture Chronic loss of joint motion of the metacarpophalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio metacarpophalangealis pollicis. Chronic loss of joint motion of the interphalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio interphalangealis pollicis. 2009-01-29T04:52:18Z HP:0005697 UMLS:C2108146 Contracture of the interphalangeal joint of the thumb Interphalangeal extension contractures of thumbs HP:0009626 Interphalangeal thumb joint contracture Chronic loss of joint motion of the interphalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio interphalangealis pollicis. This term applies if the proximal phalanx of the thumb is either small/hypoplastic or absent. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-29T05:09:41Z UMLS:C4024268 Absent/small innermost thumb bone Absent/underdeveloped innermost thumb bone HP:0009629 Aplasia/Hypoplasia of the proximal phalanx of the thumb This term applies if the proximal phalanx of the thumb is either small/hypoplastic or absent. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Absent/small innermost thumb bone Absent/underdeveloped innermost thumb bone Hypoplastic (short) proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-29T05:11:02Z HP:0004079 HP:0006073 UMLS:C1855091 Hypoplastic/small proximal phalanx of the thumb Short proximal phalanges of thumb Short proximal thumb bone Short proximal thumb phalanx HP:0009638 Short proximal phalanx of thumb Hypoplastic (short) proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Short proximal thumb bone 2009-01-29T05:19:33Z UMLS:C4024261 Absent/small outermost thumb bone Absent/underdeveloped outermost thumb bone HP:0009641 Aplasia/Hypoplasia of the distal phalanx of the thumb Absent/small outermost thumb bone Absent/underdeveloped outermost thumb bone Hypoplastic (short) distal phalanx of the thumb. 2009-01-29T05:22:06Z HP:0004085 HP:0004087 UMLS:C1862313 Hypoplastic terminal thumb phalanx Hypoplastic/small distal phalanx of the thumb Short outermost bone of the thumb Short terminal thumb phalanx Short thumb terminal phalanx Small terminal thumb phalanx HP:0009650 Short distal phalanx of the thumb Hypoplastic (short) distal phalanx of the thumb. Short outermost bone of the thumb 2009-01-29T05:29:26Z HP:0005834 UMLS:C4024256 Absent/small thumb bones Absent/underdeveloped thumb bones HP:0009658 Aplasia/Hypoplasia of the phalanges of the thumb Absent/small thumb bones Absent/underdeveloped thumb bones Hypoplastic (short) thumb phalanx. 2009-01-29T05:35:50Z HP:0004069 HP:0004071 UMLS:C4021411 Hypoplastic thumb phalanges Hypoplastic/small phalanges of the thumb Short thumb bone Short thumb phalanges HP:0009660 Short phalanx of the thumb Hypoplastic (short) thumb phalanx. Short thumb bone Abnormality of the epiphysis of the distal phalanx of the thumb. This epiphysis is located on the proximal end of the phalanx. 2009-01-29T05:49:31Z HP:0004089 UMLS:C4021410 Abnormality of terminal thumb epiphysis Abnormality of the end part of the outermost bone of the thumb HP:0009662 Abnormality of the epiphysis of the distal phalanx of the thumb Abnormality of the epiphysis of the distal phalanx of the thumb. This epiphysis is located on the proximal end of the phalanx. Abnormality of the end part of the outermost bone of the thumb This term applies if the epiphysis of the proximal phalanx of the thumb, which is located at the proximal end of the phalanx, does not appear in concordance with gender and age dependant norms as seen on x-rays. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-29T05:49:31Z UMLS:C4024254 Abnormality of end part of thumb innermost long bone HP:0009663 Abnormality of the epiphysis of the proximal phalanx of the thumb This term applies if the epiphysis of the proximal phalanx of the thumb, which is located at the proximal end of the phalanx, does not appear in concordance with gender and age dependant norms as seen on x-rays. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Abnormality of end part of thumb innermost long bone Absence of the epiphysis located at the proximal end of the proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-30T09:17:13Z UMLS:C4024253 Absent end part of thumb innermost long bone HP:0009664 Absent epiphysis of the proximal phalanx of the thumb Absence of the epiphysis located at the proximal end of the proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Absent end part of thumb innermost long bone Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-01-30T09:17:13Z UMLS:C4024250 Enlarged end part of thumb innermost long bone HP:0009667 Enlarged epiphysis of the proximal phalanx of the thumb Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Enlarged end part of thumb innermost long bone A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the proximal phalanx of the thumb. 2009-01-30T09:17:13Z UMLS:C4024246 HP:0009671 Pseudoepiphysis of the proximal phalanx of the thumb A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the proximal phalanx of the thumb. Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. 2009-01-30T09:17:13Z UMLS:C4024245 Small end part of thumb innermost long bone HP:0009672 Small epiphysis of the proximal phalanx of the thumb Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. Small end part of thumb innermost long bone Absence of the epiphysis located at the proximal end of the distal phalanx of the thumb. 2009-01-30T09:18:09Z UMLS:C4024242 Absent end part of thumb outermost long bone HP:0009675 Absent epiphysis of the distal phalanx of the thumb Absence of the epiphysis located at the proximal end of the distal phalanx of the thumb. Absent end part of thumb outermost long bone Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. 2009-01-30T09:18:09Z HP:0004092 UMLS:C4021408 Enlarged end part of thumb outermost long bone Large terminal thumb phalanx epiphysis HP:0009678 Enlarged epiphysis of the distal phalanx of the thumb Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. Enlarged end part of thumb outermost long bone A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the distal phalanx of the thumb. 2009-01-30T09:18:09Z UMLS:C4024237 Pseudoepiphysis of the outermost bone of the thumb HP:0009682 Pseudoepiphysis of the distal phalanx of the thumb A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the distal phalanx of the thumb. Pseudoepiphysis of the outermost bone of the thumb Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. 2009-01-30T09:18:09Z UMLS:C4024236 Small end part of thumb outermost bone HP:0009683 Small epiphysis of the distal phalanx of the thumb Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. Small end part of thumb outermost bone Absence of one or more epiphyses of the thumb. 2009-01-30T09:20:16Z UMLS:C4024233 HP:0009686 Absent epiphyses of the thumb Absence of one or more epiphyses of the thumb. Abnormally large size of the epiphyses of the thumb with respect to age-dependent norms. 2009-01-30T09:20:16Z UMLS:C4021406 Enlarged end part of thumb long bone Enlarged epiphyses of the thumb HP:0009689 Enlarged thumb epiphysis Abnormally large size of the epiphyses of the thumb with respect to age-dependent norms. Enlarged end part of thumb long bone A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of one or more phalanges of the thumb. 2009-01-30T09:20:16Z UMLS:C3552484 Pseudoepiphyses of the thumb HP:0009693 Pseudoepiphysis of the thumb A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of one or more phalanges of the thumb. Abnormally small size of one or more of the epiphyses of the thumb with respect to age-dependent norms. 2009-01-30T09:20:16Z UMLS:C4021402 Small end part of thumb long bone Small epiphyses of the thumb HP:0009694 Small thumb epiphysis Abnormally small size of one or more of the epiphyses of the thumb with respect to age-dependent norms. Small end part of thumb long bone Chronic loss of joint motion in one or more distal interphalangeal joints of the fingers. 2009-01-30T04:01:28Z UMLS:C4024230 HP:0009697 Contracture of the distal interphalangeal joint of the fingers Chronic loss of joint motion in one or more distal interphalangeal joints of the fingers. An abnormality of the epididymis. 2009-01-30T11:44:43Z UMLS:C4024222 Abnormality of the epididymis HP:0009714 The epididymis is the structure that connects efferent ductules to vas deferens. Abnormal epididymis morphology An abnormality of the epididymis. An abnormality of the spinal dura mater, which is the outermost of the three layers of the meninges surrounding the spinal cord. 2009-01-31T02:20:51Z UMLS:C4024214 Abnormality of the spinal dura mater HP:0009744 Abnormal spinal dura mater morphology An abnormality of the spinal dura mater, which is the outermost of the three layers of the meninges surrounding the spinal cord. A bony defect in the skull base. 2009-01-31T05:45:00Z UMLS:C1856027 Cleft in cranial base Cleft in skull base HP:0009752 Cleft in skull base A bony defect in the skull base. Cleft in cranial base Cleft in skull base Small or missing phalangeal bones of the fingers of the hand. 2009-02-02T11:38:04Z HP:0006056 HP:0006100 HP:0009801 UMLS:C1848670 Aplastic/hypoplastic phalanges Aplastic/hypoplastic phalanges of the hand Hypoplastic/absent phalanges HP:0009767 Aplasia/Hypoplasia of the phalanges of the hand Small or missing phalangeal bones of the fingers of the hand. Hypoplasia (congenital reduction in size) of the thumb. 2009-02-02T05:46:42Z HP:0001183 HP:0001186 HP:0001589 HP:0005699 HP:0006151 HP:0009628 MSH:C536903 SNOMEDCT_US:253936008 UMLS:C0431890 Hypoplastic thumb Hypoplastic thumbs Hypoplastic/small thumb Short thumb Short thumbs Small thumbs Thumb brachydactyly Thumb hypoplasia HP:0009778 Short thumb Hypoplasia (congenital reduction in size) of the thumb. Short thumb Short thumbs Small thumbs Absence or underdevelopment involving the musculature of the thigh. 2009-02-03T05:16:42Z UMLS:C4024207 Absent/small thigh muscles Absent/underdeveloped thigh muscles HP:0009786 Aplasia/Hypoplasia of the musculature of the thigh Absence or underdevelopment involving the musculature of the thigh. Absent/small thigh muscles Absent/underdeveloped thigh muscles Presence of a bifid sacral bone. 2009-02-03T05:22:25Z UMLS:C4024204 HP:0009791 Bifid sacrum Presence of a bifid sacral bone. The presence of two or more accessory spleens. 2009-02-11T05:44:01Z SNOMEDCT_US:10362008 UMLS:C0266631 Extra spleen HP:0009799 Supernumerary spleens The presence of two or more accessory spleens. Extra spleen Short (hypoplastic) phalanx of finger, affecting one or more phalanges. 2009-02-12T05:57:11Z HP:0001168 HP:0005771 HP:0006087 HP:0006126 UMLS:C0877165 Hypoplastic phalanges Hypoplastic phalanges of hands Hypoplastic/small phalanges of the hand Phalangeal hypoplasia Rudimentary phalanges Short finger bones Short phalanges Shortened phalanges HP:0009803 Short phalanx of finger Short (hypoplastic) phalanx of finger, affecting one or more phalanges. Short finger bones The absence of one or more teeth from the normal series by a failure to develop 2009-02-14T06:20:53Z UMLS:C4024202 UMLS:C4083050 Decreased tooth count Dental agenesis Failure of development of some teeth Reduced number of teeth Teeth, agenesis Decreased number of teeth Fewer teeth than normal Missing some teeth HP:0009804 Teeth agenesis needs to be confirmed by X-rays. Teeth agenesis encompasses hypodontia, oligodontia, and anodontia. The total number and the type of teeth missing should be added to the description. The clinical absence of a tooth due to a disturbed eruption should not be termed teeth agenesis but a missing tooth. Tooth agenesis The absence of one or more teeth from the normal series by a failure to develop PMID:31468724 Decreased tooth count Failure of development of some teeth Reduced number of teeth Teeth, agenesis Decreased number of teeth Fewer teeth than normal Missing some teeth A structural abnormality of a diaphysis of the arm. 2009-02-23T04:55:36Z HP:0003857 UMLS:C4021389 Abnormality involving the diaphyses of the upper limbs Abnormality of shaft of long bone of the upper limbs Diaphyseal abnormality of the upper limbs HP:0009808 Anomaly of the upper limb diaphyses A structural abnormality of a diaphysis of the arm. HPO_CONTRIBUTOR:UToronto_htrang Abnormality of shaft of long bone of the upper limbs An anomaly of one or more metaphyses of the arms. 2009-02-23T04:55:36Z HP:0003847 UMLS:C4021388 Abnormality of the wide portion of upper limb bone Abnormality of upper limb metaphysis Metaphyseal abnormality of the upper limbs HP:0009809 Abnormal upper limb metaphysis morphology An anomaly of one or more metaphyses of the arms. Abnormality of the wide portion of upper limb bone 2009-02-23T04:57:56Z UMLS:C4021387 Abnormality of the joints of the upper limbs Abnormality of upper limb joint HP:0009810 Abnormality of upper limb joint Abnormality of the joints of the upper limbs Abnormality of upper limb joint An anomaly of the joint that connects the upper and the lower arm. 2009-02-23T04:59:43Z HP:0002966 UMLS:C4021386 Abnormality of the elbow Abnormality of the elbows HP:0009811 Abnormality of the elbow An anomaly of the joint that connects the upper and the lower arm. Abnormality of the elbow Abnormality of the elbows Peromelia affecting only the upper limbs. That is, the distal parts of the arm are missing leading to stump formation. 2009-02-23T05:06:12Z UMLS:C4024199 HP:0009814 Upper limb peromelia Peromelia affecting only the upper limbs. That is, the distal parts of the arm are missing leading to stump formation. Absence (due to failure to form) or underdevelopment of the extremities. 2009-02-23T05:06:40Z HP:0002969 HP:0006497 UMLS:C0239399 Absent/small extremities Absent/underdeveloped extremities Short or absent limbs Shortened limbs HP:0009815 Aplasia/hypoplasia of the extremities Absence (due to failure to form) or underdevelopment of the extremities. Absent/small extremities Absent/underdeveloped extremities Leg shortening because of underdevelopment of one or more bones of the lower extremity. 2009-02-23T05:09:32Z HP:0003087 HP:0005884 HP:0006399 SNOMEDCT_US:253959002 UMLS:C0345371 Hypoplasia involving bones of the lower limbs Hypoplasia of the lower limbs Lower limb undergrowth Underdeveloped lower limb bones HP:0009816 Lower limb undergrowth Leg shortening because of underdevelopment of one or more bones of the lower extremity. Lower limb undergrowth Underdeveloped lower limb bones Peromelia affecting only the lower limbs. That is, the distal parts of the leg are missing leading to stump formation. 2009-02-23T05:11:07Z UMLS:C4024196 HP:0009820 Lower limb peromelia Peromelia affecting only the lower limbs. That is, the distal parts of the leg are missing leading to stump formation. Forearm shortening because of underdevelopment of one or more bones of the forearm. 2009-02-23T05:11:42Z HP:0003024 HP:0003968 HP:0006405 UMLS:C1855299 Forearm undergrowth Hypoplasia involving forearm bones Short forearm bones Short forearms Shortened forearm HP:0009821 Forearm undergrowth Forearm shortening because of underdevelopment of one or more bones of the forearm. Forearm undergrowth Short forearm bones Short forearms Shortened forearm Arm shortening because of underdevelopment of one or more bones of the upper extremity. 2009-02-23T05:13:20Z HP:0003056 HP:0006364 UMLS:C1837406 Hypoplasia involving bones of the upper limbs Short arms Shortening of the arms Upper limb undergrowth HP:0009824 Upper limb undergrowth Arm shortening because of underdevelopment of one or more bones of the upper extremity. Short arms Shortening of the arms Upper limb undergrowth Limb shortening because of underdevelopment of one or more bones of the extremities. 2009-02-23T05:16:44Z HP:0003058 HP:0005049 HP:0005057 UMLS:C0239399 Hypoplasia involving bones of the extremities Limb undergrowth Short limb Short limbs limb shortening HP:0009826 Limb undergrowth Limb shortening because of underdevelopment of one or more bones of the extremities. Limb undergrowth Short limb Short limbs limb shortening The distal parts of the limbs are missing leading to a stump formation. 2009-02-23T05:17:25Z UMLS:C4024192 HP:0009828 Peromelia The distal parts of the limbs are missing leading to a stump formation. Any anomaly of distal phalanx of finger. 2009-03-11T12:01:39Z HP:0005919 UMLS:C4021385 Abnormal terminal phalanges of the hand Abnormality of the distal phalanges of the hand Abnormality of the distal phalanx of finger Abnormality of the outermost finger bone HP:0009832 Abnormal distal phalanx morphology of finger Any anomaly of distal phalanx of finger. Abnormality of the outermost finger bone An anomaly of middle phalanx of finger. 2009-03-11T12:01:39Z UMLS:C4024191 Abnormality of the middle finger bones of the hand Abnormality of the middle phalanges of the hand HP:0009833 Abnormal middle phalanx morphology of the hand An anomaly of middle phalanx of finger. Abnormality of the middle finger bones of the hand 2009-03-11T12:01:39Z UMLS:C4024190 Abnormality of the innermost finger bones of the hand Abnormality of the proximal phalanges of the hand HP:0009834 Abnormal proximal phalanx morphology of the hand Abnormality of the innermost finger bones of the hand Absence or underdevelopment of the distal phalanges. 2009-03-11T12:10:11Z HP:0005635 HP:0006037 HP:0006066 HP:0006235 UMLS:C1861336 Absent/hypoplastic distal phalanges Absent/small outermost finger bone of the hand Absent/underdeveloped outermost finger bone of the hand Aplasia/Hypoplasia of the distal phalanges Aplastic/hypoplastic distal phalanges Hypoplastic to absent terminal phalanges Hypoplastic/aplastic distal phalanges Hypoplastic/aplastic distal phalanx Small or absent distal phalanges HP:0009835 Aplasia/Hypoplasia of the distal phalanges of the hand Absence or underdevelopment of the distal phalanges. Absent/small outermost finger bone of the hand Absent/underdeveloped outermost finger bone of the hand Small or absent distal phalanges 2009-03-11T12:15:55Z HP:0005810 HP:0006063 HP:0006148 UMLS:C1862152 Absent/hypoplastic middle phalanges Absent/small middle finger bone of the hand Absent/underdeveloped middle finger bone of the hand Aplasia/hypoplasia of middle phalanges Aplastic/hypoplastic middle phalanges Hypoplastic/aplastic middle phalanx Short to absent middle phalanges Short/absent middle phalanges HP:0009843 Aplasia/Hypoplasia of the middle phalanges of the hand Absent/small middle finger bone of the hand Absent/underdeveloped middle finger bone of the hand 2009-03-11T12:16:33Z UMLS:C4024182 Absent/small innermost finger bones of the hand Absent/underdeveloped innermost finger bones of the hand HP:0009851 Aplasia/Hypoplasia of the proximal phalanges of the hand Absent/small innermost finger bones of the hand Absent/underdeveloped innermost finger bones of the hand Short distance from the end of the finger to the most distal interphalangeal crease or the distal interphalangeal joint flexion point. That is, hypoplasia of one or more of the distal phalanx of finger. 2009-04-24T04:29:30Z HP:0001198 HP:0001202 HP:0001221 HP:0001229 HP:0005669 HP:0006075 HP:0006076 HP:0006132 HP:0006199 HP:0006223 UMLS:C1839829 Brachytelophalangy Distal phalangeal hypoplasia Hypoplasia of the distal phalanges Hypoplasia of the distal phalanges of the hand Hypoplasic terminal phalanges Hypoplastic distal phalanges Hypoplastic terminal phalanges Short distal phalanges Short outermost finger bone Terminal phalangeal hypoplasia of hand HP:0009882 This term differs from Partial absence of the finger because in that term, the phalanx must be missing, whereas in this term it may be small, but present. Distal phalangeal lengths can be assessed subjectively by comparing that digit segment to the rest of the digit, to other normal digits in that patient, or to typical patients of that age or build. Regarding the subjective definition, for individuals who do not have flexion creases, one may determine this by flexing the DIP joint and estimating the length of the terminal segment of the digit. Alternatively, one may be able to palpate the joint. Short distal phalanx of finger Short distance from the end of the finger to the most distal interphalangeal crease or the distal interphalangeal joint flexion point. That is, hypoplasia of one or more of the distal phalanx of finger. PMID:19125433 Short outermost finger bone This term applies if one or more of the distal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. 2009-04-24T04:33:55Z HP:0001228 HP:0010007 UMLS:C1849343 Bifid terminal phalanges Duplication of the outermost bone of hand Notched outermost bone of hand Partial/complete duplication of the distal phalanges of the hand HP:0009883 Duplication of the distal phalanx of hand This term applies if one or more of the distal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. Duplication of the outermost bone of hand Notched outermost bone of hand Abnormality of the growth of secondary sexual hair, which normally ensues during puberty. In males, secondary sexual hair usually comprises body hair, including underarm, abdominal, chest, and pubic hair. In females, secondary sexual hair usually comprises a lesser degree of body hair, most prominently underarm and pubic hair. 2009-04-30T06:18:33Z UMLS:C4024171 Abnormality of secondary sexual hair HP:0009888 Abnormality of secondary sexual hair Abnormality of the growth of secondary sexual hair, which normally ensues during puberty. In males, secondary sexual hair usually comprises body hair, including underarm, abdominal, chest, and pubic hair. In females, secondary sexual hair usually comprises a lesser degree of body hair, most prominently underarm and pubic hair. Abnormality of secondary sexual hair Abnormally increased hair growth with a localized distribution. 2009-04-30T06:29:20Z UMLS:C4024170 Localised abnormal hair growth Localised hirsutism Localized abnormal hair growth HP:0009889 Localized hirsutism Abnormally increased hair growth with a localized distribution. Localised abnormal hair growth Localised hirsutism Localized abnormal hair growth Complete absence of any auricular structures. 2009-04-30T06:53:41Z MSH:D065817 SNOMEDCT_US:57436000 UMLS:C0702139 UMLS:C1408788 Absent ear Absent ears Congenital absence of external ear HP:0009892 Complete absence of the auricle (external ear). The skin of the cheek passes smoothly over the aural area without definite elevation or depression. Anotia Complete absence of any auricular structures. PMID:19125421 Absent ear Absent ears Congenital absence of external ear Abnormality of the temporal bone of the skull, which is situated at the sides and base of the skull roughly underlying the region of the face known as the temple. 2009-05-01T03:33:17Z UMLS:C4024163 Abnormality of the temporal bone HP:0009911 Abnormal temporal bone morphology Abnormality of the temporal bone of the skull, which is situated at the sides and base of the skull roughly underlying the region of the face known as the temple. Underdevelopment or absence of the nose or parts thereof. 2009-05-05T06:44:04Z SNOMEDCT_US:204519007 SNOMEDCT_US:93278002 UMLS:C0685684 UMLS:C4024159 UMLS:C4280392 Decreased nasal size Decreased size of nose Hypoplasia of the nose Hypotrophic nose HP:0009924 Aplasia/Hypoplasia involving the nose Underdevelopment or absence of the nose or parts thereof. Decreased nasal size Decreased size of nose Hypoplasia of the nose Hypotrophic nose The presence of only a single nostril. 2009-05-10T10:33:56Z SNOMEDCT_US:95266003 UMLS:C0685682 Mono nostril One nostril Single nare Single nostril HP:0009932 The single opening may occur in the midline or it can occur on one side, that is, it can be symmetric or asymmetric. Although the columella is invariably absent, this is implicit and does not need to be separately specified. Single naris The presence of only a single nostril. PMID:19152422 Mono nostril One nostril Single nare Single nostril The presence of more than two nostrils. 2009-05-10T10:37:41Z UMLS:C4021372 Accessory nares Accessory nostril Extra nostril Supernumerary nares Supernumerary nostrils HP:0009934 Supernumerary naris The presence of more than two nostrils. PMID:19152422 Accessory nares Accessory nostril Extra nostril Supernumerary nares Absence or underdevelopment of the nasal septum. 2009-05-10T10:40:21Z UMLS:C4024156 Ageneis of nasal septum Underdevelopment of nasal septum Failure of development of nasal septum HP:0009935 Aplasia/Hypoplasia of the nasal septum Absence or underdevelopment of the nasal septum. Ageneis of nasal septum Underdevelopment of nasal septum Failure of development of nasal septum Excess facial hair. 2009-05-10T10:58:49Z Excessive face hair UMLS:C1850041 UMLS:C2128203 HP:0009937 Facial hirsutism Excess facial hair. Excessive face hair Lack or loss of the soft tissues between the zygomata and mandible. 2009-05-10T11:17:18Z UMLS:C4024154 Depressed cheeks Hollow cheeks Sunken cheeks HP:0009938 Sunken cheeks Lack or loss of the soft tissues between the zygomata and mandible. PMID:19125436 Depressed cheeks Hollow cheeks Sunken cheeks Complete or partial duplication of the phalanges of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones (bifid), two separate bones appearing side to side, or completely duplicated phalanges (proximal and distal phalanx of the thumb and/or 1st metacarpal). In contrast to the phalanges of the digits 2-5 (proximal, middle and distal), the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. 2009-05-15T12:51:02Z HP:0009661 UMLS:C4021370 Complete/partial duplication of phalanges of the thumb Duplicated thumbs Duplication of phalanx of thumb Duplicated thumb HP:0009942 Duplication of thumb phalanx Complete or partial duplication of the phalanges of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones (bifid), two separate bones appearing side to side, or completely duplicated phalanges (proximal and distal phalanx of the thumb and/or 1st metacarpal). In contrast to the phalanges of the digits 2-5 (proximal, middle and distal), the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Duplicated thumbs A complete duplication affecting one or more of the phalanges of the thumb. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. 2009-05-15T12:51:35Z HP:0002801 HP:0004067 UMLS:C3554724 Complete duplication of the phalanges of the thumb Complete duplication of thumb bones Digitalization of thumb Digitalization of thumbs HP:0009943 Complete duplication of thumb phalanx A complete duplication affecting one or more of the phalanges of the thumb. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. Complete duplication of thumb bones A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the thumb. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. 2009-05-15T12:51:57Z HP:0001244 HP:0004070 UMLS:C4082168 Bifid thumb Notching of thumb phalanges Partial duplication of the phalanges of the thumb Partial duplication of the thumb bones HP:0009944 Partial duplication of thumb phalanx A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the thumb. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. Partial duplication of the thumb bones This term applies if one or more of the phalanges of the 5th finger are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. 2009-05-26T02:23:38Z UMLS:C4021354 Partial/complete duplication of little finger bone Partial/complete duplication of phalanges of the 5th finger Partial/complete duplication of pinkie finger bone Partial/complete duplication of pinky finger bone HP:0009985 Duplication of phalanx of 5th finger This term applies if one or more of the phalanges of the 5th finger are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. Partial/complete duplication of little finger bone Partial/complete duplication of pinkie finger bone Partial/complete duplication of pinky finger bone A complete duplication affecting one or more of the phalanges of the 5th finger. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. 2009-05-26T02:24:20Z UMLS:C4024128 Complete duplication of the little finger bone Complete duplication of the pinkie finger bone Complete duplication of the pinky finger bone HP:0009986 Complete duplication of the phalanges of the 5th finger A complete duplication affecting one or more of the phalanges of the 5th finger. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. Complete duplication of the little finger bone Complete duplication of the pinkie finger bone Complete duplication of the pinky finger bone A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the 5th finger. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. 2009-05-26T02:24:20Z UMLS:C4024127 Partial duplication of the little finger bone Partial duplication of the pinkie finger bone Partial duplication of the pinky finger bone HP:0009987 Partial duplication of the phalanges of the 5th finger A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the 5th finger. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. Partial duplication of the little finger bone Partial duplication of the pinkie finger bone Partial duplication of the pinky finger bone Partial or complete duplication of the distal phalanx of little finger. 2009-05-26T02:24:20Z UMLS:C4021353 Duplication of the outermost little finger bone Duplication of the outermost pinkie finger bone Duplication of the outermost pinky finger bone Partial/complete duplication of the distal phalanx of the 5th finger HP:0009988 Duplication of the distal phalanx of the 5th finger Partial or complete duplication of the distal phalanx of little finger. Duplication of the outermost little finger bone Duplication of the outermost pinkie finger bone Duplication of the outermost pinky finger bone Partial or complete duplication of the fifth middle phalanx of hand. 2009-05-26T02:24:20Z UMLS:C4021352 Duplication of the middle little finger bone Duplication of the middle pinkie finger bone Duplication of the middle pinky finger bone Partial/complete duplication of the middle phalanx of the 5th finger HP:0009989 Duplication of the middle phalanx of the 5th finger Partial or complete duplication of the fifth middle phalanx of hand. Duplication of the middle little finger bone Duplication of the middle pinkie finger bone Duplication of the middle pinky finger bone Partial or complete duplication of the fifth proximal phalanx of hand. 2009-05-26T02:24:20Z UMLS:C4021351 Duplication of the innermost little finger bone Duplication of the innermost pinkie finger bone Duplication of the innermost pinky finger bone Partial/complete duplication of the proximal phalanx of the 5th finger HP:0009990 Duplication of the proximal phalanx of the 5th finger Partial or complete duplication of the fifth proximal phalanx of hand. Duplication of the innermost little finger bone Duplication of the innermost pinkie finger bone Duplication of the innermost pinky finger bone Complete duplication of the distal phalanx of little finger. 2009-05-26T02:24:33Z UMLS:C4024126 Complete duplication of the outermost little finger bone Complete duplication of the outermost pinkie finger bone Complete duplication of the outermost pinky finger bone HP:0009991 Complete duplication of the distal phalanx of the 5th finger Complete duplication of the distal phalanx of little finger. Complete duplication of the outermost little finger bone Complete duplication of the outermost pinkie finger bone Complete duplication of the outermost pinky finger bone Complete duplication of the fifth middle phalanx of hand. 2009-05-26T02:24:33Z UMLS:C4024125 Complete duplication of the middle little finger bone Complete duplication of the middle pinkie finger bone Complete duplication of the middle pinky finger bone HP:0009992 Complete duplication of the middle phalanx of the 5th finger Complete duplication of the fifth middle phalanx of hand. Complete duplication of the middle little finger bone Complete duplication of the middle pinkie finger bone Complete duplication of the middle pinky finger bone Complete duplication of the fifth proximal phalanx of hand. 2009-05-26T02:24:33Z UMLS:C4024124 Complete duplication of the innermost little finger bone Complete duplication of the innermost pinkie finger bone Complete duplication of the innermost pinky finger bone HP:0009993 Complete duplication of the proximal phalanx of the 5th finger Complete duplication of the fifth proximal phalanx of hand. Complete duplication of the innermost little finger bone Complete duplication of the innermost pinkie finger bone Complete duplication of the innermost pinky finger bone Partial duplication of the distal phalanx of little finger, seen on x-rays as a broad and/or bifid phalanx. 2009-05-26T02:24:47Z UMLS:C4021350 Bifid terminal phalanx of the 5th finger Notched outermost pinky finger bone Partial duplication of outermost little finger bone Partial duplication of outermost pinkie finger bone Partial duplication of outermost pinky finger bone HP:0009994 Partial duplication of the distal phalanx of the 5th finger Partial duplication of the distal phalanx of little finger, seen on x-rays as a broad and/or bifid phalanx. Notched outermost pinky finger bone Partial duplication of outermost little finger bone Partial duplication of outermost pinkie finger bone Partial duplication of outermost pinky finger bone Partial duplication of the fifth middle phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. 2009-05-26T02:24:47Z UMLS:C4024123 Partial duplication of the middle little finger bone Partial duplication of the middle pinkie finger bone Partial duplication of the middle pinky finger bone HP:0009995 Partial duplication of the middle phalanx of the 5th finger Partial duplication of the fifth middle phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. Partial duplication of the middle little finger bone Partial duplication of the middle pinkie finger bone Partial duplication of the middle pinky finger bone Partial or complete duplication of the fifth proximal phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. 2009-05-26T02:24:47Z UMLS:C4024122 Partial duplication of the innermost little finger bone Partial duplication of the innermost pinkie finger bone Partial duplication of the innermost pinky finger bone HP:0009996 Partial duplication of the proximal phalanx of the 5th finger Partial or complete duplication of the fifth proximal phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. Partial duplication of the innermost little finger bone Partial duplication of the innermost pinkie finger bone Partial duplication of the innermost pinky finger bone This term applies if one or more of the phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. 2009-05-26T02:28:25Z HP:0009143 UMLS:C4021349 Duplication of finger bones HP:0009997 Duplication of phalanx of hand This term applies if one or more of the phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. Duplication of finger bones A complete duplication affecting one or more of the phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, is a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. 2009-05-26T02:30:16Z UMLS:C4024121 Complete duplication of hand bones HP:0009998 Complete duplication of phalanx of hand A complete duplication affecting one or more of the phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, is a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. Complete duplication of hand bones A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. 2009-05-26T02:30:35Z UMLS:C4024120 Partial duplication of hand bones HP:0009999 Partial duplication of the phalanx of hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. Partial duplication of hand bones A complete duplication affecting one or more of the proximal phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. 2009-05-26T03:55:02Z UMLS:C4024119 Complete duplication of the innermost bones of the hand HP:0010000 Complete duplication of the proximal phalanges of the hand A complete duplication affecting one or more of the proximal phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. Complete duplication of the innermost bones of the hand A complete duplication affecting one or more of the distal phalanges of the hand. 2009-05-26T03:55:02Z UMLS:C4024118 Complete duplication of the outermost bones of the hand HP:0010001 As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accessory bone appearing in the proximo-distal axis on x-rays, is actually a different entity called a pseudoepiphysis (see corresponding terms), sometimes also referred to as hyperphalangism. Complete duplication of the distal phalanges of the hand A complete duplication affecting one or more of the distal phalanges of the hand. Complete duplication of the outermost bones of the hand A complete duplication affecting one or more of the middle phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accessory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a pseudoepiphysis (see corresponding terms) sometimes also referred to as hyperphalangism. 2009-05-26T03:55:02Z UMLS:C4024117 Complete duplication of the middle bones of the hand HP:0010002 Complete duplication of the middle phalanges of the hand A complete duplication affecting one or more of the middle phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accessory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a pseudoepiphysis (see corresponding terms) sometimes also referred to as hyperphalangism. Complete duplication of the middle bones of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the proximal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. 2009-05-26T03:55:29Z UMLS:C4024116 Partial duplication of the innermost bones of the hand HP:0010003 Partial duplication of the proximal phalanges of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the proximal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. Partial duplication of the innermost bones of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the distal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. 2009-05-26T03:55:29Z HP:0006196 UMLS:C4021348 Bifid terminal phalanges of the hand Partial duplication of the outermost bone of the hand HP:0010004 Partial duplication of the distal phalanges of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the distal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. Partial duplication of the outermost bone of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the middle phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. 2009-05-26T03:55:29Z UMLS:C4024115 Partial duplication of the middle bones of hand HP:0010005 Partial duplication of the middle phalanges of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the middle phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. Partial duplication of the middle bones of hand This term applies if one or more of the proximal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. 2009-05-26T05:29:46Z UMLS:C4021347 Duplication of the innermost bones of hand Partial/complete duplication of the proximal phalanges of the hand HP:0010006 Duplication of the proximal phalanx of hand This term applies if one or more of the proximal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. Duplication of the innermost bones of hand This term applies if one or more of the middle phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. 2009-05-26T05:29:46Z UMLS:C4021346 Duplication of the middle bones of hand Partial/complete duplication of the middle phalanges of the hand HP:0010008 Duplication of the middle phalanx of hand This term applies if one or more of the middle phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. Duplication of the middle bones of hand A structural anomaly of the first metacarpal. 2009-05-27T03:35:21Z UMLS:C4024114 Abnormality of the 1st long bone of hand Abnormality of the 1st metacarpal HP:0010009 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits. Abnormal 1st metacarpal morphology A structural anomaly of the first metacarpal. Abnormality of the 1st long bone of hand Any abnormality of the fifth metacarpal bone. 2009-05-27T03:35:21Z UMLS:C4024110 Abnormality of the 5th long bone of hand Abnormality of the 5th metacarpal HP:0010013 Abnormal 5th metacarpal morphology Any abnormality of the fifth metacarpal bone. Abnormality of the 5th long bone of hand In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). The epiphysis of the first metacarpal is localized at the proximal end (as seen in the proximal phalanges of the other digits), whereas the epiphyses of the other metacarpal bones are located at the distal end. This term applies if the epiphysis of the 1st metacarpal is in any way abnormal, referring to age and gender depending norms, as seen on x-rays. 2009-05-27T03:43:11Z UMLS:C4024109 Abnormality of the end part of the 1st long bone of hand HP:0010014 Abnormality of the epiphysis of the 1st metacarpal In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). The epiphysis of the first metacarpal is localized at the proximal end (as seen in the proximal phalanges of the other digits), whereas the epiphyses of the other metacarpal bones are located at the distal end. This term applies if the epiphysis of the 1st metacarpal is in any way abnormal, referring to age and gender depending norms, as seen on x-rays. Abnormality of the end part of the 1st long bone of hand 2009-05-27T04:02:50Z UMLS:C4024108 Absent end part of the 1st long bone of hand HP:0010015 Absent epiphysis of the 1st metacarpal Absent end part of the 1st long bone of hand Abnormally large size of the epiphyses of the 1st metacarpal with respect to age-dependent norms. 2009-05-27T04:02:50Z UMLS:C4024105 Enlarged end part of the 1st long bone of hand HP:0010018 Enlarged epiphysis of the 1st metacarpal Abnormally large size of the epiphyses of the 1st metacarpal with respect to age-dependent norms. Enlarged end part of the 1st long bone of hand The epiphysis of the first metacarpal is localized at the proximal end of the metacarpal bone although an accessory epiphysis may be located at the distal end of the metacarpal. 2009-05-27T04:02:50Z UMLS:C4024101 HP:0010022 This feature can be seen for example in Holt-Oram Syndrome. Pseudoepiphysis of the 1st metacarpal The epiphysis of the first metacarpal is localized at the proximal end of the metacarpal bone although an accessory epiphysis may be located at the distal end of the metacarpal. Abnormally small size of the epiphysis of the 1st metacarpal with respect to age-dependent norms. 2009-05-27T04:02:50Z UMLS:C4024100 Small end part of the 1st long bone of hand HP:0010023 Small epiphysis of the 1st metacarpal Abnormally small size of the epiphysis of the 1st metacarpal with respect to age-dependent norms. Small end part of the 1st long bone of hand Aplasia or Hypoplasia affecting the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). 2009-05-27T04:24:30Z UMLS:C4024098 Absent/small 1st long bone of hand Absent/underdeveloped 1st long bone of hand HP:0010026 Aplasia/Hypoplasia of the 1st metacarpal Aplasia or Hypoplasia affecting the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). Absent/small 1st long bone of hand Absent/underdeveloped 1st long bone of hand A developmental defect characterized by reduced length of the first metacarpal (long bone) of the hand. 2009-05-27T04:24:50Z HP:0001190 HP:0001499 HP:0005898 HP:0006141 UMLS:C1849311 First metacarpal hypoplasia First metacarpals hypoplastic Hypoplastic 1st metacarpal Short first metacarpal Short first metacarpals Shortened 1st long bone of hand HP:0010034 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Short 1st metacarpal A developmental defect characterized by reduced length of the first metacarpal (long bone) of the hand. Shortened 1st long bone of hand In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Aplasia or Hypoplasia affecting the 5th metacarpal. 2009-05-27T04:37:31Z UMLS:C4024085 Absent/small 5th long bone of hand Absent/underdeveloped 5th long bone of hand HP:0010045 Aplasia/Hypoplasia of the 5th metacarpal Aplasia or Hypoplasia affecting the 5th metacarpal. Absent/small 5th long bone of hand Absent/underdeveloped 5th long bone of hand Short fifth metacarpal bone. 2009-05-27T04:37:44Z HP:0005737 HP:0006004 HP:0006222 UMLS:C1861388 Fifth metacarpal hypoplasia Hypoplastic 5th metacarpal Short fifth metacarpal Short fifth metacarpals Shortened 5th long bone of hand HP:0010047 Short 5th metacarpal Short fifth metacarpal bone. Shortened 5th long bone of hand Developmental defect associated with absence of one or more metacarpal bones. 2009-05-27T04:40:58Z HP:0005911 UMLS:C1846473 Absent long bone of hand Absent metacarpal Absent metacarpals HP:0010048 Aplasia of metacarpal bones Developmental defect associated with absence of one or more metacarpal bones. Absent long bone of hand Diminished length of one or more metacarpal bones in relation to the others of the same hand or to the contralateral metacarpal. 2009-05-27T04:40:58Z HP:0001164 HP:0005695 HP:0005717 HP:0005909 HP:0006047 HP:0006183 HP:0006186 UMLS:C1837084 Brachymetacarpalia Hypoplastic metacarpal Metacarpal hypoplasia Short metacarpals Shortened long bone of hand Shortened long bones of hand Shortened metacarpals Shortening of metacarpals Short metacarpal bones HP:0010049 Short metacarpals can involve any of the metacarpal bones, and the affected ray should be specified. The assessment of isolated short metacarpal can be made by viewing the dorsum of the hand when clenched. Note that if metacarpals F2-5 are affected, the correct term is Short palm. Short metacarpal Diminished length of one or more metacarpal bones in relation to the others of the same hand or to the contralateral metacarpal. PMID:19125433 Shortened long bone of hand Short metacarpal bones Displacement of the big toe from its normal position. 2009-05-29T11:36:44Z HP:0004700 UMLS:C4021344 Displacement of big toe Displacement of the hallux HP:0010051 Deviation of the hallux Displacement of the big toe from its normal position. Displacement of big toe An abnormal shape or form of the proximal phalanx of the big toe. 2009-05-29T11:47:46Z UMLS:C4024084 Abnormal innermost big toe bone Abnormality of the proximal phalanx of the hallux HP:0010052 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the big toe is embryologically equivalent to the middle phalanges of the other digits, whereas the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Abnormal morphology of the proximal phalanx of the hallux An abnormal shape or form of the proximal phalanx of the big toe. Abnormal innermost big toe bone 2009-05-29T11:49:11Z UMLS:C4024083 Abnormality of the outermost bone of the big toe HP:0010053 Abnormality of the distal phalanx of the hallux Abnormality of the outermost bone of the big toe An anomaly of the first metatarsal bone. 2009-05-29T11:49:54Z UMLS:C4024082 Abnormality of the 1st long bone of foot HP:0010054 In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities of the first metatarsal. Abnormality of the first metatarsal bone An anomaly of the first metatarsal bone. Abnormality of the 1st long bone of foot 2009-05-29T12:00:08Z UMLS:C4024081 Abnormality of the end part of the big toe bone HP:0010056 Abnormality of the epiphyses of the hallux Abnormality of the end part of the big toe bone 2009-05-29T12:00:08Z UMLS:C4024080 Abnormal big toe bones Abnormality of the phalanges of the hallux HP:0010057 Abnormal hallux phalanx morphology Abnormal big toe bones 2009-05-29T12:10:46Z UMLS:C4024079 Absent/small big toe bone Absent/underdeveloped big toe bone HP:0010058 Aplasia/Hypoplasia of the phalanges of the hallux Absent/small big toe bone Absent/underdeveloped big toe bone Partial or complete duplication of one or more phalanx of big toe. 2009-05-29T12:10:46Z HP:0001784 HP:0005785 HP:0005851 UMLS:C1860164 UMLS:C4020691 Duplicated hallux Duplication of big toe bone Duplication of great toes Duplication of phalanx of big toe Hallucal duplication Partial/complete duplication of the phalanges of the hallux HP:0010066 Duplication of phalanx of hallux Partial or complete duplication of one or more phalanx of big toe. Duplication of big toe bone Duplication of great toes Absence or underdevelopment of the first metatarsal bone. 2009-05-29T12:13:57Z UMLS:C4024076 Absent/small 1st long bone of foot Absent/underdeveloped 1st long bone of foot HP:0010067 Aplasia/hypoplasia of the 1st metatarsal Absence or underdevelopment of the first metatarsal bone. Absent/small 1st long bone of foot Absent/underdeveloped 1st long bone of foot A developmental defect consisting in the duplication of the first metatarsal bone. 2009-05-29T12:13:57Z UMLS:C1851855 Duplicated 1st long bone of foot Duplicated first metatarsals HP:0010075 Duplication of the 1st metatarsal A developmental defect consisting in the duplication of the first metatarsal bone. Duplicated 1st long bone of foot 2009-05-29T12:16:28Z UMLS:C4024069 Absent/small outermost big toe bone Absent/underdeveloped outermost big toe bone HP:0010076 Aplasia/Hypoplasia of the distal phalanx of the hallux Absent/small outermost big toe bone Absent/underdeveloped outermost big toe bone 2009-05-29T12:16:28Z UMLS:C4021339 Duplication of the outermost bone of big toe Partial/complete duplication of the distal phalanx of the hallux HP:0010084 Duplication of the distal phalanx of the hallux Duplication of the outermost bone of big toe 2009-05-29T12:17:16Z UMLS:C4024061 Absent/small innermost big toe bone Absent/underdeveloped innermost big toe bone HP:0010085 Aplasia/Hypoplasia of the proximal phalanx of the hallux Absent/small innermost big toe bone Absent/underdeveloped innermost big toe bone Partial or complete duplication of the proximal phalanx of big toe. 2009-05-29T12:17:16Z UMLS:C4024054 Duplication of the innermost bone of big toe HP:0010093 Duplication of the proximal phalanx of the hallux Partial or complete duplication of the proximal phalanx of big toe. Duplication of the innermost bone of big toe Complete duplication of the proximal phalanx of big toe. 2009-05-29T12:18:59Z UMLS:C4024053 Complete duplication of the innermost bone of big toe HP:0010094 Complete duplication of the proximal phalanx of the hallux Complete duplication of the proximal phalanx of big toe. Complete duplication of the innermost bone of big toe Partial duplication of the proximal phalanx of big toe. 2009-05-29T12:18:59Z UMLS:C4024052 Partial duplication of the innermost bone of big toe HP:0010095 Partial duplication of the proximal phalanx of the hallux Partial duplication of the proximal phalanx of big toe. Partial duplication of the innermost bone of big toe 2009-05-29T12:19:30Z UMLS:C4024051 Complete duplication of the outermost bone of the big toe HP:0010096 Complete duplication of the distal phalanx of the hallux Complete duplication of the outermost bone of the big toe 2009-05-29T12:19:30Z HP:0008091 UMLS:C4021337 Bifid distal phalanx of hallux Notched outermost bone of big toe Partial duplication of the outermost bone of big toe HP:0010097 Partial duplication of the distal phalanx of the hallux Notched outermost bone of big toe Partial duplication of the outermost bone of big toe A developmental defect consisting in the complete duplication of the first metatarsal bone. 2009-05-29T12:20:12Z HP:0008121 UMLS:C4024050 Complete duplication of the 1st long bone of foot HP:0010098 Complete duplication of the 1st metatarsal A developmental defect consisting in the complete duplication of the first metatarsal bone. Complete duplication of the 1st long bone of foot A developmental defect consisting in the duplication of part of the first metatarsal bone. 2009-05-29T12:20:12Z UMLS:C4024049 Partial duplication of the 1st long bone of foot HP:0010099 Partial duplication of the 1st metatarsal A developmental defect consisting in the duplication of part of the first metatarsal bone. Partial duplication of the 1st long bone of foot Complete duplication of one or more phalanx of big toe. 2009-05-29T12:22:12Z UMLS:C4021336 Complete duplication of big toe bones Complete duplication of the phalanges of the hallux HP:0010100 Complete duplication of hallux phalanx Complete duplication of one or more phalanx of big toe. Complete duplication of big toe bones 2009-05-29T12:22:12Z HP:0004678 UMLS:C1855005 Partial duplication of big toe partial duplication of hallux HP:0010101 Partial duplication of the phalanges of the hallux Partial duplication of big toe Underdevelopment (hypoplasia) of the distal phalanx of big toe. 2009-05-29T12:41:37Z UMLS:C4021335 Hypoplastic/small distal phalanx of the hallux Small distal phalanx of big toe Small distal phalanx of hallux Small outermost bone of big toe HP:0010103 Short distal phalanx of hallux Underdevelopment (hypoplasia) of the distal phalanx of big toe. Small outermost bone of big toe Short first metatarsal bone. 2009-05-29T12:42:09Z HP:0004680 UMLS:C1841688 First metatarsal hypoplasia First metatarsals hypoplastic Short 1st long bone of foot HP:0010105 Short first metatarsal Short first metatarsal bone. Short 1st long bone of foot Underdevelopment (hypoplasia) of the proximal phalanx of big toe. 2009-05-29T12:43:40Z HP:0008101 HP:0008129 UMLS:C1862159 Hypoplastic proximal phalanx of the hallux Short innermost big toe bone Short proximal phalanges of halluces Short proximal phalanx of halluces Small proximal phalanx of big toe Small proximal phalanx of hallux HP:0010107 Short proximal phalanx of hallux Underdevelopment (hypoplasia) of the proximal phalanx of big toe. Short innermost big toe bone Underdevelopment (hypoplasia) of the big toe. 2009-05-29T12:46:14Z HP:0001843 HP:0001861 HP:0005610 HP:0008105 UMLS:C1865992 Hypoplastic big toes Hypoplastic hallux Short big toe Short halluces Small hallux HP:0010109 Short hallux Underdevelopment (hypoplasia) of the big toe. Short big toe Underdevelopment (hypoplasia) of a phalanx of big toe. 2009-05-29T12:49:19Z UMLS:C4021334 Hypoplastic phalanges of the hallux Short bone of big toe HP:0010111 Short phalanx of hallux Underdevelopment (hypoplasia) of a phalanx of big toe. Hypoplastic phalanges of the hallux Short bone of big toe Failure to form (agenesis) of one or more epiphyses of the big toe. 2009-05-29T01:16:38Z UMLS:C4020906 Absent end part of big toe bone Absent epiphyses of the hallux HP:0010113 Absent hallux epiphysis Failure to form (agenesis) of one or more epiphyses of the big toe. Absent end part of big toe bone 2009-05-29T01:16:38Z UMLS:C4024043 Enlarged end part of the big toe bone HP:0010116 Enlarged epiphyses of the hallux Enlarged end part of the big toe bone 2009-05-29T01:16:38Z UMLS:C4024039 HP:0010120 Pseudoepiphyses of the hallux 2009-05-29T01:16:38Z UMLS:C4024038 Small end part of the big toe bone HP:0010121 Small epiphyses of the hallux Small end part of the big toe bone 2009-05-29T01:17:54Z UMLS:C4024035 Abnormality of the end part of the outermost bone of the big toe bone HP:0010124 Abnormality of the epiphysis of the distal phalanx of the hallux Abnormality of the end part of the outermost bone of the big toe bone In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities of the epiphysis of the first metatarsal bone. 2009-05-29T01:17:54Z UMLS:C4024034 Abnormality of the end part of the 1st long bone of foot HP:0010125 Abnormality of the epiphysis of the 1st metatarsal In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities of the epiphysis of the first metatarsal bone. Abnormality of the end part of the 1st long bone of foot In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities affecting the proximal phalanx of the hallux. 2009-05-29T01:17:54Z UMLS:C4024033 Abnormality of the end part of the innermost bone of the big toe HP:0010126 Abnormality of the epiphysis of the proximal phalanx of the hallux In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities affecting the proximal phalanx of the hallux. Abnormality of the end part of the innermost bone of the big toe Failure to form (agenesis) of the epiphysis of the proximal phalanx of the hallux. 2009-05-29T01:22:23Z UMLS:C4024032 Absent end part of the innermost bone of the big toe HP:0010127 Absent epiphysis of the proximal phalanx of the hallux Failure to form (agenesis) of the epiphysis of the proximal phalanx of the hallux. Absent end part of the innermost bone of the big toe 2009-05-29T01:22:23Z UMLS:C4024029 Enlarged end part of the innermost bone of the big toe HP:0010130 Enlarged epiphysis of the proximal phalanx of the hallux Enlarged end part of the innermost bone of the big toe A pseudoepiphysis (an accessory epiphysis that does not significantly contribute to the longitudinal growth of a tubular bone) located in the proximal phalanx of the big toe. 2009-05-29T01:22:23Z UMLS:C4024025 HP:0010134 Pseudoepiphysis of the proximal phalanx of the hallux 2009-05-29T01:22:23Z UMLS:C4024024 Small end part of the innermost bone of the big toe HP:0010135 Small epiphysis of the proximal phalanx of the hallux Small end part of the innermost bone of the big toe Failure to form (agenesis) of the epiphysis of the distal phalanx of the hallux. 2009-05-29T01:22:47Z UMLS:C4024021 Absent end part of the outermost bone of the big toe HP:0010138 Absent epiphysis of the distal phalanx of the hallux Failure to form (agenesis) of the epiphysis of the distal phalanx of the hallux. Absent end part of the outermost bone of the big toe 2009-05-29T01:22:47Z UMLS:C4024018 Enlarged end part of the outermost bone of the big toe HP:0010141 Enlarged epiphysis of the distal phalanx of the hallux Enlarged end part of the outermost bone of the big toe 2009-05-29T01:22:47Z UMLS:C4024014 HP:0010145 Pseudoepiphysis of the distal phalanx of the hallux 2009-05-29T01:22:47Z UMLS:C4024013 Small end part of the outermost bone of the big toe HP:0010146 Small epiphysis of the distal phalanx of the hallux Small end part of the outermost bone of the big toe Failure to form (agenesis) of the epiphysis of the 1st metatarsal. 2009-05-29T01:24:17Z UMLS:C4024010 Absent end part of the 1st long bone of foot HP:0010149 Absent epiphysis of the 1st metatarsal Failure to form (agenesis) of the epiphysis of the 1st metatarsal. Absent end part of the 1st long bone of foot 2009-05-29T01:24:17Z UMLS:C4024007 Enlarged end part of the 1st long bone of foot HP:0010152 Enlarged epiphysis of the 1st metatarsal Enlarged end part of the 1st long bone of foot 2009-05-29T01:24:17Z UMLS:C4024003 HP:0010156 Pseudoepiphysis of the 1st metatarsal 2009-05-29T01:24:17Z UMLS:C4024002 Small end part of the 1st long bone of foot HP:0010157 Small epiphysis of the 1st metatarsal Small end part of the 1st long bone of foot 2009-05-29T01:30:42Z UMLS:C4023999 Abnormality of the end part of the toe bones Abnormality of the epiphyses of the toes HP:0010160 Abnormal toe epiphysis morphology Abnormality of the end part of the toe bones 2009-05-29T01:31:17Z UMLS:C4023998 Abnormality of the long bones of the toes Abnormality of the phalanges of the toes HP:0010161 Abnormal toe phalanx morphology Abnormality of the long bones of the toes Absence of the epiphyses of the phalanges of the toes. 2009-05-29T01:34:06Z UMLS:C4023997 Absent end part of the toe bones HP:0010162 Absent epiphyses of the toes Absence of the epiphyses of the phalanges of the toes. Absent end part of the toe bones 2009-05-29T01:34:06Z UMLS:C4023994 Enlarged end part of the toe bones HP:0010165 Enlarged epiphyses of the toes Enlarged end part of the toe bones 2009-05-29T01:34:06Z UMLS:C4023990 HP:0010169 Pseudoepiphyses of the toes 2009-05-29T01:34:06Z UMLS:C4023989 Small end part of the toe bones HP:0010170 Small epiphyses of the toes Small end part of the toe bones 2009-05-29T01:39:26Z UMLS:C4023987 Absent/small toe bones Absent/underdeveloped toe bones HP:0010173 Aplasia/Hypoplasia of the phalanges of the toes Absent/small toe bones Absent/underdeveloped toe bones Partial/complete duplication of one or more phalanx of toe. 2009-05-29T01:39:26Z UMLS:C4021328 Duplicated toe bone Partial/complete duplication of the phalanges of the toes HP:0010181 Duplication of phalanx of toe Partial/complete duplication of one or more phalanx of toe. Duplicated toe bone 2009-05-29T01:51:38Z UMLS:C4023982 Abnormality of the outermost bone of the toes HP:0010182 Abnormality of the distal phalanges of the toes Abnormality of the outermost bone of the toes 2009-05-29T01:51:38Z UMLS:C4023981 Abnormal middle bones of toe HP:0010183 Abnormality of the middle phalanges of the toes Abnormal middle bones of toe A morphological anomaly of one or more proximal phalanges of one or more toes. 2009-05-29T01:51:38Z UMLS:C4021327 Abnormal innermost toe bone Abnormality of the proximal phalanges of the toes HP:0010184 Abnormality of toe proximal phalanx A morphological anomaly of one or more proximal phalanges of one or more toes. Abnormal innermost toe bone Absence or underdevelopment of the distal phalanges of the toes. 2009-05-29T01:52:41Z HP:0005735 HP:0005818 UMLS:C4020773 UMLS:C4021326 Absent/hypoplastic terminal phalanges of toes Absent/small outermost bones of toe Absent/underdeveloped outermost bones of toe Hypoplasia/agenesis of distal phalanges of toes HP:0010185 Aplasia/Hypoplasia of the distal phalanges of the toes Absence or underdevelopment of the distal phalanges of the toes. Absent/small outermost bones of toe Absent/underdeveloped outermost bones of toe A partial or complete duplication of one or more distal phalanx of toe. 2009-05-29T01:52:41Z UMLS:C4021322 Duplication of outermost bone of toe Partial/complete duplication of the distal phalanges of the toes HP:0010193 Duplication of distal phalanx of toe A partial or complete duplication of one or more distal phalanx of toe. Duplication of outermost bone of toe 2009-05-29T01:53:35Z UMLS:C4023976 Absent/small middle bones of toe Absent/underdeveloped middle bones of toe HP:0010194 Aplasia/Hypoplasia of the middle phalanges of the toes Absent/small middle bones of toe Absent/underdeveloped middle bones of toe Partial or complete duplication of a middle phalanx of toe. 2009-05-29T01:53:35Z UMLS:C4021318 Partial/complete duplication of the middle bones of the toes Partial/complete duplication of the middle phalanges of the toes HP:0010202 Duplication of middle phalanx of toe Partial or complete duplication of a middle phalanx of toe. Partial/complete duplication of the middle bones of the toes Absence (agenesis) or underdevelopment of the proximal phalanx of the toe. 2009-05-29T01:54:18Z UMLS:C4021317 Absent/small innermost toe bones Absent/underdeveloped innermost toe bones Aplasia/Hypoplasia of the proximal phalanges of the toes HP:0010203 Aplasia/hypoplasia of proximal toe phalanx Absence (agenesis) or underdevelopment of the proximal phalanx of the toe. Absent/small innermost toe bones Absent/underdeveloped innermost toe bones Partial/complete duplication of a proximal phalanx of toe. 2009-05-29T01:54:18Z UMLS:C4021312 Duplication of innermost toe bones Partial/complete duplication of the proximal phalanges of the toes HP:0010211 Duplication of proximal phalanx of toe Partial/complete duplication of a proximal phalanx of toe. Duplication of innermost toe bones One or more bent (flexed) joints of the first (big) toe that cannot be straightened actively or passively. 2009-06-02T01:39:18Z UMLS:C4021311 Joint contracture of the big toe Joint contracture of the hallux HP:0010212 Flexion contracture of the hallux One or more bent (flexed) joints of the first (big) toe that cannot be straightened actively or passively. Joint contracture of the big toe Chronic loss of joint motion in the tarsometatarsal joint of the hallux due to structural changes in non-bony tissue. The tarsometatarsal joints of the feet are also called Lisfranc's joints. 2009-06-02T01:45:34Z UMLS:C4023968 HP:0010213 Contracture of the tarsometatarsal joint of the hallux Chronic loss of joint motion in the tarsometatarsal joint of the hallux due to structural changes in non-bony tissue. The tarsometatarsal joints of the feet are also called Lisfranc's joints. The interphalangeal joint of the big toe cannot be straightened actively or passively. 2009-06-02T01:45:34Z UMLS:C4023967 HP:0010214 Contracture of the interphalangeal joint of the hallux The interphalangeal joint of the big toe cannot be straightened actively or passively. The joint between the first metatarsal and the proximal phalanx of the first (big) toe cannot be straightened actively or passively. 2009-06-02T01:45:34Z UMLS:C4023966 HP:0010215 Contractures of the metatarsophalangeal joint of the hallux The joint between the first metatarsal and the proximal phalanx of the first (big) toe cannot be straightened actively or passively. Any abnormality of the epiphysis of the fifth metacarpal bone. 2009-07-02T04:13:00Z UMLS:C4023958 Abnormality of the end part of the long bone of little finger Abnormality of the end part of the long bone of pinkie finger Abnormality of the end part of the long bone of pinky finger HP:0010226 Abnormality of the epiphysis of the 5th metacarpal Any abnormality of the epiphysis of the fifth metacarpal bone. Abnormality of the end part of the long bone of little finger Abnormality of the end part of the long bone of pinkie finger Abnormality of the end part of the long bone of pinky finger Absence of one or more epiphyses of the phalanges of the fingers. 2009-07-06T03:31:52Z HP:0009359 UMLS:C4021310 Absent end part of fingers Absent epiphyses of the fingers HP:0010228 Absent epiphyses of the phalanges of the hand Absence of one or more epiphyses of the phalanges of the fingers. Absent end part of fingers Abnormally large size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. 2009-07-06T03:31:52Z HP:0006023 HP:0009362 UMLS:C1865036 Enlarged end part of finger bones Enlarged epiphyses of the fingers Enlarged phalangeal epiphyses HP:0010231 Enlarged epiphyses of the phalanges of the hand Abnormally large size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. Enlarged end part of finger bones A secondary ossification center in the phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-07-06T03:31:52Z HP:0009366 UMLS:C4021306 Pseudoepiphysis of the fingers HP:0010235 Pseudoepiphyses of the phalanges of the hand A secondary ossification center in the phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. Abnormally small size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. 2009-07-06T03:31:52Z HP:0009367 UMLS:C4021305 Small end part of finger bones Small epiphyses of the fingers HP:0010236 Small epiphyses of the phalanges of the hand Abnormally small size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. Small end part of finger bones Congenital hypoplasia of one or more proximal phalanx of finger. 2009-07-06T04:00:44Z HP:0005670 HP:0006138 UMLS:C1860606 Hypoplasia of the proximal phalanges of the hand Short innermost finger bones Short proximal phalanges Short proximal phalanx of finger Shortening in proximal phalanges HP:0010241 Short proximal phalanx of finger Congenital hypoplasia of one or more proximal phalanx of finger. Short innermost finger bones Short proximal phalanx of finger Any anomaly of distal epiphysis of phalanx of finger. 2009-07-06T04:21:32Z UMLS:C4023956 Abnormality of the end part of the outermost bone of finger HP:0010243 Abnormality of the epiphyses of the distal phalanx of finger Any anomaly of distal epiphysis of phalanx of finger. Abnormality of the end part of the outermost bone of finger 2009-07-06T04:21:32Z UMLS:C4023955 Abnormality of the end part of the middle hand bones HP:0010244 Abnormality of the epiphyses of the middle phalanges of the hand Abnormality of the end part of the middle hand bones 2009-07-06T04:21:32Z UMLS:C4023954 Abnormality of the end part of the innermost hand bones HP:0010245 Abnormality of the epiphyses of the proximal phalanges of the hand Abnormality of the end part of the innermost hand bones 2009-07-06T04:23:06Z UMLS:C4023953 Absent end part of the outermost hand bones HP:0010246 Absent epiphyses of the distal phalanges of the hand Absent end part of the outermost hand bones 2009-07-06T04:23:06Z UMLS:C4023950 Enlarged end part of the outermost hand bones HP:0010249 Enlarged epiphyses of the distal phalanges of the hand Enlarged end part of the outermost hand bones A secondary ossification center in the distal phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-07-06T04:23:06Z UMLS:C4023947 HP:0010253 Pseudoepiphyses of the distal phalanges of the hand 2009-07-06T04:23:06Z UMLS:C4023946 Small end part of the outermost hand bones HP:0010254 Small epiphyses of the distal phalanges of the hand Small end part of the outermost hand bones 2009-07-06T04:24:15Z UMLS:C4023943 Absent end part of the middle hand bones HP:0010257 Absent epiphyses of the middle phalanges of the hand Absent end part of the middle hand bones 2009-07-06T04:24:15Z UMLS:C4023941 Enlarged end part of the middle hand bones HP:0010260 Enlarged epiphyses of the middle phalanges of the hand Enlarged end part of the middle hand bones A secondary ossification center in the middle phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-07-06T04:24:15Z UMLS:C4023937 HP:0010264 Pseudoepiphyses of the middle phalanges of the hand 2009-07-06T04:24:15Z UMLS:C4023936 Small end part of the middle hand bones HP:0010265 Small epiphyses of the middle phalanges of the hand Small end part of the middle hand bones 2009-07-06T04:25:12Z UMLS:C4023933 Absent end part of the innermost hand bones HP:0010268 Absent epiphyses of the proximal phalanges of the hand Absent end part of the innermost hand bones 2009-07-06T04:25:12Z UMLS:C4023930 Enlarged end part of the innermost hand bones HP:0010271 Enlarged epiphyses of the proximal phalanges of the hand Enlarged end part of the innermost hand bones A secondary ossification center in the proximal phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-07-06T04:25:12Z UMLS:C4023926 HP:0010275 Pseudoepiphyses of the proximal phalanges of the hand A secondary ossification center in the proximal phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. 2009-07-06T04:25:12Z UMLS:C4023925 Small end part of the innermost hand bones HP:0010276 Small epiphyses of the proximal phalanges of the hand Small end part of the innermost hand bones Stomatitis is an inflammation of the mucous membranes of any of the structures in the mouth. 2009-07-12T09:48:56Z MSH:D013280 SNOMEDCT_US:20607006 SNOMEDCT_US:61170000 UMLS:C0038362 UMLS:C0149704 Inflammation of the mouth Gingivostomatitis HP:0010280 Stomatitis Stomatitis is an inflammation of the mucous membranes of any of the structures in the mouth. Inflammation of the mouth Gingivostomatitis A gap in the lower lip. 2009-07-12T09:50:34Z UMLS:C1856026 Cleft lower lip Cleft of the lower lip Lower labial cleft HP:0010281 Cleft lower lip A gap in the lower lip. Cleft lower lip Cleft of the lower lip Lower labial cleft Any abnormality of the salivary glands, the exocrine glands that produce saliva. 2009-07-12T10:38:51Z MSH:D012466 SNOMEDCT_US:10890000 UMLS:C0036093 UMLS:C0149772 Abnormality of the salivary glands Salivary gland disease HP:0010286 Abnormal salivary gland morphology Any abnormality of the salivary glands, the exocrine glands that produce saliva. Abnormality of the salivary glands Salivary gland disease Any abnormality of the submandibular glands, which are the salivary glands that are located beneath the floor of the mouth, superior to the digastric muscles. 2009-07-12T10:41:17Z UMLS:C4023920 Abnormality of the submaxillary glands HP:0010287 Abnormality of the submandibular glands Any abnormality of the submandibular glands, which are the salivary glands that are located beneath the floor of the mouth, superior to the digastric muscles. Abnormality of the submaxillary glands A gap (cleft) affecting one of the alveolar ridges, which are the protuberances in the mouth that contain the sockets (alveoli) of the teeth. An alveolar cleft can affect all structures of the alveolar ridge, including the gingiva, other mucosa, periosteum, alveolar bone, and teeth. Alveolar cleft occurs in response to divergence from normal development during frontonasal prominence growth, contact, and fusion. The most common alveolar portion of the cleft is located between the lateral incisor and the canine. 2009-07-12T10:47:29Z HP:0410003 SNOMEDCT_US:445306000 UMLS:C1398533 UMLS:C2919907 UMLS:C4280386 Alveolar cleft Alveolar ridge cleft Cleft anterior maxilla Cleft maxillary alveolus Cleft of alveolar ridge of maxilla Cleft of gum ridge Notch of alveolar ridge Notch of gum ridge Cleft of alveolar process Notch of alveolar process HP:0010289 The palate develops from the frontonasal and maxillary prominences between 4 and 12 weeks of gestation. During gestational weeks 4 to 7, the primary palate originates from the median palatine process, which itself originated from frontonasal prominence. The lip, alveolus, and hard palate anterior to the incisive foramen all share this origin in development. During this period, disruptions of palatal development process can result in primary palate clefting. The secondary palate develops from the lateral palatine processes originating from the maxillary prominences between 7 and 12 weeks, and the hard palate posterior to incisive foramen and the soft palate are developmental products of this process. As such, disruptions during this time will result in secondary palate clefts. The alveolus is a component of the primary palate, and alveolar cleft results from mal-development of the frontonasal prominence. As such, it is most closely related to cleft lip and cleft palate. Generally, alveolar clefts are located between the lateral incisor and canine. Cleft maxillary alveolar ridge A gap (cleft) affecting one of the alveolar ridges, which are the protuberances in the mouth that contain the sockets (alveoli) of the teeth. An alveolar cleft can affect all structures of the alveolar ridge, including the gingiva, other mucosa, periosteum, alveolar bone, and teeth. Alveolar cleft occurs in response to divergence from normal development during frontonasal prominence growth, contact, and fusion. The most common alveolar portion of the cleft is located between the lateral incisor and the canine. HPO_CONTRIBUTOR:mengelstad Cleft anterior maxilla Cleft of gum ridge Notch of alveolar ridge Notch of gum ridge Cleft of alveolar process Notch of alveolar process Absence or underdevelopment of the tongue. 2009-07-12T11:41:04Z UMLS:C4023916 UMLS:C4280384 Lingual aplasia/hypoplasia HP:0010295 Aplasia/Hypoplasia of the tongue Absence or underdevelopment of the tongue. Lingual aplasia/hypoplasia Tongue with a median apical indentation or fork. 2009-07-12T11:47:28Z SNOMEDCT_US:84557007 UMLS:C0266111 UMLS:C4255098 Bifurcated tongue Bilobed tongue Cleft tongue Forked tongue Split tongue Snake tongue HP:0010297 Bifid tongue can be associated with ankyloglossia, but this should be assessed and coded separately. Small indentations of the tip of the tongue should not be coded as a bifid tongue. Bifid tongue Tongue with a median apical indentation or fork. PMID:19125428 Bifurcated tongue Cleft tongue Forked tongue Split tongue Snake tongue Any abnormality of dentin. 2009-07-12T12:11:14Z UMLS:C4021299 Abnormal dentin Abnormality of dentin Abnormality of dentine Dentin anomaly HP:0010299 Dentin is a calcified tissue of teeth that is covered by enamel on the crown and cementum on the root and surrounds the entire pulp. Abnormal dentin morphology Any abnormality of dentin. Abnormal dentin Abnormality of dentin Abnormality of dentine A heterogeneous group of congenital spinal anomalies that result from defective closure of the neural tube early in fetal life. 2009-07-12T12:58:04Z MSH:D009436 SNOMEDCT_US:253098009 UMLS:C0027794 Incomplete closure of the vertebral arch HP:0010301 Spinal dysraphism, or neural tube defect comprises a heterogeneous group of congenital spinal anomalies that result from defective closure of the neural tube early in fetal life and anomalous development of the caudal cell mass. The anatomic features common to the entire group is an anomaly in the midline structures of the back, especially the absence of some of the neural arches, and defects of the skin, filum terminale, nerves, and spinal cord. Open forms of spinal dysraphism include myelocele, meningocele, and myelomeningocele. These open forms are often associated with hydrocephalus and Arnold-Chiari malformation type II and may be classified as spina bifida aperta. Closed forms of spinal dysraphism includ spina bifida occulta. Spinal dysraphism A heterogeneous group of congenital spinal anomalies that result from defective closure of the neural tube early in fetal life. Incomplete closure of the vertebral arch Any abnormality of the spinal meninges, the system of membranes (dura mater, the arachnoid mater, and the pia mater) which envelops the spinal cord. 2009-07-12T01:10:09Z UMLS:C4023914 Abnormality of the spinal meninges HP:0010303 Abnormal spinal meningeal morphology Any abnormality of the spinal meninges, the system of membranes (dura mater, the arachnoid mater, and the pia mater) which envelops the spinal cord. An outpouching of the spinal meninges. 2009-07-12T01:11:53Z UMLS:C4023913 HP:0010304 Spinal meningeal diverticulum An outpouching of the spinal meninges. Absence (aplasia) of the sacrum. 2009-07-12T01:13:26Z Sacrococcygeal agenesis MSH:C537221 SNOMEDCT_US:205425003 UMLS:C0344490 Absent sacrum Sacral agenesis HP:0010305 Absence of the sacrum Absence (aplasia) of the sacrum. Reduced inferior to superior extent of the thorax. 2009-07-12T02:13:42Z SNOMEDCT_US:249670005 UMLS:C0426789 Shorter than typical length between neck and abdomen HP:0010306 Short thorax Reduced inferior to superior extent of the thorax. Shorter than typical length between neck and abdomen The congenital absence of the sternum. 2009-07-12T02:21:46Z UMLS:C4023912 Aplasia of the sternum Breast bone aplasia HP:0010308 Asternia The congenital absence of the sternum. PMID:3424262 Absence or underdevelopment of the breasts. 2009-07-12T02:31:49Z UMLS:C4023911 Absent/small breasts Absent/underdeveloped breasts HP:0010311 Aplasia/Hypoplasia of the breasts Absence or underdevelopment of the breasts. Absent/small breasts Absent/underdeveloped breasts The presence of hypertrophy of the breast. 2009-07-12T02:34:30Z MSH:C536821 SNOMEDCT_US:372281005 SNOMEDCT_US:372283008 SNOMEDCT_US:372285001 UMLS:C0020565 UMLS:C0392533 UMLS:C2225524 Breast enlargement Breasts enlarged Gigantomastia Hypertrophy of the breasts Large breast Macromastia HP:0010313 Breast hypertrophy The presence of hypertrophy of the breast. Breast enlargement Breasts enlarged Gigantomastia Hypertrophy of the breasts Large breast Macromastia Absence or underdevelopment of the diaphragm. 2009-07-12T02:41:58Z UMLS:C4023910 Absent/small diaprhagm Absent/underdeveloped diaprhagm HP:0010315 Aplasia/Hypoplasia of the diaphragm Absence or underdevelopment of the diaphragm. Absent/small diaprhagm Absent/underdeveloped diaprhagm Absence or underdevelopment of the abdominal musculature. 2009-07-14T11:51:46Z UMLS:C4023909 Absent/small abdominal wall muscles Absent/underdeveloped abdominal wall muscles HP:0010318 Aplasia/Hypoplasia of the abdominal wall musculature Absence or underdevelopment of the abdominal musculature. Absent/small abdominal wall muscles Absent/underdeveloped abdominal wall muscles An anomaly of the little toe. 2009-07-16T11:37:12Z UMLS:C4023905 Abnormal 5th toe morphology Abnormality of the 5th toe Abnormality of the little toe Abnormality of the pinkie toe Abnormality of the pinky toe HP:0010322 Abnormal fifth toe morphology An anomaly of the little toe. Abnormality of the little toe Abnormality of the pinkie toe Abnormality of the pinky toe 2009-07-16T11:41:49Z UMLS:C4023893 Abnormality of the end part of the little toe bone Abnormality of the end part of the pinkie toe bone Abnormality of the end part of the pinky toe bone HP:0010341 Abnormality of the epiphyses of the 5th toe Abnormality of the end part of the little toe bone Abnormality of the end part of the pinkie toe bone Abnormality of the end part of the pinky toe bone 2009-07-16T11:41:49Z UMLS:C4023892 Abnormality of the little toe bones Abnormality of the pinkie toe bones Abnormality of the pinky toe bones HP:0010342 Abnormality of the phalanges of the 5th toe Abnormality of the little toe bones Abnormality of the pinkie toe bones Abnormality of the pinky toe bones 2009-07-16T11:41:49Z UMLS:C4023891 Absent/small little toe Absent/small pinkie toe Absent/small pinky toe Absent/underdeveloped pinky toe HP:0010343 Aplasia/Hypoplasia of the 5th toe Absent/small little toe Absent/small pinkie toe Absent/small pinky toe Absent/underdeveloped pinky toe 2009-07-16T11:41:49Z UMLS:C4021291 Displacement of the 5th toe Displacement of the little toe Displacement of the pinkie toe Displacement of the pinky toe HP:0010344 Deviation of the 5th toe Displacement of the little toe Displacement of the pinkie toe Displacement of the pinky toe One or more bent (flexed) joints of the fifth toe that cannot be straightened actively or passively. 2009-07-16T11:41:49Z UMLS:C4021290 Joint contractures of the 5th toe HP:0010345 Flexion contracture of the 5th toe One or more bent (flexed) joints of the fifth toe that cannot be straightened actively or passively. Joint contractures of the 5th toe 2009-07-16T11:52:18Z UMLS:C4023867 Absent/small little toe bones Absent/small pinkie toe bones Absent/small pinky toe bones Absent/underdeveloped pinky toe bones HP:0010383 Aplasia/Hypoplasia of the phalanges of the 5th toe Absent/small little toe bones Absent/small pinkie toe bones Absent/small pinky toe bones Absent/underdeveloped pinky toe bones Partial or complete duplication of one or more phalanx of little toe. 2009-07-16T11:52:18Z UMLS:C4020903 Duplication of the bones of the little toe Duplication of the bones of the pinkie toe Duplication of the bones of the pinky toe Duplication of the phalanges of the fifth toe Partial/complete duplication of the phalanges of the 5th toe HP:0010391 Duplication of the phalanges of the 5th toe Partial or complete duplication of one or more phalanx of little toe. Duplication of the bones of the little toe Duplication of the bones of the pinkie toe Duplication of the bones of the pinky toe 2009-07-16T11:52:18Z UMLS:C4023862 Abnormality of the outermost bone of the little toe Abnormality of the outermost bone of the pinkie toe Abnormality of the outermost bone of the pinky toe HP:0010392 Abnormality of the distal phalanx of the 5th toe Abnormality of the outermost bone of the little toe Abnormality of the outermost bone of the pinkie toe Abnormality of the outermost bone of the pinky toe 2009-07-16T11:52:18Z UMLS:C4023861 Abnormality of the middle bone of the little toe Abnormality of the middle bone of the pinkie toe Abnormality of the middle bone of the pinky toe HP:0010393 Abnormality of the middle phalanx of the 5th toe Abnormality of the middle bone of the little toe Abnormality of the middle bone of the pinkie toe Abnormality of the middle bone of the pinky toe 2009-07-16T11:52:18Z UMLS:C4023860 Abnormality of the innermost bone of the little toe Abnormality of the innermost bone of the pinkie toe Abnormality of the innermost bone of the pinky toe HP:0010394 Abnormal morphology of the proximal phalanx of the 5th toe Abnormality of the innermost bone of the little toe Abnormality of the innermost bone of the pinkie toe Abnormality of the innermost bone of the pinky toe A structural abnormality of the interventricular septum. 2009-07-27T11:59:56Z HP:0001628 Fyler:1815 UMLS:C4021264 Abnormal interventricular septum morphology Abnormality of the ventricular septum Ventricular septum abnormality HP:0010438 Abnormal ventricular septum morphology A structural abnormality of the interventricular septum. Abnormal interventricular septum morphology A congenital anomaly characterized by the presence of supernumerary fingers or toes. 2009-07-29T01:39:27Z HP:0006034 HP:0006046 HP:0006123 HP:0009605 Fyler:4103 MSH:D017689 SNOMEDCT_US:367506006 UMLS:C0152427 More than five fingers or toes on hands or feet HP:0010442 Polydactyly A congenital anomaly characterized by the presence of supernumerary fingers or toes. More than five fingers or toes on hands or feet A bifid or bifurcated appearance of the femur as seen on x-rays, possible appearing as a more or less severe bowing of the upper leg. Might be associated with hip dysplasia on the affected side. 2009-07-29T04:29:30Z UMLS:C4023824 Notched thighbone Split thighbone HP:0010443 Bifid femur A bifid or bifurcated appearance of the femur as seen on x-rays, possible appearing as a more or less severe bowing of the upper leg. Might be associated with hip dysplasia on the affected side. Notched thighbone Split thighbone Absence or underdevelopment of the spleen. 2009-09-14T10:48:29Z UMLS:C4023823 Absent/small spleen Absent/underdeveloped spleen HP:0010451 Aplasia/Hypoplasia of the spleen Absence or underdevelopment of the spleen. Absent/small spleen Absent/underdeveloped spleen Abnormality of the female genital system. 2009-09-15T08:32:09Z UMLS:C4023820 HP:0010460 Abnormality of the female internal or external genitalia. Abnormality of the female genitalia Abnormality of the female genital system. Abnormality of the male genital system. 2009-09-15T08:33:20Z UMLS:C4023819 Abnormal male genitals Abnormality of the male genitalia HP:0010461 Abnormality of the male genitalia Abnormality of the male genital system. Abnormal male genitals Abnormality of the male genitalia Aplasia or developmental hypoplasia of the ovary. 2009-09-15T08:38:35Z UMLS:C4023818 Absent/small ovary Absent/underdeveloped ovary HP:0010462 Aplasia/Hypoplasia of the ovary Aplasia or developmental hypoplasia of the ovary. Absent/small ovary Absent/underdeveloped ovary Absence or underdevelopment of the testes. 2009-09-15T09:28:46Z UMLS:C4023817 Absent/small testes Absent/underdeveloped testes HP:0010468 Aplasia/Hypoplasia of the testes Absence or underdevelopment of the testes. Absent/small testes Absent/underdeveloped testes The presence of more than two testes. 2009-09-15T09:34:18Z SNOMEDCT_US:17471001 UMLS:C0266430 Extra testes Polyorchidism HP:0010470 Supernumerary testes The presence of more than two testes. Extra testes Increased urinary excretion of oligosaccharides (low molecular weight carbohydrate chains composed of at least three monosaccharide subunits), derived from a partial degradation of glycoproteins. 2009-09-15T09:48:34Z UMLS:C4023815 HP:0010471 Oligosacchariduria Increased urinary excretion of oligosaccharides (low molecular weight carbohydrate chains composed of at least three monosaccharide subunits), derived from a partial degradation of glycoproteins. Abnormally increased excretion of porphyrins in the urine. 2009-09-15T09:57:34Z SNOMEDCT_US:44574006 UMLS:C0151861 HP:0010473 Porphyrins are natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure. One of the best-known porphyrins is heme. Porphyrinuria Abnormally increased excretion of porphyrins in the urine. Absence or underdevelopment of the urinary bladder. 2009-09-15T10:09:48Z UMLS:C4023813 Absent/small bladder Absent/underdeveloped bladder HP:0010476 Aplasia/Hypoplasia of the bladder Absence or underdevelopment of the urinary bladder. Absent/small bladder Absent/underdeveloped bladder Abnormal increase in size of the upper limbs (due to an increase of the size of cells). 2009-09-16T09:23:57Z SNOMEDCT_US:298745009 UMLS:C0575518 Increased size of upper limb HP:0010484 Hypertrophy of the upper limb Abnormal increase in size of the upper limbs (due to an increase of the size of cells). Increased size of upper limb An abnormally increased length of the metacarpal bones. 2009-09-17T10:25:37Z UMLS:C4021260 Elongated long bone of hand Increased length of metacarpals HP:0010493 Long metacarpals An abnormally increased length of the metacarpal bones. Elongated long bone of hand Abnormal increase in size of the lower limbs (due to an increase of the size of cells). 2009-09-17T11:08:38Z UMLS:C4023803 HP:0010496 Hypertrophy of the lower limb Abnormal increase in size of the lower limbs (due to an increase of the size of cells). The ability of the knee joint to extend beyond its normal range of motion (the lower leg is moved beyond a straight position with respect to the thigh). 2009-09-19T09:44:04Z UMLS:C4023802 HP:0010500 Hyperextensibility of the knee The ability of the knee joint to extend beyond its normal range of motion (the lower leg is moved beyond a straight position with respect to the thigh). Duplication of the fibula. This may occur as a part of diplopodia (accessory tarsal or metatarsal bone). Diplopodia with double fibula is an extremely rare condition. 2009-09-19T09:45:58Z UMLS:C3276742 Duplicated calf bone HP:0010503 Fibular duplication Duplication of the fibula. This may occur as a part of diplopodia (accessory tarsal or metatarsal bone). Diplopodia with double fibula is an extremely rare condition. Duplicated calf bone An abnormal increase in the length of the tibia. 2009-09-19T09:46:37Z UMLS:C4021864 Increased length of shankbone Increased length of shinbone HP:0010504 Increased length of the tibia An abnormal increase in the length of the tibia. Increased length of shankbone Increased length of shinbone An ability of the toe joints to move beyond their normal range of motion. 2009-09-19T10:15:12Z UMLS:C4023798 HP:0010510 Hypermobility of toe joints An ability of the toe joints to move beyond their normal range of motion. Toes that appear disproportionately long compared to the foot. 2009-09-19T10:40:43Z UMLS:C3150613 Increased length of toes Long toe Long toes HP:0010511 This finding must be distinguished from digits that are thin but of normal length and that of a short mid and hind foot with normal digit lengths. The affected digits should be specified. If only a subset of the digits of a limb is lengthened, the affected digits should be specified. Long toe Toes that appear disproportionately long compared to the foot. PMID:19125433 Increased length of toes Long toe Long toes Calcification within the adrenal glands. 2009-09-19T03:34:26Z SNOMEDCT_US:12286000 UMLS:C0271750 HP:0010512 This condition may occur in a wide variety of pathologies, some serious and some with no obvious consequence. Adrenal hemorrhage may be detected as an incidental finding in children in radiographic studies of the abdomen. Etiologies include hemorrhage into the adrenals at or immediately after birth, neuroblastoma, ganglioneuroblastoma, cortical carcinoma, pheochromocytoma, and cysts. Adrenal calcification Calcification within the adrenal glands. Deposition of calcium salts in the pituitary gland. 2009-09-19T04:09:21Z UMLS:C4023797 HP:0010513 Pituitary calcification Deposition of calcium salts in the pituitary gland. Hypersecretion of one or more pituitary hormones. This can occur in conditions in which deficiency in the target organ leads to decreased hormonal feedback, or as a primary condition most usually in connection with a pituitary adenoma. 2009-09-19T04:14:54Z MSH:D006964 SNOMEDCT_US:10649000 UMLS:C0020506 HP:0010514 Hyperpituitarism Hypersecretion of one or more pituitary hormones. This can occur in conditions in which deficiency in the target organ leads to decreased hormonal feedback, or as a primary condition most usually in connection with a pituitary adenoma. Absence or underdevelopment of the thymus. 2009-09-19T04:21:24Z UMLS:C3278004 UMLS:C4023796 Absent/small thymus Absent/underdeveloped thymus Thymic hypoplasia or aplasia HP:0010515 Aplasia/Hypoplasia of the thymus Absence or underdevelopment of the thymus. Absent/small thymus Absent/underdeveloped thymus Thymic hypoplasia or aplasia An abnormal elevation of phytanic acid. 2009-10-20T07:19:29Z UMLS:C4023786 Elevated level of phytanic acid Elevated levels of phytanic acid HP:0010571 Phytanic acid (3,7,11,15-tetramethyl hexadecanoic acid) is a fatty acid that is derived from chlorophyll and present in the diet. The metabolism of phytanic acid involves alpha-oxidation in the peroxisome, which converts phytanic acid to pristanic acid. Peroxisomes involved in the catabolism of very long chain fatty acids and phytanic acid. Peroxisomal malfunctioning can lead to over-accumulation of very long chain fatty acids and phytanic acid, among other things. Elevated circulating phytanic acid concentration An abnormal elevation of phytanic acid. Elevated levels of phytanic acid Any abnormality of the proximal epiphysis of the femur. sandra1 2009-10-21T01:28:23Z HP:0010589 UMLS:C4021252 Abnormality of the end part of the innermost thighbone Abnormality of the proximal femoral epiphysis HP:0010574 Note that the proximal epiphysis of the femur is often referred to as the capital femoral epiphysis from the Latin word caput for head. Abnormality of the epiphysis of the femoral head Any abnormality of the proximal epiphysis of the femur. Abnormality of the end part of the innermost thighbone The presence of developmental dysplasia of the femoral head. sandra1 2009-10-21T01:30:40Z Abnormality of femoral head development UMLS:C4021251 UMLS:C4280377 Dysplastic femoral head HP:0010575 Dysplasia of the femoral head The presence of developmental dysplasia of the femoral head. Abnormality of femoral head development sandra1 2009-10-22T02:53:19Z UMLS:C4021862 Absent end part of bone HP:0010577 Absent epiphyses Absent end part of bone Increased size of epiphyses. sandra1 2009-10-22T02:53:19Z HP:0003018 HP:0003055 HP:0005082 UMLS:C1833328 Large end part of bone Large epiphyses Widened, distorted epiphyses HP:0010580 Enlarged epiphyses Increased size of epiphyses. Large end part of bone sandra1 2009-10-22T02:53:19Z UMLS:C1841685 HP:0010584 Pseudoepiphyses Reduction in the size or volume of epiphyses. sandra1 2009-10-22T02:53:19Z HP:0005730 UMLS:C1846803 Small end part of bone HP:0010585 Small epiphyses Reduction in the size or volume of epiphyses. Small end part of bone Any abnormality of the proximal epiphysis of the tibia. sandra1 2009-10-22T03:03:04Z UMLS:C4023782 Abnormality of the end part of innermost shankbone Abnormality of the end part of innermost shinbone HP:0010591 Abnormality of the proximal tibial epiphysis Any abnormality of the proximal epiphysis of the tibia. Abnormality of the end part of innermost shankbone Abnormality of the end part of innermost shinbone sandra1 2009-10-22T03:03:34Z UMLS:C4023780 Abnormality of fibular epiphyses Abnormality of the end part of the calf bone HP:0010593 Abnormal fibular epiphysis morphology Abnormality of the end part of the calf bone Any abnormality of the proximal epiphysis of the fibula. sandra1 2009-10-22T03:04:39Z UMLS:C4023779 Abnormality of the innermost end part of calf bone HP:0010594 Abnormality of the proximal fibular epiphysis Any abnormality of the proximal epiphysis of the fibula. Abnormality of the innermost end part of calf bone Any abnormality of the proximal epiphysis of the humerus. sandra1 2009-10-22T06:40:29Z UMLS:C4023775 Abnormality of the end part of the innermost long bone in upper arm HP:0010598 Abnormality of the proximal humeral epiphysis Any abnormality of the proximal epiphysis of the humerus. Abnormality of the end part of the innermost long bone in upper arm A tumor (abnormal growth of tissue) of the skeleton. 2010-06-25T08:54:46Z NCIT:C3262 SNOMEDCT_US:442868003 UMLS:C2732838 UMLS:C4020771 Skeletal tumor Skeletal tumour Neoplasia of the skeletal system Bone neoplasm HP:0010622 Neoplasm of the skeletal system A tumor (abnormal growth of tissue) of the skeleton. Skeletal tumor Skeletal tumour Absence or underdevelopment of the anterior pituitary gland, also known as the adenohypophysis. 2009-12-05T03:03:17Z MSH:D010903 SNOMEDCT_US:62818001 UMLS:C0032008 UMLS:C4023771 Adenohypophysis HP:0010625 Anterior pituitary dysgenesis Absence or underdevelopment of the anterior pituitary gland, also known as the adenohypophysis. Adenohypophysis Underdevelopment of the anterior pituitary gland. 2009-12-05T03:04:48Z HP:0008238 UMLS:C0948740 UMLS:C1859775 Small anterior pituitary lobe Underdeveloped pituitary gland Hypoplasia of the pituitary gland HP:0010627 Anterior pituitary hypoplasia Underdevelopment of the anterior pituitary gland. Underdeveloped pituitary gland Any abnormality of a metatarsal bone epiphysis. 2009-12-06T05:58:36Z UMLS:C4021248 Abnormality of end part of long bone of foot Abnormality of metatarsal epiphysis Abnormality of the epiphyses of the metatarsals HP:0010630 Abnormal metatarsal epiphysis morphology Any abnormality of a metatarsal bone epiphysis. Abnormality of end part of long bone of foot Any abnormality of the epiphyses of the feet. 2009-12-06T06:00:04Z UMLS:C4023769 Abnormality of the end part of the foot bone HP:0010631 Abnormality of the epiphyses of the feet Any abnormality of the epiphyses of the feet. Abnormality of the end part of the foot bone Abnormality of the nasal cavity (the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures). 2009-12-17T04:56:17Z UMLS:C4023763 HP:0010640 Abnormality of the nasal cavity Abnormality of the nasal cavity (the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures). Any abnormal increase or reduction in skin elasticity. 2010-02-23T11:42:34Z UMLS:C4023760 HP:0010647 Abnormal elasticity of skin Any abnormal increase or reduction in skin elasticity. An abnormal degree of flatness of the Ala of nose, which can be defined as a reduced nasal elevation index (lateral depth of the nose from the tip of the nose to the insertion of the nasal ala in the cheek x 100 divided by the side-to-side breadth of the nasal alae). 2010-02-25T10:01:47Z UMLS:C4023759 Depressed nasal alae Flat nasal alar cartilage HP:0010649 Flat nasal alae An abnormal degree of flatness of the Ala of nose, which can be defined as a reduced nasal elevation index (lateral depth of the nose from the tip of the nose to the insertion of the nasal ala in the cheek x 100 divided by the side-to-side breadth of the nasal alae). Depressed nasal alae Flat nasal alar cartilage An abnormality of the Meninges, including any abnormality of the Dura mater, the Arachnoid mater, and the Pia mater. 2010-02-25T10:19:40Z UMLS:C4023758 Abnormality of the meninges HP:0010651 Abnormal meningeal morphology An abnormality of the Meninges, including any abnormality of the Dura mater, the Arachnoid mater, and the Pia mater. An abnormality of the Dura mater. 2010-02-25T10:29:40Z UMLS:C4023757 Abnormality of the dura mater HP:0010652 Abnormal dura mater morphology An abnormality of the Dura mater. An abnormality of the formation and mineralization of an epiphysis. 2010-02-25T09:43:04Z UMLS:C4021246 Abnormality of the mineralisation or ossification of the epiphyses Abnormal maturation of the end part of a bone HP:0010656 Abnormal epiphyseal ossification An abnormality of the formation and mineralization of an epiphysis. Abnormal maturation of the end part of a bone An abnormality of the formation and mineralization of any bone of the skeleton of hand. 2010-02-25T05:18:19Z HP:0005921 UMLS:C4021244 Abnormal ossification of hand bones Abnormality of the mineralisation and ossification of bones of the hand Abnormal maturation of the hand bones HP:0010660 Abnormal hand bone ossification An abnormality of the formation and mineralization of any bone of the skeleton of hand. Abnormal maturation of the hand bones An abnormality of the Diencephalon, which together with the cerebrum (telencephalon) makes up the forebrain. 2010-02-26T08:02:38Z UMLS:C4023752 HP:0010662 The diencephalon comprises the thalamus, hypothalamus, epithalamus, prethalamus or subthalamus and pretectum. Abnormality of the diencephalon An abnormality of the Diencephalon, which together with the cerebrum (telencephalon) makes up the forebrain. The presence of an abnormal curvature of the vertebral column. sandra1 2010-02-27T06:28:19Z UMLS:C4023747 Abnormal curve of the backbone Abnormal curve of the spine Abnormal curving of the spine Abnormality of the curvature of the vertebral column Curvature of spine Curved spine HP:0010674 Abnormal curvature of the vertebral column The presence of an abnormal curvature of the vertebral column. Abnormal curve of the backbone Abnormal curve of the spine An abnormality of the formation and mineralization of any bone of the skeleton of foot. sandra1 2010-02-28T05:27:47Z HP:0008370 HP:0009133 UMLS:C4020768 UMLS:C4021241 UMLS:C4280367 Abnormality of the mineralisation and ossification of bones of the feet Abnormal maturation of foot bones Abnormal ossification involving bones of the feet HP:0010675 Abnormal foot bone ossification An abnormality of the formation and mineralization of any bone of the skeleton of foot. Abnormal maturation of foot bones An abnormal deviation from normal levels of immunoglobulins in blood. 2010-03-22T08:17:49Z HP:0100032 UMLS:C1855755 Abnormal immunoglobulin concentration Abnormal serum immunoglobulin concentration Abnormal serum immunoglobulin levels Abnormal serum level of immunoglobulin Immunoglobulin abnormality HP:0010701 'has part' some (amount and ('inheres in' some (IMR_0002090 and ('part of' some blood))) and ('has modifier' some abnormal)) Abnormal immunoglobulin level An abnormal deviation from normal levels of immunoglobulins in blood. Abnormal serum immunoglobulin levels An increased level of gamma globulin (immunoglobulin) in the blood. 2010-03-22T08:20:07Z HP:0002852 HP:0004314 HP:0004435 MSH:D006942 SNOMEDCT_US:127388009 SNOMEDCT_US:129646001 UMLS:C0020455 UMLS:C0151669 UMLS:C0541985 UMLS:C1306857 UMLS:C2048011 Elevated immunoglobulin levels Hypergammaglobulinaemia Hypergammaglobulinemia Hyperglobulinemia Increased antibody level in blood Increased gamma globulin Increased immunoglobulin level Increased serum gamma globulin Raised immunoglobulin levels HP:0010702 In humans, immunoglobulins comprise the five antibody isotypes IgA, IgD, IgE, IgG and IgM. Increased circulating antibody level An increased level of gamma globulin (immunoglobulin) in the blood. An abnormality of the texture of the hair. 2010-04-20T09:41:53Z HP:0002295 HP:0003776 UMLS:C4023722 UMLS:C4072880 UMLS:C4072881 UMLS:C4073290 Abnormality of hair texture Abnormality of hair consistency Abnormality of hair curl pattern Abnormality of hair volume HP:0010719 Abnormality of hair texture An abnormality of the texture of the hair. Abnormality of hair texture Abnormality of hair consistency Abnormality of hair curl pattern Abnormality of hair volume An abnormality of the distribution of hair growth. 2010-04-20T09:53:15Z UMLS:C4023721 Abnormal distribution of hair Abnormal hair pattern HP:0010720 Abnormal hair pattern An abnormality of the distribution of hair growth. Abnormal distribution of hair Abnormal hair pattern A developmental defect characterized by absence of the retina. 2010-04-20T11:09:59Z UMLS:C4023718 Absent retina HP:0010728 Aplasia of the retina A developmental defect characterized by absence of the retina. Absent retina Diminished length of a metatarsal bone, with resultant proximal displacement of the associated toe. 2010-04-22T04:30:18Z HP:0001779 HP:0001865 HP:0003092 HP:0004706 HP:0005754 UMLS:C1849020 Hypoplasia of the metatarsal bones Hypoplastic metatarsals Short long bone of foot Short metatarsal bone Short metatarsals Shortened metatarsals Short metatarsal bones HP:0010743 This is a subjective assessment and one generally compares the position of the MTP joint to that of the contralateral digit or the putatively shortened ray in proportion to the other rays. The affected digits should be specified. Short metatarsal Diminished length of a metatarsal bone, with resultant proximal displacement of the associated toe. PMID:19125433 Short long bone of foot Short metatarsal bones 2010-04-22T04:33:06Z UMLS:C4023715 Small toe bones HP:0010746 Hypoplasia of the phalanges of the toes Small toe bones Positioning of a lacrimal punctum other than at the medial margins of the eyelid. 2010-04-23T09:35:56Z UMLS:C4021230 Abnormal position of the lacrimal punctum HP:0010748 The openings of the tear ducts are normally located at the medial margin of each eyelid. The opening on the lower eyelid border is more visible than the opening on the upper eyelid border. Ectopic positions can include the upper eyelid, nasal bridge, or inferior to medial aspect of the lower lid. Ectopic lacrimal punctum Positioning of a lacrimal punctum other than at the medial margins of the eyelid. PMID:19125427 Aplasia of a toe. That is, absence of all phalanges of a non-hallux digit of the foot and the associated soft tissues. 2010-04-23T03:58:25Z HP:0008084 HP:0010108 HP:0011306 UMLS:C3553754 Absent toe Absent toes Aplasia of toe Aplasia of the toes HP:0010760 This descriptor does NOT require absence of the metatarsal. The definition excludes partial absent hallux. Absent toe Aplasia of a toe. That is, absence of all phalanges of a non-hallux digit of the foot and the associated soft tissues. Absent toe Absent toes Deposition of calcium salts in a tissue or location in which calcification does not normally occur. 2010-04-27T09:52:59Z UMLS:C3806226 HP:0010766 Ectopic calcification Deposition of calcium salts in a tissue or location in which calcification does not normally occur. The presence of an abnormally large pelvis. 2010-04-29T11:03:39Z Large pelvis UMLS:C4019074 UMLS:C4072882 Large pelvis bone HP:0010779 Large pelvis bone The presence of an abnormally large pelvis. Large pelvis Large pelvis bone A tumor (abnormal growth of tissue) of the uterus. 2010-05-04T09:35:15Z Uterine cancer MSH:D014594 NCIT:C3262 SNOMEDCT_US:126908007 UMLS:C0042138 Uterine tumor Uterine tumour Uterine neoplasia HP:0010784 Uterine neoplasm A tumor (abnormal growth of tissue) of the uterus. Uterine cancer Uterine tumor Uterine tumour The presence of a neoplasm of the urinary system. 2010-05-04T09:45:25Z MSH:D014571 NCIT:C3262 SNOMEDCT_US:126879004 SNOMEDCT_US:254913005 UMLS:C0042076 Urinary tract neoplasia HP:0010786 Urinary tract neoplasm The presence of a neoplasm of the urinary system. A tumor (abnormal growth of tissue) of the genital system. 2010-05-04T09:47:50Z NCIT:C3262 UMLS:C0679347 UMLS:C4020767 Genital tumor Genital tumour Genital neoplasia HP:0010787 Genital neoplasm A tumor (abnormal growth of tissue) of the genital system. Genital tumor Genital tumour Any structural abnormality of the fifth cranial nerve. 2010-07-10T03:51:21Z UMLS:C4021226 Abnormal trigeminal nerve morphology Abnormality of the fifth cranial nerve Abnormality of the nervus trigeminus HP:0010824 Abnormal fifth cranial nerve morphology Any structural abnormality of the fifth cranial nerve. Abnormality of the eleventh cranial nerve. 2010-07-10T03:54:53Z UMLS:C4021225 Abnormality of cranial nerve XI Abnormality of the accessory nerve HP:0010825 Abnormality of the eleventh cranial nerve Abnormality of the eleventh cranial nerve. Abnormality of cranial nerve XI Abnormality of the twelfth cranial nerve. 2010-07-10T03:58:00Z UMLS:C4021224 Abnormality of cranial nerve 12 Abnormality of cranial nerve xii Abnormality of the hypoglossal nerve HP:0010826 Abnormality of the twelfth cranial nerve Abnormality of the twelfth cranial nerve. Abnormality of cranial nerve 12 Abnormality of cranial nerve xii Abnormality of the seventh cranial nerve sometimes also referred to as the facial nerve. 2010-07-10T04:04:55Z UMLS:C4021223 Abnormality of the facial nerve HP:0010827 Abnormal seventh cranial physiology Abnormality of the seventh cranial nerve sometimes also referred to as the facial nerve. An incomplete closure of the abdominal wall. 2010-08-03T09:55:15Z UMLS:C0238577 Abdominal wall defect Congenital anterior abdominal wall defect HP:0010866 Abdominal wall defect An incomplete closure of the abdominal wall. Abdominal wall defect An abnormal level of a circulating protein in the blood. 2010-09-07T01:51:12Z UMLS:C4020763 UMLS:C4020764 UMLS:C4023679 Abnormal circulating protein level Abnormality of circulating protein level Blood protein disease Serum protein abnormality HP:0010876 Abnormal circulating protein concentration An abnormal level of a circulating protein in the blood. Blood protein disease An abnormality of the umbilical cord, which is the cord connecting the developing embryo or fetus to the placenta. 2010-09-13T08:24:04Z SNOMEDCT_US:90009001 UMLS:C0266785 Umbilical cord issue HP:0010881 Abnormality of the umbilical cord An abnormality of the umbilical cord, which is the cord connecting the developing embryo or fetus to the placenta. Umbilical cord issue Any deviation from the normal concentration of a branched chain family amino acid in the blood circulation. 2010-11-11T02:53:04Z UMLS:C4023673 HP:0010892 Abnormal circulating branched chain amino acid concentration Any deviation from the normal concentration of a branched chain family amino acid in the blood circulation. Any deviation from the normal concentration of phenylalanine in the blood circulation. 2010-11-11T03:23:30Z UMLS:C4023672 Abnormality of phenylalanine metabolism HP:0010893 Abnormal circulating phenylalanine concentration Any deviation from the normal concentration of phenylalanine in the blood circulation. Any deviation from the normal concentration of a serine family amino acid in the blood circulation. 2010-11-30T05:21:41Z UMLS:C4023671 Abnormality of serine family amino acid metabolism HP:0010894 Abnormal circulating serine family amino acid concentration Any deviation from the normal concentration of a serine family amino acid in the blood circulation. Any deviation from the normal concentration of glycine in the blood circulation. 2010-11-30T05:27:24Z UMLS:C4023670 HP:0010895 Abnormal circulating glycine concentration Any deviation from the normal concentration of glycine in the blood circulation. HPO_CONTRIBUTOR:gcarletti Any deviation from the normal concentration of an aspartate family amino acid in the blood circulation. 2010-12-02T04:40:57Z UMLS:C4023667 HP:0010899 Abnormal circulating aspartate family amino acid concentration Any deviation from the normal concentration of an aspartate family amino acid in the blood circulation. Any deviation from the normal concentration of methionine in the blood circulation. 2010-12-02T05:15:22Z UMLS:C4023665 Abnormality of methionine metabolism HP:0010901 Abnormal circulating methionine concentration Any deviation from the normal concentration of methionine in the blood circulation. Any deviation from the normal concentration of a glutamine family amino acid in the blood circulation. 2010-12-03T04:30:22Z UMLS:C4023664 HP:0010902 Abnormal circulating glutamine family amino acid concentration Any deviation from the normal concentration of a glutamine family amino acid in the blood circulation. Any deviation from the normal concentration of lysine in the blood circulation. 2010-12-08T08:05:55Z UMLS:C4023660 Abnormality of lysine metabolism HP:0010908 Abnormal circulating lysine concentration Any deviation from the normal concentration of lysine in the blood circulation. HPO_CONTRIBUTOR:gcarletti Any deviation from the normal concentration of arginine in the blood circulation. 2010-12-08T08:25:05Z UMLS:C4023659 Abnormality of arginine metabolism HP:0010909 Arginine is a charged, aliphatic amino acid. Abnormal circulating arginine concentration Any deviation from the normal concentration of arginine in the blood circulation. An increased concentration of valine in the blood. 2010-12-08T08:44:27Z MSH:C536524 SNOMEDCT_US:47719001 UMLS:C0268573 High blood valine concentration HP:0010910 Hypervalinemia An increased concentration of valine in the blood. HPO_CONTRIBUTOR:gcarletti High blood valine concentration An increased concentration of leucine in the blood. 2010-12-08T08:45:56Z SNOMEDCT_US:24013007 UMLS:C0268576 High blood leucine concentration HP:0010911 Normal leucine blood levels are around 120-160 micromole per liter. Hyperleucinemia An increased concentration of leucine in the blood. HPO_CONTRIBUTOR:gcarletti High blood leucine concentration Any deviation from the normal concentration of isoleucine in the blood circulation. 2010-12-08T08:47:47Z UMLS:C4023658 HP:0010912 Abnormal circulating isoleucine concentration Any deviation from the normal concentration of isoleucine in the blood circulation. An increased concentration of isoleucine in the blood. 2010-12-08T08:49:42Z UMLS:C4023657 High blood isoleucine concentration HP:0010913 Normal isoleucine blood levels are around 60-80 micromole per liter. Hyperisoleucinemia An increased concentration of isoleucine in the blood. HPO_CONTRIBUTOR:gcarletti High blood isoleucine concentration Any deviation from the normal circulation of valine in the blood circulation. 2010-12-08T08:51:14Z UMLS:C4023656 Abnormality of valine metabolism HP:0010914 Abnormal circulating valine concentration Any deviation from the normal circulation of valine in the blood circulation. Any deviation from the normal concentration of tyrosine in the blood circulation. 2010-12-08T09:13:53Z UMLS:C4023653 HP:0010917 Abnormal circulating tyrosine concentration Any deviation from the normal concentration of tyrosine in the blood circulation. An abnormality of divalent inorganic cation homeostasis. 2011-01-06T07:47:18Z UMLS:C4023648 Abnormality of divalent inorganic cation homeostasis HP:0010927 Abnormal blood inorganic cation concentration An abnormality of divalent inorganic cation homeostasis. An abnormality of cation homeostasis. 2011-01-06T10:36:04Z UMLS:C4023646 Abnormality of cation homeostasis HP:0010929 Abnormal blood cation concentration An abnormality of cation homeostasis. An abnormality of monovalent inorganic cation homeostasis. 2011-01-06T10:38:38Z UMLS:C4023645 Abnormality of monovalent inorganic cation homeostasis HP:0010930 Abnormal blood monovalent inorganic cation concentration An abnormality of monovalent inorganic cation homeostasis. An abnormal concentration of sodium. 2011-01-06T10:40:20Z UMLS:C4023644 Abnormal blood Na+ levels Abnormal circulating Na concentration Abnormality of sodium homeostasis HP:0010931 Abnormal blood sodium concentration An abnormal concentration of sodium. Abnormal blood Na+ levels Abnormal circulating Na concentration An abnormality of a nucleobase metabolic process. 2011-01-06T10:46:17Z UMLS:C4020762 UMLS:C4023643 Abnormal nucleoside levels HP:0010932 This term is used to refers to abnormality in chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. Abnormal circulating nucleobase concentration An abnormality of a nucleobase metabolic process. An abnormality of the upper urinary tract. 2011-01-16T11:37:29Z UMLS:C4023641 Abnormality of the upper urinary tract HP:0010935 The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters. Abnormality of the upper urinary tract An abnormality of the upper urinary tract. Abnormality of the upper urinary tract An abnormality of the lower urinary tract. 2011-01-16T11:39:17Z UMLS:C4023640 HP:0010936 The lower urinary tract is a subdivision of urinary system which consists of the urinary bladder and the urethra. Abnormality of the lower urinary tract An abnormality of the lower urinary tract. An abnormality of the nasal skeleton. 2011-01-16T02:19:38Z UMLS:C4023639 UMLS:C4280361 Abnormality of the nasal skeleton Anomaly of the nasal skeleton Deformity of the bones of the nose Deformity of the nasal skeleton Distortion of the bones of the nose Distortion of the nasal skeleton Malformation of the bones of the nose Malformation of the nasal skeleton HP:0010937 Abnormal nasal skeleton morphology An abnormality of the nasal skeleton. Abnormality of the nasal skeleton Anomaly of the nasal skeleton Deformity of the bones of the nose Deformity of the nasal skeleton Distortion of the bones of the nose Distortion of the nasal skeleton Malformation of the bones of the nose Malformation of the nasal skeleton An abnormality of the external nose. 2011-01-16T02:21:10Z UMLS:C2164724 UMLS:C4023638 UMLS:C4280360 Abnormality of the external nose Anomaly of the external nose Deformity of the external nose Malformation of the external nose HP:0010938 Abnormal external nose morphology An abnormality of the external nose. Abnormality of the external nose Anomaly of the external nose Deformity of the external nose Malformation of the external nose An abnormality of the renal pelvis. 2011-01-16T03:33:55Z UMLS:C4023633 Abnormality of the renal pelvis HP:0010944 Abnormal renal pelvis morphology An abnormality of the renal pelvis. Mild pyelectasis is defined as a hypoechoic spherical or elliptical space within the renal pelvis that measures at least 5mm and not more than 10 mm. The measurement is taken on a transverse section through the fetal renal pelvis using the maximum anterior-to-posterior measurement. 2011-01-16T03:36:31Z MSH:D058536 SNOMEDCT_US:430035004 UMLS:C2317073 Fetal renal pelvic dilatation Foetal pyelectasis Foetal renal pelvic dilatation Mild fetal hydronephrosis Mild foetal hydronephrosis HP:0010945 The renal pelvis is the part of the kidney that collects urine. Fetal pyelectasis is a prenatal ultrasound finding that is diagnosed with enlargement of the renal pelvis from 4 to 10 millimeters. In many cases, fetal pyelectasis resolves spontaneously. Note that dilatation of the renal pelvis to more than 10 mm is referred to as severe pyelectasis or hydronephrosis. Measurements less than 5mm are normal, should not be designated as pyelectasis, and should not be reported (PMID:16100637). Fetal pyelectasis Mild pyelectasis is defined as a hypoechoic spherical or elliptical space within the renal pelvis that measures at least 5mm and not more than 10 mm. The measurement is taken on a transverse section through the fetal renal pelvis using the maximum anterior-to-posterior measurement. PMID:16100637 Foetal pyelectasis Foetal renal pelvic dilatation Mild foetal hydronephrosis An abnormality of the fourth ventricle. 2011-01-17T12:58:00Z UMLS:C4023630 Abnormality of the fourth ventricle HP:0010950 The fourth ventricle is the cerebral ventricle that extends from the cerebral aqueduct to the obex, and is located within the pons and the upper part of the medulla oblongata. Abnormal fourth ventricle morphology An abnormality of the fourth ventricle. Underdevelopment of the right-sided structures of the heart. 2011-01-17T03:31:37Z SNOMEDCT_US:268180007 SNOMEDCT_US:39589002 UMLS:C0265856 UMLS:C0344963 Hypoplastic right heart syndrome Underdeveloped right heart HP:0010954 Hypoplastic right heart syndrome (HRHS) causes inadequate blood flow to the lungs postnatally and thus leads to cyanosis. HRHS involves pulmonary valve atresia, hypoplasia of the right ventricle, hypoplasia of the tricuspid valve, and a small, hypoplastic pulmonary artery. As the ductus arteriosus closes postnatally, infants with HRHS become critically ill. Hypoplastic right heart Underdevelopment of the right-sided structures of the heart. Hypoplastic right heart syndrome Underdeveloped right heart Any deviation from the normal concentration of a long-chain fatty acid in the blood circulation. 2011-01-27T08:05:00Z UMLS:C4023624 HP:0010964 A long-chain fatty-acid is defined as an aliphatic monocarboxylic acid with a chain length of C13 to C18. Abnormal circulating long-chain fatty-acid concentration Any deviation from the normal concentration of a long-chain fatty acid in the blood circulation. Any deviation from the normal concentration of phytanic acid in the blood circulation. 2011-01-27T08:07:48Z UMLS:C4023623 Abnormal circulating phytanic acid level HP:0010965 Phytanic acid is a branched-chain saturated fatty acid consisting of hexadecanoic acid carrying methyl substituents at positions 3, 7, 11 and 15. Abnormal circulating phytanic acid concentration Any deviation from the normal concentration of phytanic acid in the blood circulation. Any deviation from the normal concentration of a fatty acid anion in the blood circulation. 2011-01-27T09:17:48Z UMLS:C4021209 Abnormality of fatty acid anion HP:0010966 A fatty acid anion is the conjugate base of a fatty acid. Abnormal circulating fatty-acid anion concentration Any deviation from the normal concentration of a fatty acid anion in the blood circulation. Any deviation from the normal concentration of carnitine in the blood circulation. 2011-01-27T09:19:42Z UMLS:C4020761 UMLS:C4021855 Carnitine levels abnormal HP:0010967 L-carnitine (3-hydroxy-4-N.trimethylammonium butyrate) plays a key role in facilitating the transport of long-chain fatty acids from the cytosol into the mitochondrial matrix, where they undergo 13-oxidation. Abnormal circulating carnitine concentration Any deviation from the normal concentration of carnitine in the blood circulation. HPO_CONTRIBUTOR:gcarletti An abnormality of myeloid leukocytes. 2011-02-06T09:24:46Z UMLS:C4023618 Abnormality of myeloid leukocytes HP:0010974 A myeloid leukocyte refers to a cell of the monocyte, granulocyte, or mast cell lineage. Abnormal myeloid leukocyte morphology An abnormality of myeloid leukocytes. A deviation from the normal count of B cells, i.e., the cells that are formed in the bone marrow, migrate to the peripheral lymphatic system, and mature into plasma cells or memory cells. 2011-02-06T09:38:18Z UMLS:C4021208 Abnormal number of B cells Abnormal numbers of B cells Abnormality of B cell count Abnormality of B cell numbers HP:0010975 Abnormal B cell count A deviation from the normal count of B cells, i.e., the cells that are formed in the bone marrow, migrate to the peripheral lymphatic system, and mature into plasma cells or memory cells. MP:0002458 Abnormal number of B cells Abnormal numbers of B cells An abnormal decrease from the normal count of B cells. 2011-02-06T09:44:11Z HP:0002956 UMLS:C1855067 B cell deficiency B cell lymphopenia Decreased B cell count Low B cell count Reduction in B cell number HP:0010976 Plasma B cells differentiate from B cells and secrete large amounts of antibodies. B lymphocytopenia An abnormal decrease from the normal count of B cells. Low B cell count An abnormal functioning of phagocytosis. Phagocytosis is an elegant but complex process for the ingestion and elimination of pathogens, but it is also important for the elimination of apoptotic cells and hence fundamental for tissue homeostasis. Phagocytosis can be divided into four main steps: (i) recognition of the target particle, (ii) signaling to activate the internalization machinery, (iii) phagosome formation, and (iv) phagolysosome maturation. 2011-02-06T10:31:46Z UMLS:C4023617 HP:0010977 Abnormal phagocytosis An abnormal functioning of phagocytosis. Phagocytosis is an elegant but complex process for the ingestion and elimination of pathogens, but it is also important for the elimination of apoptotic cells and hence fundamental for tissue homeostasis. Phagocytosis can be divided into four main steps: (i) recognition of the target particle, (ii) signaling to activate the internalization machinery, (iii) phagosome formation, and (iv) phagolysosome maturation. PMID:28691037 A functional abnormality of the immune system. 2011-02-07T04:28:55Z UMLS:C4023616 HP:0010978 Abnormality of immune system physiology A functional abnormality of the immune system. MP:0001790 An abnormality of the morphology or counts of the cells that make up the immune system. 2011-02-08T12:49:47Z UMLS:C4023612 HP:0010987 Abnormal cellular immune system morphology An abnormality of the morphology or counts of the cells that make up the immune system. An abnormality of the abdominal musculature. 2011-02-09T08:05:11Z UMLS:C4023608 Abnormality of the abdominal musculature HP:0010991 Abnormal morphology of the abdominal musculature An abnormality of the abdominal musculature. Any deviation from the normal concentration of a dicarboxylic acid in the blood circulation. 2011-02-10T02:01:02Z UMLS:C4023606 HP:0010995 A dicarboxylic acid is an oxoacid containing two carboxy groups. Abnormal circulating dicarboxylic acid concentration Any deviation from the normal concentration of a dicarboxylic acid in the blood circulation. Any deviation from the normal concentration of a monocarboxylic acid in the blood circulation. 2011-02-10T02:20:42Z UMLS:C4023605 HP:0010996 Abnormal circulating monocarboxylic acid concentration Any deviation from the normal concentration of a monocarboxylic acid in the blood circulation. HPO_CONTRIBUTOR:gcarletti An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often referred to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones. 2011-02-13T11:57:32Z HP:0002796 HP:0004350 HP:0005711 HP:0005741 HP:0010738 MSH:D010026 SNOMEDCT_US:49347007 UMLS:C0029464 Increased bone density Increased bone mineral density Osteosclerosis Osteosclerosis of bones HP:0011001 This term may be merged with Increased bone density in the future or made obsolete. Increased bone mineral density An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often referred to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones. Increased bone density Increased bone mineral density Abnormally increased formation of dense trabecular bone tissue. Despite the increased density of bone tissue, osteopetrotic bones tend to be more fracture-prone than normal. 2011-02-13T11:58:36Z MSH:D010022 SNOMEDCT_US:1926006 SNOMEDCT_US:367489004 UMLS:C0029454 Harder, denser, fracture-prone bones Albers-Schoenberg disease Albers-Schonberg disease Albers-Schönberg disease Marble bone disease HP:0011002 Osteopetrosis Abnormally increased formation of dense trabecular bone tissue. Despite the increased density of bone tissue, osteopetrotic bones tend to be more fracture-prone than normal. Harder, denser, fracture-prone bones An abnormality of the systemic arterial tree, which consists of the aorta and other systemic arteries. 2011-02-16T08:46:49Z HP:0002620 HP:0005114 Fyler:2600 SNOMEDCT_US:234119001 UMLS:C0151489 UMLS:C4021205 Abnormal systemic artery morphology Abnormality of the systemic arterial tree Systemic artery abnormality Arterial abnormalities HP:0011004 Abnormal systemic arterial morphology An abnormality of the systemic arterial tree, which consists of the aorta and other systemic arteries. An abnormality of the neck musculature. 2011-02-19T11:15:01Z UMLS:C4023601 Abnormality of cervical musculature Abnormality of the musculature of the neck Neck muscle issue HP:0011006 Abnormal morphology of the musculature of the neck An abnormality of the neck musculature. Abnormality of cervical musculature Abnormality of the musculature of the neck Neck muscle issue A deviation from the normal concentration of a polysaccharide in the blood circulation. 2011-02-21T09:46:11Z UMLS:C4023600 HP:0011012 Abnormal circulating polysaccharide concentration A deviation from the normal concentration of a polysaccharide in the blood circulation. A deviation from the normal concentration of a carbohydrate in the blood circulation. 2011-02-21T09:47:27Z UMLS:C4023599 HP:0011013 An abnormality of the metabolism (include abnormality of the concentration) of a carbohydrate, including monosaccharides, oligosaccharides and polysaccharides, and substances derived from them. Abnormal circulating carbohydrate concentration A deviation from the normal concentration of a carbohydrate in the blood circulation. Abnormality of glucose homeostasis. 2011-02-21T10:37:21Z UMLS:C4023598 HP:0011014 An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell. Abnormal glucose homeostasis Abnormality of glucose homeostasis. An abnormality of the concentration of glucose in the blood. 2011-02-21T10:41:13Z UMLS:C4023597 Abnormality of blood glucose concentration HP:0011015 Abnormal blood glucose concentration An abnormality of the concentration of glucose in the blood. An abnormality in a cellular process. 2011-02-22T07:05:50Z HP:0025462 UMLS:C4023595 Abnormality of cell physiology HP:0011017 Abnormal cellular physiology An abnormality in a cellular process. An abnormality of the cell cycle. 2011-02-22T07:09:31Z UMLS:C4023594 Abnormality of the cell cycle HP:0011018 Abnormality of the cell cycle An abnormality of the cell cycle. Abnormality of the cell cycle An abnormality of chromosome condensation. 2011-02-22T07:19:30Z UMLS:C4023593 HP:0011019 Abnormality of chromosome condensation An abnormality of chromosome condensation. An abnormality of the metabolism of mucopolysaccharide. 2011-02-23T07:58:02Z UMLS:C4023592 HP:0011020 Abnormality of mucopolysaccharide metabolism An abnormality of the metabolism of mucopolysaccharide. An abnormality of the gastrointestinal tract. 2011-03-01T07:52:06Z MSH:D004066 MSH:D005767 SNOMEDCT_US:119292006 SNOMEDCT_US:25374005 SNOMEDCT_US:53619000 UMLS:C0012242 UMLS:C0017178 UMLS:C4023588 Abnormality of the GI tract Abnormality of the gastrointestinal tract Digestive system disease Gastrointestinal disease HP:0011024 Abnormality of the gastrointestinal tract An abnormality of the gastrointestinal tract. Abnormality of the GI tract Abnormality of the gastrointestinal tract Digestive system disease Gastrointestinal disease Abnormal functionality of the cardiovascular system. 2011-03-03T10:23:19Z UMLS:C4023587 Abnormality of cardiovascular system physiology HP:0011025 Abnormal cardiovascular system physiology Abnormal functionality of the cardiovascular system. Aplasia or developmental hypoplasia of the vagina. 2011-03-02T06:17:46Z UMLS:C4023586 Absent/small vagina Absent/underdeveloped vagina HP:0011026 Aplasia/Hypoplasia of the vagina Aplasia or developmental hypoplasia of the vagina. Absent/small vagina Absent/underdeveloped vagina An abnormality of the fallopian tube. 2011-03-02T06:36:01Z UMLS:C0281842 Abnormality of the fallopian tube HP:0011027 The Fallopian tubes (also known as oviducts, uterine tubes, and salpinges) are ducts that lead from the ovaries into the uterus. Abnormal fallopian tube morphology An abnormality of the fallopian tube. An abnormality of blood circulation. 2011-03-03T10:25:21Z UMLS:C4020760 UMLS:C4023585 Blood circulation disorder HP:0011028 Abnormality of blood circulation An abnormality of blood circulation. The presence of hemorrhage within the body. 2011-03-03T10:26:26Z UMLS:C1390214 Internal bleeding Internal haemorrhage HP:0011029 Internal hemorrhage The presence of hemorrhage within the body. Internal bleeding Internal haemorrhage An abnormality of the homeostasis (concentration) of transition element cation. 2011-03-04T07:59:31Z UMLS:C4023584 Abnormality of transition element cation homeostasis HP:0011030 Abnormal blood transition element cation concentration An abnormality of the homeostasis (concentration) of transition element cation. An abnormality of the homeostasis (concentration) of iron cation. 2011-03-04T08:01:07Z UMLS:C4023583 HP:0011031 Abnormality of iron homeostasis An abnormality of the homeostasis (concentration) of iron cation. An abnormality of the regulation of body fluids. 2011-03-05T09:09:27Z SNOMEDCT_US:1860003 SNOMEDCT_US:190902006 UMLS:C2364164 Abnormality of fluid regulation Fluid imbalance HP:0011032 Abnormality of fluid regulation An abnormality of the regulation of body fluids. Abnormality of fluid regulation Fluid imbalance An abnormality of the cortex of the kidney. 2011-03-06T11:31:39Z UMLS:C4023580 Abnormality of renal cortex morphology HP:0011035 Abnormal renal cortex morphology An abnormality of the cortex of the kidney. An altered ability of the kidneys to void urine and/or specific substances. 2011-03-06T12:28:55Z MP:0005555 UMLS:C4023579 HP:0011036 Abnormality of renal excretion An altered ability of the kidneys to void urine and/or specific substances. A decreased rate of urine production. 2011-03-06T12:33:12Z UMLS:C3887784 HP:0011037 A reduction in the overall amount of urine output. Decreased urine output A decreased rate of urine production. An abnormality of renal absorption. 2011-03-06T12:38:04Z UMLS:C4023578 Abnormal renal resorption Abnormality of renal resorption HP:0011038 Abnormal renal tubular resorption An abnormality of renal absorption. An abnormality of the intrahepatic bile duct. 2011-03-07T07:54:11Z UMLS:C4023577 Abnormality of the intrahepatic bile duct HP:0011040 Abnormal intrahepatic bile duct morphology An abnormality of the intrahepatic bile duct. Aplasia or developmental hypoplasia of the cervical vertebral column. 2011-03-09T08:29:34Z UMLS:C4023576 Absent/small cervical spine Absent/underdeveloped cervical spine HP:0011041 Aplasia/Hypoplasia of the cervical spine Aplasia or developmental hypoplasia of the cervical vertebral column. Absent/small cervical spine Absent/underdeveloped cervical spine An abnormal concentration of potassium. 2011-03-09T11:00:32Z UMLS:C4023575 Abnormal blood K concentration Abnormality of potassium homeostasis HP:0011042 Abnormal blood potassium concentration An abnormal concentration of potassium. Abnormal blood K concentration A localized form of periodontitis. 2011-03-10T12:26:35Z Limited area of gum disease Localised gum disease Localized gum disease UMLS:C4023559 UMLS:C4280344 Localised periodontal disease Localised periodontitis Localized periodontal disease HP:0011059 Localized periodontitis A localized form of periodontitis. Limited area of gum disease Localised gum disease Localized gum disease Localised periodontal disease Localised periodontitis Localized periodontal disease An abnormality of the structure or composition of the teeth. 2011-03-10T01:44:04Z UMLS:C4023557 Abnormality of tooth part Abnormality of tooth structure HP:0011061 Abnormality of dental structure An abnormality of the structure or composition of the teeth. Abnormality of tooth part Abnormality of tooth structure The presence of one or more teeth additional to the normal number. 2011-03-10T02:52:19Z HP:0000672 MSH:D014096 SNOMEDCT_US:266414008 SNOMEDCT_US:367534004 SNOMEDCT_US:8666004 UMLS:C0040457 Extra teeth Hyperdontia Increased number of teeth Increased tooth count Supernumerary teeth Supplemental dentition Supplemental teeth Tooth, supernumerary Supernumary dentition Supernumary teeth More teeth than normal HP:0011069 Age-related physiological sequential eruption should be taken into account during evaluation. The type and the location of the additional tooth/teeth should be added to the description. Supernumerary teeth are uncommon (in 0.21% of deciduous dentitions and in 0.9% of permanent dentitions), and often abnormal positioning of a normal number of teeth is wrongly classified as supernumerary teeth. Supernumerary teeth are most frequent in the upper maxilla, and typically, a single additional tooth is present. We discourage the use of distodens, distomolars (an extra fourth molar posterior to the third molar), paramolars (supernumerary tooth in the molar region) but rather to mention the presence of the supernumerary tooth mesial to or distal to a tooth from the normal series. Diagnosing a supernumerary tooth may require radiographic examination. A supernumerary tooth present between the maxillary central incisors is called mesiodens. Supernumerary tooth The presence of one or more teeth additional to the normal number. PMID:31468724 Extra teeth Hyperdontia Increased number of teeth Increased tooth count Supplemental dentition Supplemental teeth Supernumary dentition Supernumary teeth More teeth than normal 2011-03-10T03:56:41Z MSH:C538215 SNOMEDCT_US:109493006 UMLS:C0399379 UMLS:C4082200 Absence of tooth root Agenesis of tooth root Aplasia of tooth root Missing tooth root Rootless teeth Teeth without roots Tooth with dentin dysplasia type i HP:0011072 Rootless teeth Absence of tooth root Agenesis of tooth root Aplasia of tooth root Missing tooth root Rootless teeth Teeth without roots Tooth with dentin dysplasia type i A localized form of developmental hypoplasia of the dental enamel. 2011-03-10T05:13:09Z UMLS:C4023550 UMLS:C4280339 Localised hypoplasia of dental enamel Localised hypoplasia of tooth enamel Localized hypoplasia of tooth enamel Localised dysplasia of tooth enamel Localized dysplasia of tooth enamel HP:0011074 Localized hypoplasia of dental enamel A localized form of developmental hypoplasia of the dental enamel. Localised hypoplasia of dental enamel Localised hypoplasia of tooth enamel Localized hypoplasia of tooth enamel Localised dysplasia of tooth enamel Localized dysplasia of tooth enamel An abnormality of the outflow tract of the left ventricle. 2011-06-05T04:15:50Z SNOMEDCT_US:253545000 UMLS:C0344916 Abnormality of the left ventricular outflow tract HP:0011103 Abnormal left ventricular outflow tract morphology An abnormality of the outflow tract of the left ventricle. Inflammation of the tonsils that has occurred repeatedly. The definition of recurrent may vary somewhat, but the criteria used recently as a measure of severity were five or more episodes of true tonsillitis per year, symptoms recurring for at least a year, and episodes that are disabling and that prevent normal functioning. In some cases recurrent tonsillitis may be related to immunosusceptibility. Evidence exists for a genetic predisposition for recurrent tonsillitis. 2011-06-10T07:46:38Z MSH:D014069 SNOMEDCT_US:90176007 UMLS:C0040425 Recurrent inflammation of tonsils HP:0011110 Recurrent tonsillitis Inflammation of the tonsils that has occurred repeatedly. The definition of recurrent may vary somewhat, but the criteria used recently as a measure of severity were five or more episodes of true tonsillitis per year, symptoms recurring for at least a year, and episodes that are disabling and that prevent normal functioning. In some cases recurrent tonsillitis may be related to immunosusceptibility. Evidence exists for a genetic predisposition for recurrent tonsillitis. PMID:15897415 Recurrent inflammation of tonsils An abnormality of the concentration or function of circulating immune proteins. 2011-06-12T08:58:47Z UMLS:C4023536 HP:0011111 Abnormality of immune serum protein physiology An abnormality of the concentration or function of circulating immune proteins. An abnormality in the production or cellular release of a cytokine (i.e., any of the non-antibody proteins made by inflammatory leukocytes and some non-leukocytic cells that affect the behavior of other cells). 2011-06-12T09:07:24Z MP:0003009 UMLS:C4023534 HP:0011113 Abnormality of cytokine secretion An abnormality in the production or cellular release of a cytokine (i.e., any of the non-antibody proteins made by inflammatory leukocytes and some non-leukocytic cells that affect the behavior of other cells). An abnormality of the nasal dorsum, also known as the nasal ridge. 2011-06-12T09:37:47Z UMLS:C4021202 UMLS:C4280332 Abnormality of the dorsum of nose Abnormality of the nasal dorsum Abnormality of the nasal ridge Anomaly of the nasal ridge Abnormal morphology of dorsum of nose Crooked dorsum of nose Crooked nasal dorsum Crooked nasal ridge Deformity of the dorsum of the nose Deformity of the nasal dorsum Deformity of the nasal ridge Malformation of the dorsum of nose Malformation of the nasal dorsum Malformation of the nasal ridge HP:0011119 The nasal ridge is the midline prominence of the nose, extending from the nasal root to the tip. Abnormal nasal dorsum morphology An abnormality of the nasal dorsum, also known as the nasal ridge. PMID:19152422 Abnormality of the dorsum of nose Abnormality of the nasal ridge Abnormal morphology of dorsum of nose Crooked dorsum of nose Crooked nasal dorsum Crooked nasal ridge Deformity of the dorsum of the nose Deformity of the nasal dorsum Deformity of the nasal ridge Malformation of the dorsum of nose Malformation of the nasal dorsum Malformation of the nasal ridge Any morphological abnormality of the skin. 2011-06-12T10:03:23Z Fyler:4133 UMLS:C4023528 Abnormal skin morphology Abnormal skin structure Abnormality of skin morphology HP:0011121 Abnormal skin morphology Any morphological abnormality of the skin. Abnormal skin morphology Abnormal skin structure Any abnormality of the physiological function of the skin. 2011-06-12T10:05:14Z UMLS:C4023527 Abnormality of skin physiology HP:0011122 Abnormality of skin physiology Any abnormality of the physiological function of the skin. Abnormality of skin physiology The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. 2011-06-12T10:06:04Z HP:0002727 HP:0007423 MP:0004947 MSH:D003872 SNOMEDCT_US:703938007 UMLS:C0011603 UMLS:C3875321 Abnormal tendency to infections of the skin Inflammatory abnormality of the skin Skin inflammation Dermatitis Inflammatory skin disease HP:0011123 Inflammatory abnormality of the skin The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. Inflammatory abnormality of the skin Skin inflammation An abnormality of the morphology of the epidermis. 2011-06-12T10:11:28Z UMLS:C4023526 Abnormality of epidermal morphology HP:0011124 Abnormal epidermal morphology An abnormality of the morphology of the epidermis. Absence or developmental hypoplasia of the sweat glands. 2011-06-19T02:01:50Z UMLS:C4023520 Absent/small sweat glands Absent/underdeveloped sweat glands HP:0011135 Aplasia/Hypoplasia of the sweat glands Absence or developmental hypoplasia of the sweat glands. Absent/small sweat glands Absent/underdeveloped sweat glands An abnormality of the skin adnexa (skin appendages), which are specialized skin structures located within the dermis and focally within the subcutaneous fatty tissue, comprising three histologically distinct structures: (1) the pilosebaceous unit (hair follicle and sebaceous glands); (2) the eccrine sweat glands; and (3) the apocrine glands. 2011-06-19T06:25:34Z UMLS:C4023518 Abnormal skin appendage Abnormality of skin adnexa morphology HP:0011138 Abnormal skin adnexa morphology An abnormality of the skin adnexa (skin appendages), which are specialized skin structures located within the dermis and focally within the subcutaneous fatty tissue, comprising three histologically distinct structures: (1) the pilosebaceous unit (hair follicle and sebaceous glands); (2) the eccrine sweat glands; and (3) the apocrine glands. Abnormal skin appendage Gastric duplication is a usually cystic malformation of gastrointestinal tract, usually attached to the greater curvature of the stomach and has no communication with the stomach. 2011-06-25T08:57:09Z UMLS:C4021201 Gastric duplication cyst HP:0011139 Gastric duplication usually presents as gastric outlet obstruction. They are usually spherical in form, do not communicate with the stomach, and are generally localized at the greater curvature. In some cases they may exhibit adhesion to the pancreas and even communicate with aberrant pancreatic ducts. Gastric duplication is more frequent in females. It is generally either diagnosed in infancy because of symptoms of gastric outlet obstruction or is an incidental finding in adulthood. Gastric duplication Gastric duplication is a usually cystic malformation of gastrointestinal tract, usually attached to the greater curvature of the stomach and has no communication with the stomach. A spherical hollow structure with a smooth muscle coat, lined by a mucous membrane, and attached to any part of the gastrointestinal tract, from the base of the tongue to the anus. 2011-06-25T09:02:50Z SNOMEDCT_US:33257003 UMLS:C0266019 GI duplication HP:0011140 Gastrointestinal duplication A spherical hollow structure with a smooth muscle coat, lined by a mucous membrane, and attached to any part of the gastrointestinal tract, from the base of the tongue to the anus. PMID:21218094 GI duplication An abnormal shape of occiput. 2011-12-03T10:14:06Z Abnormal shape of posterior head Abnormal shape of the back of the head UMLS:C4023459 Abnormal shape of posterior cranium Abnormal shape of posterior skull Abnormal shape of the back of the skull HP:0011217 Abnormal shape of the occiput An abnormal shape of occiput. Abnormal shape of posterior head Abnormal shape of the back of the head Abnormal shape of posterior cranium Abnormal shape of posterior skull Abnormal shape of the back of the skull An abnormal shape of the frontal part of the head. 2011-12-03T10:26:03Z UMLS:C4023458 Abnormal morphology of the frontal region Abnormal shape of the forehead Dysmorphic forehead Dysmorphic frontal region HP:0011218 Abnormal shape of the frontal region An abnormal shape of the frontal part of the head. Abnormal morphology of the frontal region Abnormal shape of the forehead Dysmorphic forehead Dysmorphic frontal region Facial height (length) is more than two standard deviations below the mean (objective); or an apparent decrease in the height (length) of the face (subjective). 2011-12-07T09:01:18Z UMLS:C4023457 Decreased height of face Decreased length of face Decreased vertical dimension of face Short face Short facies Vertical Facial Deficiency Vertical deficiency of face Vertical facial insufficiency Vertical hypoplasia of face Vertical insufficiency of face Vertical shortening of face HP:0011219 Objective measurement of face height is made with sliding calipers from the nasion, just above the depth of the nasal root to the gnathion, the inferior border of the mandible, both in the midline. Note that short face is distinct from wide face. Short face Facial height (length) is more than two standard deviations below the mean (objective); or an apparent decrease in the height (length) of the face (subjective). PMID:19125436 Decreased height of face Decreased length of face Decreased vertical dimension of face Short face Short facies Vertical Facial Deficiency Vertical deficiency of face Vertical facial insufficiency Vertical hypoplasia of face Vertical insufficiency of face Vertical shortening of face 2011-12-30T02:51:16Z UMLS:C4023437 HP:0011277 Abnormality of the urinary system physiology An abnormal amount of hydrogencarbonate in the urine. 2011-12-30T02:57:55Z UMLS:C4023435 Abnormality of urine HCO3 concentration HP:0011279 Abnormality of urine bicarbonate level An abnormal amount of hydrogencarbonate in the urine. Abnormality of urine HCO3 concentration An abnormality of calcium concentration in the urine. 2011-12-30T03:27:02Z UMLS:C4023434 Abnormality of urine Ca concentration Abnormality of urine Ca2+ concentration HP:0011280 Abnormality of urine calcium concentration An abnormality of calcium concentration in the urine. Abnormality of urine Ca concentration Abnormality of urine Ca2+ concentration An abnormality of the hindbrain, also known as the rhombencephalon. 2012-01-01T01:22:36Z UMLS:C4021170 Abnormal shape of hindbrain Abnormality of hindbrain morphology Abnormality of the hindbrain HP:0011282 The hindbrain consists of two main structures: The pons and the cerebellum. Abnormal hindbrain morphology An abnormality of the hindbrain, also known as the rhombencephalon. Abnormal shape of hindbrain An abnormality of the metencephalon. The metencephalon is the part of the hindbrain that consists of the pons and the cerebellum. 2012-01-01T01:24:14Z UMLS:C4023432 Abnormality of the metencephalon HP:0011283 Abnormal metencephalon morphology An abnormality of the metencephalon. The metencephalon is the part of the hindbrain that consists of the pons and the cerebellum. A morphological abnormality of a digit, i.e., of a finger or toe. 2012-02-11T07:16:22Z UMLS:C3550704 Abnormality of digit Abnormality of fingers or toes Digital anomalies HP:0011297 Abnormal digit morphology A morphological abnormality of a digit, i.e., of a finger or toe. Abnormality of fingers or toes The total absence of the foot, with no bony elements distal to the tibia or fibula. 2012-02-11T11:20:59Z SNOMEDCT_US:371197005 UMLS:C0265624 Absent foot Aplasia of the foot Apodia HP:0011301 Absent foot The total absence of the foot, with no bony elements distal to the tibia or fibula. PMID:19125433 Absent foot An abnormality of size or shape of the long bones. 2012-02-12T02:31:03Z HP:0100713 HP:0100714 HP:0100715 UMLS:C4021165 Abnormal shape of long bone Abnormality of long bone morphology Abnormality of the tubular bones HP:0011314 Abnormal long bone morphology An abnormality of size or shape of the long bones. Abnormal shape of long bone An abnormality of the fontanelle. 2012-02-25T02:34:36Z UMLS:C4020755 Anomaly of the fontanelles HP:0011328 The fontanelles are the regions in an infant's calvaria that are covered by a thick membrane that normally ossify in the first two years of life. Abnormality of fontanelles An abnormality of the fontanelle. PMID:12825844 Any anomaly of a cranial suture, that is one of the six membrane-covered openings in the incompletely ossified skull of the fetus or newborn infant. 2012-02-25T03:33:56Z UMLS:C4023412 Abnormality of cranial sutures Abnormality of the bregma sutures Abnormality of the calvarium sutures Abnormality of the cranial sutures Abnormality of the skull suture HP:0011329 Abnormality of cranial sutures Any anomaly of a cranial suture, that is one of the six membrane-covered openings in the incompletely ossified skull of the fetus or newborn infant. Abnormality of cranial sutures 2012-02-26T11:00:17Z UMLS:C4023408 Abnormality of mouth size Anomaly of mouth size HP:0011337 Abnormality of mouth size Abnormality of mouth size Anomaly of mouth size An abnormality of the outline, configuration, or contour of the mouth. 2012-02-26T01:05:23Z Fyler:4874 UMLS:C4023407 Abnormality of mouth shape Anomaly of mouth shape Unusual mouth shape HP:0011338 Abnormality of mouth shape An abnormality of the outline, configuration, or contour of the mouth. HPO_CONTRIBUTOR:DDD_jhurst Abnormality of mouth shape Anomaly of mouth shape Unusual mouth shape Increased width of the upper lip. 2012-02-26T01:58:08Z UMLS:C3151495 Elongation of upper lip Increased height of upper lip Increased vertical length of upper lip Long upper lip HP:0011341 Long upper lip Increased width of the upper lip. HPO_CONTRIBUTOR:DDD_jhurst Elongation of upper lip Increased height of upper lip Increased vertical length of upper lip Long upper lip An abnormality of the skin that is not localized to any one particular region. 2012-03-01T01:55:07Z UMLS:C4021157 Generalised abnormality of skin Generalized abnormality of skin HP:0011354 Generalized abnormality of skin An abnormality of the skin that is not localized to any one particular region. Generalised abnormality of skin Generalized abnormality of skin A lesion of the skin that is located in a specific region rather than being generalized. 2012-03-01T02:37:43Z UMLS:C0850826 Localised skin lesion Localized skin lesion HP:0011355 Localized skin lesion A lesion of the skin that is located in a specific region rather than being generalized. Localised skin lesion Localized skin lesion An abnormal amount of hair. 2012-03-01T08:46:57Z HP:0002115 HP:0011357 UMLS:C4023397 UMLS:C4023401 Abnormal hair quantity Abnormality of hair density HP:0011362 Abnormal hair quantity An abnormal amount of hair. Abnormal hair quantity Absence of the inner ear due to a developmental defect. 2012-03-07T08:23:52Z SNOMEDCT_US:71973003 UMLS:C0266604 Absent inner ear Aplasia of the labyrinth Labyrinthine aplasia Michel deformity HP:0011372 Aplasia of the inner ear is usually diagnosed on MR or CT imaging. Aplasia of the inner ear Absence of the inner ear due to a developmental defect. HPO_CONTRIBUTOR:DDD_dfitzpatrick Absent inner ear Incomplete formation of the cochlear partition. The scala vestibuli and scala tympani separated by the cochlear partition, except in the apical turn where the two scalae are in continuity via the helicotrema. 2012-03-07T08:24:55Z UMLS:C4023392 HP:0011373 Incomplete partition of the cochlea Incomplete formation of the cochlear partition. The scala vestibuli and scala tympani separated by the cochlear partition, except in the apical turn where the two scalae are in continuity via the helicotrema. Absence of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. 2012-03-07T08:31:27Z UMLS:C4023390 Absent cochlea HP:0011375 Cochlear aplasia Absence of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. HPO_CONTRIBUTOR:dfitzpatrick Absent cochlea An abnormality of the function of the inner ear. 2012-03-09T04:58:30Z UMLS:C4023382 Functional abnormality of the inner ear HP:0011389 The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium. Functional abnormality of the inner ear An abnormality of the function of the inner ear. HPO_CONTRIBUTOR:DDD_dfitzpatrick Functional abnormality of the inner ear A structural anomaly of the internal part of the ear. 2012-03-09T04:59:24Z UMLS:C4023381 Morphological abnormality of the inner ear HP:0011390 The inner ear contains the cochlea and the semicircular canals. Abnormal inner ear morphology A structural anomaly of the internal part of the ear. 2012-03-09T05:03:30Z UMLS:C4023380 Morphological abnormality of the nerves of the inner ear HP:0011391 Abnormal inner ear nerve morphology Absence or underdevelopment of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. 2012-03-09T05:37:50Z UMLS:C4023378 Absent/small cochlea Absent/underdeveloped cochlea HP:0011395 Aplasia/Hypoplasia of the cochlea Absence or underdevelopment of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. Absent/small cochlea Absent/underdeveloped cochlea 2012-03-15T11:05:13Z UMLS:C4023372 Abnormal umbilical cord blood vessels HP:0011403 Abnormal umbilical cord blood vessel morphology 2012-03-15T10:10:35Z SNOMEDCT_US:249174002 UMLS:C0426234 Placental calcification HP:0011415 Calcified placenta Increased length of the umbilical cord. 2012-03-15T10:12:55Z SNOMEDCT_US:237261008 UMLS:C0405028 Long umbilical cord HP:0011417 Long umbilical cord Increased length of the umbilical cord. Long umbilical cord An increased consentration of zinc in the blood. 2012-03-17T08:54:44Z UMLS:C0854520 UMLS:C0856208 Hyperzincemia HP:0011424 Increased serum zinc An increased consentration of zinc in the blood. An finding upon obstetric ultrasound examination performed at around 16 to 20 weeks of gestation that is abnormal but not clearly identifiable as a fetal anatomic malformation or growth restriction. Such findings are known as soft markers since they are associated with increased risk for fetal aneuploidy or other disorders. 2012-03-17T04:26:01Z UMLS:C4023366 Foetal ultrasound soft marker HP:0011425 The screening ultrasound at 16 to 20 weeks should evaluate 8 markers, 5 of which (thickened nuchal fold, echogenic bowel, mild ventriculomegaly, echogenic focus in the heart, and choroid plexus cyst) are associated with an increased risk of fetal aneuploidy, and in some cases with nonchromosomal problems, while 3 (single umbilical artery, enlarged cisterna magna, and pyelectasis) are only associated with an increased risk of nonchromosomal abnormalities when seen in isolation (PMID:16100637). Fetal ultrasound soft marker An finding upon obstetric ultrasound examination performed at around 16 to 20 weeks of gestation that is abnormal but not clearly identifiable as a fetal anatomic malformation or growth restriction. Such findings are known as soft markers since they are associated with increased risk for fetal aneuploidy or other disorders. PMID:16100637 Foetal ultrasound soft marker An abnormality of the medulla oblongata, the lower half of the brainstem. 2012-03-18T01:51:24Z UMLS:C4021148 Abnormality of the medulla oblongata Abnormality of the myencephalon HP:0011441 The medulla oblongata, which is often referred to simply as the medulla, comprises the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures. Abnormal medulla oblongata morphology An abnormality of the medulla oblongata, the lower half of the brainstem. An anomaly of the control or production of movement in the central nervous system. 2012-03-18T02:29:04Z UMLS:C4023354 Abnormality of central motor function HP:0011442 Abnormal central motor function An anomaly of the control or production of movement in the central nervous system. 2012-03-18T02:40:46Z UMLS:C4023353 Abnormality of coordination Coordination issue HP:0011443 Abnormality of coordination Abnormality of coordination Coordination issue Cognitive, psychiatric, or memory anomaly. 2012-03-18T04:23:59Z UMLS:C4023352 Abnormality of higher mental function HP:0011446 This includes abnormalities in speech, mood, emotions, behavior, and cognition. Abnormality of mental function A type of infection of the central nervous system that can be regarded as a sign of a pathological susceptibility to infection. 2012-03-18T05:57:29Z MSH:D002494 SNOMEDCT_US:128117002 UMLS:C0007684 Central nervous system infection HP:0011450 Unusual CNS infection Central nervous system infection An abnormality of the function of the middle ear. 2012-03-19T09:33:03Z UMLS:C4021846 Functional abnormality of the middle ear HP:0011452 The middle ear comprises the tympanic cavity in the temporal bone of the skull behind the eardrum, and is separated from the outer ear by the ear drum. The tympanic cavity contains the auditory ossicles (malleus, incus, stapes) that vibrate when exposed to sound, forming a chain that extends to the oval window of the inner ear and whose main function is to amplify sound. Additionally, the middle ear connects to the back of the throat and nose through the Eustachian tube. Functional abnormality of the middle ear An abnormality of the function of the middle ear. Functional abnormality of the middle ear A subjective manifestation of disease localized to the abdomen. 2012-03-25T05:35:45Z UMLS:C0740651 HP:0011458 Abdominal symptom Absence or underdevelopment of the gallbladder. 2012-03-25T07:40:20Z UMLS:C4023344 Absent/small gallbladder Absent/underdeveloped gallbladder HP:0011466 Aplasia/Hypoplasia of the gallbladder Absence or underdevelopment of the gallbladder. Absent/small gallbladder Absent/underdeveloped gallbladder A developmental defect in which the gallbladder fails to form. 2012-03-25T07:41:14Z MSH:C562564 SNOMEDCT_US:86507001 UMLS:C0266251 Absent gallbladder Agenesis of the gallbladder Aplasia of the gallbladder HP:0011467 Absent gallbladder A developmental defect in which the gallbladder fails to form. Absent gallbladder 2012-03-26T08:16:03Z UMLS:C4023341 Abnormal shape of small intestinal villus Abnormality of small intestinal villus morphology HP:0011472 Abnormal small intestinal villus morphology Abnormal shape of small intestinal villus The enteric villi are atrophic or absent. 2012-03-26T08:18:31Z SNOMEDCT_US:275403002 SNOMEDCT_US:75581001 UMLS:C0267456 UMLS:C0554101 UMLS:C1833058 UMLS:C1859541 UMLS:C2677378 UMLS:C4020747 Atrophy of small intestinal villi Villous degeneration Biopsy shows villous atrophy Duodenal villous atrophy Small intestine biopsy shows villous atrophy Variable degree of villous atrophy HP:0011473 Villous atrophy The enteric villi are atrophic or absent. Villous degeneration Biopsy shows villous atrophy Duodenal villous atrophy Small intestine biopsy shows villous atrophy Variable degree of villous atrophy An abnormality of the lacrimal punctum, an opening on the eyelid close to the medial canthus that drains tears from the conjunctival sac into the lacrimal duct in the same eyelid. 2012-04-01T09:08:05Z UMLS:C4023337 Abnormality of the lacrimal punctum HP:0011479 Abnormal lacrimal punctum morphology An abnormality of the lacrimal punctum, an opening on the eyelid close to the medial canthus that drains tears from the conjunctival sac into the lacrimal duct in the same eyelid. An abnormality of the lacrimal duct, a duct that drain tears from the conjunctiva, via the lacrimal puncta, into the lacrimal sac. 2012-04-01T09:11:55Z UMLS:C1858567 Abnormality of the lacrimal canaliculus Abnormality of the lacrimal duct HP:0011481 Abnormal lacrimal duct morphology An abnormality of the lacrimal duct, a duct that drain tears from the conjunctiva, via the lacrimal puncta, into the lacrimal sac. Abnormality of the lacrimal gland, i.e., of the almond-shaped gland that secretes the aqueous layer of the tear film for each eye. 2012-04-01T09:35:54Z UMLS:C4023336 Abnormality of the lacrimal gland HP:0011482 Abnormal lacrimal gland morphology Abnormality of the lacrimal gland, i.e., of the almond-shaped gland that secretes the aqueous layer of the tear film for each eye. Abnormality of the corneal endothelium, that is, the single layer of cells on the inner surface of the cornea. 2012-04-02T10:18:50Z UMLS:C4023332 Abnormality of corneal endothelium HP:0011488 Abnormal corneal endothelium morphology Abnormality of the corneal endothelium, that is, the single layer of cells on the inner surface of the cornea. Abnormal migration of corneal endothelium. 2012-04-02T10:20:17Z UMLS:C4023331 HP:0011489 Can be seen in posterior polymorphous corneal dystrophy. Abnormal migration of corneal endothelium Abnormal migration of corneal endothelium. HPO_CONTRIBUTOR:DDD_ncarter Abnormality of Descemet's membrane, which is the basement membrane of the corneal endothelium. 2012-04-02T10:23:11Z UMLS:C4023330 Abnormality of Descemet's membrane HP:0011490 Abnormal Descemet membrane morphology Abnormality of Descemet's membrane, which is the basement membrane of the corneal endothelium. An abnormality of the stroma of cornea, also known as the substantia propria of cornea. 2012-04-02T10:28:49Z UMLS:C4023328 Abnormality of corneal stroma HP:0011492 Abnormal corneal stroma morphology An abnormality of the stroma of cornea, also known as the substantia propria of cornea. HPO_CONTRIBUTOR:DDD_ncarter Abnormality of the corneal epithelium, that is of the epithelial tissue that covers the front of the cornea. 2012-04-03T07:10:49Z UMLS:C4023326 Abnormality of corneal epithelium HP:0011495 Abnormal corneal epithelium morphology Abnormality of the corneal epithelium, that is of the epithelial tissue that covers the front of the cornea. An abnormal shape of the lens. 2012-04-06T09:16:11Z UMLS:C4023314 Abnormality of lens shape HP:0011526 Abnormality of lens shape An abnormal shape of the lens. Abnormality of lens shape Congenital defect characterized by underdevelopment of the tricuspid valve. 2012-04-08T10:22:38Z Fyler:1720 UMLS:C4023294 Tricuspid valve hypoplasia Underdeveloped tricuspid valve HP:0011573 Hypoplastic tricuspid valve Congenital defect characterized by underdevelopment of the tricuspid valve. HPO_CONTRIBUTOR:DDD_dbrown Underdeveloped tricuspid valve Abnormally short chordae tendineae of the mitral valve. 2012-04-08T12:01:44Z UMLS:C4023288 HP:0011580 The chordae tendineae connect the papillary muscles to the tricuspid valve and the mitral valve in the heart. Short chordae tendineae of the mitral valve Abnormally short chordae tendineae of the mitral valve. An abnormality of the pulmonary situs, i.e., of the sidedness of the morphological right and left lungs, which is defined by characteristics such as the number of lobes per lung and the relationship of the pulmonary arteries to their bronchi. 2012-04-08T09:20:13Z UMLS:C4023271 Abnormality of pulmonary situs HP:0011615 Abnormal pulmonary situs morphology An abnormality of the pulmonary situs, i.e., of the sidedness of the morphological right and left lungs, which is defined by characteristics such as the number of lobes per lung and the relationship of the pulmonary arteries to their bronchi. HPO_CONTRIBUTOR:DDD_dbrown A developmental defect of the pericardium with congenital onset. 2012-04-08T10:05:20Z UMLS:C4023261 HP:0011628 Congenital defect of the pericardium A developmental defect of the pericardium with congenital onset. HPO_CONTRIBUTOR:DDD_dbrown No pericardium around the heart, occurring as a congenital defect, not the result of a surgical pericardectomy. 2012-04-08T10:06:22Z Fyler:1910 SNOMEDCT_US:253732001 UMLS:C0345140 Absent pericardium Congenital absence of the pericardium HP:0011629 Total absence of the pericardium No pericardium around the heart, occurring as a congenital defect, not the result of a surgical pericardectomy. HPO_CONTRIBUTOR:DDD_dbrown Absent pericardium Congenital absence of the pericardium An abnormality of the coronary sinus, which is formed by the union of the great cardiac vein and the left marginal vein and terminates in the right atrium. The coronary sinus functions to o collect deoxygenated blood from the myocardium of the heart and drain it into the right atrium. 2012-04-09T09:02:09Z Fyler:2840 SNOMEDCT_US:253323000 UMLS:C0344680 Abnormality of the coronary sinus HP:0011642 Abnormal coronary sinus morphology An abnormality of the coronary sinus, which is formed by the union of the great cardiac vein and the left marginal vein and terminates in the right atrium. The coronary sinus functions to o collect deoxygenated blood from the myocardium of the heart and drain it into the right atrium. HPO_CONTRIBUTOR:DDD_dbrown A venous pouch within the left ventricular wall, with a neck opening into the coronary sinus. 2012-04-09T09:12:28Z SNOMEDCT_US:447661004 UMLS:C3163894 Diverticulum of the coronary sinus HP:0011644 Coronary sinus diverticulum A venous pouch within the left ventricular wall, with a neck opening into the coronary sinus. HPO_CONTRIBUTOR:DDD_dbrown PMID:3138904 An abnormality of the pulmonary veins. 2012-04-11T08:45:48Z SNOMEDCT_US:111322000 SNOMEDCT_US:128585006 SNOMEDCT_US:199113001 UMLS:C0265914 Abnormality of lung veins HP:0011718 The right superior, right inferior, left superior, and left inferior pulmonary veins carry oxygenated blood to the left atrium. Abnormality of the pulmonary veins An abnormality of the pulmonary veins. Abnormality of lung veins Defect or defects of the morphogenesis of the right heart identifiable at birth. 2012-04-11T08:56:19Z UMLS:C4023219 HP:0011723 Congenital malformation of the right heart An abnormality in the range and ease of motion of joints across their normal range. 2012-04-18T07:09:28Z UMLS:C4023216 HP:0011729 Abnormality of joint mobility An abnormality in the range and ease of motion of joints across their normal range. Any structural anomaly of the adrenal glands. 2012-04-21T08:04:29Z UMLS:C4023213 Abnormality of adrenal morphology HP:0011732 Abnormal adrenal morphology Any structural anomaly of the adrenal glands. A functional abnormality of the adrenal glands. 2012-04-21T08:05:42Z HP:0002855 UMLS:C4023212 HP:0011733 Abnormality of adrenal physiology A functional abnormality of the adrenal glands. Absent development of the adrenal gland. 2012-04-21T09:46:49Z MSH:C538429 SNOMEDCT_US:702615004 SNOMEDCT_US:83190008 UMLS:C0266273 HP:0011743 Adrenal gland agenesis Absent development of the adrenal gland. An abnormality of the adenohypophysis, which is also known as the anterior lobe of the pituitary gland. 2012-04-22T11:17:00Z MSH:D010900 SNOMEDCT_US:399244003 UMLS:C0032002 UMLS:C4023206 Pituitary disease HP:0011747 Abnormality of the anterior pituitary An abnormality of the adenohypophysis, which is also known as the anterior lobe of the pituitary gland. An abnormality of the neurohypophysis, which is also known as the posterior lobe of the hypophysis. 2012-04-22T01:20:33Z UMLS:C4023204 Abnormality of the neurohypophysis Abnormality of the posterior pituitary HP:0011751 Abnormal posterior pituitary morphogenesis An abnormality of the neurohypophysis, which is also known as the posterior lobe of the hypophysis. Abnormality of the neurohypophysis Abnormal development of the neurohypophysis during embryonic growth and development. 2012-04-22T01:42:04Z UMLS:C4021123 Neurohypophysis dysplasia Posterior pituitary dysplasia HP:0011753 Posterior pituitary dysgenesis Abnormal development of the neurohypophysis during embryonic growth and development. Neurohypophysis dysplasia Absence of the neurohypophysis owing to a developmental defect. 2012-04-22T01:55:35Z UMLS:C4023203 Neurohypophysis agenesis HP:0011756 Posterior pituitary agenesis Absence of the neurohypophysis owing to a developmental defect. Neurohypophysis agenesis Underdevelopment of the neurohypophysis. 2012-04-22T01:56:23Z UMLS:C4023202 Neurohypophysis hypoplasia HP:0011757 Posterior pituitary hypoplasia Underdevelopment of the neurohypophysis. Neurohypophysis hypoplasia A structural abnormality of the parathyroid gland. 2012-04-22T04:08:26Z UMLS:C4023199 Abnormality of the parathyroid morphology HP:0011766 Abnormal parathyroid morphology A structural abnormality of the parathyroid gland. A functional abnormality of the parathyroid gland. 2012-04-22T04:09:13Z Parathyroid issue UMLS:C4023198 Parathyroid dysfunction HP:0011767 Abnormality of the parathyroid physiology A functional abnormality of the parathyroid gland. Parathyroid issue Parathyroid dysfunction Abnormal embryonic development of the parathyroid gland. 2012-04-22T04:20:41Z UMLS:C4023197 HP:0011768 Parathyroid dysgenesis Abnormal embryonic development of the parathyroid gland. A structural abnormality of the thyroid gland. 2012-04-22T05:54:57Z UMLS:C4023195 Abnormal shape of thyroid gland Abnormality of thyroid morphology HP:0011772 Abnormal thyroid morphology A structural abnormality of the thyroid gland. Abnormal shape of thyroid gland Neoplasm categorized according to type of histological abnormality. 2012-04-22T06:57:50Z UMLS:C4023186 HP:0011792 Neoplasm by histology Neoplasm categorized according to type of histological abnormality. Neoplasm categorized according to the anatomical site of origin of the neoplasm. 2012-04-22T07:00:13Z UMLS:C4023185 HP:0011793 Neoplasm by anatomical site Neoplasm categorized according to the anatomical site of origin of the neoplasm. 2012-04-23T07:27:57Z UMLS:C4023183 Abnormality of facial soft tissue Anomaly of facial soft tissue Deformity of facial soft tissue Malformation of facial soft tissue HP:0011799 Abnormality of facial soft tissue Abnormality of facial soft tissue Anomaly of facial soft tissue Deformity of facial soft tissue Malformation of facial soft tissue Posterior positions and/or vertical shortening of the infraorbital and perialar regions, or increased concavity of the face and/or reduced nasolabial angle. 2012-04-24T07:46:05Z HP:0040199 Small midface UMLS:C1853242 UMLS:C2673410 UMLS:C4280320 UMLS:C4280321 Decreased size of midface Flat midface Hypoplasia of midface Midface deficiency Midface hypoplasia Midface retrusion Midface, flat Retrusive midface Underdevelopment of midface Decreased projection of midface Hypotrophic midface HP:0011800 Midface retrusion Posterior positions and/or vertical shortening of the infraorbital and perialar regions, or increased concavity of the face and/or reduced nasolabial angle. PMID:19125436 Small midface Decreased size of midface Midface deficiency Midface hypoplasia Midface retrusion Retrusive midface Underdevelopment of midface Decreased projection of midface Hypotrophic midface Visually assessable vertical indentation, cleft, or depression of the nasal bridge, ridge and tip. 2012-04-25T08:09:58Z MSH:C535441 SNOMEDCT_US:204521002 UMLS:C0221363 UMLS:C4280318 UMLS:C4280319 Bifid nasal bridge Indentation or clefting of the nose Cleft nasal bridge Cleft nose Indented bridge of nose HP:0011803 This is a bundled term, but as it is useful in practice it is kept here. If it is only an indentation or cleft of the nasal tip, this should be coded as Bifid nasal tip. Bifid nose Visually assessable vertical indentation, cleft, or depression of the nasal bridge, ridge and tip. PMID:19152422 Bifid nasal bridge Indentation or clefting of the nose Cleft nasal bridge Cleft nose Indented bridge of nose A functional abnormality of a skeletal muscle. 2012-04-25T02:00:15Z UMLS:C4023182 Abnormality of muscle physiology Issue with muscle function HP:0011804 Abnormal muscle physiology A functional abnormality of a skeletal muscle. Issue with muscle function A structural abnormality of a skeletal muscle. 2012-04-25T02:00:34Z HP:0003735 UMLS:C4023181 Abnormal muscle morphology Abnormality of muscle morphology Abnormally shaped muscle Issue with muscle structure HP:0011805 Abnormal skeletal muscle morphology A structural abnormality of a skeletal muscle. Abnormally shaped muscle Issue with muscle structure Decreased intensity of the patellar reflex (also known as the knee jerk reflex). 2012-04-27T08:38:22Z UMLS:C3277184 Decreased knee jerk reflex Decreased patellar reflexes HP:0011808 Decreased patellar reflex Decreased intensity of the patellar reflex (also known as the knee jerk reflex). Decreased knee jerk reflex Decreased patellar reflexes An abnormality of one or more of the set of bones that make up the facial skeleton. 2012-04-29T04:37:30Z SNOMEDCT_US:433096001 UMLS:C2315229 Abnormality of facial skeleton Anomaly of facial skeleton Abnormality of facial bones Anomaly of facial bones Deformity of facial skeleton Deformity of the facial bones Malformation of facial bones Malformation of facial skeleton HP:0011821 The facial skeleton comprises the mandible, maxilla, frontal bone, nasal bones, and zygoma, as well as the inferior nasal concha, the lacrimal bones, the palatine bone, and the vomer. Abnormal facial skeleton morphology An abnormality of one or more of the set of bones that make up the facial skeleton. Abnormality of facial skeleton Anomaly of facial skeleton Abnormality of facial bones Anomaly of facial bones Deformity of facial skeleton Deformity of the facial bones Malformation of facial bones Malformation of facial skeleton Abnormality of the oral mucosa. 2012-05-01T10:43:40Z UMLS:C4023170 Abnormality of lining of mouth Abnormality of mucosa of mouth Abnormality of oral mucosa Abnormality of oral mucous membrane HP:0011830 Abnormal oral mucosa morphology Abnormality of the oral mucosa. Abnormality of lining of mouth Abnormality of mucosa of mouth Abnormality of oral mucous membrane A deviation from the normal count of T cells. 2012-05-06T10:43:44Z UMLS:C4021113 Abnormal number of T cells Abnormality of T cell number HP:0011839 Abnormal T cell count A deviation from the normal count of T cells. Abnormal number of T cells Abnormality of T cell number A functional anomaly of T cells. 2012-05-06T10:44:50Z HP:0005402 UMLS:C4023166 HP:0011840 Abnormality of T cell physiology A functional anomaly of T cells. An abnormality of the form, structure, or size of the skeletal system. 2012-05-07T08:08:37Z UMLS:C4023165 Abnormality of skeletal morphology Abnormally shaped skeletal HP:0011842 Abnormal skeletal morphology An abnormality of the form, structure, or size of the skeletal system. Abnormally shaped skeletal An abnormality of the function of the skeletal system. 2012-05-07T08:09:43Z UMLS:C4023164 Abnormality of musculoskeletal physiology HP:0011843 Abnormal musculoskeletal physiology An abnormality of the function of the skeletal system. An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles. 2012-05-07T08:12:26Z UMLS:C4023163 HP:0011844 Abnormal appendicular skeleton morphology An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles. Any anomaly in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. 2012-05-15T07:39:58Z MP:0008271 UMLS:C4023161 UMLS:C4280317 Abnormal bone maturation HP:0011849 All bones are formed by the replacement by osteocytes of mesenchyme-derived connective tissue. Intramembranous ossification refers to the direct replacement of primitive mesenchyme with bone, and is responsible for bones such as the calvarium (e.g., frontals, parietals, interparietal) and the clavicula. In endochondral ossification, the mesenchyme differentiates into a cartilaginous intermediate, which serves as a template (anlange) that is subsequently removed and replaced by bone. Most bones are formed via endochondral ossification, including those at the base of the skull, the vertebral column, pectoral and pelvic regions and long bones of the extremities. A reduction in the amount of mineralized bone compared with that expected for a given developmental age. In clinicakl parlance, reduced ossification and delayed ossification are often used synonymously, but in principle a bone delayed ossification in a child can display normal ossification at a later developmental stage. The HPO will therefore treat poor, reduced, and decreased officiation as synonymous, and delayed ossification as a specific kind of reduced ossification. Abnormal bone ossification Any anomaly in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. PMID:18157903 MP:0008271 Abnormal bone ossification Abnormal bone maturation Any structural anomaly of the connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. 2012-05-27T01:32:04Z UMLS:C4023158 HP:0011862 Abnormal bone collagen fibril morphology Any structural anomaly of the connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011642 Any anomaly in the formation of the bony substance of the sternum. 2012-05-27T04:08:55Z HP:0006624 UMLS:C1860243 Abnormal maturation of breastbone Sternal ossification center abnormalities Sternal ossification centre abnormalities HP:0011863 The sternum develops from two cartilaginous bars, situated one on either side of the median plane and connected with the cartilages of the upper nine ribs of its own side. During development, the two cartilaginous bars fuse with each other to form the cartilaginous sternum. This in turn is ossified from six centers: one in the manubrium, four in the body of the sternum, and one in the xiphoid process. Abnormal sternal ossification Any anomaly in the formation of the bony substance of the sternum. Abnormal maturation of breastbone Sternal ossification centre abnormalities Any anomaly in the function of thrombocytes. 2012-05-30T05:32:11Z UMLS:C0855740 HP:0011869 Abnormal platelet function Any anomaly in the function of thrombocytes. Abnormal number of platelets per volume of blood. In a healthy adult, a normal platelet count is between 150,000 and 450,000 per microliter of blood. 2012-05-30T08:11:13Z SNOMEDCT_US:165558001 UMLS:C0580317 HP:0011873 Abnormal platelet count Abnormal number of platelets per volume of blood. In a healthy adult, a normal platelet count is between 150,000 and 450,000 per microliter of blood. An anomaly in platelet form, ultrastructure, or intracellular organelles. 2012-05-31T03:43:59Z UMLS:C0855742 Abnormal shape of platelets HP:0011875 Abnormal platelet morphology An anomaly in platelet form, ultrastructure, or intracellular organelles. Abnormal shape of platelets Anomalous size of platelets. Most normal sized platelets are 1.5 to 3 micrometers in diameter. Large platelets are 4 to 7 micrometers. Giant platelets are larger than 7 micrometers and usually 10 to 20 micrometers. 2012-05-31T03:46:13Z UMLS:C4023152 HP:0011876 Abnormal platelet volume Anomalous size of platelets. Most normal sized platelets are 1.5 to 3 micrometers in diameter. Large platelets are 4 to 7 micrometers. Giant platelets are larger than 7 micrometers and usually 10 to 20 micrometers. Average platelet volume above the upper limit of the normal reference interval. 2012-05-31T03:58:17Z UMLS:C1096367 Large platelets HP:0011877 Mean platelet volume (MPV) is a measure of the average size of platelets, with a typical reference range of 7.5 to 11.5 femtoliters (fL). Increased mean platelet volume Average platelet volume above the upper limit of the normal reference interval. Large platelets A reduced concentration of vitamin K. 2012-06-02T05:21:14Z MSH:D014813 SNOMEDCT_US:52675005 UMLS:C0042880 HP:0011892 Low levels of vitamin K Number of leukocytes per volume of blood beyond normal limits. 2012-06-02T05:32:39Z SNOMEDCT_US:165509000 UMLS:C0580531 Abnormal white blood cell count HP:0011893 Abnormal leukocyte count Number of leukocytes per volume of blood beyond normal limits. Abnormal white blood cell count Anomaly in the level or the function of hemoglobin, the oxygen-carrying protein of erythrocytes. 2012-06-03T03:53:23Z UMLS:C0349705 Abnormal Hb Abnormal haemoglobin HP:0011902 Abnormal hemoglobin Anomaly in the level or the function of hemoglobin, the oxygen-carrying protein of erythrocytes. Abnormal Hb Abnormal haemoglobin An anomaly of a metacarpophalangeal joint. 2012-06-03T11:03:36Z UMLS:C4023132 Abnormality of metacarpophalangeal joint Abnormality of the knuckle HP:0011911 Abnormal metacarpophalangeal joint morphology An anomaly of a metacarpophalangeal joint. Abnormality of the knuckle An anomaly of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. 2012-06-05T08:51:23Z UMLS:C4023131 HP:0011912 Abnormality of the glenoid fossa An anomaly of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. Abnormal calcification in the cardiovascular system. 2012-06-05T10:35:58Z UMLS:C4023128 HP:0011915 Cardiovascular calcification Abnormal calcification in the cardiovascular system. Underdevelopment (hypoplasia) of the fifth toe. 2012-06-08T08:25:00Z UMLS:C4021111 Short fifth toe Short little toe Short pinkie toe Short pinky toe HP:0011917 Short 5th toe Underdevelopment (hypoplasia) of the fifth toe. Short little toe Short pinkie toe Short pinky toe One or more digit that appears disproportionately short compared to the hand/foot, whereby either the entire digit or a specific phalanx is shortened. 2012-06-10T09:18:42Z UMLS:C1860176 UMLS:C4023124 Short digit Very short digits HP:0011927 Note that the term brachydactyly is reserved for specific patterns of short digits, see HP:0001156. Short digit One or more digit that appears disproportionately short compared to the hand/foot, whereby either the entire digit or a specific phalanx is shortened. Short digit Very short digits Developmental hypoplasia (shortening) of proximal phalanx of toe. 2012-06-10T10:06:30Z UMLS:C4023123 Short innermost toe bone HP:0011928 Short proximal phalanx of toe Developmental hypoplasia (shortening) of proximal phalanx of toe. Short innermost toe bone An infection of the upper or lower respiratory tract. 2012-06-21T08:26:36Z MSH:D012141 SNOMEDCT_US:275498002 UMLS:C0035243 Respiratory infection Respiratory tract infection Respiratory infections HP:0011947 Respiratory tract infection An infection of the upper or lower respiratory tract. Respiratory infection Respiratory tract infection Respiratory infections Any deviation from the normal concentration of citrulline in the blood circulation. 2012-07-18T08:21:59Z UMLS:C4023103 HP:0011965 Citrulline is an alpha-amino acid that is a key intermediate in the urea cycle. Abnormal circulating citrulline concentration Any deviation from the normal concentration of citrulline in the blood circulation. An increased concentration of citrulline in the blood. 2012-07-18T08:23:22Z UMLS:C4023102 HP:0011966 Elevated plasma citrulline An increased concentration of citrulline in the blood. A functional abnormality of neutrophils. 2012-07-19T10:56:37Z UMLS:C4023093 HP:0011990 Abnormality of neutrophil physiology A functional abnormality of neutrophils. A deviation from the normal range of neutrophil cell counts in the circulation. 2012-07-19T10:59:14Z UMLS:C4023092 Abnormal neutrophil cell number HP:0011991 Abnormal neutrophil count A deviation from the normal range of neutrophil cell counts in the circulation. An abnormal form or size of neutrophils. 2012-07-19T11:00:27Z UMLS:C4023091 Abnormality of neutrophil morphology HP:0011992 Abnormal neutrophil morphology An abnormal form or size of neutrophils. An abnormality of the interatrial septum. 2012-07-19T11:34:27Z Fyler:2002 SNOMEDCT_US:253363004 UMLS:C0344722 Abnormal interatrial septum morphology Abnormality of the atrial septum HP:0011994 Abnormal atrial septum morphology An abnormality of the interatrial septum. Abnormal interatrial septum morphology Elevated concentration of galactose in the urine. 2012-07-26T10:31:35Z SNOMEDCT_US:71690006 UMLS:C0268157 Increased urinary galactose level HP:0012023 Galactosuria Elevated concentration of galactose in the urine. Increased urinary galactose level Elevated concentration of galactose in the blood. 2012-07-26T10:35:58Z MSH:D005693 SNOMEDCT_US:190745006 SNOMEDCT_US:190749000 UMLS:C0016952 UMLS:C4023071 Galactosemia HP:0012024 Hypergalactosemia is used here to mean the increased concentration of galactose in the blood. Note that the word galactosemia is occasionally used with the same meaning but more commonly denotes the disease entity called galactosemia caused by mutations in the galactose-1-phosphate uridyltransferase gene (MIM:230400). Hypergalactosemia Elevated concentration of galactose in the blood. Deviation from the normal concentration of ornithine in the blood circulation. 2012-07-26T10:48:59Z UMLS:C4023070 HP:0012025 Ornithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. Ornithine is a naturally occurring, non-proteinogenic amino acid found in meat, fish, dairy and eggs. Abnormal circulating ornithine concentration Deviation from the normal concentration of ornithine in the blood circulation. Increased concentration of ornithine in the blood. 2012-07-26T10:49:54Z MSH:D015799 SNOMEDCT_US:276426004 SNOMEDCT_US:33985005 UMLS:C0599035 High blood ornithine levels HP:0012026 Hyperornithinemia Increased concentration of ornithine in the blood. High blood ornithine levels An abnormal concentration of a hormone in the urine. 2012-07-27T01:29:51Z UMLS:C4023069 Abnormality of urine hormone level HP:0012029 Abnormal urine hormone level An abnormal concentration of a hormone in the urine. Inability to elicit tendon reflexes in the upper limbs. 2012-08-01T12:24:31Z UMLS:C2674177 HP:0012046 Areflexia of upper limbs Inability to elicit tendon reflexes in the upper limbs. Increased concentration of disaccharide in the urine. 2012-08-04T02:54:28Z UMLS:C4023062 HP:0012066 Excess amount of disaccharides such as mannosyl-N-acetylglucosamine excreted in the urine. Increased urinary disaccharide excretion Increased concentration of disaccharide in the urine. An increased concentration of keratan sulfate in the urine. 2012-08-04T03:20:15Z UMLS:C4023060 Keratan sulphate excretion in urine HP:0012069 Keratan sulfate is a a glycosaminoglycan. Keratan sulfate excretion in urine An increased concentration of keratan sulfate in the urine. Keratan sulphate excretion in urine An increased concentration of chondroitin sulfate (CHEBI:37397) in the urine. 2012-08-04T03:22:36Z UMLS:C4023059 Chondroitin sulphate excretion in urine HP:0012070 Chondroitin sulfate refers to a class of 10-60 kDa glycosaminoglycan sulfates, which are widely distributed in cartilage. Chondroitin sulfate excretion in urine An increased concentration of chondroitin sulfate (CHEBI:37397) in the urine. Chondroitin sulphate excretion in urine Excretion of urine with an acid pH, i.e., having an increased hydrogen ion concentration. SNOMEDCT_US:21806007 UMLS:C0278026 Acidic urine HP:0012072 Aciduria Excretion of urine with an acid pH, i.e., having an increased hydrogen ion concentration. Acidic urine An abnormally increased size of the cerebellum compared to other brain structures. 2012-08-18T05:29:26Z UMLS:C3278024 HP:0012081 Enlarged cerebellum An abnormally increased size of the cerebellum compared to other brain structures. Any abnormality of the size of the skeletal muscle cell. 2012-08-20T03:19:54Z UMLS:C4023051 Abnormality of skeletal muscle fibre size HP:0012084 Abnormality of skeletal muscle fiber size Any abnormality of the size of the skeletal muscle cell. Abnormality of skeletal muscle fibre size The presence of 10 or more white cells per cubic millimeter in a urine specimen, 3 or more white cells per high-power field of unspun urine, a positive result on Gram staining of an unspun urine specimen, or a urinary dipstick test that is positive for leukocyte esterase. 2012-08-20T09:10:26Z MSH:D011776 SNOMEDCT_US:275765006 SNOMEDCT_US:4800001 UMLS:C0034359 High urine neutrophil count Leukocyturia HP:0012085 Pyuria The presence of 10 or more white cells per cubic millimeter in a urine specimen, 3 or more white cells per high-power field of unspun urine, a positive result on Gram staining of an unspun urine specimen, or a urinary dipstick test that is positive for leukocyte esterase. PMID:25760357 High urine neutrophil count An anomaly in the surface contour of mitochondria. 2012-09-08T11:02:39Z UMLS:C4023050 HP:0012087 Abnormal mitochondrial shape An anomaly in the surface contour of mitochondria. MP:0011633 2012-08-20T09:16:38Z UMLS:C4023049 Abnormality of pancreas morphology Abnormally shaped pancreas HP:0012090 Abnormal pancreas morphology Abnormally shaped pancreas An anomaly of the function of the pancreas. 2012-08-20T09:17:10Z UMLS:C4023048 HP:0012091 Abnormality of pancreas physiology An anomaly of the function of the pancreas. A functional anomaly of the acinar gland portion of the pancreas that secretes digestive enzymes. 2012-08-20T09:17:46Z UMLS:C4021103 Abnormal exocrine pancreatic function HP:0012092 Abnormality of exocrine pancreas physiology A functional anomaly of the acinar gland portion of the pancreas that secretes digestive enzymes. Abnormal exocrine pancreatic function A function abnormality of the endocrine pancreas. 2012-08-20T09:18:18Z UMLS:C4023047 HP:0012093 Abnormality of endocrine pancreas physiology A function abnormality of the endocrine pancreas. A deviation from the normal size of the pancreas. 2012-08-20T09:19:08Z UMLS:C4023046 Abnormal pancreas size HP:0012094 Abnormal pancreas size A deviation from the normal size of the pancreas. Abnormal pancreas size A deviation from the normal number of mitochondria per cell. 2012-09-08T11:03:33Z UMLS:C4023043 HP:0012102 Abnormal mitochondrial number A deviation from the normal number of mitochondria per cell. An anomaly of the mitochondrion, the membranous cytoplasmic organelle the interior of which is subdivided by cristae. The mitochondrion is a self replicating organelle that is the site of tissue respiration. 2012-09-08T11:05:06Z UMLS:C4020732 UMLS:C4023042 Mitochondrial abnormalities HP:0012103 Abnormality of the mitochondrion An anomaly of the mitochondrion, the membranous cytoplasmic organelle the interior of which is subdivided by cristae. The mitochondrion is a self replicating organelle that is the site of tissue respiration. Mitochondrial abnormalities Underdevelopment of the pons. 2012-09-10T05:35:36Z UMLS:C1848529 Pontine hypoplasia HP:0012110 Hypoplasia of the pons Underdevelopment of the pons. An abnormality of the concentration of a glucocorticoid in the blood. 2012-09-16T04:22:26Z UMLS:C4023038 HP:0012111 Abnormality of circulating glucocorticoid level An abnormality of the concentration of a glucocorticoid in the blood. Inflammation of the liver. 2012-09-16T05:03:29Z MSH:D006505 SNOMEDCT_US:128241005 UMLS:C0019158 Liver inflammation HP:0012115 Hepatitis Inflammation of the liver. Liver inflammation Deviation from normal concentration of albumin in the blood. 2012-09-16T05:14:53Z UMLS:C4023036 Abnormal albumin level HP:0012116 Abnormal circulating albumin concentration Deviation from normal concentration of albumin in the blood. Abnormal albumin level Elevation in the concentration of albumin in the blood. 2012-09-16T05:15:41Z High albumin SNOMEDCT_US:119248009 UMLS:C1142113 High blood albumin levels Hyperalbuminaemia HP:0012117 Hyperalbuminemia Elevation in the concentration of albumin in the blood. High albumin High blood albumin levels Increased concentration of uracil in the urine. 2012-09-16T06:53:53Z UMLS:C4021833 High urine uracil levels HP:0012127 Uraciluria Increased concentration of uracil in the urine. High urine uracil levels An anomaly of erythroid lineage cells, that is, of the erythropoietic cells in the lineage leading to and including erythrocytes. 2012-09-16T07:14:03Z UMLS:C4020862 Abnormality of cells of the erythroid lineage HP:0012130 Abnormal erythroid lineage cell morphology An anomaly of erythroid lineage cells, that is, of the erythropoietic cells in the lineage leading to and including erythrocytes. A deviation from the normal count of erythroid precursor cells, that is, erythroid lineage cells in the bone marrow. 2012-09-16T07:17:18Z UMLS:C4023033 HP:0012131 Abnormal number of erythroid precursors A deviation from the normal count of erythroid precursor cells, that is, erythroid lineage cells in the bone marrow. Increased count of erythroid precursor cells, that is, erythroid lineage cells in the bone marrow. 2012-09-16T07:19:21Z UMLS:C0014800 UMLS:C1838111 UMLS:C3552917 Bone marrow biopsy shows erythroid hyperplasia Bone marrow smear shows erythroid hyperplasia HP:0012132 Erythroid hyperplasia Increased count of erythroid precursor cells, that is, erythroid lineage cells in the bone marrow. Bone marrow biopsy shows erythroid hyperplasia Bone marrow smear shows erythroid hyperplasia Decreased count of erythroid precursor cells, that is, erythroid lineage cells in the bone marrow. 2012-09-16T07:21:19Z MSH:D000741 SNOMEDCT_US:167923006 SNOMEDCT_US:41614006 UMLS:C0178416 UMLS:C0542035 Erythroblastopenia Erythroid hypoplasia in the bone marrow HP:0012133 Erythroid hypoplasia Decreased count of erythroid precursor cells, that is, erythroid lineage cells in the bone marrow. Erythroid hypoplasia in the bone marrow An anomaly of cells involved in the formation of a granulocytes, that is, of the granulocytopoietic cell. 2012-09-16T08:02:11Z UMLS:C4023031 Abnormality of cells of the granulocytic lineage HP:0012135 Abnormal granulocytopoietic cell morphology An anomaly of cells involved in the formation of a granulocytes, that is, of the granulocytopoietic cell. 2012-09-16T08:09:13Z UMLS:C4023029 HP:0012137 Abnormal number of granulocyte precursors 2012-09-16T08:09:36Z UMLS:C4023028 HP:0012138 Granulocytic hyperplasia Decreased number of granulocyte precursors in the bone marrow. 2012-09-16T08:09:56Z SNOMEDCT_US:416627004 UMLS:C1534864 HP:0012139 Granulocytic hypoplasia Decreased number of granulocyte precursors in the bone marrow. Any structural anomaly of megakaryocytes. Mature blood platelets are released from the cytoplasm of megakaryocytes, which are bone-marrow resident cells. 2012-09-16T08:20:38Z UMLS:C4023026 Abnormality of cells of the megakaryocyte lineage HP:0012143 Abnormal megakaryocyte morphology Any structural anomaly of a myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. 2012-09-16T08:21:37Z UMLS:C4023025 HP:0012144 Abnormal monocyte morphology 2012-09-16T08:21:57Z UMLS:C4023024 HP:0012145 Abnormality of multiple cell lineages in the bone marrow An decrease in the level of triglycerides in the blood. 2012-09-20T06:39:11Z UMLS:C0542037 Decreased circulating Tg levels Decreased plasma Tg levels Low blood triglyceride levels HP:0012153 Hypotriglyceridemia An decrease in the level of triglycerides in the blood. Decreased circulating Tg levels Decreased plasma Tg levels Low blood triglyceride levels A developmental defect resulting in the presence of fewer than the normal number of digits. 2013-02-16T10:44:40Z UMLS:C3887496 HP:0012165 Oligodactyly A developmental defect resulting in the presence of fewer than the normal number of digits. An anomaly of the natural killer cell, which is a lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors. It also regulates immune responses via cytokine release and direct contact with other cells. 2013-02-23T10:02:16Z UMLS:C4021098 Abnormal NK cells Abnormality of natural killer cells HP:0012176 Abnormal natural killer cell morphology An anomaly of the natural killer cell, which is a lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors. It also regulates immune responses via cytokine release and direct contact with other cells. PMID:21212348 Abnormal NK cells A functional anomaly of the natural killer cell. 2013-02-23T10:03:37Z UMLS:C4023012 HP:0012177 Abnormal natural killer cell physiology A functional anomaly of the natural killer cell. Reduced ability of the natural killer cell to function in the adaptive immune response. 2013-02-23T10:05:33Z UMLS:C1839969 HP:0012178 Reduced natural killer cell activity Reduced ability of the natural killer cell to function in the adaptive immune response. An increase in the concentration of bile acid in the blood. 2013-03-12T11:56:40Z UMLS:C4023004 HP:0012202 Increased serum bile acid concentration An increase in the concentration of bile acid in the blood. An anomaly of the mobility of ejaculated sperm. 2013-03-12T12:23:21Z UMLS:C0855512 Abnormal sperm motility HP:0012206 Abnormal sperm motility An anomaly of the mobility of ejaculated sperm. Abnormal sperm motility An abnormal reduction in the mobility of ejaculated sperm. 2013-03-12T12:23:59Z UMLS:C4023002 Asthenospermia Asthenozoospermia Reduced sperm motility HP:0012207 Reduced sperm motility An abnormal reduction in the mobility of ejaculated sperm. Reduced sperm motility Any structural anomaly of the kidney. 2013-03-14T07:41:11Z HP:0000792 HP:0004726 HP:0004735 HP:0008712 Fyler:4512 SNOMEDCT_US:44513007 UMLS:C0266292 Abnormal kidney morphology Abnormally shaped kidney Kidney malformation Kidney structure issue Renal malformation Structural anomalies of the renal tract Structural kidney abnormalities Structural renal anomalies HP:0012210 Abnormal renal morphology Any structural anomaly of the kidney. Abnormal kidney morphology Abnormally shaped kidney Kidney malformation Kidney structure issue Structural kidney abnormalities An abnormal functionality of the kidney. 2013-03-14T07:43:34Z HP:0000082 HP:0000087 HP:0005566 HP:0008646 SNOMEDCT_US:39539005 UMLS:C0151746 Abnormal kidney function Abnormal renal function Abnormality of renal physiology Kidney function issue Renal functional abnormality HP:0012211 Abnormal renal physiology An abnormal functionality of the kidney. Abnormal kidney function Abnormal renal function Kidney function issue Marked decrease in the number of granulocytes. 2013-03-31T09:42:50Z UMLS:C0702094 HP:0012234 Agranulocytosis is defined as an absolute neutrophil count less than 500 cells/microliter. Agranulocytosis Marked decrease in the number of granulocytes. A structural or developmental anomaly of any of the tissues involved in the genital system. 2013-04-02T07:02:20Z UMLS:C4021096 Abnormal genital system morphology HP:0012243 Abnormal reproductive system morphology A structural or developmental anomaly of any of the tissues involved in the genital system. MP:0002160 A structural anomaly of the respiratory system. 2013-04-07T09:11:09Z Fyler:4235 UMLS:C4022992 HP:0012252 Abnormal respiratory system morphology A structural anomaly of the respiratory system. Any structural anomaly of the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. 2013-04-07T09:12:48Z UMLS:C4022991 HP:0012253 Abnormal respiratory epithelium morphology Any structural anomaly of the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. MP:0010942 An abnormally reduced concentration of glycine in the blood. 2013-04-07T03:54:41Z UMLS:C4022973 Low blood glycine levels HP:0012277 Hypoglycinemia An abnormally reduced concentration of glycine in the blood. Low blood glycine levels Any deviation from the normal concentration of serine in the blood circulation. 2013-04-07T03:57:10Z UMLS:C4022972 HP:0012278 Abnormal circulating serine concentration Any deviation from the normal concentration of serine in the blood circulation. Reduced concentration of serine in the blood. 2013-04-07T03:57:25Z UMLS:C4022971 Low blood serine levels HP:0012279 Hyposerinemia Reduced concentration of serine in the blood. Low blood serine levels Reduced size of the proximal epiphysis of the tibia. 2013-04-09T07:36:38Z UMLS:C4022969 Small end part of innermost shankbone Small end part of innermost shinbone HP:0012284 Small proximal tibial epiphyses Reduced size of the proximal epiphysis of the tibia. Small end part of innermost shankbone Small end part of innermost shinbone An abnormal functionality of the hypothalamus. 2013-04-09T07:51:07Z UMLS:C4022968 HP:0012285 The hypothalamus is linked vascularly with the anterior lobe of the pituitary gland and thereby controls the secretion of pituitary hormones. Abnormal hypothalamus physiology An abnormal functionality of the hypothalamus. Any structural anomaly of the hypothalamus. 2013-04-09T07:53:16Z HP:0002443 UMLS:C4021095 Abnormal shape of hypothalamus Abnormality of hypothalamus morphology Abnormality of the hypothalamus HP:0012286 The hypothalamus is a cone-shaped cerebral structure that projects downward, ending in the pituitary (infundibular) stalk, a tubular connection to the pituitary gland. It is linked vascularly with the anterior lobe of the pituitary gland and thereby controls the secretion of pituitary hormones. Abnormal hypothalamus morphology Any structural anomaly of the hypothalamus. Abnormal shape of hypothalamus Abnormality of the occipital bone of the skull. 2013-04-11T06:21:12Z UMLS:C4022964 Abnormality of the occipital bone HP:0012294 Abnormal occipital bone morphology Abnormality of the occipital bone of the skull. Increased length of the middle phalanx of finger. 2013-04-12T05:46:43Z UMLS:C4022960 Long middle bone of finger HP:0012298 Long middle phalanx of finger Increased length of the middle phalanx of finger. Long middle bone of finger Increased length of the distal phalanx of finger. 2013-04-12T05:48:52Z UMLS:C4021865 Long outermost bone of finger HP:0012299 Long distal phalanx of finger Increased length of the distal phalanx of finger. Long outermost bone of finger An anomaly of the arch of aorta. 2013-08-06T10:06:07Z Fyler:2700 SNOMEDCT_US:448742006 UMLS:C3163801 Abnormality of the aortic arch HP:0012303 Abnormal aortic arch morphology An anomaly of the arch of aorta. Underdevelopment of the arch of aorta. 2013-08-06T10:10:36Z Fyler:2704 SNOMEDCT_US:60787001 UMLS:C0265881 Aortic arch hypoplasia Underdeveloped aortic arch HP:0012304 Hypoplastic aortic arch Underdevelopment of the arch of aorta. Underdeveloped aortic arch An anomaly of the process of rib bone formation. 2013-08-10T09:31:03Z UMLS:C4022957 Abnormal maturation of rib bones HP:0012306 Abnormal rib ossification An anomaly of the process of rib bone formation. Abnormal maturation of rib bones An anomaly in the number of monocytes, which are myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. 2013-08-10T12:07:14Z SNOMEDCT_US:165540007 SNOMEDCT_US:165541006 UMLS:C0580319 Abnormal monocyte number HP:0012310 Abnormal monocyte count An anomaly in the number of monocytes, which are myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. An increased number of circulating monocytes. 2013-08-10T12:09:16Z SNOMEDCT_US:19636003 UMLS:C0085702 High blood monocyte number HP:0012311 Monocytosis An increased number of circulating monocytes. High blood monocyte number An decreased number of circulating monocytes. 2013-08-10T12:10:07Z SNOMEDCT_US:165539005 UMLS:C0427544 Low blood monocyte number HP:0012312 Monocytopenia An decreased number of circulating monocytes. Low blood monocyte number An anomaly of the celiac artery. 2013-08-12T08:47:21Z UMLS:C4022954 Abnormal coeliac artery morphology Abnormality of the celiac artery Abnormality of the coeliac artery HP:0012326 The celiac artery (celiac trunk or truncus coeliacus) is the first major branch of the abdominal aorta. Abnormal celiac artery morphology An anomaly of the celiac artery. Abnormal coeliac artery morphology Abnormality of the coeliac artery A structural abnormality of the autonomic nervous system. 2013-09-13T07:52:31Z UMLS:C4022953 HP:0012331 Abnormal autonomic nervous system morphology A structural abnormality of the autonomic nervous system. A functional abnormality of the autonomic nervous system. 2013-09-13T07:53:55Z HP:0002271 HP:0002387 HP:0002459 HP:0007310 UMLS:C4022952 Autonomic dysfunction Autonomic dysregulation Dysautonomia HP:0012332 Abnormal autonomic nervous system physiology A functional abnormality of the autonomic nervous system. An abnormality of the metabolism of folic acid, which is also known as vitamin B9. 2013-09-13T08:38:06Z UMLS:C4022951 HP:0012335 Abnormality of folate metabolism An abnormality of the metabolism of folic acid, which is also known as vitamin B9. An anomaly in the processes involved in the maintenance of an internal equilibrium. 2013-09-13T09:23:23Z MP:0001764 UMLS:C4022950 HP:0012337 Abnormal homeostasis An anomaly in the processes involved in the maintenance of an internal equilibrium. MP:0001764 Abnormal homeostasis A decreased concentration of potassium(1+) in the urine. 2013-10-03T10:21:51Z SNOMEDCT_US:54781007 UMLS:C0268024 Decreased urinary K Hypokaliuria Hypokaluria Low urine potassium levels HP:0012364 Decreased urinary potassium A decreased concentration of potassium(1+) in the urine. Decreased urinary K Low urine potassium levels An abnormally decreased phosphate concentration in the urine. 2013-10-03T10:25:06Z SNOMEDCT_US:91632005 UMLS:C0268077 Low urine phosphate levels HP:0012365 Hypophosphaturia An abnormally decreased phosphate concentration in the urine. Low urine phosphate levels Absence of concavity or convexity of the face when viewed in profile. 2013-10-13T01:49:13Z UMLS:C1853241 Flat face Flat facial profile Flat facial shape Flat facies HP:0012368 A useful guide is to imagine that a line connecting the glabella to the anterior most part of the mandible touches the top of the philtrum where it meets the base of the columella. The glabella is the most prominent point on the frontal bone above the root of the nose. If the superior philtrum is anterior to this line the face is convex, if the superior philtrum is posterior to this line the face is concave. Flat face Absence of concavity or convexity of the face when viewed in profile. PMID:19125436 Flat face Flat facial profile Flat facial shape Flat facies A structural anomaly of the globe of the eye, or bulbus oculi. 2013-10-13T03:44:43Z HP:0000489 HP:0012374 Fyler:4863 UMLS:C4022925 Abnormal eye structure Abnormality of the globe Abnormally shaped eye HP:0012372 previously: Abnormal globe morphology Abnormal eye morphology A structural anomaly of the globe of the eye, or bulbus oculi. Abnormal eye structure Abnormally shaped eye A functional anomaly of the eye. 2013-10-13T03:45:37Z UMLS:C4022924 Abnormal eye physiology HP:0012373 Abnormal eye physiology A functional anomaly of the eye. Abnormal eye physiology Concentration or activity of an enzyme is above or below the limits of normal in the blood circulation. 2013-10-15T08:58:55Z UMLS:C4022922 HP:0012379 Abnormal circulating enzyme concentration or activity Concentration or activity of an enzyme is above or below the limits of normal in the blood circulation. MP:0005584 The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers or toes cannot be extended to 180 degrees by either active or passive extension. 2013-10-20T08:08:19Z SNOMEDCT_US:29271008 UMLS:C0685409 Permanent flexion of the finger or toe HP:0012385 Camptodactyly The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers or toes cannot be extended to 180 degrees by either active or passive extension. Permanent flexion of the finger or toe Reduced intensity of muscle tendon reflexes in the upper limbs. Reflexes are elicited by stretching the tendon of a muscle, e.g., by tapping. 2013-11-07T07:42:49Z UMLS:C1836835 HP:0012391 Hyporeflexia of upper limbs Reduced intensity of muscle tendon reflexes in the upper limbs. Reflexes are elicited by stretching the tendon of a muscle, e.g., by tapping. Reduced intensity of muscle tendon reflexes in jaw. 2013-11-07T07:43:29Z UMLS:C4022918 Mandibular hyporeflexia HP:0012392 The jaw jerk is elicited by the examiner placing the tip of the index finger on a relaxed jaw, one that is about one-third open. One then taps briskly on the index finger with the other hand and notes the speed as the mandible is flexed. Jaw hyporeflexia Reduced intensity of muscle tendon reflexes in jaw. Mandibular hyporeflexia An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. 2013-11-10T04:59:20Z SNOMEDCT_US:312391003 UMLS:C0476337 Abnormal blood gas level HP:0012415 Abnormal blood gas level An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. Abnormal blood gas level An inflammation of the choroid and retina. 2013-11-11T08:10:29Z MSH:D002825 SNOMEDCT_US:46627006 UMLS:C0008513 HP:0012424 Chorioretinitis is a form of posterior uveitis. Note that the term Chorioretinitis suggests that the origin of the process is predominantly in the choroid while Retinitis suggests that the process is mainly in the retina. Chorioretinitis An inflammation of the choroid and retina. PMID:16196117 An abnormality of actions or reactions of a person taking place during interactions with others. 2013-11-23T08:37:01Z UMLS:C4020726 UMLS:C4021087 Abnormal social behavior Abnormal social behaviour Abnormal social interactions HP:0012433 Abnormal social behavior Abnormal social behavior Abnormal social behaviour Abnormal social interactions A structural anomaly of the gallbladder. 2013-11-23T01:13:40Z UMLS:C4022904 Abnormal gallbladder structure Abnormal shape of gallbladder HP:0012437 Abnormal gallbladder morphology A structural anomaly of the gallbladder. Abnormal gallbladder structure Abnormal shape of gallbladder A functional anomaly of the gallbladder. 2013-11-23T01:17:00Z UMLS:C4022903 HP:0012438 Abnormal gallbladder physiology A functional anomaly of the gallbladder. A functional abnormality of the biliary tree. 2013-11-23T02:14:51Z UMLS:C4022902 HP:0012439 Abnormal biliary tract physiology A functional abnormality of the biliary tree. A structural abnormality of the biliary tree. 2013-11-23T02:15:33Z UMLS:C4021086 Anomaly of the biliary tract HP:0012440 Abnormal biliary tract morphology A structural abnormality of the biliary tree. A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. 2013-11-23T02:38:00Z UMLS:C4021085 Abnormal shape of brain Abnormality of brain morphology Abnormality of the brain HP:0012443 Abnormal brain morphology A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. Abnormal shape of brain Abnormality of the brain Partial or complete wasting (loss) of brain tissue that was once present. 2013-11-23T02:46:15Z SNOMEDCT_US:278849000 SNOMEDCT_US:418143002 SNOMEDCT_US:52522001 UMLS:C0154671 UMLS:C0235946 Brain degeneration Brain wasting HP:0012444 Brain atrophy Partial or complete wasting (loss) of brain tissue that was once present. Brain degeneration Brain wasting Calcification, that is, pathological deposition of calcium salts in the tunica media of arteries. 2013-11-24T10:50:45Z UMLS:C4022896 HP:0012456 Medial arterial calcification causes stiffening and decreased compliance of the affected arteries. Medial arterial calcification Calcification, that is, pathological deposition of calcium salts in the tunica media of arteries. An increased level of iron in liver tissues. 2013-11-24T12:54:57Z UMLS:C4022891 Increased iron concentration in liver Increased liver iron level HP:0012465 This abnormality can be measured by liver biopsy or by hepatic magnetic resonance imaging. Elevated hepatic iron concentration An increased level of iron in liver tissues. PMID:10922422 PMID:14668426 Increased iron concentration in liver Increased liver iron level An anomaly of cerebral veins. 2013-11-28T08:01:32Z UMLS:C4022888 Abnormality of cerebral veins HP:0012480 Abnormal cerebral vein morphology An anomaly of cerebral veins. Inflammation of the spinal cord. 2013-11-29T08:10:12Z MSH:D009187 SNOMEDCT_US:41370002 UMLS:C0026975 Inflammation of spinal cord HP:0012486 Myelitis Inflammation of the spinal cord. Inflammation of spinal cord Inflammation of adipose tissue. 2013-11-29T09:28:11Z MSH:D015434 SNOMEDCT_US:22125009 UMLS:C0030326 Inflammation of adipose tissue Inflammation of fat tissue HP:0012490 Panniculitis most commonly affects the skin and characterized by reddened subcutaneous nodules. Panniculitis Inflammation of adipose tissue. Inflammation of adipose tissue Inflammation of fat tissue An anomaly of the pituitary gland. 2013-11-30T09:34:21Z MSH:D010900 SNOMEDCT_US:399244003 UMLS:C0032002 Abnormality of the pituitary gland disorder of pituitary gland HP:0012503 Abnormal pituitary gland morphology An anomaly of the pituitary gland. A deviation from the normal size of the pituitary gland. 2013-11-30T09:36:04Z UMLS:C4022874 HP:0012504 Abnormal size of pituitary gland A deviation from the normal size of the pituitary gland. An abnormally increased size of the pituitary gland. 2013-11-30T09:36:45Z SNOMEDCT_US:237718009 UMLS:C0342422 HP:0012505 Enlarged pituitary gland An abnormally increased size of the pituitary gland. An abnormally decreased size of the pituitary gland. 2013-11-30T09:37:34Z UMLS:C4022873 HP:0012506 Small pituitary gland An abnormally decreased size of the pituitary gland. An anomaly of the circle of Willis, also known as the cerebral arterial circle. 2013-12-09T07:03:02Z UMLS:C4022868 Abnormality of the cerebral arterial circle HP:0012518 The circle of Willis is a circulatory anastomosis in the brain comprised of the anterior cerebral arteries, the anterior communicating artery, the internal carotid arteries, the posterior cerebral arteries, and the posterior communicating arteries. Abnormal circle of Willis morphology An anomaly of the circle of Willis, also known as the cerebral arterial circle. Abnormality of the cerebral arterial circle A deviation from the normal discoid platelet shape. 2013-12-15T08:55:03Z UMLS:C4022866 HP:0012524 Abnormal platelet shape A deviation from the normal discoid platelet shape. An anomaly in the communication from a neuron to a target across a synapse. This is a four step process, comprising (i) synthesis and storage of neurotransmitters; (ii) neurotransmitter release; (iii) activation of postsynaptic receptors by the neurotransmitter; and (iv) inactivation of the neurotransmitter. Thus, this term is defined as an anomaly of neurotransmitter metabolic process. 2013-12-15T10:12:31Z UMLS:C4021083 Abnormality of neurotransmitter metabolism HP:0012535 Abnormal synaptic transmission An anomaly in the communication from a neuron to a target across a synapse. This is a four step process, comprising (i) synthesis and storage of neurotransmitters; (ii) neurotransmitter release; (iii) activation of postsynaptic receptors by the neurotransmitter; and (iv) inactivation of the neurotransmitter. Thus, this term is defined as an anomaly of neurotransmitter metabolic process. MP:0003635 Increased concentration of beta-alanine in the blood. 2014-01-04T01:37:23Z UMLS:C4021080 High blood beta-alanine levels Hyperbetaalaninemia HP:0012556 Hyperbeta-alaninemia Increased concentration of beta-alanine in the blood. High blood beta-alanine levels A structural anomaly of the nephron. 2014-01-16T12:49:04Z UMLS:C4022838 Abnormality of the nephron HP:0012575 Abnormal nephron morphology A structural anomaly of the nephron. HPO_CONTRIBUTOR:Eurenomics_fschaefer Atrophy of the kidney. 2014-01-16T03:21:19Z SNOMEDCT_US:197659005 UMLS:C0341698 Kidney degeneration HP:0012585 Renal atrophy Atrophy of the kidney. Kidney degeneration An abnormal amount of urine production. 2014-01-16T03:59:33Z UMLS:C3693260 HP:0012590 Abnormal urine output An abnormal amount of urine production. HPO_CONTRIBUTOR:Eurenomics_ewuehl An abnormality in the concentration of electrolytes in the urine. 2014-01-16T05:44:11Z UMLS:C4022833 Urinary electrolyte imbalance HP:0012591 Abnormal urinary electrolyte concentration An abnormality in the concentration of electrolytes in the urine. PMID:25215103 Increased concentration of albumin in the urine. 2014-01-16T05:49:16Z MSH:D000419 SNOMEDCT_US:274769005 UMLS:C0001925 HP:0012592 Albuminuria Increased concentration of albumin in the urine. HPO_CONTRIBUTOR:Eurenomics_fschaefer An abnormal concentration of potassium(1+) in the urine. 2014-01-16T06:11:59Z UMLS:C4022829 Abnormal urine K concentration HP:0012598 Abnormal urine potassium concentration An abnormal concentration of potassium(1+) in the urine. HPO_CONTRIBUTOR:Eurenomics_fschaefer Abnormal urine K concentration An abnormal phosphate concentration in the urine. 2014-01-16T06:14:49Z UMLS:C4022828 HP:0012599 Abnormal urine phosphate concentration An abnormal phosphate concentration in the urine. HPO_CONTRIBUTOR:Eurenomics_ewuehl An abnormal concentration of sodium in the urine. 2014-01-16T06:19:27Z UMLS:C4022825 Abnormal urine Na concentration Abnormal urine Na+ levels HP:0012603 Abnormal urine sodium concentration An abnormal concentration of sodium in the urine. HPO_CONTRIBUTOR:Eurenomics_fschaefer An abnormally decreased sodium concentration in the urine. 2014-01-16T06:22:09Z UMLS:C4022824 Low urine sodium levels HP:0012604 Hyponatriuria An abnormally decreased sodium concentration in the urine. HPO_CONTRIBUTOR:Eurenomics_ewuehl Low urine sodium levels An increased concentration of sodium(1+) in the urine. 2014-01-16T06:22:44Z HP:0003608 UMLS:C3671887 Increased urinary sodium HP:0012605 Hypernatriuria An increased concentration of sodium(1+) in the urine. HPO_CONTRIBUTOR:Eurenomics_ewuehl An abnormal concentration of magnesium the urine. 2014-01-17T11:37:50Z UMLS:C4022823 Abnormal urine magnesium concentration HP:0012607 Abnormal urine magnesium concentration An abnormal concentration of magnesium the urine. HPO_CONTRIBUTOR:Eurenomics_ewuehl Abnormal urine magnesium concentration An increased concentration of magnesium the urine. 2014-01-17T11:38:51Z UMLS:C2673443 HP:0012608 Hypermagnesiuria An increased concentration of magnesium the urine. HPO_CONTRIBUTOR:Eurenomics_fschaefer An decreased concentration of magnesium the urine. 2014-01-17T11:39:31Z UMLS:C3203528 Decreased urine magnesium Low urine magnesium levels HP:0012609 Hypomagnesiuria An decreased concentration of magnesium the urine. HPO_CONTRIBUTOR:Eurenomics_fschaefer Decreased urine magnesium Low urine magnesium levels Abnormal concentration of sulfate in the urine. 2014-01-17T11:58:23Z UMLS:C4022821 Abnormal urinary sulphate concentration HP:0012612 Abnormal urinary sulfate concentration Abnormal concentration of sulfate in the urine. Abnormal urinary sulphate concentration Elevated concentration of SO4(2-), i.e., sulfate, in the urine. 2014-01-17T11:58:51Z UMLS:C4022820 Increased urinary sulphate HP:0012613 Increased urinary sulfate Elevated concentration of SO4(2-), i.e., sulfate, in the urine. Increased urinary sulphate An anomalous finding in the examination of the urine for cells. 2014-01-17T12:01:16Z SNOMEDCT_US:310439007 UMLS:C0587955 HP:0012614 Abnormal urine cytology An anomalous finding in the examination of the urine for cells. HPO_CONTRIBUTOR:Eurenomics_ewuehl A developmental anomaly associated with the failure of rectum, vagina, and bladder to separate. 2014-01-17T12:27:06Z UMLS:C4022816 HP:0012620 Cloacal abnormality A developmental anomaly associated with the failure of rectum, vagina, and bladder to separate. A functional anomaly of the nervous system. 2014-01-19T08:02:46Z UMLS:C4022811 Abnormality of nervous system physiology HP:0012638 Abnormal nervous system physiology A functional anomaly of the nervous system. A structural anomaly of the nervous system. 2014-01-19T08:03:08Z Fyler:4135 Fyler:4300 UMLS:C4022810 Abnormal shape of nervous system Abnormality of nervous system morphology HP:0012639 Abnormal nervous system morphology A structural anomaly of the nervous system. Abnormal shape of nervous system Increase in size of a peripheral nerve. This finding can be appreciated by palpation along the axis of the nerve. 2014-02-01T12:44:16Z UMLS:C2675074 Enlarged peripheral nerves HP:0012645 This feature can be appreciated by imaging studies (magnetic resonancy tomography), by palpation along the axis of a nerve, and by biopsy, and may be caused by axonal swelling or by myelin thickening. The differential diagnosis of enlarged peripheral nerves includes leprosy, hereditary motor and sensory neuropathy type 1 (about 30% of patients), but not type 2 (the axonal form), some other polyneuropathies, neurofibromatosis, and nerve tumors. A good review is available in Practical Neurology, 2003,3:40-45 by Michael Donaghy (no pubmed id). Enlarged peripheral nerve Increase in size of a peripheral nerve. This finding can be appreciated by palpation along the axis of the nerve. Enlarged peripheral nerves Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. 2014-02-01T01:25:42Z UMLS:C4022805 Abnormal inflammatory response HP:0012647 Abnormal inflammatory response Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. Abnormal inflammatory response An abnormal reduction in the inflammatory response to injury or infection. 2014-02-01T01:29:24Z UMLS:C4022804 Decreased inflammatory response HP:0012648 Decreased inflammatory response An abnormal reduction in the inflammatory response to injury or infection. Decreased inflammatory response A abnormal increase in the inflammatory response to injury or infection. 2014-02-01T01:29:58Z UMLS:C4022803 HP:0012649 Increased inflammatory response A abnormal increase in the inflammatory response to injury or infection. An abnormal build up of iron (Fe) in brain tissue. 2014-03-13T07:22:40Z UMLS:C4021076 Brain iron deposition Iron accumulation in brain HP:0012675 Iron accumulation in brain An abnormal build up of iron (Fe) in brain tissue. Iron accumulation in brain An anomaly of the pineal gland,a small endocrine gland in the brain that produces melatonin. 2014-03-22T12:46:36Z UMLS:C4022783 HP:0012680 Abnormality of the pineal gland An anomaly of the pineal gland,a small endocrine gland in the brain that produces melatonin. A structural abnormality of the pineal gland. 2014-03-22T12:50:21Z UMLS:C4022782 Abnormality of pineal morphology HP:0012681 The pineal gland typically measures 7 x 6 x 3mm in size and is located in a groove between the laterally placed thalamic bodies. Abnormal pineal morphology A structural abnormality of the pineal gland. HPO_CONTRIBUTOR:UToronto_htrang Accumulation of calcium salts in the pineal gland. 2014-03-22T12:51:57Z UMLS:C1398718 HP:0012682 This feature can be appreciated on skull radiography. Pineal gland calcification Accumulation of calcium salts in the pineal gland. An abnormal increase or decrease in the quantity of three-dimensional space taken up by the pineal gland. 2014-03-22T01:08:48Z UMLS:C4022781 HP:0012684 This feature is typically assessed by magnetic resonance tomography of the brain. Abnormal pineal volume An abnormal increase or decrease in the quantity of three-dimensional space taken up by the pineal gland. HPO_CONTRIBUTOR:UToronto_htrang An abnormal reduction in the quantity of three-dimensional space taken up by the pineal gland. 2014-03-22T01:10:12Z UMLS:C4022780 HP:0012685 Decreased pineal volume An abnormal reduction in the quantity of three-dimensional space taken up by the pineal gland. HPO_CONTRIBUTOR:UToronto_htrang PMID:24456088 An abnormal elevation in the quantity of three-dimensional space taken up by the pineal gland. 2014-03-22T01:11:33Z UMLS:C4022779 HP:0012686 Increased pineal volume An abnormal elevation in the quantity of three-dimensional space taken up by the pineal gland. HPO_CONTRIBUTOR:UToronto_htrang A functional abnormality of the pineal gland. 2014-03-22T01:15:36Z UMLS:C4022778 HP:0012688 Abnormality of pineal physiology A functional abnormality of the pineal gland. HPO_CONTRIBUTOR:UToronto_htrang A structural abnormality of a diaphysis of the leg. 2014-03-22T06:14:15Z UMLS:C4022767 Anomaly of shaft of long bone of lower limb HP:0012699 Anomaly of lower limb diaphyses A structural abnormality of a diaphysis of the leg. HPO_CONTRIBUTOR:UToronto_htrang Anomaly of shaft of long bone of lower limb A functional anomaly of the large intestine. 2014-03-22T06:20:38Z UMLS:C4022766 HP:0012700 Abnormal large intestine physiology A functional anomaly of the large intestine. Abnormality in the space in the meninges beneath the arachnoid membrane and above the pia mater that contains the cerebrospinal fluid. 2014-03-22T07:45:24Z UMLS:C4022765 Abnormality of the subarachnoid space HP:0012703 Abnormal subarachnoid space morphology Abnormality in the space in the meninges beneath the arachnoid membrane and above the pia mater that contains the cerebrospinal fluid. HPO_CONTRIBUTOR:UToronto_htrang Abnormal structure of the gastrointestinal tract. 2014-03-23T01:09:02Z UMLS:C4021073 Abnormal shape of the digestive system Morphological abnormality of the GI tract Morphological abnormality of the gastrointestinal tract Morphological anomaly of the digestive system HP:0012718 Abnormal gastrointestinal tract morphology Abnormal structure of the gastrointestinal tract. Abnormal shape of the digestive system Morphological abnormality of the GI tract Abnormal functionality of the gastrointestinal tract. 2014-03-23T01:10:47Z UMLS:C4022755 Functional abnormality of the GI tract GI dysfunction HP:0012719 Functional abnormality of the gastrointestinal tract Abnormal functionality of the gastrointestinal tract. Functional abnormality of the GI tract GI dysfunction A vascular malformation resulting from a developmental error of venous tissue composed of dysmorphic channels lined by flattened endothelium and exhibiting slow turnover. A venous malformation may present as a blue patch on the skin ranging to a soft blue mass. Venous malformations are easily compressible and usually swell in thewhen venous pressure increases (e.g., when held in a dependent position or when a child cries). They may be relatively localized or quite extensive within an anatomic region. 2014-03-23T01:20:33Z SNOMEDCT_US:297222002 UMLS:C2937220 Venous malformations HP:0012721 Venous malformations are always present at birth, and usually involve the skin of the face, limbs, or trunk. Venous malformation A vascular malformation resulting from a developmental error of venous tissue composed of dysmorphic channels lined by flattened endothelium and exhibiting slow turnover. A venous malformation may present as a blue patch on the skin ranging to a soft blue mass. Venous malformations are easily compressible and usually swell in thewhen venous pressure increases (e.g., when held in a dependent position or when a child cries). They may be relatively localized or quite extensive within an anatomic region. Venous malformations Impaired conduction of cardiac impulse occurring anywhere along the conduction pathway. 2014-03-23T01:32:14Z MSH:D006327 SNOMEDCT_US:233916004 UMLS:C0018794 HP:0012722 Heart block Impaired conduction of cardiac impulse occurring anywhere along the conduction pathway. An abnormality of the anus or rectum. 2014-03-23T02:48:00Z MSH:D000071056 SNOMEDCT_US:33225004 UMLS:C3495676 HP:0012732 Anorectal anomaly An abnormality of the anus or rectum. A discrete abnormal tissue mass that protrudes into the lumen of the small intestine and is attached to the intestinal wall either by a stalk, pedunculus, or a broad base. 2014-03-23T03:50:25Z SNOMEDCT_US:399723004 UMLS:C1302645 HP:0012737 Small intestinal polyp A discrete abnormal tissue mass that protrudes into the lumen of the small intestine and is attached to the intestinal wall either by a stalk, pedunculus, or a broad base. Excessive fat around the stomach and abdomen. 2014-03-23T05:00:05Z MSH:D056128 SNOMEDCT_US:248311001 UMLS:C0311277 Abdominal obesity Central obesity HP:0012743 Abdominal obesity Excessive fat around the stomach and abdomen. Abdominal obesity Central obesity Failure of the femur to develop. 2014-03-23T05:14:34Z SNOMEDCT_US:47276000 UMLS:C0265629 Absent femur Absent thighbone Aplasia of the femur HP:0012744 Femoral aplasia Failure of the femur to develop. Absent thighbone A structural anomaly of a neuron. Neurons are electrically excitable cells that transmit signals throughout the body. Neurons employ both electrical and chemical components in the transmission of information. Neurons are connected to other neurons at synapses and connected to effector organs or cells at neuroeffector junctions. 2014-04-02T05:12:30Z UMLS:C4022739 Abnormal neuron shape Abnormal neuronal morphology HP:0012757 Abnormal neuron morphology A structural anomaly of a neuron. Neurons are electrically excitable cells that transmit signals throughout the body. Neurons employ both electrical and chemical components in the transmission of information. Neurons are connected to other neurons at synapses and connected to effector organs or cells at neuroeffector junctions. HPO_CONTRIBUTOR:KI_phemming PMID:28723006 Abnormal neuron shape A reduced ability to participate in the back-and-forth flow of social interaction appropriate to culture and developmental level, which is normally characterized by an influence of the behavior of one person on the behavior of another person. 2014-04-03T12:52:44Z UMLS:C4022736 Impaired social reciprocity HP:0012760 Reduced social reciprocity Impaired social reciprocity A deviation from normal size of the placenta. 2014-04-07T12:11:29Z UMLS:C4022732 HP:0012767 Abnormal placental size A deviation from normal size of the placenta. A structural anomaly of the ciliary body. 2014-04-07T04:00:10Z UMLS:C4022726 Abnormality of the ciliary body HP:0012776 Abnormal ciliary body morphology A structural anomaly of the ciliary body. HPO_CONTRIBUTOR:CINEAS_asollie Chronic loss of joint motion in a finger due to structural changes in non-bony tissue. 2014-04-20T04:09:34Z UMLS:C1857304 Flexion deformity of finger HP:0012785 Note that the term camptodactyly refers to a painless flexion contracture of the proximal interphalangeal (PIP) joint and not to a finger joint contracture in general. Flexion contracture of finger Chronic loss of joint motion in a finger due to structural changes in non-bony tissue. An anomaly of the process of formation of bone in the humerus. 2014-04-24T10:23:43Z UMLS:C4022722 Abnormal maturation of long bone in upper arm HP:0012791 Abnormal humeral ossification An anomaly of the process of formation of bone in the humerus. Abnormal maturation of long bone in upper arm A lack of bone mineralization of one or more body of thoracic vertebra. 2014-04-24T11:05:14Z UMLS:C4022721 HP:0012792 Absent ossification of thoracic vertebral bodies A lack of bone mineralization of one or more body of thoracic vertebra. Underdevelopment of part or all of the female external reproductive organs (which include the mons pubis, labia majora, labia minora, Bartholin glands, and clitoris). 2014-05-27T08:14:55Z UMLS:C4022715 Underdeveloped female external genitalia HP:0012815 Hypoplastic female external genitalia Underdevelopment of part or all of the female external reproductive organs (which include the mons pubis, labia majora, labia minora, Bartholin glands, and clitoris). Underdeveloped female external genitalia Inflammation of the myocardium. 2014-05-28T09:01:32Z MSH:D009205 SNOMEDCT_US:50920009 UMLS:C0027059 Inflammation of heart muscle HP:0012819 Myocarditis can be caused by a variety of bacterial and viral infections. Enteroviruses, especially coxsackievirus B, and adenovirus and parvovirus B19 are often associated with acute myocarditis. Exposure to drug treatment, physical stimuli such as radiation and heat, metabolic disorders, immune disorders, and pregnancy are also causes of myocarditis. Many cases of myocarditis are idiopathic. Myocarditis presents with non-specific symptoms including chest pain, dyspnoea, and palpitations, and thus often mimics more common disorders such as coronary artery disease. In some patients, cardiac MRI and endomyocardial biopsy can help identify myocarditis, predict risk of cardiovascular events, and guide treatment. Myocarditis Inflammation of the myocardium. PMID:21304213 PMID:22185868 PMID:22361396 Inflammation of heart muscle Any structural anomaly of a reproductive cell. 2014-06-09T10:01:49Z UMLS:C4022704 Abnormal shape of a reproductive cell Abnormally shaped germ cell Abnormally shaped reproductive cell HP:0012862 Abnormal germ cell morphology Any structural anomaly of a reproductive cell. Abnormally shaped reproductive cell A structural anomaly of a male reproductive cell. 2014-06-09T10:05:33Z UMLS:C4022703 HP:0012863 Abnormal male germ cell morphology A structural anomaly of a male reproductive cell. A structural anomaly of sperm. 2014-06-09T10:07:03Z MSH:D000072660 SNOMEDCT_US:236817003 UMLS:C0403824 Abnormal shape of sperm Teratospermia Teratozoospermia HP:0012864 Abnormal sperm morphology A structural anomaly of sperm. Abnormal shape of sperm An abnormal functionality of the male genital system. 2014-06-09T11:20:46Z UMLS:C4020716 Abnormal male genital system physiology HP:0012874 Abnormal male reproductive system physiology An abnormal functionality of the male genital system. Abnormality in the process of ejection of semen (usually carrying sperm) from the male reproductive tract. 2014-06-09T11:21:29Z SNOMEDCT_US:386674000 UMLS:C2937350 HP:0012875 Abnormal ejaculation Abnormality in the process of ejection of semen (usually carrying sperm) from the male reproductive tract. Difficulty of a male in achieving orgasm. 2014-06-09T11:29:28Z SNOMEDCT_US:15405008 UMLS:C0234047 Delayed ejaculation HP:0012878 Retarded ejaculation Difficulty of a male in achieving orgasm. PMID:24528812 Delayed ejaculation Inability to ejaculate. 2014-06-09T11:33:16Z SNOMEDCT_US:248782001 SNOMEDCT_US:42288005 UMLS:C0278106 Ejaculatory incompetence HP:0012879 Anejaculation Inability to ejaculate. PMID:24528812 An anomaly of the neck of the uterus (lower part of the uterus), called the uterine cervix. 2014-06-11T09:40:02Z UMLS:C4022694 Abnormality of the uterine cervix HP:0012888 Abnormal uterine cervix morphology An anomaly of the neck of the uterus (lower part of the uterus), called the uterine cervix. Hypertrophy of one or more muscles innervated by the facial nerve (the seventh cranial nerve). 2014-06-23T10:58:42Z UMLS:C4022691 UMLS:C4280307 Increased size of facial muscles Large facial muscles Hyperplasia of facial muscles HP:0012892 Facial muscle hypertrophy Hypertrophy of one or more muscles innervated by the facial nerve (the seventh cranial nerve). HPO_CONTRIBUTOR:UToronto_htrang Increased size of facial muscles Large facial muscles Hyperplasia of facial muscles Muscle hypertrophy affecting the muscles of the neck. 2014-06-23T10:59:17Z Increased size of neck muscles UMLS:C4022690 UMLS:C4280306 Hypertrophy of cervical muscles Large neck muscles Overgrowth of neck muscles Hyperplasia of neck muscles HP:0012893 Neck muscle hypertrophy Muscle hypertrophy affecting the muscles of the neck. HPO_CONTRIBUTOR:UToronto_htrang Increased size of neck muscles Hypertrophy of cervical muscles Large neck muscles Overgrowth of neck muscles Hyperplasia of neck muscles Muscle hypertrophy affecting the scapular muscles. 2014-06-23T11:00:11Z UMLS:C4022688 HP:0012895 Scapular muscle hypertrophy Muscle hypertrophy affecting the scapular muscles. HPO_CONTRIBUTOR:UToronto_htrang A coloboma of the ciliary body. UMLS:C4072884 Ciliary body coloboma Any structural anomaly of a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. 2017-12-22T14:32:10Z Abnormal myeloid cell morphology Any functional abnormality of erythrocytes (red-blood cells). 2018-09-28T23:39:07Z Abnormal erythrocyte physiology Any deviation from the normal number of eosinophils per volume in the blood circulation. 2018-10-17T13:48:52Z Abnormal eosinophil count Any deviation of the concentration of one or more proteins in the urine. 2019-07-05T16:29:22Z Abnormal urine protein level 2016-08-12T11:24:56Z Abnormal vascular morphology A structural anomaly of the tiny blood vessels that connect arterioles with venules and whose walls act as semipermeable membranes that mediate the diffusion of fluids and gases between the blood circulation and body tissues. 2016-08-12T11:42:27Z Abnormal capillary morphology A functional anomaly of the tiny blood vessels that connect arterioles with venules and whose walls act as semipermeable membranes that mediate the diffusion of fluids and gases between the blood circulation and body tissues. 2016-08-12T11:56:48Z Abnormal capillary physiology 2016-08-27T13:44:32Z Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. Abnormality of the digestive system A functional anomaly of the digestive system. 2016-08-27T13:58:05Z Abnormality of digestive system physiology A structural anomaly of the digestive system. 2016-08-27T13:58:23Z Abnormality of digestive system morphology Abnormal digestive system morphology Abnormal form of the progenitor cells committed to the erythroid lineage. 2016-09-02T11:14:05Z Abnormal morphology of erythroid progenitor cell Anomalous form of the proerythroblast, i.e., the immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. 2016-09-02T11:16:54Z Abnormal proerythroblast morphology Partial or complete wasting (loss) of hypothalamus tissue that was once present. 2016-09-26T09:07:40Z Atrophy of the hypothalamus Hypothalamic atrophy Passage of many stools containing blood. 2016-10-15T13:58:14Z Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Bloody diarrhoea Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea. Bloody diarrhea Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Bloody diarrhoea Structural abnormality of the hypothalamus related to defective development. 2016-10-28T06:41:35Z Hypothalamic dysgenesis Note that the term hypothalamic dysgenesis is generally used to refer to a morphological abnormality of the hypothalamus that is of presumed developmental (rather than acquired) origin. Dysgenesis of the hypothalamus A structural anomaly of the mucous lining of the small intestine. 2016-11-15T11:57:47Z Abnormal small intestinal mucosa morphology Ectopic deposition of calcium salts found in the gingiva. 2016-11-27T14:27:44Z Gingival calcifications Gingival calcification Ectopic deposition of calcium salts found in the gingiva. PMID:25928877 A functional anomaly of the hepatobiliary system 2016-12-04T12:05:04Z Abnormality of hepatobiliary system physiology Any physiological abnormality of the esophagus. 2016-12-18T13:39:06Z Abnormality of esophagus physiology Abnormality of oesophagus physiology Functional abnormality of the esophagus Functional abnormality of the oesophagus Abnormal esophagus physiology Abnormality of oesophagus physiology Functional abnormality of the oesophagus An anomaly of arterial function. 2017-02-03T12:08:38Z Abnormal arterial physiology An anomaly of the margin of the cornea overlapped by the sclera. 2017-02-12T23:58:19Z Abnormality of the corneal limbus Abnormal corneal limbus morphology An anomaly of cellular morphology or physiology. 2017-02-13T00:29:35Z Abnormal cellular phenotype Abnormal bone tissue formation (ossification) affecting the sacrum. 2017-02-20T14:45:33Z Abnormal ossification of the sacrum Any anomaly of the structure of the spleen. 2017-04-23T10:55:52Z Splenic lesion Abnormal spleen morphology Any anomaly of the function of the spleen. 2017-04-23T10:56:59Z Abnormal spleen physiology Any anomaly of the structure of the larynx. 2017-04-23T12:44:49Z Abnormal larynx morphology Any anomaly of the function of the larynx. 2017-04-23T12:46:36Z Abnormal larynx physiology Any structural anomaly of the bronchi, i.e., of the airways leading from the trachea to the lungs. 2017-04-23T12:50:43Z HP:0002109 Abnormality of the bronchi Abnormal bronchus morphology Any anomaly of the function of the bronchi. 2017-04-23T12:51:32Z Abnormal bronchus physiology Inflammation (due to infection or irritation) of the pharynx. 2017-04-24T00:03:24Z Pharyngitis Any deviation from the normal range of concentration of a metabolite in the cerebrospinal fluid. 2017-05-05T10:24:32Z HP:0032207 Abnormal CSF metabolite level Abnormal cerebrospinal fluid metabolite concentration Abnormal CSF metabolite concentration Abnormal CSF metabolite level Any deviation from the normal range of a protein concentration in the cerebrospinal fluid. 2017-05-05T10:32:59Z Abnormal CSF protein level Abnormal CSF protein concentration CSF total protein level is below the lower limit of normal. 2017-05-05T10:34:12Z Decreased CSF protein Decreased cerebrospinal fluid total protein Hypoproteinorrhachia Low CSF total protein Decreased CSF protein concentration CSF total protein level is below the lower limit of normal. PMID:27388694 Low CSF total protein CSF albumin level is below the lower limit of normal. 2017-05-05T10:46:15Z Low CSF albumin Decreased CSF albumin concentration CSF albumin level is below the lower limit of normal. PMID:27388694 Low CSF albumin Any anomaly of cell structure. 2017-05-07T11:14:54Z Abnormal cell morphology An abnormality of the processes that maintain the redox environment of a cell or compartment within a cell, that is, the balance between reduction and oxidation chemical reactions. 2017-05-07T11:17:15Z Abnormality of redox activity Any structural anomaly of the bladder. 2017-05-14T17:07:03Z Abnormality of bladder morphology Abnormal bladder morphology A congenital anomaly characterized by the presence of two bladders. 2017-05-14T17:16:59Z Bladder duplication A congenital anomaly characterized by the presence of two bladders. PMID:25657554 Abnormal increased in length of the chordae tendinae of the mitral valve. 2017-05-17T23:42:26Z Elongated chordae tendinae of the mitral valve A structural anomaly of the chordae tendinae of the mitral valve, whose main function is to transmit the contraction and relaxation of the papillary muscles during the cardiac cycle, thus ensuring the closing of the leaflets of the mitral valve. 2017-05-17T23:44:02Z Abnormal morphology of the chordae tendinae of the mitral valve A structural anomaly of the chordae tendinae of the mitral valve, whose main function is to transmit the contraction and relaxation of the papillary muscles during the cardiac cycle, thus ensuring the closing of the leaflets of the mitral valve. PMID:23304176 Any structural anomaly of the principal vein draining blood from the upper portion of the body and delivering it to the right ventricle of the heart. 2017-12-15T23:00:56Z Fyler:2820 Abnormal superior vena cava morphology Any structural anomaly of the principal vein draining blood from the upper portion of the body and delivering it to the right ventricle of the heart. MP:0006064 Any structural anomaly of the principal vein draining blood from the lower portion of the body. 2017-12-15T23:02:17Z Fyler:2810 Abnormal inferior vena cava morphology Any structural anomaly of the principal vein draining blood from the lower portion of the body. MP:0006063 Any structural abnormality of the left atrium. 2017-12-15T23:54:09Z Fyler:3010 Abnormal left atrium morphology Any structural abnormality of the right atrium. 2017-12-15T23:56:01Z Fyler:1770 Abnormal right atrium morphology A structural abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. 2019-04-26T17:40:47Z Abnormal ureter morphology A functional abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. 2019-04-26T17:43:08Z Abnormal ureter physiology A growth protruding from the mucous membrane of the ureter. Ureteral polyps can be attached to the ureter by a broad base or a thin stalk. 2019-04-26T17:44:45Z NCIT:C4530 Polyp of the ureter Ureter polyp Ureteral polyp A growth protruding from the mucous membrane of the ureter. Ureteral polyps can be attached to the ureter by a broad base or a thin stalk. NCIT:C4530 Any structural anomaly of the neck region. Abnormal neck morphology Congenital absence of the cervix. SNOMEDCT_US:37687000 UMLS:C0266404 Absent cervix Aplasia of the cervix Cervical aplasia Cervical agenesis Absent cervix UMLS:C4020714 UMLS:C4022678 Abnormal female reproductive system physiology Abnormal female genital system physiology Abnormal female reproductive system physiology Abnormal female reproductive system physiology Abnormal female genital system physiology A morphological anomaly of the nasal cartilage. UMLS:C4022670 Abnormality of cartilage of nose Abnormality of the nasal cartilage Anomaly of cartilage of nose Anomaly of nasal cartilage Deformity of cartilage of nose Deformity of nasal cartilage Malformation of cartilage of nose Malformation of nasal cartilage Abnormal nasal cartilage morphology Abnormality of cartilage of nose Abnormality of the nasal cartilage Anomaly of cartilage of nose Anomaly of nasal cartilage Deformity of cartilage of nose Deformity of nasal cartilage Malformation of cartilage of nose Malformation of nasal cartilage Lack of a palpable nasal cartilage. MSH:C562753 SNOMEDCT_US:232381002 UMLS:C4022669 UMLS:C4082198 Absent cartilage of nose Absent nasal cartilage Agenesis of cartilage of nose Agenesis of nasal cartilage Failure of development of cartilage of nose Failure of development of nasal cartilage Missing cartilage of nose Missing nasal cartilage This feature may be accompanied by a deficiency of the nasal bone. Absence of the nasal cartilage may lead to a Depressed nasal tip, which should be coded separately. Absent nasal cartilage Lack of a palpable nasal cartilage. PMID:19152422 eom:73e4e8bb2eec316d Absent cartilage of nose Absent nasal cartilage Agenesis of cartilage of nose Agenesis of nasal cartilage Failure of development of cartilage of nose Failure of development of nasal cartilage Missing cartilage of nose Missing nasal cartilage Incomplete duplication of the ureter. UMLS:C3887498 Bifid ureter Incomplete duplication of the ureter. PMID:23513084 A bent (flexed) finger or toe joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. UMLS:C1839864 Flexion contracture of digit A morphological anomaly of the lateral ventricle. UMLS:C4022662 Abnormality of lateral ventricle There are two lateral ventricles, one on each side of the brain. The lateral ventricle resembles a C-shaped structure that begins at an inferior horn in the temporal lobe, travels through a body in the parietal lobe and frontal lobe, and ultimately terminates at the interventricular foramen of Monro where each lateral ventricle connects to the central third ventricle. Abnormal lateral ventricle morphology An anomalous amount of protein present in or on the surface of muscle fibers. This feature may be appreciate upon immunohistochemical investigation of muscle biopsy tissue. UMLS:C4022653 Abnormal muscle fibre protein expression Abnormal muscle fiber protein expression Abnormal muscle fibre protein expression An anomaly of the inner mucous membrane of the uterus. UMLS:C4022620 Abnormality of the endometrium Abnormal endometrium morphology An anomaly of the inner mucous membrane of the uterus. A structural anomaly of the liver located predominantly in the hepatocytes as opposed to stromal cells. UMLS:C4022605 Abnormal liver parenchyma morphology A structural anomaly of the liver located predominantly in the hepatocytes as opposed to stromal cells. PMID:11157536 Inflammation of the biliary ductal system, affecting the intrahepatic or extrahepatic portions, or both. MSH:D002761 SNOMEDCT_US:82403002 UMLS:C0008311 Bile duct inflammation Cholangitis is characterized by biliary epithelial damage with inflammatory cell infiltration. Some cholangitis is also associated with ductal and periductal fibrosis. Cholangitis Inflammation of the biliary ductal system, affecting the intrahepatic or extrahepatic portions, or both. PMID:21994886 Bile duct inflammation Abnormal growth of tissue projecting from a mucous membrane of the endocervix. MSH:D002583 SNOMEDCT_US:123841004 SNOMEDCT_US:65576009 UMLS:C0007855 UMLS:C0007873 Cervical tumor Cervical tumour Cervical polyp Abnormal growth of tissue projecting from a mucous membrane of the endocervix. PMID:21270291 Cervical tumor Cervical tumour Abnormally large size of glomeruli. UMLS:C4022604 Glomerulomegaly is a histologic finding that can be present in idiopathic pulmonary hypertension, congenital cyanotic heart disease, morbid obesity associated with sleep apnea syndrome, sickle cell disease, and polycythemic states. Glomerulomegaly Abnormally large size of glomeruli. PMID:21115671 PMID:9402101 Abnormality of vascular function. UMLS:C4022603 Abnormal vascular physiology Abnormality of vascular function. Abnormalities of the overall muscle bulk based on clinical observation. UMLS:C4022563 Abnormality of muscle size Abnormality of muscle size Abnormalities of the overall muscle bulk based on clinical observation. Abnormality of muscle size Underdevelopment of the deltoid muscle. HP:0009039 HP:0009044 UMLS:C1868170 Deltoid muscle hypoplasia Hypoplasia of deltoid muscle Underdevelopment of the deltoid muscle. Thrombosis of the portal vein and/or its tributaries, which include the splenic vein and the superior and inferior mesenteric veins. SNOMEDCT_US:17920008 UMLS:C0155773 Blood clot in portal vein Portal vein thrombosis (PVT) can occur within the main portal vein, or it can occur in the branches of the portal vein within the liver itself. It can be an occluding thrombus or nonoccluding, with a clot present but continued blood flow through the vessel. The sequela of a long-standing PVT is cavernous formation of the portal vein, which represents bridging collaterals around the occlusion. Portal vein thrombosis Thrombosis of the portal vein and/or its tributaries, which include the splenic vein and the superior and inferior mesenteric veins. PMID:21960890 Blood clot in portal vein An obstruction in the veins of the liver caused by a blood clot (thrombosis). MSH:D006502 SNOMEDCT_US:38739001 UMLS:C0019154 Blood clot in liver vein Hepatic venous thrombosis Hepatic vein thrombosis An obstruction in the veins of the liver caused by a blood clot (thrombosis). Blood clot in liver vein The term splanchnic vein thrombosis encompasses Budd-Chiari syndrome (hepatic vein thrombosis), extrahepatic portal vein obstruction (EHPVO), and mesenteric vein thrombosis; the word splanchnic is used to refer to the visceral organs (of the abdominal cavity). UMLS:C4022560 Blood clot in splanchnic vein Splanchnic vein thrombosis The term splanchnic vein thrombosis encompasses Budd-Chiari syndrome (hepatic vein thrombosis), extrahepatic portal vein obstruction (EHPVO), and mesenteric vein thrombosis; the word splanchnic is used to refer to the visceral organs (of the abdominal cavity). PMID:20532730 Blood clot in splanchnic vein The presence of multiple polyps in the large intestine. UMLS:C4022556 Large intestinal polyposis The presence of multiple polyps in the large intestine. Lack of recognizable penile structures. HP:0040316 SNOMEDCT_US:204908001 SNOMEDCT_US:59981001 UMLS:C0555231 Absent penis Aphallia Aplasia of the penis Penis aplasia Absence of the penis is always accompanied by abnormal position of the meatus (usually in the perineum, sometimes in the rectum), may be accompanied by Cryptorchidism, and is often associated with non-genital anomalies, which all should be coded separately. Absent penis should be differentiated from a penis concealed within pre-pubic fat tissue. Absent penis Lack of recognizable penile structures. PMID:23650202 Absent penis An abnormal flattening of an epiphysis of femur. UMLS:C1850642 Flattended end part of thigh bone Flattened femoral epiphysis An abnormal flattening of an epiphysis of femur. Flattended end part of thigh bone Lack of ossification of the sacrum. UMLS:C2675562 Absence of sacrum ossification Unossified sacrum Lack of ossification of the sacrum. A deviation from the normal number of vertebrae in the spinal column. UMLS:C4022523 Abnormal number of vertebrae A deviation from the normal number of vertebrae in the spinal column. UMLS:C4022522 Decreased number of vertebrae An increase in the vertical distance between adjacent vertebral bodies, observed as an increase in the intervertebral disc space. UMLS:C4022513 Increased intervertebral space An increase in the vertical distance between adjacent vertebral bodies, observed as an increase in the intervertebral disc space. An anomaly in the number of macrophages. UMLS:C4022509 Abnormal macrophage count An anomaly in the number of macrophages. UMLS:C4072991 Yellow/white lesions of the retina A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. UMLS:C4073120 Abnormal ocular adnexa morphology Any structural anomaly of the heart and great vessels. HP:0001632 HP:0002564 HP:0002565 UMLS:C4049796 Abnormality of cardiovascular system morphology Cardiovascular malformations HP:0030680 Abnormal cardiovascular system morphology Any structural anomaly of the muscular columns which project from the inner surface of the right and left ventricles of the heart (cardiac trabeculae, trabeculae carneae). UMLS:C4073289 Abnormal morphology of myocardial trabeculae Inflammation of the vagina that can result from a spectrum of conditions that cause vaginal and sometimes vulvar symptoms, such as itching, burning, irritation, odor, and vaginal discharge. MSH:D014627 SNOMEDCT_US:30800001 UMLS:C0042267 Vulvovaginitis The most common infectious causes of vaginitis are bacterial vaginosis, vulvovaginal candidiasis, and trichomoniasis. Physicians traditionally diagnose vaginitis using the combination of symptoms, physical examination, pH of vaginal fluid, microscopy, and the whiff test. Vaginitis Increase in size of the right atrium. Fyler:1771 Fyler:2859 SNOMEDCT_US:67751000119106 UMLS:C0748427 Dilated right atrium Enlarged heart right atrium Right atrial dilatation This feature can be appreciated on chext radiography, MRI, or CT. Right atrial enlargement Increase in size of the right atrium. Any structural anomaly of the tongue. UMLS:C4280755 Abnormal tongue morphology Increase in size of the tonsils, small collections of lymphoid tissue facing into the aerodigestive tract on either side of the back part of the throat. SNOMEDCT_US:46689006 UMLS:C0272386 Enlargment of tonsils Tonsillar hypertrophy tonsils large/hypertrophy Enlarged tonsils Increase in size of the tonsils, small collections of lymphoid tissue facing into the aerodigestive tract on either side of the back part of the throat. Lack of observable tonsillar tissue. SNOMEDCT_US:249393008 SNOMEDCT_US:300277007 UMLS:C0576999 Hypoplastic tonsils Tonsillar hypoplasia Absent tonsils Lack of observable tonsillar tissue. An anomaly of venous function. UMLS:C4280744 Abnormality of venous physiology An anomaly of venous function. A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. UMLS:C4280730 Abnormal pulmonary circulation Abnormality of respiratory circulation Abnormality of pulmonary circulation A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. An anomaly of the muscular contractions that propel food though the gastrointestinal tract. Abnormal GI motility Abnormal gastrointestinal motility An anomaly of the muscular contractions that propel food though the gastrointestinal tract. Abnormal GI motility Supernumerary clitoris. The word bifid indicates the presence of a split clitoris, as opposed to a supernumerary clitoris, which could be described as duplicated clitoris. Duplicated clitoris An anomaly of the wave-like muscle contractions of the digestive tract. Abnormal peristalsis An anomaly of the wave-like muscle contractions of the digestive tract. An anomaly of the electrical conduction physiology of the heart. 2017-03-17T17:47:04Z Abnormality of cardiovascular system electrophysiology A structural anomaly affecting a blood vessel involved in the circulation of the heart, i.e., the superior or inferior vena cava, the pulmonary arteries, the pulmonary veins, and the aorta. 2017-04-18T13:00:44Z Abnormal morphology of the great vessels 2017-04-18T13:14:14Z Abnormal aortic physiology An abnormality of the structure of the pulmonary artery. 2017-04-18T13:29:12Z Abnormal pulmonary artery morphology An abnormality of the structure of the pulmonary veins. 2017-04-18T13:38:34Z Fyler:3000 Abnormal pulmonary vein morphology An abnormality of the function of the pulmonary veins. 2017-04-18T13:38:42Z Abnormal pulmonary vein physiology A chronic deviation from normal pressure in the systemic arterial system. 2017-04-18T13:55:40Z Abnormal systemic BP Abnormal systemic blood pressure Abnormal systemic BP A deviation from the normal concentration of serum bile acid concentration. 2017-05-13T12:45:39Z There are two major bile acids, cholic acid and chenodeoxycholic acid, which are synthesised in the hepatocyte by the cytochrome P450-mediated oxidation of cholesterol. These bile acids are secreted into the biliary canaliculi as sodium salts and conjugated with glycine, taurine, sulphate or glucuronic acid, and stored in the gall bladder until excreted into the intestinal lumen in response to a fatty meal. Enterohepatic circulation of bile salts is associated with conversion of the primary bile salts to secondary bile salts by bacerial enyzmes. The total bile pool of about 4 grams is recirculated about 5 to 10 times per day. Because serum bile salt concentration can increase by two to five times after a meal it is important that bile salts are measured while the subject is fasting. Abnormal serum bile acid concentration A reduction in the concentration of bile acid in the blood. 2017-05-13T13:02:06Z Decreased serum bile acid concentration An elevation in bone density in one or more tarsal bones of the foot. Sclerosis is normally detected on a radiograph as an area of increased opacity. 2017-05-27T14:41:39Z Tarsal sclerosis 2017-05-28T22:32:58Z Abnormal ovarian morphology Any anomaly of ovarian function. 2017-05-28T22:33:50Z Abnormal ovarian physiology Any anomaly of the structure of an organ ofthe endocrine system. 2017-05-28T23:11:43Z Abnormal endocrine morphology Any anomaly of the function of the endocrine system. 2017-05-28T23:12:36Z Abnormal endocrine physiology An anomalous response to a test that is designed to probe the function of the endocrine system. 2017-05-28T23:14:39Z Abnormal response to endocrine stimulation test Any anomaly of the structure of the breast. 2017-06-30T15:41:38Z Abnormal breast morphology Any anomaly of the function of the breast. 2017-06-30T15:42:09Z Abnormal breast physiology Any anomaly of the structure of the humerus. 2017-05-30T01:22:39Z Abnormal humerus morphology Any anomaly of the structure of the uterus 2017-05-30T02:52:38Z Abnormal uterus morphology Hepatocytes (liver parenchymal cells) exhibit a bloated appearance because of expansion of the cytoplasm by accumulated material. 2017-06-10T15:30:13Z Storage in hepatocytes Any anomolous structure of the renal corpuscle, which is the initial component of the nephron that filters blood. The renal corpuscle consists of a knot of capillaries (glomerulus) that is surrounded by a double-walled capsule (Bowman capsule) that opens into a renal tubule. 2017-08-12T18:30:25Z Abnormal renal corpuscle morphology Increase in size of the left atrium. 2017-08-13T21:38:04Z Fyler:3011 Fyler:3020 Enlarged heart left atrium Left atrial enlargement An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall. 2017-08-26T20:56:01Z Peripheral artery calcification Peripheral arterial calcification can be observed on radiographs and may be classified as either medial (linear calcifications in a train-track pattern) or atherosclerotic (distinct, nodular calcifications). A number of other techniques may also be used to detect peripheral arterial calcification including computed tomographic (CT) and magnetic resonance (MR) imaging, duplex ultrasonography, measurement of pulse wave velocity, echocardiography, planar radiographs, and indirectly, the ankle-brachial index. A discussion on the ontological description of peripheral arterial calcification can be found here: https://github.com/obophenotype/human-phenotype-ontology/issues/6877. Peripheral arterial calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall. PMID:24402839 PMID:26811161 An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall of the leg. 2017-08-26T21:03:24Z Lower extremity peripheral artery calcification GitHub issue: https://github.com/obophenotype/human-phenotype-ontology/issues/6877 Lower extremity peripheral arterial calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall of the femoral artery. 2017-08-26T21:04:24Z Femoral arterial calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall of the iliac artery. 2017-08-26T21:05:02Z Iliac arterial calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in an artery that is located within the skull (intracranial). 2017-08-26T21:30:38Z Intracranial arterial calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the internal carotid artery. 2017-08-26T21:32:35Z Internal carotid artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in a cerebral artery. 2017-08-26T21:34:47Z Cerebral artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in abdominal aorta. 2017-08-26T21:44:24Z Abdominal aortic calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in a carotid artery. 2017-08-26T21:52:52Z Carotid artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the external carotid artery. 2017-08-26T21:53:48Z External carotid artery calcification Any abnormality in the multiplication or reproduction of cells, which may result in the expansion of a cell population. 2017-09-02T15:54:47Z Abnormal cell proliferation An impaired immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). 2017-09-03T15:36:45Z Impaired adaptive immune response Impaired antigen-specific response Any anomaly of lymphocyte function. 2017-09-04T12:08:45Z Abnormal lymphocyte physiology Any structural anomaly of the chordae tendinae of the tricuspid valve. The chordae tendineae connect the papillary muscles to the tricuspid valve. 2017-09-17T13:37:09Z Abnormal tricuspid chordae tendinae morphology Any functional anomaly of the mitral valve. 2017-09-17T22:37:40Z Abnormal mitral valve physiology Any deviation from the normal range of the hormones produced by the thyroid gland. 2017-09-21T01:56:23Z Abnormal thyroid hormone level Thyroid hormones (TH) are involved in the regulation of metabolism, proliferation, and growth of most tissues. Serum TH levels are tightly controlled by the hypothalamic, pituitary, and thyroid (HPT) axis to deliver appropriate amounts of TH to target tissues. The two major THs (T3 and T4) are iodothyrosines synthesized by the thyroid gland under the control of thyrotropin/thyroid stimulating hormone (TSH), a glycoprotein heterodimer that is produced by the pituitary gland. TSH, in turn, is regulated by thyrotropin releasing hormone (TRH), a tripeptide generated by the hypothalamus that is released into its own portal system to reach the pituitary. Both the production of TRH and TSH are under negative feedback control determined by the circulating free TH concentrations. Abnormal circulating thyroid hormone concentration Any deviation from the normal range of the hormones produced by the thyroid gland. PMID:28932413 Any anomaly of the progression of electrical impulses through the heart. 2017-09-24T22:36:44Z Abnormality of cardiac conduction Abnormality of cardiac conduction system Cardiac conduction abnormalities Cardiac conduction defects Heart conduction disorder The conduction system of the heart initiates and coordinates the electric signal that causes the rhythmic and synchronized contractions of the atria and ventricles. In higher vertebrates, this system comprises the sinuatrial (SAN) and atrioventricular nodes (AVN) and the wiring of the ventricles. The latter comprises the atrioventricular bundle (AVB), the left and right bundle branches (BBs), and the peripheral ventricular conduction system (PVCS). Cardiac conduction abnormality Any functional defect of the mitral or tricuspid valve. 2017-12-17T15:17:45Z Abnormal atrioventricular valve physiology Any functional defect of the tricuspid valve. 2017-12-17T15:19:13Z Abnormal tricuspid valve physiology Any functional abnormality of a cardiac valve. 2017-12-17T15:21:49Z Abnormal heart valve physiology Abnormal level of metabolite or other abnormal analyte result in a stool test. 2017-12-17T21:04:26Z HP:0032483 Abnormal faeces composition Abnormal feces composition Abnormal faecal test result Abnormal fecal test result Abnormal stool composition Abnormal faeces composition Abnormal faecal test result Any structural anomaly of the ear. 2017-12-18T00:20:14Z Fyler:4867 Abnormal ear morphology Any functional anomaly of the ear. 2017-12-18T00:20:24Z Abnormal ear physiology A developmental defect in which the coronary sinus fails to form. 2018-01-28T12:02:56Z Fyler:2841 Absent coronary sinus A developmental defect in which the coronary sinus fails to form. PMID:24551710 Any deviation from the normal concentration of glycerol in the blood. 2018-02-25T14:28:46Z Abnormal circulating glycerol level Any deviation from the normal number of basophils per volume in the blood circulation. 2018-04-04T01:11:52Z Abnormal basophil count An abnormally increased count of basophils per volume in the blood circulation. 2018-04-04T01:15:24Z Basophilia Increased basophil count An abnormally reduced count of basophils per volume in the blood circulation. 2018-04-04T01:16:02Z Decreased basophil count A functional anomaly of the mouth (which is also known as the oral cavity). 2018-04-29T14:50:56Z The physiological functions of the mouth include salivary gland secretory function, mastication (chewing) and preparation of food for swallowing. Abnormal oral physiology Any structural anomaly of the mouth, which is also known as the oral cavity. 2018-04-29T14:55:47Z Abnormal oral morphology Any anomaly of a reflex, i.e., of an automatic response mediated by the nervous system (a reflex does not need the intervention of conscious thought to occur). 2018-05-02T01:05:40Z Abnormal reflex A reduced concentration of zinc in the blood. 2018-05-04T02:05:49Z Decreased serum zinc A reduced concentration of zinc in the blood. HPO_CONTRIBUTOR:RGD_gthayman PMID:16518702 Abnormal reduction in the count of eosinophils in the blood per volume. 2018-05-13T20:35:28Z Decreased eosinophil count Abnormal reduction in the count of eosinophils in the blood per volume. A functional abnormality affecting one or more of the cranial nerves, which emerge directly from the brain stem. 2018-06-23T13:49:43Z Abnormal cranial nerve physiology Any structural anomaly of the portal venous sytem, which comprises all of the veins draining the abdominal part of the digestive tract, including the lower esophagus but excluding the lower anal canal. The portal vein conveys blood from viscera and ramifies like an artery at the liver, ending at the sinusoids. Tributaries of the portal vein, which make up the portal venous system, are the splenic, superior mesenteric, left gastric, right gastric, paraumbilical, and cystic veins. 2018-07-05T13:39:22Z Abnormal portal venous system morphology Any structural anomaly of the portal venous sytem, which comprises all of the veins draining the abdominal part of the digestive tract, including the lower esophagus but excluding the lower anal canal. The portal vein conveys blood from viscera and ramifies like an artery at the liver, ending at the sinusoids. Tributaries of the portal vein, which make up the portal venous system, are the splenic, superior mesenteric, left gastric, right gastric, paraumbilical, and cystic veins. PMID:11796904 Anomaly where the intestinal and the splenic venous drainage bypass the liver and drain into systemic veins through other possible venous shunts. 2018-07-05T13:42:31Z CAPV Missing portal vein Congenital absence of portal vein Anomaly where the intestinal and the splenic venous drainage bypass the liver and drain into systemic veins through other possible venous shunts. PMID:18932274 PMID:2053351 CAPV Any deviation from the normal concentration of urea nitrogen in the blood. 2018-07-07T23:29:10Z Abnormal BUN concentration Abnormal blood urea nitrogen concentration Abnormal BUN concentration Any deviation from the normal concentration of a carbohydrate in the urine. 2018-07-08T12:53:24Z Carbohydrates, also known as saccharides, comprise mono-, d-, and oligosaccharides (substances from endogenous metabolism or from exogenous sources such as diet). Most saccharides except glucose are readily excreted in the urine, reflecting dieteray consuption. Increased sacchardie levels may indicate an enzyme defect or other disease if a certain type of saccharide or a certain profile is found. Abnormal urine carbohydrate level Any deviation from the normal concentration of a carboxylic acid in the urine. 2018-07-08T13:01:16Z Carboxylic acid refers to an organic compound that contains a carboxyl group (-COOH). Abnormal urine carboxylic acid level An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. 2018-09-03T00:17:49Z Abnormality of the ocular adnexa A functional anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. 2018-09-03T00:18:45Z Abnormal ocular adnexa physiology Underdevelopment of the carotid canal, which normally is a circular aperture in the temporal bone of the skull through which the internal carotid artery and the carotid plexus of nerves traverse. 2018-09-16T10:47:06Z Hypoplastic carotid canal A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. 2018-11-04T22:23:03Z Unusual infection A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. PMID:22052638 Any functional abnormality of the part of the nervous system that consists of the nerves and ganglia outside of the brain and spinal cord. 2018-11-17T16:57:55Z Abnormal peripheral nervous system physiology An unusual infection classified by the affected body part. 2018-12-09T12:17:59Z Unusual infection by anatomical site An elevated circulating concentration of folic acid, which is also known as vitamin B9. 2018-12-09T14:04:29Z Increased blood folate concentration An abnormal level of an analyte measured in the blood. 2019-01-12T13:45:59Z Abnormal circulating metabolite concentration Any structural anomaly of the sebaceous glands. 2019-01-26T14:26:26Z Sebaceous glands are found all over the human body except on the palms of the hands and soles of the feet. The glands are numerous on the face and scalp and are sparse in areas such as the back. They can number as many as 400-900 glands/cm2 on the face. Sebaceous glands are usually found in association with a hair follicle, which, together, is referred to as a pilosebaceous unit. The sebaceous gland is located in association with the upper portion of the hair follicle, where it is not affected by the hair cycle. Sebaceous glands can be unilobular or multilobular. Although a majority of sebaceous glands are part of a pilosebaceous unit, some glands can be found without an associated hair follicle. Sebaceous glands secrete sebum, which contains cholesterol, cholesteryl esters, squalene, fatty acids, diglycerides and triglycerides, and wax esters. Abnormal sebaceous gland morphology Any structural anomaly of the sebaceous glands. PMID:17975220 Any deviation from the normal concentration of a metabolite in a tissue. 2019-01-27T11:56:39Z Abnormal tissue metabolite concentration An abnormality in the function of the chemical reactions related to processes including conversion of food to enter, synthesis of proteins, lipids, nucleic acids, and carbohydrates, or the elimination of waste products. 2019-01-27T12:48:52Z Abnormal metabolism 2019-01-27T16:44:33Z Abnormal immune system morphology Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. 2019-01-27T20:07:59Z Increased BP Increased blood pressure Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. PMID:9137951 Increased BP Any deviation from the normal cell count per volume of granulocytes in the blood circulation. 2019-02-14T10:54:57Z Granulocytes belong to the innate immune system and make up the largest proportion of white blood cells. They are myeloid cells and can be classified as neutrophil granulocytes (neutrophils), eosinophils, basophils, monocytes, and mast cells. Abnormal granulocyte count Increased level of phenylalanine in urine. 2019-02-23T16:46:17Z Increased level of phenylalanine in urine Phenylalaninuria Increased level of phenylalanine in urine. PMID:18566668 Any deviation from the normal level of growth hormone (GH) in the blood circulation. GH or somatotropin is a peptide hormone that stimulates growth, cell reproduction, and cell regeneration. Its secretion from the pituitary is regulated by the neurosecretory nuclei of the hypothalamus, which can release Growth hormone-releasing hormone (GHRH or somatocrinin) and Growth hormone-inhibiting hormone (GHIH or somatostatin) into the hypophyseal portal venous blood surrounding the pituitary. GH is secreted in a pulsatile manner, which is one of the reasons why an isolated measurement of its blood concentration is not meaningful. 2019-02-23T18:15:25Z Abnormal somatotropin level Abnormal growth hormone level An abnormally low blood pH (usually defined as less than 7.35). 2019-02-23T18:37:21Z When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Acidemia An abnormally low blood pH (usually defined as less than 7.35). PMID:24381489 An abnormally high blood pH (usually defined as 7.41 or above). 2019-02-23T18:42:24Z When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Alkalemia An abnormally high blood pH (usually defined as 7.41 or above). PMID:24381489 Pulmonary bullae are rounded focal regions of emphysema with a thin wall which measure more than 1 cm in diameter. They are often subpleural in location and are typically larger in the apices. In some cases, bullae can be very large and result in compression of adjacent lung tissue. A giant bulla is arbitrarily defined as one that occupies at least one third of the volume of a hemithorax. When large, bullae can simulate pneumothorax. The most common cause is paraseptal emphysema but bullae may also be seen in association with centrilobular emphysema. 2019-03-03T17:45:09Z Pulmonary bullae Blebs and bullae are commonly subpleural and are mostly seen in both upper lobes in patients with coexisting centrilobular and paraseptal emphysema. Pulmonary bulla Pulmonary bullae are rounded focal regions of emphysema with a thin wall which measure more than 1 cm in diameter. They are often subpleural in location and are typically larger in the apices. In some cases, bullae can be very large and result in compression of adjacent lung tissue. A giant bulla is arbitrarily defined as one that occupies at least one third of the volume of a hemithorax. When large, bullae can simulate pneumothorax. The most common cause is paraseptal emphysema but bullae may also be seen in association with centrilobular emphysema. PMID:18195376 PMID:20028879 PMID:24106540 Pulmonary bullae Underdevelopment of the ureter. 2019-04-04T09:26:25Z Hypoplasia of the ureter Ureter hypoplasia Ureteral hypoplasia Underdevelopment of the ureter. A deviation from the normal level of a nucleobase in the urine. Nucleobases are nitrogen-containing biological compounds that form nucleosides: adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U). Abnormal urinary nucleobase concentration Any structural anomaly of the renal tubular epithelial cells (RTEC), a layer of cells in the outer layer of the renal tubule. These cells play a role in the absorption of substances such as glucose and amino from the primary urine. Abnormal renal tubular epithelial morphology A deviation of urine pH from the normal range of 4.5 to 7.8. Urine pH typically is 5 as a result of daily net acid excretion. The interpretation of the urine pH depends on the medical context. Abnormal urine pH A neoplasm that affects the female reproductive system. NCIT:C3053 Female reproductive system neoplasm Any structural anomaly of the fetal part of the placenta, which is known as the chorion. Abnormal chorion morphology Any structural anomaly of the fetal part of the placenta, which is known as the chorion. PMID:18755720 Absence or underdevelopment of the thyroid gland. Aplasia/Hypoplasia of the thyroid gland An elevated level of an aromatic amino acid in the urine. Increased aromatic amino acid level in urine An abnormally increased level of tyrosine in the urine. Increased tyrosine in urine Tyrosinuria An elevated level of an glutamine family amino acid in the urine. Increased glutamine family amino acid level in urine An elevated level of an aspartate family amino acid in the urine. Increased aspartate family amino acid level in urine An increased level in the urine of an alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. Elevated urinary non-proteinogenic amino acid level Increased urinary non-proteinogenic amino acid level An increased level of a serine family amino acid in the urine. Increased serine family amino acid in urine An elevated level of a proteinogenic amino acid in the urine. These are the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Increased proteinogenic amino acid level in urine An elevated level of a proteinogenic amino acid in the blood circulation. These are the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. 2020-08-29T11:59:15Z Abnormal circulating proteinogenic amino acid concentration Any deviation from the normal concentration in the blood circulation of an alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. 2020-08-29T12:04:47Z Abnormal circulating non-proteinogenic amino acid concentration Inflammation of the lining of the upper small intestine (duodenum). 2020-09-03T12:01:20Z Duodenal inflammation The diagnosis of duodenitis is made when there is infiltration by inflammatory cells with changes in villous architecture and surface and crypt epithelium. Duodenitis can be graded according to the amount of neutrophilic and plasma cell infiltration, villous height, Brunner's gland hyperplasia with prolapse into the lamina propria and gastric metaplasia. Duodenitis Inflammation of the lining of the upper small intestine (duodenum). PMID:16679353 An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body. 2020-09-05T13:35:03Z Abnormality of the musculoskeletal system Inflammation of the lining of the middle section of the small intestine. 2020-09-15T10:25:52Z Jejunitis Inflammation of the lining of the middle section of the small intestine. PMID:26420973 A structural anomaly of the pharynx. 2020-09-20T11:17:40Z Abnormal pharynx morphology A functional anomaly of the pharynx. 2020-09-20T11:18:32Z Abnormal pharynx physiology Any deviation from the normal amount of a pyrimidine compound in the urine. Pyrimidines and pyrimidine derivatives are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms. The nucleotides cytosine, thymine and uracil are pyrimidines. 2020-09-24T09:15:07Z Abnormal urinary pyrimidine level Presence of one or more manifestations of the acute phase response. Acute phase proteins (APP) are blood proteins primarily synthesized by hepatocytes as part of the acute phase response (APR). The APR is part of the early-defense or innate immune system, which is triggered by different stimuli including trauma, infection, stress, neoplasia, and inflammation. The APR results in a complex systemic reaction with the goal of reestablishing homeostasis and promoting healing. 2020-11-29T16:35:16Z Acute phase response Presence of one or more manifestations of the acute phase response. Acute phase proteins (APP) are blood proteins primarily synthesized by hepatocytes as part of the acute phase response (APR). The APR is part of the early-defense or innate immune system, which is triggered by different stimuli including trauma, infection, stress, neoplasia, and inflammation. The APR results in a complex systemic reaction with the goal of reestablishing homeostasis and promoting healing. PMID:20034426 PMID:30137854 Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein). 2020-12-01T11:42:14Z Abnormal blood vessel morphology Any deviation from the normal amount of a metabolite in urine. 2020-12-01T12:00:51Z As water reabsorption in kidneys affect urinary solute concentrations, various methods are applied to normalize the measured concentration. Frequently, concentrations are reported as a ratio to urinary creatinine. The HPO terms in this subhierarchy therefore use the word 'level' to indicate that appropriate normalization has been performed before concluding that the amount of the indicated metabolite is abnormal. Abnormal urine metabolite level Inflammation of the cartilage of the nose. 2020-12-23T14:31:16Z Nose chondritis Nasal chondritis Inflammation of the cartilage of the nose. PMID:33108101 Activation of the brain's innate immune system in response to an inflammatory challenge and is characterized by a host of cellular and molecular changes within the brain. 2021-01-09T17:51:49Z Neuroinflammation 2021-01-09T23:02:44Z Abnormal circulating bilirubin concentration Pre-capillary pulmonary hypertension is a haemodynamic condition characterised by elevated mean pulmonary artery pressure (mPAP over 20 mmHg) and pulmonary vascular resistance (PVR 3 Wood units or more) accompanied by normal pulmonary artery wedge pressure (PAWP not more than 15 mmHg). 2021-01-24T14:20:32Z Precapillary pulmonary hypertension Pre-capillary pulmonary hypertension Pre-capillary pulmonary hypertension is a haemodynamic condition characterised by elevated mean pulmonary artery pressure (mPAP over 20 mmHg) and pulmonary vascular resistance (PVR 3 Wood units or more) accompanied by normal pulmonary artery wedge pressure (PAWP not more than 15 mmHg). PMID:30545968 Deposition of calcium salts in the leaflets (cusps) of the mitral valve. 2021-02-03T13:41:58Z Mitral valve leaflet calcification A functional abnormality of a white blood cell. 2021-05-08T13:50:44Z Abnormal leukocyte physiology Anomalous structure of a blood vessel in the kidney. 2021-05-16T17:27:46Z Abnormal renal vascular morphology An anomalous structure of an artery located in the kidney. 2021-05-16T17:29:18Z Abnormal kidney arterial blood vessel morphology Abnormal intrarenal artery morphology Structural or functional abnormalities of the fetus. Note that this section comprises terms that describe abnormalities that are specific to the fetus or differ from the corresponding general terms. A term from anywhere in the Human Phenotype Ontology can be applied to a fetus if appropriate. 2021-11-27T19:01:00Z Fetal anomaly Any structural anomaly of the fetus. 2021-11-27T19:03:05Z Structural fetal anomaly Structural foetal anomaly Abnormal fetal morphology Structural foetal anomaly An anomalous structural finding of the fetal gastrointestinal system. Terms in this subhierarchy are restricted to findings that can only be observed in the prenatal period. Other HPO terms can also be used to describe fetal phenotypes. 2022-04-10T11:11:27Z Abnormal fetal gastrointestinal system morphology An abnormal strcutural of the zone (lobe) of the cerebral cortex that is located inferior to the lateral fissure on other cerebral hemispheres. 2022-04-10T13:13:34Z Abnormal temporal lobe morphology An anomalous structural finding of the fetal genitourinary system. Terms in this subhierarchy are restricted to findings that can only be observed in the prenatal period. Other HPO terms can also be used to describe fetal phenotypes. 2022-04-10T18:07:18Z Abnormal fetal genitourinary system morphology An anomaly of the corneal reflex that normally induces involuntary blinking of the eyelids following contact of the cornea. 2022-04-23T11:42:49Z The corneal reflex can be tested by touching the cornea lightly with a cotton tip. The normal response to to blink (shut the eyelids) immediately. To evaluate the corneal reflex, the examiner uses a cotton-tipped applicator, the tip of which has been pulled into a thin strand. The examiner stabilizes the patient's head by placing a hand on the patient's eyebrow and head. The patient is asked to look to the left side as the cotton tip is brought in from the right side to touch the right cornea gently. Abnormal corneal reflex An anomaly of the corneal reflex that normally induces involuntary blinking of the eyelids following contact of the cornea. PMID:30480980 Absence or underdevelopment of the midbrain (mesencephalon). 2022-05-21T15:34:06Z Aplasia/Hypoplasia of the mesencephalon Aplasia/Hypoplasia of the midbrain A developmental defect characterized by absence or underdevelopment of one or more facial bone. 2022-05-21T15:47:04Z Aplasia/Hypoplasia of facial bones Erythroblasts with multiple nuclei. Erythroblasts are nucleated precrusor cells of erythrocytes that are localized to the bone marrow. Normally, erythroblasts have a single nucleus. The abnormal finding of erythrocytes with two or more nuclei may be related to defects in cytokinesis. 2022-05-28T21:45:14Z Bone marrow: multinucleated erythroblasts Multinucleate erythroblast Binucleated erythroblast Double-nucleated erythroblast Multinucleated erythroblast Erythroblasts with multiple nuclei. Erythroblasts are nucleated precrusor cells of erythrocytes that are localized to the bone marrow. Normally, erythroblasts have a single nucleus. The abnormal finding of erythrocytes with two or more nuclei may be related to defects in cytokinesis. PMID:11994986 PMID:23744492 2022-09-05T10:59:04Z Abnormal muscle tissue metabolite concentration A limitation in the passive range of motion of the elbow resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin. 2022-09-30T12:50:12Z Elbow contracture A limitation in the passive range of motion of the elbow resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin. A contracture prevents movement of the associated body part. 2022-09-30T12:53:13Z Contracture To assess a joint contracture, the passive or active range of motion (ROM) of a joint with a contracture is assessed by moving the joint through its natural range with no active effort from the individual. The angular distance of the joint motion and the loss of ROM in a contracture is recorded through comparison with the contralateral joint or normative values. Conventionally, a joint contracture is named according to the joint involved and the direction opposite the lack of range. For example, inability to fully extend the knee is referred to as a knee flexion contracture, compared to inability to bend (flex) the knee, which is referred to as a knee extension contracture. Contractures in neuromuscular diseases develop due to intrinsic myotendinous structural changes and extrinsic factors. Known contributing extrinsic factors include decreased ability to actively move a limb through its full range of motion, immobility or static positioning for prolonged periods of time, and agonist antagonist muscle imbalance. Intrinsic muscle tissue alterations in dystrophic myopathies contribute to contracture formation. The most significant histologic changes are those of muscle fiber loss, abnormal residual dystrophic muscle fibers, segmental necrosis of muscle fibers, and increased amounts of adipose tissue, connective tissue, and fibrosis. Joint contracture A limitation in the passive range of motion of the elbow resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin. A contracture prevents movement of the associated body part. PMID:22938881 PMID:26247029 PMID:30928194 2022-11-24T00:18:11Z Abnormal joint physiology Inflammation of glans penis 2022-11-26T13:37:26Z Balanitis An increased level of uracil in the cerebrospinal fluid. 2022-12-03T23:24:34Z Increased CSF uracil concentration Abnormal increase in the size of the epididymis. 2022-12-04T18:11:08Z Epididymis enlarged Enlarged epididymis A developmental defect characterized by underdevelopment of hte portal vein. 2023-02-19T18:35:18Z Hypoplasia of the portal veins Portal vein hypoplasia The concentration of a metabolite in the liver is above or below the limits of normal. 2023-03-19T15:38:07Z Abnormal liver metabolite concentration Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the shoulder joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. 2023-03-25T12:27:46Z Shoulder contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the shoulder joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. PMID:16214063 PMID:24975760 PMID:31282072 A structural abnormality of the knee joint or surrounding structures. 2023-03-25T13:22:12Z Abnormal knee morphology A functional anomaly of the knee joint. 2023-03-25T13:23:25Z Abnormal knee physiology Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the knee joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. 2023-03-25T13:24:29Z Contracture of knee Contracture of the knees Knee contractures Knee contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of the knee joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. PMID:16214063 PMID:24975760 PMID:31282072 Knee contractures A structural anomaly of the ankle. 2023-03-25T13:30:08Z Abnormal ankle morphology A functional anomaly of the ankle. 2023-03-25T13:31:03Z Abnormal ankle physiology Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of a toe joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. 2023-03-26T15:48:09Z Toe joint contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of a toe joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. PMID:16214063 PMID:24975760 PMID:31282072 2023-03-26T15:52:39Z Ankle contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of a finger joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. 2023-03-26T16:07:41Z Finger joint contracture Lack of full passive range of motion (restrictions in flexion, extension, or other movements) of a finger joint resulting from structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules and/or skin. PMID:16214063 PMID:24975760 PMID:31282072 Concentration or activity of an enzyme is above or below the limits of normal. 2023-03-26T18:12:26Z Abnormal enzyme concentration or activity Abnormality of a sperm function including protection of paternal DNA, traversing the female reproductive tract, oocyte localisation, penetration of the zona pellucida, oocyte activation and centriole deposition. 2023-07-01T11:30:00Z Abnormal sperm physiology Concentration of calcitonin, a 32-amino acid polypeptide hormone that is produced primarily by the parafollicular cells of the thyroid, in the blood circulation outside of normal limits. 2023-07-08T23:22:54Z Abnormal circulating calcitonin concentration A structural anomaly of the anus. 2023-07-09T12:37:28Z Abnormal anus morphology A functional anomaly of the anus. 2023-07-09T12:39:28Z Abnormal anus physiology A tumor (abnormal growth of tissue) of the digestive system. 2023-07-09T14:37:49Z Digestive system neoplasm Any structural abnormality of the femoral artey, a large blood vessel that provides oxygenated blood to lower extremity structures and in part to the lower anterior abdominal wall. 2023-07-20T20:50:38Z Abnormal femoral artery morphology Any structural abnormality of the femoral artey, a large blood vessel that provides oxygenated blood to lower extremity structures and in part to the lower anterior abdominal wall. PMID:30855850 UMLS:C4022500 Abnormality of corneal shape UMLS:C4022493 Decreased mitochondrial number UMLS:C4022492 Increased mitochondrial number UMLS:C4022480 Absent/small 5th long bone of foot Absent/underdeveloped 5th long bone of foot Aplasia/Hypoplasia of the fifth metatarsal bone Absent/small 5th long bone of foot Absent/underdeveloped 5th long bone of foot UMLS:C4022473 Underdeveloped diaphragm Hypoplasia of the diaphragm Underdeveloped diaphragm UMLS:C4021858 Abnormality of nasal hair Abnormality of nose hair Abnormality of nasal hair Abnormality of nasal hair Abnormality of nose hair UMLS:C4022461 Calcification of ribs UMLS:C4022459 Decreased fat tissue Decreased adipose tissue Decreased fat tissue SNOMEDCT_US:445144002 UMLS:C0239337 UMLS:C4073131 Abnormal limbs Abnormality of limbs Limb anomaly Dysmelia Abnormality of limbs Abnormal limbs Abnormality of limbs Limb anomaly Dysmelia UMLS:C4022456 Abnormality of limb bone Abnormality of limb bone Abnormality of limb bone HP:0040066 UMLS:C4022455 UMLS:C4022457 Abnormal morphology of bones of the lower limbs Abnormal shape of bones of the lower limbs Abnormality of lower limb bone Abnormal lower limb bone morphology Abnormal shape of bones of the lower limbs Abnormality of lower limb bone UMLS:C4022454 UMLS:C4022458 Abnormal morphology of bones of the upper limbs Abnormal shape of bones of the upper limbs Abnormality of upper limb bone Abnormal upper limb bone morphology Abnormal shape of bones of the upper limbs Abnormality of upper limb bone HP:0040073 UMLS:C4022452 Abnormality of forearm bone Abnormal forearm bone morphology Abnormality of forearm bone MSH:D007018 SNOMEDCT_US:74728003 UMLS:C0020635 Hypopituitarism Any deviation from the normal concentration of folate in the blood circulation. UMLS:C4021037 Abnormal serum folate Abnormality of folate in blood Folate is an essential water-soluble vitamin (vitamin B9) that is found in green leafy vegetables, cereals, legumes, and fruit. As a major methyl group donor, it plays an important role in one-carbon metabolism and is involved in DNA, RNA, and protein synthesis, in addition to its significant role in energy production and normal cell division. Low blood folate concentration is associated with an increased risk for neural tube defects during pregnancy. Abnormal blood folate concentration Abnormal serum folate Any abnormality in the total number of lymphocytes in the blood. SNOMEDCT_US:165534000 UMLS:C0580550 Abnormal lymphocyte count Abnormal lymphocyte counts Abnormal number of lymphocytes Abnormal numbers of lymphocytes Abnormality of lymphocyte number Abnormal lymphocyte count Abnormal lymphocyte count Abnormal lymphocyte counts Abnormal number of lymphocytes Abnormal numbers of lymphocytes Abnormality of lymphocyte number Any deviation from the normal overall count of natural killer (NK) cells in the circulation or a deviation from the normal distribution of NK cell subtypes. UMLS:C4021036 Abnormal NK cell count Abnormal number of natural killer cells Abnormality of natural killer cell count In human peripheral blood, five NK cell subpopulations can be defined on the basis of the relative expression of the markers CD16 and CD56: (1) CD56bright CD16- (50-70% of CD56bright), (2) CD56bright CD16dim (30-50% of CD56bright), (3) CD56dim CD16-, (4) CD56dim CD16bright, and (5) CD56- CD16bright. In healthy individuals, populations (3) and (5) are numerically in the minority. Abnormal natural killer cell count Any deviation from the normal overall count of natural killer (NK) cells in the circulation or a deviation from the normal distribution of NK cell subtypes. PMID:19278419 Abnormal NK cell count Abnormal number of natural killer cells Abnormality of natural killer cell count An abnormality of the tympanic membrane UMLS:C4022447 Abnormality of the eardrum The tympanic membrane is considered to be the border of middle and outer ear. Abnormality of the tympanic membrane Abnormality of the eardrum A deviation from the normal concentration of cobalamin (vitamin B12) in the blood. Vitamin B12 is one of the eight B vitamins. UMLS:C4021032 Abnormal serum cobalamin level Abnormal vitamin B12 level A deviation from the normal concentration of cobalamin (vitamin B12) in the blood. Vitamin B12 is one of the eight B vitamins. UMLS:C0235760 Abnormal serum iron concentration UMLS:C4022420 Abnormal liver iron concentration Abnormal liver iron level Abnormal hepatic iron concentration Abnormal liver iron concentration Abnormal liver iron level UMLS:C4022416 Dicarboxylic acidemia An increased amount of carboxylic acid in the urine. UMLS:C4022413 Elevated urinary carboxylic acid UMLS:C1398367 Localised osteoporosis Localized osteoporosis Localised osteoporosis UMLS:C4073132 Abnormal shape of pelvis bone Abnormal pelvis bone morphology Abnormal shape of pelvis bone UMLS:C4073139 Abnormality of lingual muscle Abnormality of the tongue muscle Abnormality of the tongue muscle Abnormality of lingual muscle Abnormality of the tongue muscle UMLS:C4073140 Abnormality of extrinsic lingual muscle Abnormality of extrinsic muscle of tongue Abnormality of extrinsic lingual muscle Any deviation from the normal concentration of a phospholipid in the blood circulation. UMLS:C4073141 Abnormal level of phospholipids Abnormal circulating phospholipid concentration An abnormally increased head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. UMLS:C4083076 Increased head circumference Increased head circumference Increased head circumference An abnormally reduced head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. Microcephaly is defined as a head circumference (HC) that is great than two standard deviations below the mean of age- and gender-matched population based samples. Severe microcephaly is defined with an HC that is three standard deviations below the mean. SNOMEDCT_US:271611007 UMLS:C0424688 Decreased head circumference Although HC measures skull size, it typically also reflects overall brain volume and has been described as a widely used proxy of neural growth and brain size. Brain size outside of normal values is an important risk factor for cognitive and motor delay. Microcephaly at birth has been termed primary microcephaly and that acquired after birth is secondary microcephaly. Decreased head circumference An abnormally reduced head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. Microcephaly is defined as a head circumference (HC) that is great than two standard deviations below the mean of age- and gender-matched population based samples. Severe microcephaly is defined with an HC that is three standard deviations below the mean. PMID:26505062 Decreased head circumference Recurrent abnormal consumption of food, liquids, or objects that could have negative consequences for the individual. UMLS:C4073150 Abnormal consumption behaviour Abnormal consumption behavior Abnormal consumption behaviour An abnormal concentration of insulin in the body. HP:0040215 UMLS:C4073160 Abnormal insulin level Abnormal circulating insulin concentration A decreased concentration of insulin in the blood. UMLS:C2748055 Hypoinsulinemia Less than normal number of natural killer cells, a type of lymphocyte in the innate immune system with an ability to mediate cytotoxicity and produce cytokines after the ligation of a germline-encoded activation receptor. UMLS:C1855767 Reduced NK cell number Reduced natural killer cell number Reduced natural killer cell count Less than normal number of natural killer cells, a type of lymphocyte in the innate immune system with an ability to mediate cytotoxicity and produce cytokines after the ligation of a germline-encoded activation receptor. PMID:23993353 Reduced NK cell number Lack of natural killer cells, a type of lymphocyte in the innate immune system that contains cytoplasmic granzymes, i.e., small granules with perforin and proteases that allow natural killer cells to form pores in the cell membrane of the target cell through which the granzymes and associated molecules can enter, inducing apoptosis. UMLS:C4073163 Absent NK cells Absent natural killer cells Lack of natural killer cells, a type of lymphocyte in the innate immune system that contains cytoplasmic granzymes, i.e., small granules with perforin and proteases that allow natural killer cells to form pores in the cell membrane of the target cell through which the granzymes and associated molecules can enter, inducing apoptosis. Absent NK cells UMLS:C4280723 Abnormal size of the dental root UMLS:C4280722 Hypoplasia of the dental root Clincial phenotype characterized by delayed bleeding accelerated break down of blood clot (fibrinolysis) UMLS:C4280719 Abnormality of the fibrinolytic system requested and created by members of the BRIDGE consortium Abnormality of fibrinolysis UMLS:C4280696 Abnormal size of the clitoris UMLS:C4280695 Increased size of the clitoris UMLS:C4280694 Decreased size of the clitoris UMLS:C4280693 Aplasia/Hypoplasia of the clitoris Absence or underdevelopment of the nasopharyngeal adenoids. UMLS:C4280290 Adenoids small or absent Aplastic/Hypoplastic nasopharyngeal adenoids A deviation in the size of nasopharyngeal adenoids. UMLS:C4280692 Abnormal size of nasopharyngeal adenoids A deviation in the size of nasopharyngeal adenoids. Underdevelopment of the nasopharyngeal adenoids. UMLS:C4280691 Underdeveloped nasopharyngeal adenoids Hypoplastic nasopharyngeal adenoids An abnormal decrease in the size of nasopharyngeal adenoids. UMLS:C4280689 Decreased size of nasopharyngeal adenoids An abnormal decrease in the size of nasopharyngeal adenoids. An abnormal increase in the size of nasopharyngeal adenoids. SNOMEDCT_US:111591002 SNOMEDCT_US:276442006 UMLS:C0149825 UMLS:C0455938 Adenoid hypertrophy Adenoids large Increased size of nasopharyngeal adenoids Abnormal increase in muscle size and mass of one or both arms not due to training. UMLS:C4280687 Upper limb muscle hypertrophy An abnormal resistance to glucose, i.e., a reduction in the ability to maintain glucose levels in the blood stream within normal limits following oral or intravenous administration of glucose. MP:0005291 UMLS:C0151671 Decreased glucose tolerance Glucose tolerance decreased Impaired glucose tolerance An abnormal resistance to glucose, i.e., a reduction in the ability to maintain glucose levels in the blood stream within normal limits following oral or intravenous administration of glucose. A structural anomaly of the muscles of the trunk and head. Abnormality of axial muscles Abnormal axial muscle morphology Axial muscle atrophy Duplication of tongue Tongue duplicated Tongue duplication Duplicated tongue Double upper lip Duplication of the upper lip An increased concentration of glycerol in the urine. Increased urinary glycerol Increased concentration of glycerol in the blood. Pseudohypertriglyceridemia In glycerol kinase deficiency, the increased glycerol concentration has been noted to cause false-positive results of hypertriglyceridemia, a phenomenon called pseudohypertriglyceridemia. Hyperglycerolemia Increased concentration of glycerol in the blood. PMID:23415440 Low serum iron Decreased serum iron An abnormal deviation from normal levels of immunoglobulins in body fluids, such as mucous. Abnormal immunoglobulin level in body fluid An elevation from normal levels of immunoglobulins in body fluids, such as mucous. Increased immunoglobulin level in body fluid An reduction from normal levels of immunoglobulins in body fluids, such as mucous. Decreased immunoglobulin level in body fluid A neural tube defect arises when the neural tube, the embryonic precursor of the brain and spinal cord, fails to close during neurulation. The cranial region (anencephaly) or the low spine (open spina bifida; myelomeningocele) are most commonly affected although, in the severe NTD craniorachischisis, almost the entire neural tube remains open, from midbrain to low spine. MSH:D009436 SNOMEDCT_US:253098009 UMLS:C0027794 Abnormality of neural tube closure Neural tube defect A neural tube defect arises when the neural tube, the embryonic precursor of the brain and spinal cord, fails to close during neurulation. The cranial region (anencephaly) or the low spine (open spina bifida; myelomeningocele) are most commonly affected although, in the severe NTD craniorachischisis, almost the entire neural tube remains open, from midbrain to low spine. PMID:19808787 Abnormal morphology of a specific peripheral nerve UMLS:C4022400 Abnormal peripheral nerve morphology by anatomical site Abnormally decreased concentration of hydrogencarbonate in the urine. UMLS:C4022399 Decreased urine HCO3 concentration Decreased urine bicarbonate concentration Decreased urine HCO3 concentration SNOMEDCT_US:238090007 UMLS:C0342892 Hypolipidemia Defect or defects of the morphogenesis of the left heart identifiable at birth. UMLS:C4022397 Congenital malformation of the left heart Any structural anomaly of the central compartment of the thoracic cavity. HP:0100722 UMLS:C4022395 Abnormality of the mediastinum Abnormal mediastinum morphology UMLS:C4022394 Abnormality of the thoracic cavity UMLS:C4073166 Abnormality of jaw muscles Abnormality of jaw muscles Abnormality of jaw muscles Any abnormality of the brachial nerve plexus. UMLS:C4073176 Abnormality of the brachial nerve plexus Concentration of alpha-fetoprotein in the blood circulation outside normal limits. UMLS:C4073179 Abnormal circulating alpha-fetoprotein concentration Concentration of alpha-fetoprotein in the blood circulation below the lower limit of normal. UMLS:C4073295 Decreased circulating alpha-fetoprotein concentration An anomaly of the size of the testicle (the male gonad). UMLS:C4073180 Abnormality of the testis size UMLS:C4073181 Aplasia/hypoplasia involving bones of the extremities UMLS:C4073182 Decreased carnitine level in liver Inflammation in any serous cavity. Serositis Inflammation in any serous cavity. The ability of the knee to move past its normal range of motion, (knee hyperextension is greater than 10 degrees). Knee joint over-flexibility Knee joint hypermobility The ability of the knee to move past its normal range of motion, (knee hyperextension is greater than 10 degrees). PMID:28599980 Knee joint over-flexibility Hip joint hypermobility Any morphological abnormality of the cervical vertebral column. SNOMED_CT:298391004 Abnormal cervical spine morphology A tumor (abnormal growth of tissue) of the breast. 2010-05-14T09:45:09Z HP:0010623 MSH:D001943 NCIT:C3262 SNOMEDCT_US:126926005 UMLS:C1458155 Breast tumor Breast tumour Tumours of the breast Neoplasia of the breast HP:0100013 Neoplasm of the breast A tumor (abnormal growth of tissue) of the breast. Breast tumor Breast tumour Tumours of the breast Folds of membranous tissue (peritoneum, mesothelium) attached to the wall of the abdomen and enclosing viscera. Examples include the mesentery for the small intestine; the transverse mesocolon, which attaches the transverse portion of the colon to the back wall of the abdomen; and the mesosigmoid, which enfolds the sigmoid portion of the colon. Cells of the same embryologic origin also surround the other organs of the body such as the lungs (pleura) or the heart (pericardium). 2010-05-25T11:20:36Z UMLS:C4022389 Abnormality of mesentery morphology Abnormality of the mesentery HP:0100016 Abnormal mesentery morphology Folds of membranous tissue (peritoneum, mesothelium) attached to the wall of the abdomen and enclosing viscera. Examples include the mesentery for the small intestine; the transverse mesocolon, which attaches the transverse portion of the colon to the back wall of the abdomen; and the mesosigmoid, which enfolds the sigmoid portion of the colon. Cells of the same embryologic origin also surround the other organs of the body such as the lungs (pleura) or the heart (pericardium). An abnormality of movement with a neurological basis characterized by changes in coordination and speed of voluntary movements. 2010-05-28T11:48:50Z HP:0001294 MSH:D009069 SNOMEDCT_US:60342002 UMLS:C0026650 Abnormality of movement Movement disorder Unusual movement HP:0100022 Movement disorders are characterized by the phenotypic abnormalities including abnormal involuntary movements, akathisia, akinesia, athetosis, ataxia, ballismus, bradykinesia, chorea, dyskinesia, dystonia, and myoclonus tics, tremor, spasms, and stereotypy. Abnormality of movement An abnormality of movement with a neurological basis characterized by changes in coordination and speed of voluntary movements. Abnormality of movement Movement disorder Unusual movement 2010-06-24T10:00:02Z UMLS:C4022344 Absent end part of the little toe bone Absent end part of the pinkie toe bone Absent end part of the pinky toe bone HP:0100077 Absent epiphyses of the 5th toe Absent end part of the little toe bone Absent end part of the pinkie toe bone Absent end part of the pinky toe bone 2010-06-24T10:00:02Z UMLS:C4022341 Enlarged end part of the little toe bone Enlarged end part of the pinkie toe bone Enlarged end part of the pinky toe bone HP:0100080 Enlarged epiphyses of the 5th toe Enlarged end part of the little toe bone Enlarged end part of the pinkie toe bone Enlarged end part of the pinky toe bone 2010-06-24T10:00:02Z UMLS:C4022337 HP:0100084 Pseudoepiphyses of the 5th toe 2010-06-24T10:00:02Z UMLS:C4022336 Small end part of the little toe bone Small end part of the pinkie toe bone Small end part of the pinky toe bone HP:0100085 Small epiphyses of the 5th toe Small end part of the little toe bone Small end part of the pinkie toe bone Small end part of the pinky toe bone 2010-06-24T10:02:41Z UMLS:C4022324 Abnormality of the end part of the outermost bone of the little toe Abnormality of the end part of the outermost bone of the pinkie toe Abnormality of the end part of the outermost bone of the pinky toe HP:0100097 Abnormality of the epiphysis of the distal phalanx of the 5th toe Abnormality of the end part of the outermost bone of the little toe Abnormality of the end part of the outermost bone of the pinkie toe Abnormality of the end part of the outermost bone of the pinky toe 2010-06-24T10:02:41Z UMLS:C4022323 Abnormality of the end part of the middle bone of the little toe Abnormality of the end part of the middle bone of the pinkie toe Abnormality of the end part of the middle bone of the pinky toe HP:0100098 Abnormality of the epiphysis of the middle phalanx of the 5th toe Abnormality of the end part of the middle bone of the little toe Abnormality of the end part of the middle bone of the pinkie toe Abnormality of the end part of the middle bone of the pinky toe 2010-06-24T10:02:41Z UMLS:C4022322 Abnormality of the end part of the innermost bone of the little toe Abnormality of the end part of the innermost bone of the pinkie toe Abnormality of the end part of the innermost bone of the pinky toe HP:0100099 Abnormality of the epiphysis of the proximal phalanx of the 5th toe Abnormality of the end part of the innermost bone of the little toe Abnormality of the end part of the innermost bone of the pinkie toe Abnormality of the end part of the innermost bone of the pinky toe Abnormality of the growth of the axillary hair. Axillary hair is part of the secondary sexual hair, which normally ensues during puberty. 2010-06-24T10:17:00Z UMLS:C4022287 HP:0100134 Abnormality of the axillary hair Abnormality of the growth of the axillary hair. Axillary hair is part of the secondary sexual hair, which normally ensues during puberty. 2010-06-24T05:03:31Z UMLS:C4022219 Absent end part of the outermost bone of the little toe Absent end part of the outermost bone of the pinkie toe Absent end part of the outermost bone of the pinky toe HP:0100202 Absent epiphysis of the distal phalanx of the 5th toe Absent end part of the outermost bone of the little toe Absent end part of the outermost bone of the pinkie toe Absent end part of the outermost bone of the pinky toe 2010-06-24T05:03:31Z UMLS:C4022216 Enlarged end part of the outermost bone of the little toe Enlarged end part of the outermost bone of the pinkie toe Enlarged end part of the outermost bone of the pinky toe HP:0100205 Enlarged epiphysis of the distal phalanx of the 5th toe Enlarged end part of the outermost bone of the little toe Enlarged end part of the outermost bone of the pinkie toe Enlarged end part of the outermost bone of the pinky toe 2010-06-24T05:03:31Z UMLS:C4022212 HP:0100209 Pseudoepiphysis of the distal phalanx of the 5th toe 2010-06-24T05:03:31Z UMLS:C4022211 Small end part of the outermost bone of the little toe Small end part of the outermost bone of the pinkie toe Small end part of the outermost bone of the pinky toe HP:0100210 Small epiphysis of the distal phalanx of the 5th toe Small end part of the outermost bone of the little toe Small end part of the outermost bone of the pinkie toe Small end part of the outermost bone of the pinky toe 2010-06-24T05:04:00Z UMLS:C4022208 Absent end part of the middle bone of the little toe Absent end part of the middle bone of the pinkie toe Absent end part of the middle bone of the pinky toe HP:0100213 Absent epiphysis of the middle phalanx of the 5th toe Absent end part of the middle bone of the little toe Absent end part of the middle bone of the pinkie toe Absent end part of the middle bone of the pinky toe 2010-06-24T05:04:00Z UMLS:C4022205 Enlarged end part of the middle bone of the little toe Enlarged end part of the middle bone of the pinkie toe Enlarged end part of the middle bone of the pinky toe HP:0100216 Enlarged epiphysis of the middle phalanx of the 5th toe Enlarged end part of the middle bone of the little toe Enlarged end part of the middle bone of the pinkie toe Enlarged end part of the middle bone of the pinky toe A pseudoepiphysis (an accessory epiphysis that does not significantly contribute to the longitudinal growth of a tubular bone) located in the middle phalanx of the fifth toe. 2010-06-24T05:04:00Z UMLS:C4022201 HP:0100220 Pseudoepiphysis of the middle phalanx of the 5th toe 2010-06-24T05:04:00Z UMLS:C4022200 Small end part of the middle bone of the little toe Small end part of the middle bone of the pinkie toe Small end part of the middle bone of the pinky toe HP:0100221 Small epiphysis of the middle phalanx of the 5th toe Small end part of the middle bone of the little toe Small end part of the middle bone of the pinkie toe Small end part of the middle bone of the pinky toe 2010-06-24T05:04:53Z UMLS:C4022197 Absent end part of the innermost bone of the little toe Absent end part of the innermost bone of the pinkie toe Absent end part of the innermost bone of the pinky toe HP:0100224 Absent epiphysis of the proximal phalanx of the 5th toe Absent end part of the innermost bone of the little toe Absent end part of the innermost bone of the pinkie toe Absent end part of the innermost bone of the pinky toe 2010-06-24T05:04:53Z UMLS:C4022194 Enlarged end part of the innermost bone of the little toe Enlarged end part of the innermost bone of the pinkie toe Enlarged end part of the innermost bone of the pinky toe HP:0100227 Enlarged epiphysis of the proximal phalanx of the 5th toe Enlarged end part of the innermost bone of the little toe Enlarged end part of the innermost bone of the pinkie toe Enlarged end part of the innermost bone of the pinky toe A pseudoepiphysis (an accessory epiphysis that does not significantly contribute to the longitudinal growth of a tubular bone) located in the proximal phalanx of the fifth toe. 2010-06-24T05:04:53Z UMLS:C4022190 HP:0100231 Pseudoepiphysis of the proximal phalanx of the 5th toe 2010-06-24T05:04:53Z UMLS:C4022189 Small end part of the innermost bone of the little toe Small end part of the innermost bone of the pinkie toe Small end part of the innermost bone of the pinky toe HP:0100232 Small epiphysis of the proximal phalanx of the 5th toe Small end part of the innermost bone of the little toe Small end part of the innermost bone of the pinkie toe Small end part of the innermost bone of the pinky toe Osteomas are bony growths found most commonly on the skull and mandible; however, they may occur in any bone of the body. Osteomas do not usually cause clinical problems and do not become malignant. 2010-07-08T11:38:30Z MSH:D010016 NCIT:C3296 SNOMEDCT_US:302858007 SNOMEDCT_US:83612000 UMLS:C0029440 HP:0100246 Osteoma Osteomas are bony growths found most commonly on the skull and mandible; however, they may occur in any bone of the body. Osteomas do not usually cause clinical problems and do not become malignant. Deposition of calcium salts in muscle tissue. 2010-07-09T12:32:25Z SNOMEDCT_US:446993003 UMLS:C2960760 Skeletal muscle calcinosis HP:0100249 Calcification of muscles Deposition of calcium salts in muscle tissue. Calcium deposition affecting the Meninges. 2010-07-14T03:41:34Z UMLS:C4022181 HP:0100250 In general, meningeal calcifications are plaque-like and bilateral as seen on CT-scans. Meningeal calcification Calcium deposition affecting the Meninges. The presence of dysplastic regions in metaphyseal regions. 2010-07-14T05:15:56Z HP:0000948 HP:0005002 HP:0005636 HP:0005704 HP:0005899 HP:0006427 MSH:C536252 SNOMEDCT_US:27837003 UMLS:C0265294 HP:0100255 Metaphyseal dysplasia The presence of dysplastic regions in metaphyseal regions. A form of polydactyly in which the extra digit or digits are localized on the side of the thumb or great toe. 2010-07-20T11:00:32Z SNOMEDCT_US:205135003 UMLS:C0345354 Polydactyly, preaxial HP:0100258 Preaxial polydactyly A form of polydactyly in which the extra digit or digits are localized on the side of the thumb or great toe. Polydactyly, preaxial A form of polydactyly in which the extra digit or digits are localized on the side of the fifth finger or fifth toe. 2010-07-20T11:00:32Z HP:0005808 MSH:C562429 UMLS:C0220697 Polydactyly, postaxial Postaxial hexadactyly HP:0100259 Postaxial polydactyly A form of polydactyly in which the extra digit or digits are localized on the side of the fifth finger or fifth toe. An abnormality of the structure or form of the tendons, also often called sinews. 2010-07-20T01:20:19Z UMLS:C4021026 Abnormal shape of tendon Abnormality of the sinew HP:0100261 A tendon (or sinew) is a tough band of fibrous connective tissue that usually connects muscle to bone and is capable of withstanding tension. Tendons are similar to ligaments and fascia as they are all made of collagen except that ligaments join one bone to another bone, and fascia connect muscles to other muscles. Tendons and muscles work together and can only exert a pulling force. Abnormal tendon morphology An abnormality of the structure or form of the tendons, also often called sinews. Abnormal shape of tendon The presence of an increased amount of muscle fibers with an increased diameter. This feature can be ascertained by microscopic examination of a muscle biopsy sample. Together with fiber size variation and atrophied muscle fibers, and hypertrophied muscle fibers are commonly found in myopathies. 2010-08-10T01:57:00Z SNOMEDCT_US:42091004 UMLS:C0333759 Muscle fiber hypertrophy Muscle fibre hypertrophy HP:0100293 Muscle hypertrophy can be assessed at the whole-muscle level (macroscopic methods) or the muscle fiber level (microscopic methods). This term refers to hypertrophy assessed at the microscopic level. Hypertrophied muscle fibers 2010-08-10T01:58:24Z HP:0100294 SNOMEDCT_US:67867005 UMLS:C0333751 Muscle fiber degeneration Muscle fibre atrophy Muscle fibre degeneration HP:0100295 Muscle fiber atrophy Muscle fiber degeneration Muscle fibre degeneration Immunological states where the immune system produces harmful responses upon reexposure to sensitising antigens. 2010-09-16T06:00:43Z UMLS:C0237653 HP:0100326 Immunologic hypersensitivity Immunological states where the immune system produces harmful responses upon reexposure to sensitising antigens. https://www.st-andrews.ac.uk/~gdk/bl4217web/Gp3%20Ref%20list/hypersensitivity%20printed.pdf 2010-11-11T03:44:27Z UMLS:C4022134 HP:0100346 Fibular deviation of the 5th toe The proximal interphalangeal joint of the fifth toe cannot be straightened actively or passively. UMLS:C4021016 Camptodactyly of the 5th toe Camptodactyly of the fifth toe HP:0100351 Contractures of the proximal interphalangeal joint of the 5th toe The proximal interphalangeal joint of the fifth toe cannot be straightened actively or passively. The distal interphalangeal joint of the 5th toe cannot be straightened actively or passively. UMLS:C4022130 Contracture of the outermost hinge joint of the 5th toe HP:0100355 Contractures of the distal interphalangeal joint of the 5th toe The distal interphalangeal joint of the 5th toe cannot be straightened actively or passively. Contracture of the outermost hinge joint of the 5th toe The joint between the fifth metatarsal and the proximal phalanx of the fifth toe cannot be straightened actively or passively. UMLS:C4022126 HP:0100359 Contracture of the metatarsophalangeal joint of the 5th toe The joint between the fifth metatarsal and the proximal phalanx of the fifth toe cannot be straightened actively or passively. A limitation in the passive range of motion of a joint of the upper limb resulting from loss of elasticity in the periarticular tissues owing to structural changes of non-bony tissues, such as muscles, tendons, ligaments, joint capsules or skin. 2010-11-11T04:18:29Z UMLS:C2750635 Contractures of the joints of the upper limbs HP:0100360 Upper-limb joint contracture Developmental hypoplasia of one or more phalanx of little toe. UMLS:C4021012 Hypoplastic/small phalanges of the 5th toe Short little toe bone Short phalanx of the fifth toe Short pinkie toe bone Short pinky toe bone HP:0100368 Short phalanx of the 5th toe Developmental hypoplasia of one or more phalanx of little toe. Short little toe bone Short pinkie toe bone Short pinky toe bone UMLS:C4022120 Absent/small outermost little toe bone Absent/small outermost pinkie toe bone Absent/small outermost pinky toe bone Absent/underdeveloped outermost pinky toe bone HP:0100371 Aplasia/Hypoplasia of the distal phalanx of the 5th toe Absent/small outermost little toe bone Absent/small outermost pinkie toe bone Absent/small outermost pinky toe bone Absent/underdeveloped outermost pinky toe bone UMLS:C4022117 Absent/small middle 5th toe bone Absent/underdeveloped middle bone of little toe Absent/underdeveloped middle bone of pinkie toe Absent/underdeveloped middle bone of pinky toe HP:0100374 Aplasia/Hypoplasia of the middle phalanx of the 5th toe Absent/small middle 5th toe bone Absent/underdeveloped middle bone of little toe Absent/underdeveloped middle bone of pinkie toe Absent/underdeveloped middle bone of pinky toe Absence (agenesis) or underdevelopment of the proximal phalanx of the 5th toe. UMLS:C4022114 Absent/small innermost little toe bone Absent/small innermost pinkie toe bone Absent/small innermost pinky toe bone Absent/underdeveloped innermost 5th toe bone HP:0100377 Aplasia/hypoplasia of the proximal phalanx of the 5th toe Absence (agenesis) or underdevelopment of the proximal phalanx of the 5th toe. Absent/small innermost little toe bone Absent/small innermost pinkie toe bone Absent/small innermost pinky toe bone Absent/underdeveloped innermost 5th toe bone Developmental hypoplasia of the distal phalanx of little toe. UMLS:C4021006 Hypoplastic/small distal phalanx of the 5th toe Short distal phalanx of the fifth toe Short outermost bone of the little toe Short outermost bone of the pinkie toe Short outermost bone of the pinky toe HP:0100391 Short distal phalanx of the 5th toe Developmental hypoplasia of the distal phalanx of little toe. Short outermost bone of the little toe Short outermost bone of the pinkie toe Short outermost bone of the pinky toe Developmental hypoplasia of the middle phalanx of the 5th toe. UMLS:C4021003 Hypoplastic/small middle phalanx of the 5th toe Short middle bone of little toe Short middle bone of pinkie toe Short middle bone of pinky toe Short middle phalanx of the fifth toe HP:0100394 Short middle phalanx of the 5th toe Developmental hypoplasia of the middle phalanx of the 5th toe. Hypoplastic/small middle phalanx of the 5th toe Short middle bone of little toe Short middle bone of pinkie toe Short middle bone of pinky toe Developmental hypoplasia of the proximal phalanx of fifth toe. UMLS:C4021000 Hypoplastic/small proximal phalanx of the 5th toe Short innermost bone of little toe Short innermost bone of pinkie toe Short innermost bone of pinky toe Short proximal phalanx of the fifth toe HP:0100397 Short proximal phalanx of the 5th toe Developmental hypoplasia of the proximal phalanx of fifth toe. Hypoplastic/small proximal phalanx of the 5th toe Short innermost bone of little toe Short innermost bone of pinkie toe Short innermost bone of pinky toe Short proximal phalanx of the fifth toe Partial or complete duplication of the distal phalanx of little toe. UMLS:C4020997 Duplication of the distal phalanx of the fifth toe Duplication of the outermost bone of the fifth toe Duplication of the outermost bone of the little toe Duplication of the outermost bone of the pinkie toe Duplication of the outermost bone of the pinky toe Partial/complete duplication of the distal phalanx of the 5th toe HP:0100400 Duplication of the distal phalanx of the 5th toe Partial or complete duplication of the distal phalanx of little toe. Duplication of the outermost bone of the fifth toe Duplication of the outermost bone of the little toe Duplication of the outermost bone of the pinkie toe Duplication of the outermost bone of the pinky toe Partial or complete duplication of the proximal phalanx of fifth toe. UMLS:C4020991 Duplication of the innermost bone of the little toe Duplication of the innermost bone of the pinkie toe Duplication of the innermost bone of the pinky toe Duplication of the proximal phalanx of the fifth toe Partial/complete duplication of the proximal phalanx of the 5th toe HP:0100406 Duplication of the proximal phalanx of the 5th toe Partial or complete duplication of the proximal phalanx of fifth toe. Duplication of the innermost bone of the little toe Duplication of the innermost bone of the pinkie toe Duplication of the innermost bone of the pinky toe Complete duplication of the distal phalanx of little toe. UMLS:C4020988 Complete duplication of the distal phalanx of the fifth toe Complete duplication of the outermost bone of the little toe Complete duplication of the outermost bone of the pinkie toe Complete duplication of the outermost bone of the pinky toe HP:0100409 Complete duplication of the distal phalanx of the 5th toe Complete duplication of the distal phalanx of little toe. Complete duplication of the outermost bone of the little toe Complete duplication of the outermost bone of the pinkie toe Complete duplication of the outermost bone of the pinky toe Complete duplication of the proximal phalanx of fifth toe. UMLS:C4020984 Complete duplication of the innermost bone of the little toe Complete duplication of the innermost bone of the pinkie toe Complete duplication of the innermost bone of the pinky toe Complete duplication of the proximal phalanx of the fifth toe HP:0100415 Complete duplication of the proximal phalanx of the 5th toe Complete duplication of the proximal phalanx of fifth toe. Complete duplication of the innermost bone of the little toe Complete duplication of the innermost bone of the pinkie toe Complete duplication of the innermost bone of the pinky toe The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers cannot be extended to 180 degrees by either active or passive extension. 2010-12-14T10:46:57Z HP:0005651 HP:0005662 HP:0005713 HP:0005801 HP:0005821 HP:0006195 HP:0006218 HP:0006240 HP:0009698 SNOMEDCT_US:202281000 UMLS:C0409348 Camptodactyly of hands Camptodactyly of proximal interphalangeal joint Contractures of the proximal interphalangeal joints of the fingers Flexion contractures of proximal interphalangeal joints Permanent flexion of the finger Proximal interphalangeal finger joint contractures HP:0100490 Note that some restrict the use of the term to inability to extend the proximal interphalangeal joint of the fifth finger. We do not restrict the term in this way. This term should not be used if the patient has Clenched hand. A similar effect can be created by radial angulation within the distal phalanx with thickening of the epiphysis, which is called Kirner deformity or dystelephalangy. The affected digits should be specified. Camptodactyly of finger The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers cannot be extended to 180 degrees by either active or passive extension. PMID:19125433 Permanent flexion of the finger 2010-12-14T10:58:11Z HP:0100239 UMLS:C4020971 Abnormality of lower limb joint Abnormality of the joints of the lower limbs HP:0100491 Abnormality of lower limb joint Abnormality of lower limb joint Abnormality of the joints of the lower limbs A decreased concentration of ammonia in the blood. 2010-12-17T03:54:51Z UMLS:C4022041 HP:0100493 Hypoammonemia A decreased concentration of ammonia in the blood. HPO_CONTRIBUTOR:gcarletti Any structural anomaly of mast cells, which are found in almost all tissues and contain numerous basophilic granules and are capable of releasing large amounts of histamine and heparin upon activation. 2010-12-17T04:02:08Z SNOMEDCT_US:397017008 UMLS:C1301149 Abnormality of mast cells Abnormality of mastocytes HP:0100494 Mast cells (or mastocytes) can be found in several types of tissues and contain many granules rich in histamine and heparin. Although best known for their role in allergy and anaphylaxis, mast cells play an important protective role as well, being intimately involved in wound healing and defense against pathogens. Mast cells possess a non-lobed nucleus and can work with basophils in the immune defense against worms. Their cell membrane is covered with Fc recepros that may be attached to class E antibodies. Abnormal mast cell morphology Any structural anomaly of mast cells, which are found in almost all tissues and contain numerous basophilic granules and are capable of releasing large amounts of histamine and heparin upon activation. The presence of an increased number of mast cells and CD34+ mast cell precursors in the body. 2010-12-17T04:06:36Z MSH:D008415 SNOMEDCT_US:125541005 SNOMEDCT_US:397007003 UMLS:C0024899 HP:0100495 Mastocytosis The presence of an increased number of mast cells and CD34+ mast cell precursors in the body. 2010-12-17T04:25:31Z UMLS:C4022039 HP:0100498 Deviation of toes 2010-12-17T04:26:14Z UMLS:C4020970 Lateral deviation of toes HP:0100500 Fibular deviation of toes A reduced circulating concentration of folic acid, which is also known as vitamin B9. 2010-12-17T06:13:04Z MSH:D005494 SNOMEDCT_US:190633005 UMLS:C0016412 Folate deficiency Vitamin B9 deficiency HP:0100507 Reduced blood folate concentration A reduced circulating concentration of folic acid, which is also known as vitamin B9. Folate deficiency An anomaly in the metabolism of a vitamin. 2010-12-17T06:17:22Z UMLS:C4022036 Abnormality of vitamin metabolism HP:0100508 Vitamins are organic substances that are essential in minute quantities and not produced within the body, instead being present in natural foodstuffs. Vitamins act as coenzymes or precursors of coenzymes in the regulation of metabolic processes. Abnormality of vitamin metabolism An anomaly in the metabolism of a vitamin. Abnormality of vitamin metabolism 2010-12-17T06:19:15Z UMLS:C4022035 Abnormality of vitamin D metabolism HP:0100511 Abnormality of vitamin D metabolism Abnormality of vitamin D metabolism A reduced concentration of Vitamin D. 2010-12-17T06:19:35Z MSH:D014808 SNOMEDCT_US:34713006 UMLS:C0042870 Deficient in vitamin D Vitamin D deficiency HP:0100512 Low levels of vitamin D Deficient in vitamin D Vitamin D deficiency A reduced concentration of vitamin E in the blood circulation. Vitamin E is a lipophilic vitamin that is also known as alpha-tocopherol. 2010-12-17T06:20:12Z MSH:D014811 SNOMEDCT_US:54137008 UMLS:C0042875 Alpha-tocopherol deficiency Low levels of vitamin E Vitamin E deficiency HP:0100513 Decreased circulating vitamin E concentration A reduced concentration of vitamin E in the blood circulation. Vitamin E is a lipophilic vitamin that is also known as alpha-tocopherol. PMID:30559825 Alpha-tocopherol deficiency Vitamin E deficiency Concentration of vitamin E in the blood circulation outside of normal limits. 2010-12-17T06:20:30Z UMLS:C4022034 HP:0100514 Abnormal circulating vitamin E concentration The presence of a neoplasm of the ureter. 2010-12-20T10:35:11Z MSH:D014516 NCIT:C3262 SNOMEDCT_US:126882009 SNOMEDCT_US:363458004 UMLS:C0041955 UMLS:C0153619 Neoplasia of the ureters ureter, cancer of HP:0100516 Neoplasm of the ureter The presence of a neoplasm of the ureter. Absence of urine, clinically classified as below 50ml/day. 2010-12-20T10:41:00Z MSH:D001002 SNOMEDCT_US:2472002 UMLS:C0003460 Absent urine output HP:0100519 Anuria Absence of urine, clinically classified as below 50ml/day. Absent urine output Congenital duplication of all or part of a limb. 2010-12-20T11:32:41Z SNOMEDCT_US:34488005 UMLS:C0265551 Dimelia Limb duplication HP:0100524 Limb duplication Limb duplication An abnormality of phosphate homeostasis or concentration in the body. 2010-12-20T11:58:32Z UMLS:C4022032 Abnormality of phosphate homeostasis HP:0100529 Abnormal blood phosphate concentration An abnormality of phosphate homeostasis or concentration in the body. Any deviation from the normal concentration in the blood circulation of a hormone that is involved in the regulation of phosphate and calcium. 2010-12-20T12:00:26Z UMLS:C4022031 Abnormal Ca-PHOS regulating hormone level Abnormal Ca2+ PO4 regulating hormone level HP:0100530 Abnormal circulating calcium-phosphate regulating hormone concentration Abnormal Ca-PHOS regulating hormone level Abnormal Ca2+ PO4 regulating hormone level Inflammation of the eye, parts of the eye or the periorbital region. 2010-12-20T03:53:42Z HP:0007891 UMLS:C4020969 Inflammatory abnormality of the eye Ocular inflammation HP:0100533 Inflammatory abnormality of the eye Inflammation of the eye, parts of the eye or the periorbital region. Inflammatory abnormality of the eye An abnormal site of the kidney. 2010-12-20T06:43:50Z UMLS:C4020968 Abnormal localisation of kidneys HP:0100542 Abnormal localization of kidney An abnormal site of the kidney. Abnormal localisation of kidneys Abnormal cognition is characterized by deficits in thinking, reasoning, or remembering. 2010-12-20T06:50:32Z HP:0002128 HP:0002129 HP:0002302 HP:0002337 HP:0002441 HP:0006972 HP:0006998 HP:0007211 MSH:D060825 SNOMEDCT_US:386806002 UMLS:C0338656 UMLS:C0683322 Abnormality of cognition Cognitive abnormality Cognitive defects Cognitive deficits Cognitive impairment Intellectual impairment HP:0100543 An individual with cognitive impairment may experience difficulties in remembering, learning new things, concentrating, or making decisions. Cognitive impairment Abnormality of cognition Cognitive abnormality Cognitive defects Cognitive deficits Cognitive impairment Intellectual impairment An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. 2010-12-21T02:12:53Z UMLS:C4020967 Abnormal shape of forebrain Abnormality of forebrain morphology Abnormality of the forebrain HP:0100547 Abnormal forebrain morphology An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. Abnormal shape of forebrain An abnormality of the formation and mineralization of one or more vertebrae. 2010-12-21T04:50:43Z UMLS:C4020966 Abnormal bone maturation of vertebra Abnormal vertebral ossification Abnormality of ossification/mineralisation of vertebrae HP:0100569 Abnormally ossified vertebrae An abnormality of the formation and mineralization of one or more vertebrae. Abnormal bone maturation of vertebra A cardiac diverticulum is a rare congenital malformation which is either fibrous or muscular. 2010-12-21T05:11:26Z UMLS:C4020965 Ventricular diverticulum HP:0100571 Cardiac diverticulum A cardiac diverticulum is a rare congenital malformation which is either fibrous or muscular. A fibrous cardiac diverticulum refers to an aneurysm and usually appears as an isolated congenital anomaly. 2010-12-21T05:14:00Z UMLS:C4020964 Congenital ventricular aneurysm HP:0100572 Fibrous cardiac diverticulum A fibrous cardiac diverticulum refers to an aneurysm and usually appears as an isolated congenital anomaly. 2010-12-21T05:14:00Z UMLS:C4022021 HP:0100573 Muscular cardiac diverticulum Inflammation of the urinary bladder. 2010-12-27T12:49:16Z MSH:D003556 SNOMEDCT_US:38822007 UMLS:C0010692 Cystitis of the urinary bladder Urinary bladder inflammation HP:0100577 Urinary bladder inflammation Inflammation of the urinary bladder. Urinary bladder inflammation An inflammation of the endocardium, the inner layer of the heart, which usually involves the heart valves. 2010-12-27T02:57:48Z MSH:D004696 SNOMEDCT_US:56819008 UMLS:C0014118 HP:0100584 Endocarditis An inflammation of the endocardium, the inner layer of the heart, which usually involves the heart valves. An abnormality of the retractable fold of skin that covers the tip of the penis. 2010-12-27T03:13:07Z UMLS:C4022016 Abnormality of the preputium HP:0100587 Abnormal preputium morphology The presence of calcium deposition in cartilage. 2010-12-27T04:35:28Z UMLS:C4022015 HP:0100593 Calcification of cartilage The nostrils (the paired channels of the nose) are not present. 2010-12-27T05:07:16Z HP:0100597 UMLS:C4020707 UMLS:C4020963 Abouphalia Aplasia of the nares Missing nostrils Aplasia/Hypoplasia of the nares HP:0100596 Absent nares The nostrils (the paired channels of the nose) are not present. Missing nostrils A general term for inflammation of the muscles without respect to the underlying cause. 2010-12-28T11:14:59Z MSH:D009220 SNOMEDCT_US:128496001 SNOMEDCT_US:26889001 UMLS:C0027121 Muscle inflammation HP:0100614 Many such conditions are considered likely to be caused by autoimmune conditions, rather than directly due to infection, although autoimmune conditions can be activated or exacerbated by infections. It is also a documented side effect of the lipid-lowering drugs such as statins and fibrates. Elevation of creatine kinase in blood is indicative of myositis. Myositis A general term for inflammation of the muscles without respect to the underlying cause. Muscle inflammation 2010-12-28T04:14:55Z UMLS:C4020962 Wide rib cage Wide thorax HP:0100625 Enlarged thorax Wide rib cage The presence of a diverticulum of the esophagus. 2010-12-29T02:22:08Z MSH:D004936 SNOMEDCT_US:204667006 SNOMEDCT_US:414133009 UMLS:C0014854 Esophageal pouch HP:0100628 A diverticulum is a blind ended outpouching through the wall of a tubular organ or bounded cavity. Esophageal diverticulum The presence of a diverticulum of the esophagus. Inflammation of the thyroid gland. 2010-12-29T06:08:32Z MSH:D013966 SNOMEDCT_US:82119001 UMLS:C0040147 Thyroid gland inflammation HP:0100646 Thyroiditis Inflammation of the thyroid gland. Thyroid gland inflammation An anomaly of the cerebral blood vessels. 2010-12-30T11:39:15Z UMLS:C4022001 Abnormality of the cerebral blood vessels Abnormality of the cerebral vasculature HP:0100659 Abnormal cerebral vascular morphology An anomaly of the cerebral blood vessels. PMID:30335330 Abnormality of the cerebral blood vessels Inflammation of cartilage. 2010-12-30T12:57:50Z SNOMEDCT_US:46176001 UMLS:C0008439 Cartilage inflammation HP:0100662 Chondritis Inflammation of cartilage. Cartilage inflammation A developmental disorder in which there is a duplication the entire intestine or of a portion of the intestine. 2010-12-30T01:23:50Z SNOMEDCT_US:3845008 UMLS:C0266166 UMLS:C4020702 Bowel duplication Gut duplication HP:0100668 Intestinal duplication A developmental disorder in which there is a duplication the entire intestine or of a portion of the intestine. Bowel duplication Gut duplication A developmental disorder in which there is a duplication of a portion of the muscle and submucosa of the esophagus without epithelial duplication. 2010-12-30T02:08:38Z SNOMEDCT_US:66865009 UMLS:C0266135 HP:0100681 Esophageal duplication is a rare cause of mediastinal mass. An esophageal duplication may be a simple epithelial cyst or duplication that contains muscle and submucosa but not epithelium. In most cases, the duplication is located in the lower thrid of the esophagus, and the most common associated symptom is difficulty in swallowing. Esophageal duplication occurs because of maldevelopment of the posterior division of embryonic foregut. Esophageal duplication A developmental disorder in which there is a duplication of a portion of the muscle and submucosa of the esophagus without epithelial duplication. PMID:10464795 2011-02-18T04:58:48Z UMLS:C4021995 HP:0100691 Abnormality of the curvature of the cornea An abnormality of the Arachnoid mater. 2011-03-31T12:43:27Z UMLS:C4020955 Abnormality of the arachnoid mater Abnormality of the arachnoidea HP:0100700 Abnormal arachnoid mater morphology An abnormality of the Arachnoid mater. An abnormality of the pia mater. 2011-03-31T12:44:41Z UMLS:C4021994 Abnormality of the pia mater HP:0100701 Abnormal pia mater An abnormality of the pia mater. An abnormality of the glia cell. 2011-04-03T02:33:49Z UMLS:C4021993 Abnormality of the glial cells HP:0100705 Glia are nonneuronal cells of the nervous system that provide physical support, respond to injury, regulate the composition of the extracellular milieu, guide neuronal migration during development, and exchange metabolites with neurons. Abnormal glial cell morphology An abnormality of the glia cell. An abnormality of the thoracic vertebral column. 2011-05-05T09:37:17Z UMLS:C4021989 Abnormality of the thoracic spine HP:0100711 Abnormal thoracic spine morphology An abnormality of the thoracic vertebral column. Any structural abnormality of the lumbar vertebral column. 2011-05-05T09:37:33Z UMLS:C4021988 Abnormality of the lumbar spine HP:0100712 Abnormal lumbar spine morphology Any structural abnormality of the lumbar vertebral column. A sectoral indentation of the crystalline lens, usually due to zonular weakness or absence. 2011-06-06T02:16:53Z SNOMEDCT_US:204134008 UMLS:C0344516 HP:0100719 Lens coloboma A sectoral indentation of the crystalline lens, usually due to zonular weakness or absence. 2011-06-06T04:50:47Z UMLS:C2748652 Big face Large face Large facies HP:0100729 Large face Big face Large face Large facies An anomaly of one or more epiphyses of one or more vertebrae. 2011-06-06T05:13:08Z UMLS:C4020953 Abnormal shape of the end part of the vertebra bone Abnormality of the vertebral epiphyses Abnormality of vertebral epiphysis morphology HP:0100734 Abnormal vertebral epiphysis morphology Abnormal shape of the end part of the vertebra bone 2011-06-06T06:20:18Z MSH:D012004 NCIT:C3262 SNOMEDCT_US:126847008 UMLS:C0034885 Rectal tumor Rectal tumour HP:0100743 Neoplasm of the rectum Rectal tumor Rectal tumour 2011-06-07T10:01:04Z UMLS:C4021978 Abnormal spit Abnormality of salivation HP:0100755 Abnormality of salivation Abnormal spit Abnormality of salivation An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. 2011-06-07T10:40:36Z HP:0003012 MSH:D008206 SNOMEDCT_US:111590001 SNOMEDCT_US:234087005 SNOMEDCT_US:3305006 SNOMEDCT_US:362971004 UMLS:C0024228 UMLS:C4021976 Lymphatic disease HP:0100763 Abnormality of the lymphatic system An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. An abnormality of the tonsils. 2011-06-07T10:43:35Z UMLS:C4021975 HP:0100765 Abnormality of the tonsils An abnormality of the tonsils. A structural anomaly of the vessel that contains or conveys lymph fluid. 2011-06-07T10:44:54Z UMLS:C4021974 Abnormality of the lymphatic vessels HP:0100766 Abnormal lymphatic vessel morphology A structural anomaly of the vessel that contains or conveys lymph fluid. https://en.wikipedia.org/wiki/Lymphatic_vessel An abnormality of the placenta, the organ that connects the developing fetus to the uterine wall to enable nutrient uptake, waste elimination, and gas exchange. 2011-06-07T11:03:03Z SNOMEDCT_US:169957005 SNOMEDCT_US:33552005 UMLS:C1306893 Abnormality of the placenta Placental issue HP:0100767 The placenta is a fetomaternal organ. The fetal portion of the placenta is the villous chorion and the maternal portion is the decidua basalis. The two portions are connected by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Abnormal placenta morphology An abnormality of the placenta, the organ that connects the developing fetus to the uterine wall to enable nutrient uptake, waste elimination, and gas exchange. Placental issue Excessively active peristalsis (wave of contraction of the tubular organs of the gastrointestinal tract) marked by excessive rapidity of the passage of food through the stomach and intestine. 2011-06-07T11:53:08Z Stomach churning SNOMEDCT_US:271838002 SNOMEDCT_US:80306002 UMLS:C0232474 UMLS:C0857071 HP:0100770 Hyperperistalsis Excessively active peristalsis (wave of contraction of the tubular organs of the gastrointestinal tract) marked by excessive rapidity of the passage of food through the stomach and intestine. Stomach churning http://www.healthhype.com/stomach-churning-sensation-feeling-causes-remedies.html Reduced or inadequate peristalsis, with resultant slow passage of contents through the digestive tract. 2011-06-07T11:53:08Z SNOMEDCT_US:77853002 UMLS:C0232475 UMLS:C4020700 Intestinal hypoperistalsis HP:0100771 Hypoperistalsis Reduced or inadequate peristalsis, with resultant slow passage of contents through the digestive tract. Intestinal hypoperistalsis Excessive growth or abnormal thickening of bone tissue. 2011-06-07T05:17:19Z MSH:D015576 SNOMEDCT_US:13814009 SNOMEDCT_US:203514008 UMLS:C0020492 Bone Hypertrophy Bone overgrowth HP:0100774 Hyperostosis refers to a localized bone overgrowth process (as opposed to sclerosis, which refers to a generalized disturbance with increased bone density). Hyperostosis Excessive growth or abnormal thickening of bone tissue. Bone overgrowth An anomaly of the sacroiliac joint, which connects the base of the spine (sacrum) to the ilium (a hip bone). 2011-06-07T05:52:24Z UMLS:C0262621 Abnormality of the sacroiliac joint HP:0100781 The sacroiliac joint (SIJ) is a true diarthrodial joint: matching articular surfaces separated by a joint space containing synovial fluid and enveloped by a fibrous capsule. It does, however, have unique characteristics not typically found in other diarthrodial joints. The SIJ has fibrocartilage in addition to hyaline cartilage. There is discontinuity of the posterior capsule. Rather than being smooth, the articular surfaces have many ridges and depressions that minimize movement and enhance stability. Primary stability, however, is attributed to the many adjacent ligaments. Abnormal sacroiliac joint morphology An anomaly of the sacroiliac joint, which connects the base of the spine (sacrum) to the ilium (a hip bone). PMID:16700283 A congenital underdevelopment (aplasia or hypoplasia) of the pancreas. 2011-06-09T11:45:58Z UMLS:C4021968 Absent/small pancreas Absent/underdeveloped pancreas HP:0100800 Aplasia/Hypoplasia of the pancreas A congenital underdevelopment (aplasia or hypoplasia) of the pancreas. Absent/small pancreas Absent/underdeveloped pancreas The middle finger is more than 2 SD above the mean for newborns 27 to 41 weeks EGA or above the 97th centile for children from birth to 16 years of age AND the five digits retain their normal length proportions relative to each other (i.e., it is not the case that the middle finger is the only lengthened digit), or, Fingers that appear disproportionately long compared to the palm of the hand. 2011-06-09T01:13:15Z HP:0006010 UMLS:C1858091 Long fingers HP:0100807 Long fingers The middle finger is more than 2 SD above the mean for newborns 27 to 41 weeks EGA or above the 97th centile for children from birth to 16 years of age AND the five digits retain their normal length proportions relative to each other (i.e., it is not the case that the middle finger is the only lengthened digit), or, Fingers that appear disproportionately long compared to the palm of the hand. PMID:19125433 Long fingers An outpouching of the gastric wall. 2011-06-09T01:43:31Z MSH:D013273 SNOMEDCT_US:75198005 UMLS:C0038355 Stomach diverticulum HP:0100808 Gastric diverticulum may be asymptomatic or may present with a vague sensation of fullness or discomfort in the upper abdomen, or with acute upper gastrointestinal bleed or perforation. Gastric diverticulum An outpouching of the gastric wall. PMID:22257431 Congenital absence or underdevelopment of the colon. 2011-06-09T01:54:57Z UMLS:C4021964 Absent/small colon Absent/underdeveloped colon HP:0100811 Aplasia/Hypoplasia of the colon Congenital absence or underdevelopment of the colon. Absent/small colon Absent/underdeveloped colon Increase in the number or proportion of lymphocytes in the blood. 2011-06-09T05:32:57Z HP:0012141 MSH:D008218 SNOMEDCT_US:67023009 UMLS:C0024282 High lymphocyte count HP:0100827 Lymphocytosis Increase in the number or proportion of lymphocytes in the blood. High lymphocyte count An abnormal increase in the total number of T cells detected in the blood. 2011-06-09T05:34:46Z UMLS:C4021960 Increase in T cell count Increase in T cell number HP:0100828 Increased T cell count Vitamin K is a fat-soluble vitamin with a role in promoting the coagulation cascade. 2011-06-09T05:46:50Z UMLS:C4021958 Abnormality of vitamin K metabolism HP:0100831 Abnormality of vitamin K metabolism Vitamin K is a fat-soluble vitamin with a role in promoting the coagulation cascade. Abnormality of vitamin K metabolism The presence of a neoplasm of the small intestine. 2011-06-09T06:03:02Z NCIT:C3262 SNOMEDCT_US:126832004 UMLS:C0345832 Small intestine tumor Small intestine tumour HP:0100833 An estimated 40% of small bowel cancers are adenocarcinomas, 40% are carcinoids, 15% are sarcomas (GI stromal tumors), and less than 5% are lymphomas. Neoplasm of the small intestine The presence of a neoplasm of the small intestine. Small intestine tumor Small intestine tumour The presence of a neoplasm of the large intestine. 2011-06-09T06:03:45Z MSH:D015179 NCIT:C3262 SNOMEDCT_US:126837005 UMLS:C0009404 Large intestine tumor Large intestine tumour HP:0100834 Neoplasm of the large intestine The presence of a neoplasm of the large intestine. Large intestine tumor Large intestine tumour Abnormalities in the intensity, frequency, or duration of emotional experiences. 2011-06-23T11:07:13Z UMLS:C4020949 Abnormal emotion processing Abnormal emotion/affect behaviour Abnormal mood/emotion/affect Abnormal mood/emotion/affect/thought Emotion dysregulation HP:0100851 Abnormal emotion An abnormal fear-induced behavior includes observable actions. This behavior is characterized by abnormal responses to fear or abnormal fear levels. Examples of such behavior include avoiding fear-inducing situations. 2011-06-23T11:13:16Z HP:0001296 UMLS:C4018849 Abnormal fear-induced behaviour Abnormal fear/anxiety-related behavior Abnormal fear/anxiety-related behaviour HP:0100852 Internal responses to fear, which are experienced by an individual and do not necessarily involve clear behavioral changes (observable actions), should be labeled with a term for fear-related cognition, such as HP:5200230. Abnormal fear-induced behavior Abnormal fear/anxiety-related behaviour Decreased ossification of the vertebral bodies. 2011-11-30T09:59:32Z UMLS:C4021953 HP:0100856 Poorly ossified vertebrae Decreased ossification of the vertebral bodies. 2011-11-30T10:47:46Z UMLS:C4021950 Absent femoral head HP:0100862 Aplasia of the femoral head Absent femoral head 2011-11-30T10:48:08Z UMLS:C4021949 Absent neck of thighbone HP:0100863 Aplasia of the femoral neck Absent neck of thighbone An abnormally short femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). 2011-11-30T10:48:34Z HP:0003032 HP:0008779 HP:0008793 UMLS:C1836184 Hypoplasia of the femoral neck Hypoplastic femoral neck Short femoral necks Short neck of thighbone HP:0100864 Short femoral neck An abnormally short femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). Short neck of thighbone Underdevelopment of the iliac bones. 2011-11-30T11:11:24Z UMLS:C1849063 Short pelvis bones HP:0100866 Short iliac bones Underdevelopment of the iliac bones. PMID:29019756 Short pelvis bones Cystic, urine-containing intrarenal cavities lined with transitional cell epithelium that communicate through a narrow channel with the collecting system. 2011-12-01T02:29:09Z SNOMEDCT_US:433036004 UMLS:C2315541 Caliceal diverticulum Pelvic diverticulum Renal pelvic diverticulum HP:0100877 Renal diverticulum Cystic, urine-containing intrarenal cavities lined with transitional cell epithelium that communicate through a narrow channel with the collecting system. 2011-12-01T02:32:26Z SNOMEDCT_US:198319004 UMLS:C0151994 Enlarged uterus HP:0100878 Enlarged uterus Enlarged uterus 2011-12-01T02:33:12Z SNOMEDCT_US:66998000 UMLS:C0392039 Enlarged ovaries HP:0100879 Enlarged ovaries Enlarged ovaries An abnormality in the placement of the ocular globe (eyeball). 2011-12-13T04:25:29Z UMLS:C4021946 Abnormality of eyeball location Abnormality of eyeball position Abnormality of globe position HP:0100886 Abnormality of globe location An abnormality in the placement of the ocular globe (eyeball). Abnormality of eyeball location Abnormality of eyeball position Abnormality of globe position An abnormality in the size of the ocular globe (eyeball). 2011-12-13T04:25:29Z HP:0010725 UMLS:C4021945 Abnormality of eyeball size Eye size difference HP:0100887 Abnormality of globe size An abnormality in the size of the ocular globe (eyeball). Abnormality of eyeball size Eye size difference An abnormality of the Common bile duct, a tube-like anatomic structure in the human gastrointestinal tract, formed by the union of the Common hepatic duct and the Cystic duct from the gall bladder. 2011-12-01T04:52:13Z UMLS:C4020944 Abnormality of the common bile duct Abnormality of the ductus choledochus HP:0100889 Abnormal ductus choledochus morphology An abnormality of the Common bile duct, a tube-like anatomic structure in the human gastrointestinal tract, formed by the union of the Common hepatic duct and the Cystic duct from the gall bladder. An elevation in bone density in one or more foot bones. Sclerosis is normally detected on a radiograph as an area of increased opacity. 2011-12-02T11:12:32Z UMLS:C4020931 Increased bone density in foot bone Sclerosis of bones of the feet HP:0100925 Sclerosis of foot bone An elevation in bone density in one or more foot bones. Sclerosis is normally detected on a radiograph as an area of increased opacity. Increased bone density in foot bone Any structural abnormality of the medulla of the kidney. 2011-12-12T10:02:15Z HP:0005582 UMLS:C4021911 Abnormality of the renal medulla HP:0100957 The renal pyramids of the adult kidney resemble a cone with a broad base adjacent to the renal cortex and the narrow apex that is termed papilla. The adult renal medulla is made up of 10-18 pyramids. A pyramid consists of the medullary collecting ducts, loops of Henle, vasa recta (straight capillaries) and the interstitium. The main function of the medulla is to regulate concentration of the urine. The urine flows from the collecting ducts into the renal calyces and pelvis. Abnormal renal medulla morphology Any structural abnormality of the medulla of the kidney. PMID:22343825 The presence of multiple polyps in the intestine. 2010-06-09T11:38:54Z Growths in inner lining of intestine MSH:D044483 UMLS:C0744333 UMLS:C1257915 Multiple intestinal polyps Gastrointestinal polyps HP:0200008 Intestinal polyposis The presence of multiple polyps in the intestine. Growths in inner lining of intestine Gastrointestinal polyps Disproportionately small hand. SNOMEDCT_US:299032009 UMLS:C0575802 Disproportionately small hands Small hand Small hands HP:0200055 Small hand Disproportionately small hand. Disproportionately small hands Small hand Small hands Multiple abnormal growths that arise from the lining of the large intestine (colon or rectum) and protrude into the intestinal lumen. 2013-05-31T01:19:31Z SNOMEDCT_US:399505005 UMLS:C0949059 Colorectal polyps HP:0200063 Colorectal polyposis 2013-05-31T01:29:16Z HP:0007912 HP:0007945 SNOMEDCT_US:247177004 UMLS:C0521683 HP:0200065 Chorioretinal degeneration Median longitudinal ear length greater than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. UMLS:C1848657 Long ear Long ears The commonly used term Macrotia is a bundled term comprising increased length and width (surface area). Long ear Median longitudinal ear length greater than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. PMID:19152421 eom:2028381d5c61842a Long ear Long ears Median longitudinal ear length less than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. UMLS:C3551041 Short ear Short ears The commonly used term Microtia is a bundled term comprising decreased length and width (surface area). Short ear Median longitudinal ear length less than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. PMID:19152421 eom:2cff5ac9b681fc73 Short ear Short ears An abnormality of the vomer. UMLS:C4020914 Abnormality of vomer Abnormality of vomer bone Defect of vomer Abnormal vomer morphology Abnormality of vomer bone Abnormality of the first branch of the internal carotid artery. UMLS:C4073185 Ophthalmic artery anomaly The ophthalmic artery (OA) is the first branch of the internal carotid artery distal to the cavernous sinus. Branches of the OA supply all the structures in the orbit as well as some structures in the nose, face and meninges. Abnormality of ophthalmic artery Abnormality of the first branch of the internal carotid artery. Ophthalmic artery anomaly Any abnormality of the part of the nervous system that consists of the nerves and ganglia outside of the brain and spinal cord. UMLS:C4073187 Abnormality of the peripheral nervous system Abnormality of the peripheral nervous system Any abnormality of the part of the nervous system that consists of the nerves and ganglia outside of the brain and spinal cord. Abnormality of the peripheral nervous system Any abnormality of the part of the peripheral nervous system associated with sensation and skeletal muscle voluntary control of body movements. UMLS:C4073188 The SoNS consists of afferent and efferent nerves. Afferent nerves are responsible for relaying sensation to the central nervous system; efferent nerves are responsible for stimulating muscle contraction, including all the non-sensory neurons connected with skeletal muscles and skin. Abnormality of the somatic nervous system Any abnormality of the part of the peripheral nervous system associated with sensation and skeletal muscle voluntary control of body movements. Any abnormality of the somatic nerve plexus. UMLS:C4073189 Abnormality of somatic nerve plexus Any abnormality of the somatic nerve plexus. An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system. UMLS:C4073193 Abnormality of ganglion Abnormal ganglion morphology An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system. https://en.wikipedia.org/wiki/Ganglion An abnormality of nerve cell cluster or a group of nerve cell bodies located in the peripheral autonomic nervous system. UMLS:C4073194 Abnormality of ganglion of peripheral nervous system Abnormal peripheral nervous system ganglion morphology An abnormality of nerve cell cluster or a group of nerve cell bodies located in the peripheral autonomic nervous system. https://en.wikipedia.org/wiki/Ganglion An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system of the cranium. UMLS:C4073195 Abnormality of cranial ganglion Abnormal cranial ganglion morphology An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system of the cranium. https://en.wikipedia.org/wiki/Ganglion Any abnormality of the periodontium. 2017-06-20T21:40:50Z Abnormality of the periodontium Abnormal periodontium morphology A gap in the lip or lips. 2017-06-20T22:17:35Z Cleft lip Cleft of the lip Cleft lip Cleft lip Any abnormality in the activation of T cells, i.e. the change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. 2017-06-22T19:07:54Z Abnormal T lymphocyte activation Abnormal T-cell activation Abnormal T-lymphocyte activation Abnormal T cell activation Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. 2017-09-20T00:22:53Z Fyler:4447 Abnormal liver morphology Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. MP:0000598 Any structural anomaly of the hollow epithelial tube found on the dorsal side of the vertebrate embryo that develops into the central nervous system (i.e. brain and spinal cord). 2017-09-20T00:25:37Z Fyler:4339 Abnormal neural tube morphology Any structural anomaly of the hollow epithelial tube found on the dorsal side of the vertebrate embryo that develops into the central nervous system (i.e. brain and spinal cord). MP:0002151 An increase in the level of ribose in the urine. 2018-01-30T00:47:12Z Ribose is a pentose monosaccharide. Increased level of ribose in urine An increase in the level of ribose in the urine. PMID:14988808 An increase in the level of ribose in the cerebrospinal fluid. 2018-01-30T00:47:46Z Increased level of ribose in cerebrospinal fluid Increased level of ribose in CSF An increase in the level of ribose in the cerebrospinal fluid. PMID:14988808 Any abnormality of the chest muscles. 2018-05-01T17:37:03Z Muscle issues in the chest Abnormality of the chest musculature Abnormal morphology of the chest musculature Muscle issues in the chest Any abnormality of the back muscles. 2018-05-01T17:38:59Z Muscle issues in the back Abnormality of the back musculature Muscle issues in the back Any abnormality of the shoulder muscles. 2018-05-01T17:39:54Z Abnormality of the shoulder musculature Muscle issues in the shoulder Abnormal morphology of the shoulder musculature Muscle issues in the shoulder An increase in the level of ketone bodies (acetoacetic acid, beta-hydroxybutyric acid, and acetone) in the blood. 2018-05-21T17:36:23Z Elevated circulating ketone body concentration Increased level of ketone bodies in blood Ketonemia Hyperketonemia An increase in the level of ketone bodies (acetoacetic acid, beta-hydroxybutyric acid, and acetone) in the blood. PMID:27036365 Increased level of ketone bodies in blood A reduced concentration of folic acid, which is also known as vitamin B9 in the cerebrospinal fluid. 2018-09-12T00:12:26Z Folate deficiency in cerebrospinal fluid Cerebral folate deficiency is usually measured as low levels of folate in the CSF, in the presence of normal folate metabolism outside the nervous system. Folate deficiency in CSF A reduced concentration of folic acid, which is also known as vitamin B9 in the cerebrospinal fluid. PMID:15581159 An abnormality in any umbilical cord measurement performed after birth, such as the blood gas level. 2018-09-12T00:35:41Z Abnormal cord blood measurement An abnormality in any umbilical cord measurement performed after birth, such as the blood gas level. PMID:7926229 2018-09-12T00:44:12Z Abnormal blood gas level in cord blood Partial or complete wasting (loss) of the pituitary gland. 2018-10-30T19:54:09Z Atrophic pituitary Pituitary gland atrophy Atrophic pituitary gland Partial or complete wasting (loss) of the pituitary gland. DOI:10.1530/endoabs.44.EP82 An abnormal form or size of neutrophils in the cerebrospinal fluid. Abnormality of neutrophil morphology in cerebrospinal fluid Abnormality of neutrophil morphology in CSF An abnormal form or size of neutrophils in the cerebrospinal fluid. Absence of the sebaceous gland, the holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts. Absence of sebaceous glands Absent sebaceous glands Absence of the sebaceous gland, the holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts. MP:0000647 An abnormality of the frontal bone. UMLS:C4021873 Abnormality of the bone of the forehead Abnormality of the frontal bone Abnormal morphology of frontal bone Anomaly of the frontal bone Deformity of the frontal bone Malformation of the frontal bone Abnormal frontal bone morphology An abnormality of the frontal bone. HPO_CONTRIBUTOR:GOC_MG Abnormality of the bone of the forehead Abnormal morphology of frontal bone Anomaly of the frontal bone Deformity of the frontal bone Malformation of the frontal bone An abnormality of the ethmoid bone UMLS:C4021869 Abnormality of ethmoid bone Anomaly of the ethmoid bone Deformity of the ethmoid bone Malformation of the ethmoid bone Abnormal ethmoid bone morphology An abnormality of the ethmoid bone HPO_CONTRIBUTOR:GOC_MG Anomaly of the ethmoid bone Deformity of the ethmoid bone Malformation of the ethmoid bone An abnormality of any of the muscles of the pharynx. UMLS:C4073197 Abnormality of muscles of the pharynx Abnormality of musculature of pharynx Abnormality of pharyngeal musculature Abnormality of pharynx musculature Abnormal morphology of musculature of pharynx An abnormality of any of the muscles of the pharynx. An abnormality of the muscles of the structure of the nose. UMLS:C4073200 Abnormality of muscle of nose Abnormality of musculature of the nose Abnormality of nasal musculature Abnormality of nasal musculature An abnormality of the muscles of the structure of the nose. Abnormality of muscle of nose Abnormality of musculature of the nose Abnormality of nasal musculature The capability that a small joint (or a group of joints) has to move, passively and/or actively, beyond normal limits along physiological axes. Small joints include metacarpophalangeal joints, proximal interphalangeal joints, second to fifth metatarsophalangeal joints, and wrists. 2024-01-07T09:36:17Z Small joint hypermobilty The capability that a large joint (or a group of joints) has to move, passively and/or actively, beyond normal limits along physiological axes. Large joints include shoulders, elbows, hips, knees, and ankles. 2024-01-07T09:39:20Z Large joint hypermobilty Inflammation of the urethra. Urethritis is characterized by discharge, dysuria and/or urethral discomfort but may be asymptomatic. Common etiologies include gonococcal urethritis as well as infection by chlamydia trachomatis, mycoplasma genitalium, ureaplasma urealyticum, trichomonas vaginalis, anaerobes, herpes simplex virus, and adenovirus. Urethritis Inflammation of the urethra. PMID:26220178 Underdevelopment of the musculature of the pelvis. 2017-05-25T16:53:10Z Hypoplasia of the musculature of the pelvis Any abnormality in the proportion natural killer subsets relative to the total number of natural killer cells. 2018-01-08T19:18:59Z Abnormal natural killer subset distribution A decreased amount of valine in the blood. 2018-10-01T14:47:05Z Low blood valine concentration Hypovalinemia A decreased amount of valine in the blood. Low blood valine concentration An decreased concentration of tyrosine in the blood. 2018-10-01T15:01:56Z Decreased tyrosine in blood Low blood tyrosine concentration Hypotyrosinemia An decreased concentration of tyrosine in the blood. Decreased tyrosine in blood Low blood tyrosine concentration An increased amount of serine in the blood. 2018-10-01T16:54:02Z Elevated circulating serine levels High blood serine levels Increased serine blood concentration Hyperserinemia High blood serine levels Increased serine blood concentration A decreased amount of phenylalanine in the blood. 2018-10-03T19:58:21Z Decreased blood phenylalanine Low blood phenylalanine Hypophenylalaninemia A decreased amount of phenylalanine in the blood. Decreased blood phenylalanine Low blood phenylalanine A decreased amount of lysine in the blood. 2018-10-03T20:04:58Z Decreased blood lysine Low blood lysine levels Hypolysinemia A decreased amount of lysine in the blood. Decreased blood lysine Low blood lysine levels Decreased amount of leucine in the blood. 2018-10-04T13:17:00Z Decreased blood concentration of leucine Low blood leucine levels Hypoleucinemia Decreased amount of leucine in the blood. Decreased blood concentration of leucine Low blood leucine levels A decreased amount of isoleucine in the blood. 2018-10-04T13:22:24Z Decreased blood isoleucine concentration Low blood isoleucine levels Hypoisoleucinemia A decreased amount of isoleucine in the blood. Decreased blood isoleucine concentration Low blood isoleucine levels Any deviation from the normal concentration of glutamate in the blood circulation. 2018-10-04T14:22:57Z Abnormality of glutamate metabolism Abnormal circulating glutamate concentration Concentration of glutamate in the blood circulation above the upper limit of normal. 2018-10-04T14:29:35Z HP:0410068 High blood glutamate levels Increased blood glutamate concentration Increased level of L-glutamic acid in blood Under normal circumstances, plasma glutamate concentration is 5-100 microM/L, the whole blood concentration is 150-300 microM/L while in the brain's ECF it is only 0.3-2 microM/L. Hyperglutamatemia Concentration of glutamate in the blood circulation above the upper limit of normal. PMID:22949847 PMID:7623444 High blood glutamate levels Increased blood glutamate concentration Under normal circumstances, plasma glutamate concentration is 5-100 microM/L, the whole blood concentration is 150-300 microM/L while in the brain's ECF it is only 0.3-2 microM/L. PMID:22949847 An increased amount of arginine levels in the blood. 2018-10-05T14:45:02Z High blood arginine levels Increased blood arginine concentration Hyperargininemia An increased amount of arginine levels in the blood. High blood arginine levels Increased blood arginine concentration An abnormal decrease in ornithine in the blood. 2018-10-12T13:25:49Z Decreased blood ornithine concentrations Low blood ornithine levels Hypoornithinemia An abnormal decrease in ornithine in the blood. Decreased blood ornithine concentrations Low blood ornithine levels Any deviation from the normal concentration of a carboxylic acid in the cerebrospinal fluid. 2019-02-25T15:15:53Z Abnormal CSF carboxylic acid concentration Any deviation from the normal concentration of amino acids in the cerebrospinal fluid. 2019-02-25T15:20:22Z HP:0032364 Abnormal CSF amino acid level Abnormal amino acid levels in cerebrospinal fluid Abnormal cerebrospinal fluid amino acid level Abnormal CSF amino acid concentration Any deviation from the normal concentration of amino acids in the cerebrospinal fluid. PMID:715764 Abnormal amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of branched-chain amino acids in the cerebrospinal fluid. 2019-02-25T15:24:13Z Abnormal branched-chain amino acid levels in cerbrospinal fluid Abnormal CSF branched chain amino acid concentration Any deviation from the normal concentration of branched-chain amino acids in the cerebrospinal fluid. PMID:715764 Abnormal branched-chain amino acid levels in cerbrospinal fluid PMID:715764 Any deviation from the normal concentration of valine in the cerebrospinal fluid. 2019-02-25T15:28:13Z Abnormal valine levels in cerebrospinal fluid Abnormal CSF valine concentration Any deviation from the normal concentration of valine in the cerebrospinal fluid. PMID:715764 Abnormal valine levels in cerebrospinal fluid PMID:715764 Any increased amount from normal of valine in the cerebrospinal fluid. 2019-02-25T15:37:57Z High valine levels in cerebrospinal fluid Increased CSF valine concentration Any increased amount from normal of valine in the cerebrospinal fluid. PMID:715764 High valine levels in cerebrospinal fluid PMID:715764 Any decreased amount from normal of valine in the cerebrospinal fluid. 2019-02-25T15:40:23Z Low valine levels in cerebrospinal fluid Decreased CSF valine concentration Any decreased amount from normal of valine in the cerebrospinal fluid. PMID:715764 Low valine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of leucine in the cerebrospinal fluid. 2019-02-25T15:52:19Z Abnormal leucine levels in cerebrospinal fluid Abnormal CSF leucine concentration Any deviation from the normal concentration of leucine in the cerebrospinal fluid. PMID:715764 Abnormal leucine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of leucine in the cerebrospinal fluid. 2019-02-25T15:52:49Z Low leucine levels in cerebrospinal fluid Decreased CSF leucine concentration Abnormally decreased levels of leucine in the cerebrospinal fluid. PMID:715764 Low leucine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of leucine in cerebrospinal fluid. 2019-02-25T15:53:12Z High leucine levels in cerebrospinal fluid Increased CSF leucine concentration Abnormally increased levels of leucine in cerebrospinal fluid. PMID:715764 High leucine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of isoleucine in the cerebrospinal fluid. 2019-02-25T16:24:44Z Abnormal isoleucine levels in cerebrospinal fluid Abnormal CSF isoleucine concentration Any deviation from the normal concentration of isoleucine in the cerebrospinal fluid. PMID:715764 Abnormal isoleucine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of isoleucine in cerebrospinal fluid. 2019-02-25T16:25:11Z High levels of isoleucine in cerebrospinal fluid Increased CSF isoleucine concentration Abnormally increased levels of isoleucine in cerebrospinal fluid. PMID:715764 High levels of isoleucine in cerebrospinal fluid PMID:715764 Abnormally decreased levels of isoleucine in cerebrospinal fluid. 2019-02-25T16:25:36Z Low levels of isoleucine in cerebrospinal fluid Decreased CSF isoleucine concentration Abnormally decreased levels of isoleucine in cerebrospinal fluid. PMID:715764 Low levels of isoleucine in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of glutamine-family amino acids in the cerebrospinal fluid. 2019-02-25T16:41:53Z Abnormal glutamine family amino acid levels in cerebrospinal fluid Abnormal CSF glutamine family amino acid concentration Any deviation from the normal concentration of glutamine-family amino acids in the cerebrospinal fluid. PMID:715764 Abnormal glutamine family amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of glutamic acid in the cerebrospinal fluid. 2019-02-25T16:56:56Z Abnormal glutamic acid levels in cerebrospinal fluid Abnormal CSF glutamate concentration Any deviation from the normal concentration of glutamic acid in the cerebrospinal fluid. PMID:715764 Abnormal glutamic acid levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of glutamic acid in cerebrospinal fluid. 2019-02-25T16:57:13Z High glutamic acid levels in cerebrospinal fluid Increased CSF glutamate concentration Abnormally increased levels of glutamic acid in cerebrospinal fluid. PMID:715764 High glutamic acid levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of glutamic acid in cerebrospinal fluid. 2019-02-25T16:57:30Z Low glutamic acid levels in cerebrospinal fluid Decreased CSF glutamate concentration Abnormally decreased levels of glutamic acid in cerebrospinal fluid. PMID:715764 Low glutamic acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of arginine in the cerebrospinal fluid. 2019-02-25T17:12:23Z Abnormal arginine levels in cerebrospinal fluid Abnormal CSF arginine concentration Any deviation from the normal concentration of arginine in the cerebrospinal fluid. PMID:715764 Abnormal arginine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of arginine in cerebrospinal fluid. 2019-02-25T17:12:38Z High arginine levels in cerebrospinal fluid Increased CSF arginine concentration Abnormally increased levels of arginine in cerebrospinal fluid. PMID:715764 High arginine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of arginine in cerebrospinal fluid. 2019-02-25T17:12:54Z Low arginine levels in cerebrospinal fluid Decreased CSF arginine concentration Abnormally decreased levels of arginine in cerebrospinal fluid. PMID:715764 Low arginine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of aspartate-family amino acids in the cerebrospinal fluid. 2019-02-25T18:30:37Z Abnormal aspartate-family amino acid levels in cerebrospinal fluid Abnormal CSF aspartate family amino acid concentration Any deviation from the normal concentration of aspartate-family amino acids in the cerebrospinal fluid. PMID:715764 Any deviation from the normal concentration of lysine in the cerebrospinal fluid. 2019-02-25T18:31:42Z Abnormal lysine levels in cerebrospinal fluid Abnormal CSF lysine concentration Any deviation from the normal concentration of lysine in the cerebrospinal fluid. PMID:715764 Abnormal lysine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of lysine in cerebrospinal fluid. 2019-02-25T18:31:54Z Low lysine levels in cerebrospinal fluid Decreased CSF lysine concentration Abnormally decreased levels of lysine in cerebrospinal fluid. PMID:715764 Low lysine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of lysine in cerebrospinal fluid. 2019-02-25T18:32:16Z High lysine levels in cerebrospinal fluid Increased CSF lysine concentration Any deviation from the normal concentration of methionine in the cerebrospinal fluid. 2019-02-25T18:58:00Z Abnormal methionine levels in cerebrospinal fluid Abnormal CSF methionine concentration Any deviation from the normal concentration of methionine in the cerebrospinal fluid. PMID:715764 Abnormal methionine levels in cerebrospinal fluid PMID:715764 Concentration of methionine in the cerebrospinal fluid above the upper limit of normal. 2019-02-25T18:58:44Z High methionine levels in cerebrospinal fluid Increased CSF methionine concentration Concentration of methionine in the cerebrospinal fluid above the upper limit of normal. PMID:715764 High methionine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of aromatic amino acids in the cerebrospinal fluid. 2019-02-25T19:28:05Z Abnormal aromatic amino acid levels in cerebrospinal fluid Abnormal CSF aromatic amino acid concentration Any deviation from the normal concentration of aromatic amino acids in the cerebrospinal fluid. PMID:715764 Abnormal aromatic amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of phenylalanine in the cerebrospinal fluid. 2019-02-25T19:28:51Z Abnormal phenylalanine levels in cerebrospinal fluid Abnormal CSF phenylalanine concentration Any deviation from the normal concentration of phenylalanine in the cerebrospinal fluid. PMID:715764 Abnormal phenylalanine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of tyrosine in the cerebrospinal fluid. 2019-02-25T19:48:03Z Abnormal tyrosine levels in cerebrospinal fluid Abnormal CSF tyrosine concentration Any deviation from the normal concentration of tyrosine in the cerebrospinal fluid. PMID:715764 Abnormal tyrosine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of tyrosine in cerebrospinal fluid. 2019-02-25T19:53:00Z High tyrosine levels in cerebrospinal fluid Increased CSF tyrosine concentration Abnormally increased levels of tyrosine in cerebrospinal fluid. PMID:715764 High tyrosine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of tyrosine in cerebrospinal fluid. 2019-02-25T19:53:22Z Low tyrosine levels in the cerebrospinal fluid Decreased CSF tyrosine concentration Abnormally decreased levels of tyrosine in cerebrospinal fluid. PMID:715764 Low tyrosine levels in the cerebrospinal fluid PMID:715764 Abnormally increased levels of phenylalanine in cerebrospinal fluid. 2019-02-25T20:13:37Z High phenylalanine levels in cerebrospinal fluid Increased CSF phenylalanine concentration Abnormally increased levels of phenylalanine in cerebrospinal fluid. PMID:715764 High phenylalanine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of phenylalanine in cerebrospinal fluid. 2019-02-25T20:13:51Z Low phenylalanine levels in cerebrospinal fluid Decreased CSF phenylalanine concentration Abnormally decreased levels of phenylalanine in cerebrospinal fluid. PMID:715764 Low phenylalanine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of serine-family amino acids in the cerebrospinal fluid. 2019-02-25T20:27:34Z Abnormal serine-family amino acid levels in cerebrospinal fluid Abnormal CSF serine family amino acid concentration Any deviation from the normal concentration of serine-family amino acids in the cerebrospinal fluid. PMID:715764 Abnormal serine-family amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of serine in the cerebrospinal fluid. 2019-02-25T20:30:42Z Abnormal serine levels in cerebrospinal fluid Abnormal CSF serine concentration Any deviation from the normal concentration of serine in the cerebrospinal fluid. PMID:715764 Abnormal serine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of serine in cerebrospinal fluid. 2019-02-25T20:32:30Z High serine levels in cerebrospinal fluid Increased CSF serine concentration Abnormally increased levels of serine in cerebrospinal fluid. PMID:715764 High serine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of serine in cerebrospinal fluid. 2019-02-25T20:32:46Z Low serine levels in cerebrospinal fluid Decreased CSF serine concentration Abnormally decreased levels of serine in cerebrospinal fluid. PMID:715764 Low serine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of glycine in the cerebrospinal fluid. 2019-02-25T20:40:09Z Abnormal glycine levels in cerebrospinal fluid Abnormal CSF glycine concentration Any deviation from the normal concentration of glycine in the cerebrospinal fluid. PMID:715764 Abnormally increased levels of glycine in cerebrospinal fluid. 2019-02-25T20:40:30Z High glycine levels in cerebrospinal fluid Increased CSF glycine concentration Abnormally increased levels of glycine in cerebrospinal fluid. PMID:715764 High glycine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of albumin in the cerebrospinal fluid. 2019-02-26T15:00:29Z Abnormal albumin levels in cerebrospinal fluid Abnormal CSF albumin concentration Any deviation from the normal concentration of albumin in the cerebrospinal fluid. PMID:27067000 Abnormal albumin levels in cerebrospinal fluid PMID:27067000 2019-02-26T15:00:54Z High albumin levels in cerebrospinal fluid Abnormally increased levels of albumin in cerebrospinal fluid. Increased CSF albumin concentration High albumin levels in cerebrospinal fluid PMID:27067000 Abnormally increased levels of albumin in cerebrospinal fluid. PMID:27067000 Any deviation from the normal concentration of ornithine in the cerebrospinal fluid. 2019-02-26T15:36:15Z Abnormal ornithine levels in cerebrospinal fluid Abnormal CSF ornithine concentration Any deviation from the normal concentration of ornithine in the cerebrospinal fluid. PMID:20551690 Abnormal ornithine levels in cerebrospinal fluid PMID:20551690 Abnormally increased levels of ornithine in cerebrospinal fluid. 2019-02-26T15:36:36Z High ornithine levels in cerebrospinal fluid Increased CSF ornithine concentration Abnormally increased levels of ornithine in cerebrospinal fluid. PMID:20551690 High ornithine levels in cerebrospinal fluid PMID:20551690 Any deviation from the normal concentration of citrulline in the cerebrospinal fluid. 2019-02-26T15:48:42Z Abnormal citrulline levels in cerebrospinal fluid Abnormal CSF citrulline concentration Any deviation from the normal concentration of citrulline in the cerebrospinal fluid. PMID:16793028 Abnormal citrulline levels in cerebrospinal fluid PMID:16793028 Abnormally increased levels of citrulline in cerebrospinal fluid. 2019-02-26T15:49:01Z High citrulline levels in cerebrospinal fluid Increased CSF citrulline concentration Abnormally increased levels of citrulline in cerebrospinal fluid. PMID:16793028 High citrulline levels in cerebrospinal fluid PMID:16793028 The most dramatic and severe form of hair loss characterized by an absence of hair follicles. 2019-08-21T15:12:23Z Atrichia The most dramatic and severe form of hair loss characterized by an absence of hair follicles. PMID:14676077 Any structural anomaly of an inner ear epithelium. 2014-07-15T23:41:38Z UMLS:C4073211 HP:3000002 Abnormal inner ear epithelium morphology An abnormality of a buccal mucosa. 2015-08-07T00:13:17Z UMLS:C4073228 Abnormality of buccal mucosa Abnormality of cheek mucosa Abnormality of inside lining of cheek HP:3000019 Abnormal buccal mucosa morphology Abnormality of cheek mucosa Abnormality of inside lining of cheek An abnormality of a cartilage of external ear. 2015-08-07T00:15:54Z UMLS:C4073231 HP:3000022 Abnormality of cartilage of external ear Any structural abnormality of a facial artery, one of the branches of the external carotid artery. 2015-08-07T00:16:03Z UMLS:C4073233 Abnormality of facial artery HP:3000024 Abnormal facial artery morphology Any structural abnormality of a facial artery, one of the branches of the external carotid artery. An abnormality of an orbit of skull. 2015-08-07T00:27:07Z UMLS:C4073239 Abnormality of bones of the orbit of the skull Abnormality of bony orbit of skull Abnormality of the bony eye socket Abnormality of the orbital bones of skull HP:3000030 Abnormal morphology of bony orbit of skull Abnormality of bones of the orbit of the skull Abnormality of the bony eye socket Abnormality of the orbital bones of skull Any abnormality of nasopharyngeal adenoids. 2015-08-07T00:27:21Z UMLS:C4073241 Abnormality of adenoids Abnormality of nasopharyngeal adenoids Abnormality of nasopharyngeal tonsil Abnormality of pharyngeal tonsil HP:3000033 The adenoid, a mass of lymphatic tissue situated posterior to the nasal cavity, in the roof of the nasopharynx, where the nose blends into the throat. Abnormal nasopharyngeal adenoid morphology Abnormality of adenoids Abnormality of nasopharyngeal tonsil Abnormality of pharyngeal tonsil The adenoid, a mass of lymphatic tissue situated posterior to the nasal cavity, in the roof of the nasopharynx, where the nose blends into the throat. An abnormality of a cartilage of nasal septum. 2015-08-07T00:27:26Z UMLS:C4073242 Abnormality of cartilage of nasal septum Abnormality of cartilage of septum of nose Anomaly of cartilage of nasal septum Deformity of cartilage of nasal septum Malformation of cartilage of nasal septum HP:3000034 Abnormality nasal septum cartilage morphology Abnormality of cartilage of nasal septum Abnormality of cartilage of septum of nose Anomaly of cartilage of nasal septum Deformity of cartilage of nasal septum Malformation of cartilage of nasal septum An abnormality of a blood vessel of the head, including branches of the arterial and venous systems of the head. 2015-08-07T00:36:02Z UMLS:C4073244 Abnormality of blood vessel of head Abnormality of head blood vessel Abnormality of vasculature of head HP:3000036 Abnormal head blood vessel morphology An abnormality of a blood vessel of the head, including branches of the arterial and venous systems of the head. Abnormality of blood vessel of head Abnormality of head blood vessel An abnormality of a blood vessel of the neck, including branches of the arterial and venous systems of the neck. 2015-08-07T00:36:06Z UMLS:C4073245 Abnormality of blood vessel of neck Abnormality of neck blood vessel Abnormality of the cervical blood vessels Abnormality of the cervical vasculature Abnormality of the vasculature of the neck HP:3000037 Abnormal neck blood vessel morphology An abnormality of a blood vessel of the neck, including branches of the arterial and venous systems of the neck. Abnormality of blood vessel of neck Abnormality of neck blood vessel An abnormality of an external carotid artery. 2015-08-07T00:36:24Z Abnormality of carotid artery Disorder of carotid artery UMLS:C4073249 HP:3000041 Abnormality of external carotid artery Abnormality of carotid artery Disorder of carotid artery Any structural abnormality of a jugular vein. 2015-08-07T01:04:39Z UMLS:C4073250 Abnormality of jugular vein HP:3000042 Abnormal jugular vein morphology Abnormality of jugular vein An abnormality of a facial vein. 2015-08-07T01:04:44Z UMLS:C4073251 Abnormal vein of face Abnormality of facial vein HP:3000043 Abnormal facial vein morphology Abnormal vein of face Abnormality of facial vein An abnormality of a genioglossus muscle. 2015-08-07T01:04:53Z UMLS:C4073253 HP:3000045 Abnormality of genioglossus muscle Any structural anomaly of the glossopharyngeal nerve, the ninth paired cranial nerve (CN IX). 2015-08-07T01:08:41Z UMLS:C4073255 Abnormality of glossopharyngeal nerve HP:3000047 The glossopharyngeal nerve originates in the medulla oblongata. It Innervates the oropharynx, carotid body and sinus, as well as the posterior third of the tongue (where it mediates taste sensation), the middle ear cavity and the Eustachian tube. Additionally, it innervates the stylopharyngeus muscle of the pharynx. Abnormal glossopharyngeal nerve morphology An abnormality of an odontoid tissue. 2015-08-07T01:08:54Z UMLS:C4073258 Abnormality of hard tissues of teeth Abnormality of odontoid tissue Abnormality of tooth hard tissue HP:3000050 Abnormal odontoid tissue morphology An abnormality of a hyoglossus muscle. 2015-08-07T01:08:58Z UMLS:C4073259 Abnormality of hyoglossus muscle HP:3000051 Abnormal hyoglossus muscle morphology Any structural abnormality of the hyoid bone (hyoid), a small U-shaped (horseshoe-shaped) solitary bone, situated in the midline of the neck anteriorly at the base of the mandible and posteriorly at the fourth cervical vertebra. 2015-08-07T01:09:03Z UMLS:C4073260 Abnormality of hyoid bone HP:3000052 Abnormal hyoid bone morphology Any structural abnormality of the hyoid bone (hyoid), a small U-shaped (horseshoe-shaped) solitary bone, situated in the midline of the neck anteriorly at the base of the mandible and posteriorly at the fourth cervical vertebra. PMID:30969548 A structural anomaly of the hypopharyx, which is the most inferior portion of the pharynx. The hypopharynx continues from the oropharynx at the pharyngoepiglottic fold superiorly and extends inferiorly to the level of the inferior aspect of the cricoid cartilage, which marks the beginning of the cervical esophagus. 2015-08-07T01:09:07Z UMLS:C4073261 Abnormality of hypopharynx Abnormality of lower pharynx HP:3000053 Abnormal hypopharynx morphology A structural anomaly of the hypopharyx, which is the most inferior portion of the pharynx. The hypopharynx continues from the oropharynx at the pharyngoepiglottic fold superiorly and extends inferiorly to the level of the inferior aspect of the cricoid cartilage, which marks the beginning of the cervical esophagus. Abnormality of hypopharynx Abnormality of lower pharynx An abnormality of an artery of lower lip. 2015-08-07T03:18:34Z UMLS:C4073264 Abnormality of the inferior labial artery HP:3000056 Abnormality of artery of lower lip An abnormality of an internal carotid artery. 2015-08-07T03:19:02Z UMLS:C1860488 Abnormality of internal carotid artery HP:3000062 Abnormal internal carotid artery morphology An abnormality of an internal jugular vein. 2015-08-07T03:19:06Z UMLS:C4073270 HP:3000063 Abnormality of internal jugular vein An abnormality of an intrinsic muscle of tongue. 2015-08-07T03:19:10Z UMLS:C4073271 Abnormality of intrinsic lingual muscle HP:3000064 Abnormality of intrinsic muscle of tongue Abnormality of intrinsic lingual muscle An abnormality of a lacrimal artery. 2015-08-07T03:38:25Z UMLS:C4073272 Abnormality of lacrimal artery HP:3000065 Abnormal lacrimal artery morphology An abnormality of a lacrimal sac. 2015-08-07T03:38:31Z UMLS:C4073273 Abnormality of lacrimal sac HP:3000066 Abnormal lacrimal sac morphology Any structural abnormality of a lingual artery. 2015-08-07T03:39:06Z UMLS:C4073281 Abnormality of lingual artery HP:3000074 Abnormal lingual artery morphology Any structural anomaly of a lingual nerve. 2015-08-07T03:39:10Z UMLS:C4073282 Abnormality of lingual nerve HP:3000075 The lingual nerve (LN) is one of the two terminal branches of the posterior division of the mandibular nerve. It supplies the general sensation to the mucosa of the anterior two-thirds of the tongue, the sublingual mucosa, the mandibular lingual gingiva and the floor of the mouth.The chorda tympani nerve, a branch of the facial nerve joins this nerve carrying taste fibers from the anterior two third of the tongue and parasympathetic fibers to the submandibular ganglion. Abnormal lingual nerve morphology Any structural anomaly of a lingual nerve. PMID:27662622 A structural abnormality of a mandibular symphysis. 2015-08-07T03:39:28Z UMLS:C4073286 Abnormality of mandible symphysis HP:3000079 Abnormal mandibular symphysis morphology A structural defect associated with abnormal development of the lung. 2021-06-09T12:13:11Z Developmental pulmonary anomaly Abnormal lung development Any structural anomaly of the iliac artery. 2021-11-24T01:28:09Z The common iliac artery originates from the aorta and divides into the internal and external iliac arteries, supplying oxygenated blood to the lower extremities (via the external iliac artery), the pelvis and its viscera (via internal iliac artery) as well as the peritoneum, psoas major muscle, ureter, and surrounding tissues. Abnormal iliac artery morphology The state of having abnormal relationships with others. This does not describe specific aspects of one's social aptitudes but rather a state which may come about from these aptitudes, such as lacking peer relationships, lacking close friends, or having a relational network that is abnormal given one's cultural context. Abnormal relationship Social disinhibition Abnormal response to social norms A repeating behavior that is either immediately unproductive or has negative long-term consequences. This includes harmful coping mechanisms such as addictive behavior and failure to control impulses and compulsions. Recurrent maladaptive behavior Congenital abnormality with cleft (gap or opening) in the craniofacial bones. Craniofacial cleft includes facial cleft, orofacial clef, and cleft of the jaw. Craniofacial cleft Congenital abnormality with cleft (gap or opening) in the craniofacial bones. Craniofacial cleft includes facial cleft, orofacial clef, and cleft of the jaw. data item data item information content entity information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type A clinically prescribed procedure, therapy, intervention, or recommendation. 2018-11-16T20:07:28Z OGMS:0000096 health care process medical action health care process OGMS:0000096 All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. 2018-11-16T20:08:29Z NCIT:C25218 NCIT:C49236 OAE:0000094 OGMS:0000112 An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. therapeutic procedure All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. ISBN-10:0124105165 An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. NCIT:C49236 Any procedure or test to diagnose a disease or disorder. 2018-11-16T20:10:20Z NCIT:C18020 OGMS:0000104 diagnostic technique procedure diagnostic testing diagnostic procedure Any procedure or test to diagnose a disease or disorder. NCIT:C18020 A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. 2018-11-16T20:10:35Z ERO:0000378 NCIT:C15329 NCIT:C17173 NCRO:0000228 OAE:0000067 SCDO:1000017 operation surgery surgical intervention surgical operation surgical procedure A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. NCIT:C15329 Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy. 2018-11-16T20:10:50Z NCIT:C17369 imaging procedure medical imaging therapeutic imaging procedure therapeutic imaging technique clinical imaging procedure Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy. NCIT:C17369 Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting for diagnosis, treatment, or therapy. 2018-11-16T20:11:26Z NCIT:C25294 clinical lab testing clinical laboratory testing clinical testing lab testing clinical laboratory procedure A test that involves the administration of contrast dye and X-ray imaging in order to be able to see soft tissue within the body. Dye can be added intravenously, ingested, or other methods. 2023-02-22T20:05:27Z radiographic imaging with contrast dye radiography with contrast dye radiograph imaging with contrast dye obsolete therapeutic intervention true Behavioral or regulatory nutritional interventions aim at modifying nutritional intake which have an impact on health outcomes. 2018-11-16T20:12:00Z nutritional intervention nutrition intervention Behavioral or regulatory nutritional interventions aim at modifying nutritional intake which have an impact on health outcomes. Cognitive and behavioral interventions are therapies that are designed to decrease symptoms and foster the belief that one has control over thoughts, beliefs, attitudes, and skills to facilitate coping. 2018-11-16T20:12:16Z NCIT:C116519 NCIT:C15184 NCIT:C64345 cognitive and behavioral therapies cognitive and behavioral therapy cognitive and behavioural intervention cognitive behavior therapy cognitive behavioral therapy cognitive behaviour therapy cognitive behavioural therapy cognitive and behavioral intervention Cognitive and behavioral interventions are therapies that are designed to decrease symptoms and foster the belief that one has control over thoughts, beliefs, attitudes, and skills to facilitate coping. PMID:22796302 The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. 2018-11-16T20:12:31Z NCIT:C15302 OGMS:0000115 PT physiatric procedure physical medicine procedure physical therapeutics physical therapy procedure physiotherapy physiotherapy procedure physical therapy The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. NCIT:C15302 PT A surgery performed on specific region of the body. 2023-02-24T15:24:21Z surgical procedure on body region surgery by body site Complementary and alternative medicine (CAM) or “complementary health approaches” are a group of diverse medical and health care practices and products that are not presently considered to be part of conventional medicine. 2019-01-07T19:24:28Z NCIT:C51976 SCDO:0000271 CAM therapy complementary or alternative medical procedure complementary medicine complementary therapy complementary and alternative medical therapy Complementary and alternative medicine (CAM) or “complementary health approaches” are a group of diverse medical and health care practices and products that are not presently considered to be part of conventional medicine. NCCIH Treatment of a disease by means of exposure of the target or the whole body to radiation. Radiation therapy is often used as part of curative therapy and occasionally as a component of palliative treatment for cancer. Other uses include total body irradiation prior to transplantation. 2018-11-16T20:20:38Z NCIT:C15313 OGMS:0000116 RT radiation radiation therapy procedure radiotherapeutics radiotherapy radiation therapy Treatment of a disease by means of exposure of the target or the whole body to radiation. Radiation therapy is often used as part of curative therapy and occasionally as a component of palliative treatment for cancer. Other uses include total body irradiation prior to transplantation. NCIT:C15313 RT A type of treatment that uses substances derived from or made by living organisms to treat disease; this includes both naturally occurring and synthetic products. 2018-11-16T20:20:54Z NCIT:C15187 BRM therapy biologic therapies biological response modifier therapy biological therapy biotheraphy biologic therapy A type of treatment that uses substances derived from or made by living organisms to treat disease; this includes both naturally occurring and synthetic products. NCIT:C15187 BRM therapy Cell therapy is therapy in which cellular material is injected into a patient. 2018-11-16T20:21:19Z NCIT:C70601 cell therapy cellular therapies cellular therapy Cell therapy is therapy in which cellular material is injected into a patient. PMID:24471045 A therapy or action designed to prevent disease or ailment. 2018-11-16T20:21:49Z preventative clinical measure preventative medical action preventative therapeutics preventative therapies preventive medical action preventive medical measure preventative therapy A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. 2018-11-16T20:22:04Z NCIT:C63333 biomarker assessment biomarker measurement biomarker test biomarker analysis A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. PMID:20978388 A radiographic examination of the esophagus in which the esophagusis made visible by barium or a water-soluble contrast administered orally prior to the examination. 2023-02-22T20:53:16Z contrast examination of the esophagus barrium swallow test of the esophagus esophography with contrast A behavioral modification or implementation of a behavior designed to prevent disease or ailment. 2018-11-16T20:22:48Z behavioral preventative therapeutics behavioral preventive care behavioral preventive therapy preventative behavior therapy preventative behavioral therapy behavioral preventative care An approach that improves the quality of life of patients and their families facing the problems associated with life-threatening illness, through the prevention and relief of suffering by means of early identification and impeccable assessment and treatment of pain and other problems, physical, psychosocial, and spiritual’. 2018-11-16T20:23:01Z NCIT:C101516 NCIT:C15747 comfort care palliative therapeutics symptom management supportive care palliative care An approach that improves the quality of life of patients and their families facing the problems associated with life-threatening illness, through the prevention and relief of suffering by means of early identification and impeccable assessment and treatment of pain and other problems, physical, psychosocial, and spiritual’. PMID:27162584 A service delivery system that provides palliative care/medicine when life expectancy is 6 months or less and when curative or life-prolonging therapy is no longer indicated. 2018-11-16T20:23:10Z NCIT:C15252 hospice care A service delivery system that provides palliative care/medicine when life expectancy is 6 months or less and when curative or life-prolonging therapy is no longer indicated. PMID:22190887 Treatment with an agent that can alter brain chemistry leading to mood and/or behaviorial changes. 2023-02-23T18:26:42Z mood altering drug therapy mood and behavior-altering agent therapy Any surgical procedure conducted on the camera-type eye. 2023-02-24T15:25:58Z camera-type eye surgical procedure eye procedure eye surgery surgery of the eye surgical procedure on the eye Care for patients with a progressive life-limiting disease with a prognosis of months or less. 2019-01-09T20:15:05Z NCIT:C67359 end-of-life treatment management end-of life care Care for patients with a progressive life-limiting disease with a prognosis of months or less. PMID:23796586 The production of heat in a body part by high-frequency electrical currents to stimulate circulation, relieve pain, cauterization, or destroy tissue. 2023-03-02T20:01:36Z diathermy A therapy using microwaves to focus on and heat up tissue with high water content, such as muscle. 2023-03-02T20:08:03Z microwave diathermy A deep heating modality that uses high-frequency acoustic vibrations within body tissues for the treatment of certain medical conditions, such as the alleviation of pain, muscle spasms, and joint contractures. 2023-03-02T20:08:31Z therapeutic ultrasound therapeutic ultrasound diathermy ultrasound diathermy therapy ultrasound therapy Quantification of cell characteristics, including morphological or physiological parameter of one or more cells in order to determine the health of the patient and/or detect disease. 2023-03-03T21:22:53Z clinical cell assessment clinical cell measurement clinical cell test cell measurement A form of deep heat therapy can induce vasodilatation, elevation of pain threshold, reduction in muscle spasm, acceleration of cellular metabolism, increased soft tissue extensibility, increase blood flow, decrease joint pain and stiffness, reduce inflammation, faster resolution of edema, and accelerate wound healing. 2023-03-02T20:15:39Z SWD radio-frequency diathermy short-wave diathermy shortwave diathermy radio frequency heating short wave diathermy A form of deep heat therapy can induce vasodilatation, elevation of pain threshold, reduction in muscle spasm, acceleration of cellular metabolism, increased soft tissue extensibility, increase blood flow, decrease joint pain and stiffness, reduce inflammation, faster resolution of edema, and accelerate wound healing. PMID:31748973 Any medical procedure used to sustain the life of a patient in critical condition. 2019-01-09T20:25:04Z NCIT:C95171 OMIT:0009105 life support care Any medical procedure used to sustain the life of a patient in critical condition. NCIT:C95171 obsolete therapeutic avoidance of behavior true A measurement of the shape, structure, form, and size of cells from a patient to determine if there is disease and/or infection. 2023-03-03T21:25:21Z morphology evaluation cell morphology assessment All manners of treatment to relieve illness and injury of a particular body site or system. 2023-03-20T19:58:58Z therapeutic procedure by site obsolete therapeutic mental or psychological behavior avoidance true obsolete stress avoidance true obsolete smoking avoidance true A clinical recommendation to avoid preventable diseases by vaccination or otherwise lowering risk for certain diseases. 2019-01-11T19:39:19Z disease avoidance preventable disease avoidance recommendation Avoidance of an illness or infection that can be spread from person to person, animal to person, animal to animal or person to animal by taking precautionary measures, such as good hygiene practices or vaccines. 2019-01-11T19:39:37Z avoid communicable disease communicable disease prevention communicable disease avoidance obsolete physiologic state true A medical requirement or recommendation of avoiding or preventing Dehydration. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Dehydration avoidance avoid Dehydration recommendation dehydration prevention recommendation A medical requirement or recommendation of avoiding or preventing Hypertension. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Hypertension avoidance avoid Hypertension recommendation hypertension prevention recommendation A medical requirement or recommendation of avoiding or preventing Obesity. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Obesity avoidance avoid Obesity recommendation obesity prevention recommendation A medical requirement or recommendation of avoiding or preventing Inflammatory abnormality of the skin. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Inflammatory abnormality of the skin avoidance avoid Inflammatory abnormality of the skin recommendation inflammation of the skin prevention recommendation Recommendation by a clinician to avoid exercise or physical activity. 2019-01-11T20:11:57Z avoid exercise avoidance of physical activity recommendation rest recommendation avoidance of physical activity therapeutic recommendation physical activity avoidance recommendation A recommendation by a clinician or therapist to avoid any impact activities to prevent medical issues or help the physical wellbeing of a patient. 2019-01-11T20:12:16Z impact sports avoidance therapeutic recommendation to avoid impact activities impact activities avoidance recommendation A recommendation by a clinician or therapist to avoid isometric exercises to prevent medical issues or help the physical wellbeing of a patient. 2019-01-11T20:13:10Z therapeutic recommendation to avoid isometric exercise isometric exercise avoidance recommendation A clinical recommendation to avoid or refrain from certain environmental exposures in order to maintain health or ameliorate symptoms. 2019-01-11T20:50:37Z therapeutic avoidance of environmental exposure A clinical recommendation to avoid or refrain from unnecessary radiation exposure. 2019-01-11T20:50:51Z radiation exposure avoidance A clinical recommendation to avoid or refrain from unnecessary sulight exposure. 2019-01-11T20:56:19Z sunlight avoidance A clinical recommendation to avoid the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. 2019-01-11T20:56:39Z food consumption avoidance nutrition intake avoidance Use of a substance introduced into a living organism with therapeutic or diagnostic purpose. 2019-01-15T18:20:06Z CHEBI:52217 drug treatment medication therapy pharmaceutical drug pharmaceutical treatment pharmacological treatment Medical treatment by means of drugs. pharmacotherapy Medical treatment by means of drugs. Use of a drug to treat or prevent bacterial infections. 2019-01-15T18:59:44Z CHEBI:36047 antibacterial treatment antibiotic agent therapy treatment with an anti-bacterial drug treatment with an anti-bacterial medication treatment with an anti-bacterial therapy treatment with an antibacterial agent treatment with an antibacterial drug treatment with an antibacterial medication treatment with an antibacterial therapy treatment with antibacterial drug antibacterial agent therapy Use of a substance that inhibits or prevents the proliferation of neoplasms. 2019-01-15T19:01:01Z anticancer agent therapy CHEBI:35610 NCIT:C274 anti-neoplastic agent therapy antineoplastic drug therapy cytostatic agent therapy cytostatic drug therapy treatment with anti-cancer drug treatment with anti-cancer medication treatment with anti-neoplastic drug treatment with anti-neoplastic medication treatment with antineoplastic agent treatment with antineoplastic drug treatment with antineoplastic medication antineoplastic therapy Sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. 2019-01-15T19:02:35Z NCIT:C39774 aerobic activity aerobic exercise A medical recommendation of sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. aerobic exercise therapy Sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. NCIT:C39774 A medical recommendation of sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. NCIT:C39774 The administration of oxygen to an individual, usually to aid in respiration. 2019-01-15T19:14:17Z MeSH:D010102 NCIT:C94624 oxygen inhalation therapy oxygen supplementation oxygen support therapy Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed) supplemental oxygen therapy The administration of oxygen to an individual, usually to aid in respiration. NCIT:C94624 Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed) MeSH:D010102 A procedure designed to help you breathe easier when your lungs have been damaged by disease. The goal of the surgery is to remove the area of the lung most affected by disease, allowing the remaining lung to function more efficiently, and improve your breathing ability and quality of life. 2019-01-15T19:14:42Z lung volume reduction surgery Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species. 2019-01-15T19:15:04Z NCIT:C15342 NCIT:C15431 OBI:0000105 transplant procedure transplantation transplantation surgery transplantation surgical procedure grafting procedure transplantation procedure Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species. NCIT:C15342 obsolete lung transplantation surgical procedure true NCIT:C15271 hepatic transplantation liver grafting liver transplantation surgical transplantation of the liver obsolete liver transplantation true A clinical recommendation to avoid or refrain from unnecessary chemical exposure. 2019-01-15T19:31:56Z chemical exposure avoidance The use of ultrasound to produce images of structures in the human body. 2019-01-15T19:32:35Z ERO:0001325 NCIT:C17230 diagnostic ultrasound medical sonography sonography ultrasound procedure 2D ultrasounds produce a flat image of the organs. 3D images show three-dimensional external images of organs or fetus. 4D ultrasounds generates an image that is continuously updated, like amoving image. A procedure that uses high-energy sound waves to look at tissues and organs inside the body. The sound waves make echoes that form pictures of the tissues and organs on a computer screen (sonogram). Ultrasound may be used to help diagnose diseases, such as cancer. It may also be used during pregnancy to check the fetus (unborn baby) and during medical procedures, such as biopsies. Also called ultrasonography. ultrasonography procedure obsolete liver ultrasound procedure true A procedure to measure pancreatic secretion to discriminate between pancreatic and nonpancreatic causes of malabsorption. 2019-01-15T19:35:19Z NCIT:C97101 pancreatic function assessment pancreatic function testing The quantitative measurement of digestive system tests to diagnose or treat a digestive disorder using clinical laboratory procedures, imaging tests, endoscopic or other procedures. 2019-01-15T19:35:36Z digestive system testing The act of receiving professional guidance in resolving personal conflicts and emotional problems. 2019-01-19T19:44:32Z NCIT:C15308 NCIT:C61547 NCIT:C63474 behaviour therapy behavioural counseling counseling intervention psychotherapy behavioral counseling The act of receiving professional guidance in resolving personal conflicts and emotional problems. NCIT:C61547 counseling intervention NCIT:C61547 Counseling designed to guide and support an individual to overcome alcohol dependence. 2019-01-19T19:46:47Z NCIT:C150658 alcoholism counseling Counseling designed to guide and support an individual to overcome alcohol dependence. NCIT:C150658 The process whereby an expert in hereditary disorders provides information about risk and clinical burden of a disorder or disorders to patients or relatives in families with genetic disorders as an aid to making informed and responsible decisions about marriage, children, early diagnosis, and handling disability. 2019-01-19T19:48:00Z NCIT:C15240 SCDO:0000443 genetic counseling The process whereby an expert in hereditary disorders provides information about risk and clinical burden of a disorder or disorders to patients or relatives in families with genetic disorders as an aid to making informed and responsible decisions about marriage, children, early diagnosis, and handling disability. NCIT:C15240 A wide range of techniques and psychotherapies aimed at controlling a person's level of stress. 2019-01-19T19:49:24Z NCIT:C67032 therapy for stress therapy to relieve stress stress management stress therapy stress management therapy A process by which a health professional provides education, recommendations, or interventions to help clients stop using tobacco products. (ACC) 2019-01-19T19:51:07Z NCIT:C101244 smoking cessation counseling smoking cessation tobacco cessation counseling A process by which a health professional provides education, recommendations, or interventions to help clients stop using tobacco products. (ACC) NCIT:C101244 smoking cessation The practice of piercing specific points on the body with very thin sterile needles in order to relieve pain or induce regional anesthesia. 2019-01-19T20:30:57Z NCIT:C15176 acupuncture therapy The practice of piercing specific points on the body with very thin sterile needles in order to relieve pain or induce regional anesthesia. NCIT:C15176 Continuous and profound contemplation or musing on a subject or series of subjects of a deep or abstruse nature; contemplation of spiritual matters 2019-01-19T20:32:30Z NCIT:C51975 SCDO:0000741 meditation therapy Continuous and profound contemplation or musing on a subject or series of subjects of a deep or abstruse nature; contemplation of spiritual matters NCIT:C51975 An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems. 2019-01-19T20:34:15Z NCIT:C64897 yoga therapy An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems. NCIT:C64897 An alternative medical system that focuses on the relationship between bodily structure (primarily that of the spine) and function, and how that relationship affects the preservation and restoration of health. Chiropractors use manipulative therapy as an integral treatment tool. 2019-01-19T20:35:28Z NCIT:C15204 chiropractic therapies chiropractic treatment chiropratic medicine chiropractic therapy An alternative medical system that focuses on the relationship between bodily structure (primarily that of the spine) and function, and how that relationship affects the preservation and restoration of health. Chiropractors use manipulative therapy as an integral treatment tool. NCIT:C15204 A therapeutic method of manipulation, methodical pressure, friction, and kneading of the body. (from Taber's) 2019-01-19T20:36:55Z NCIT:C15276 massage massage and body work massage therapy A therapeutic method of manipulation, methodical pressure, friction, and kneading of the body. (from Taber's) NCIT:C15276 Any alteration or treatment in an individual's diet with a planned goal, usually designed to improve the individual's overall health. 2019-01-19T20:39:14Z NCIT:C15447 diet behavioral nutritional intervention dietary intervention Any alteration or treatment in an individual's diet with a planned goal, usually designed to improve the individual's overall health. NCIT:C15447 The restriction of energy (calorie) intake below the amount required for weight maintenance. 2019-01-19T20:39:29Z LCD intake calorie restricted food intake carorie restriction in food intake low calorie diet intake primarily food‐based low‐calorie diet intake calorie restrictive diet intake The restriction of energy (calorie) intake below the amount required for weight maintenance. PMID:23748374 LCD intake Delivery of enteral nutrition via a tube placed into the stomach, duodenum, or jejunum. 2019-01-19T20:40:39Z NCIT:C93322 EN intake enteral nutrition support intake enteral tube feeding nutrition intake tube feeding nutrition intake enteral nutrition intake Delivery of enteral nutrition via a tube placed into the stomach, duodenum, or jejunum. NCIT:C93322 EN intake obsolete alcohol intake avoidance true A medical requirement or recommendation of avoiding the consumption of large amounts of alcohol. 2019-01-19T20:54:50Z excessive alcohol avoidance A clinical recommendation to avoid foods with high concentrations of estrogen. 2019-01-19T20:55:05Z Some processed foods and soy contain large amounts of estrogen. estrogen-containing food avoidance obsolete excessive iron consumption avoidance true A clinical recomendation to avoid high-protein diets which may worsen kidney function. 2019-01-19T21:00:36Z excessive protein consumption avoidance Clinical recommendation to avoid fasting due to health risks. 2019-01-19T21:01:13Z fasting avoidance Abstinence from all or some kinds of food or drink, particularly for religious observance, medical nutrition therapy, or prior to a medical procedure. 2019-01-19T21:01:21Z NCIT:C63663 NPO fasting nil per os therapeutic fasting intermittant fasting fasting intervention Abstinence from all or some kinds of food or drink, particularly for religious observance, medical nutrition therapy, or prior to a medical procedure. PMID:16630428 PMID:27499591 NPO obsolete food consumption avoidance true obsolete meat consumption avoidance true obsolete nut consumption avoidance true obsolete seafood consumption avoidance true obsolete mussel consumption avoidance true obsolete iron supplementation avoidance true obsolete saffron consumption avoidance true The addition of one or more elements and/or chemical compounds that are either absent or deficient in an individual's daily diet. 2019-01-19T21:07:25Z NCIT:C15425 nutritional supplementation The addition of one or more elements and/or chemical compounds that are either absent or deficient in an individual's daily diet. NCIT:C15425 Addition of multivitamin preparation to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-01-19T09:00:01Z NCIT:C1654 dietary supplementation of multivitamin preparation multivitamin preparation supplemental intake supplementation of multivitamin preparation supplementation with multivitamin A dietary supplement containing all or most of the vitamins that may not be readily available in the diet. Vitamins may be classified according to their solubility either in lipids (vitamins A, D, E, K, F) or in water (vitamins C, B-complex). Present in minute amounts in various foods, vitamins are essential to maintaining normal metabolism and biochemical functions. multivitamin supplementation A dietary supplement containing all or most of the vitamins that may not be readily available in the diet. Vitamins may be classified according to their solubility either in lipids (vitamins A, D, E, K, F) or in water (vitamins C, B-complex). Present in minute amounts in various foods, vitamins are essential to maintaining normal metabolism and biochemical functions. NCIT:C1654 Addition of iron atom to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-01-30T09:00:01Z dietary supplementation of iron atom iron atom supplemental intake oral iron supplementation supplementation of iron atom iron replacement therapy Oral iron supplementation is an effective and well‐studied option to replenish iron stores. iron supplementation Oral iron supplementation is an effective and well‐studied option to replenish iron stores. PMID:28328083 Addition of vitamin C to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of vitamin C supplementation of vitamin C vitamin C supplemental intake vitamin C supplementation Addition of vitamin D to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-01-19T09:00:01Z dietary supplementation of vitamin D supplementation of vitamin D vitamin D supplemental intake vitamin D supplementation obsolete amino acid supplementation true Addition of food antioxidant to a diet for adequate and complete nutrition. http://orcid.org/0000-0001-7941-2961 2019-01-19T21:12:19Z NCIT:C67025 antioxidant therapy dietary supplementation of food antioxidant food antioxidant supplemental intake supplementation of food antioxidant Treatment with antioxidants in order to protect cells against damage caused by oxygen-free radicals. food antioxidant supplementation Treatment with antioxidants in order to protect cells against damage caused by oxygen-free radicals. NCIT:C67025 Administration of nutritional support by means of a tube passed into the stomach. 2019-01-19T21:13:59Z NCIT:C73430 gastrogavage nutrition intake gavage nutrition intake Administration of nutritional support by means of a tube passed into the stomach. NCIT:C73430 Total parenteral nutrition formulated for intravenous administration in patients who cannot eat or cannot get enough nutrients from the foods they eat. It is a liquid mixture of proteins, carbohydrates, fats, vitamins, minerals and other nutrients. 2019-01-19T21:16:22Z NCIT:C29484 TNA intake TPN intake total nutrient admixture intake hyperalimentation total parenteral nutrition intake Total parenteral nutrition formulated for intravenous administration in patients who cannot eat or cannot get enough nutrients from the foods they eat. It is a liquid mixture of proteins, carbohydrates, fats, vitamins, minerals and other nutrients. NCIT:C29484 TPN intake Any action taken for the purpose of improving or maintaining an individual's memory. 2019-01-19T21:26:54Z NCIT:C116526 working memory interventions memory aids memory intervention A behavioral modification or implementation of a behavior designed to prevent smoking. 2019-01-19T21:33:17Z NCIT:C16114 prevent smoking smoking prevention A behavioral modification or implementation of a behavior designed to prevent smoking. The prevention of conception or impregnation by the use of devices or drugs or surgery. 2019-01-19T21:34:14Z NCIT:C37932 birth control conception prevention contraceptive management pregnancy prevention contraceptive pregnancy prevention The prevention of conception or impregnation by the use of devices or drugs or surgery. NCIT:C37932 birth control NCIT:C37932 Immunization is the process whereby a person is made immune or resistant to an infectious disease, typically by the administration of a vaccine. 2019-01-19T21:36:12Z NCIT:C15258 OBI:1110094 immunization preventive immunization preventative immunization Immunization is the process whereby a person is made immune or resistant to an infectious disease, typically by the administration of a vaccine. WHO immunization NCIT:C15258 OBI:1110094 Active immunity refers to the process of exposing the body to an antigen to generate an adaptive immune response: the response takes days/weeks to develop but may be long lasting—even lifelong. 2019-01-20T00:31:42Z IDO:0000498 NCIT:C15416 VO:0000491 active immunization Active immunity refers to the process of exposing the body to an antigen to generate an adaptive immune response: the response takes days/weeks to develop but may be long lasting—even lifelong. PMID:18045976 Passive immunity refers to the process of providing IgG antibodies to protect against infection; it gives immediate, but short-lived protection. 2019-01-20T00:31:52Z NCIT:C15259 OBI:0001174 VO:0000492 passive immunization Passive immunity refers to the process of providing IgG antibodies to protect against infection; it gives immediate, but short-lived protection. PMID:18045976 The intentional exposure to a disease in order to achieve immunization. 2019-01-20T00:36:49Z disease exposure immunization The use of any device, marker, or other means for the purpose of detecting the presence of disease, usually in asymptomatic individuals. 2019-01-20T00:39:19Z NCIT:C15419 disease screening The use of any device, marker, or other means for the purpose of detecting the presence of disease, usually in asymptomatic individuals. NCIT:C15419 Testing conducted utilizing a manual or microprocessor audiometer to test for hearing loss. 2019-01-20T00:42:26Z NCIT:C38036 audiometry test hearing exam procedure hearing testing procedure audiometry exam audiometric testing Testing conducted utilizing a manual or microprocessor audiometer to test for hearing loss. NCIT:C38036 The use of any device, marker, or other means for the purpose of detecting the presence Neoplasm, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z 2019-01-20T00:45:24Z NCIT:C15406 Neoplasm screening cancer screening The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. 2019-01-20T00:46:22Z NCIT:C15709 genetic analysis genetic testing The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. NCIT:C15709 obsolete prenatal screening true obsolete biopsy procedure true A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ to examine the structural architecture and/or remove abnormal tissues. 2019-01-20T01:01:22Z NCIT:C16546 endoscopic exam endoscopy endoscopic procedure A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ to examine the structural architecture and/or remove abnormal tissues. NCIT:C16546 endoscopy NCIT:C16546 A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular portion of a specific body part or body location. 2019-01-20T01:03:18Z endoscopy by body location location specific endoscopy endoscopy by site A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ using a specific endoscopic technique. 2019-01-20T01:03:28Z endoscopy by type specific type endoscopy specific technique endoscopy An endoscopic technique that allows deep intubation of the small intestine while using a standard endoscope. An inflatable balloon attached to the endoscope's tip acts as a stabilizer and a second balloon that is advanced ahead of the endoscope acts as a pulling device. 2019-01-20T18:48:29Z NCIT:C64865 balloon-guided endoscopy balloon-guided endoscopic procedure An endoscopic technique that allows deep intubation of the small intestine while using a standard endoscope. An inflatable balloon attached to the endoscope's tip acts as a stabilizer and a second balloon that is advanced ahead of the endoscope acts as a pulling device. NCIT:C64865 Endoscopy that employs the use of tissue stains to increase tissue contrast, and enhance the ability to identify various tissue dysplasia and other abnormalities. 2019-01-20T18:51:12Z NCIT:C116476 chromoendoscopy Endoscopy that employs the use of tissue stains to increase tissue contrast, and enhance the ability to identify various tissue dysplasia and other abnormalities. NCIT:C116476 A low-cost, high-resolution imaging tool consisting of a 1-mm diameter fiber-optic bundle that produces subcellular imaging at 1,000x magnification and 4 micrometer resolution, allowing for minimally invasive bioimaging. 2019-01-20T19:03:17Z NCIT:C116480 HRME high-resolution microendoscopy A low-cost, high-resolution imaging tool consisting of a 1-mm diameter fiber-optic bundle that produces subcellular imaging at 1,000x magnification and 4 micrometer resolution, allowing for minimally invasive bioimaging. NCIT:C116480 HRME A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. NCIT:C17007 PET scan positron emission tomography procedure A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. NCIT:C17007 PET scan NCIT:C17007 Ultrasound imaging following the administration of a microbubble contrast agent. 2019-01-21T20:17:52Z NCIT:C148281 CEUS contrast-enhanced ultrasound procedure Ultrasound imaging following the administration of a microbubble contrast agent. NCIT:C148281 CEUS A postmortem examination of the body that includes an examination of the internal organs and structures after dissection to determine the cause of death and the nature of pathological changes. 2019-01-21T20:33:46Z NCIT:C25153 autopsy autopsy procedure A postmortem examination of the body that includes an examination of the internal organs and structures after dissection to determine the cause of death and the nature of pathological changes. NCIT:C25153 A procedure to examine and define cellular anatomy or function. The test results are often used by a clinician to diagnose disease or disordered function. 2019-01-21T20:36:01Z NCIT:C49132 clinical cytological procedure diagnostic cytological procedure clinical cytological testing A biospecimen collection and staining procedure in which secretions and superficial cells of the cervix are collected and stained with the Papanicolaou stain followed by microscopic examination to identify the presence of abnormal cells. 2019-01-21T20:38:23Z Papanicolaou smear procedure cervical smear procedure pap testing cervical cancer screening pap smear examination A biospecimen collection and staining procedure in which secretions and superficial cells of the cervix are collected and stained with the Papanicolaou stain followed by microscopic examination to identify the presence of abnormal cells. NCIT:C17348 Papanicolaou smear procedure NCIT:C17348 cervical smear procedure NCIT:C17348 pap testing NCIT:C17348 A diagnostic technique for lung cancer detection. Looks for abnormal cell cytology in sputum. 2019-01-21T20:45:16Z NCIT:C16192 sputum cytology testing sputum smear examination sputum smear testing sputum cytology examination A diagnostic technique for lung cancer detection. Looks for abnormal cell cytology in sputum. NCIT:C16192 Examination of the cells in urine. 2019-01-21T20:47:27Z urine cytology testing urine cytology examination Examination of the cells in urine. NCIT:C94473 Technique or procedure used for the study of the microanatomy of tissues and their cellular structure; usually involves microscopic examination of tissue slices. 2019-01-21T21:04:01Z NCIT:C16680 histological procedure histological testing histological examination Technique or procedure used for the study of the microanatomy of tissues and their cellular structure; usually involves microscopic examination of tissue slices. NCIT:C16680 obsolete clinical pathology procedure true A procedure to determine the number of cells in a clinical sample. 2019-01-21T21:16:16Z NCIT:C48938 cell count clinical pathology cell count clinical cell count A procedure to determine the number of cells in a clinical sample. NCIT:C48938 A procedure to measure hematopoietic components and investigate hematologic disorders in a blood sample. 2019-01-21T21:22:45Z NCIT:C49286 blood testing hematology procedure hematology testing The determination of the maximum amount of oxygen that can be combined chemically with hemoglobin in a volume of blood. 2019-01-21T21:29:03Z NCIT:C96614 OXYCAP testing oxygen capacity measurement oxygen capacity testing oxygen capacity assessment The determination of the maximum amount of oxygen that can be combined chemically with hemoglobin in a volume of blood. NCIT:C96614 OXYCAP testing A measure of the volume of red blood cells expressed as a percentage of the total blood volume. Normal in males is 43-49%, in females 37-43%. 2019-01-21T21:32:32Z NCIT:C64796 EVF testing HCT PCV measurement erythrocyte volume fraction testing hematocrit measurement hematocrit testing packed cell volume measurement hematocrit assessment A measure of the volume of red blood cells expressed as a percentage of the total blood volume. Normal in males is 43-49%, in females 37-43%. NCIT:C64796 EVF testing HCT PCV measurement packed cell volume measurement NCIT:C64796 A medical recommendation to avoid a particular therapy, intervention, medication, or procedure. 2019-01-07T19:23:10Z avoid procedure avoid therapy avoid activity avoid drug avoid medication therapeutic avoidance intervention A medical recommendation to avoid a particular therapy, intervention, medication, or procedure. Administration of intravenous infusions of alpha-1 proteinase inhibitor at regular schedules is a specific therapy for individuals with alpha-1 antitrypsin deficiency (AATD) with pulmonary involvement. 2019-01-22T17:27:25Z augmentation therapy Administration of intravenous infusions of alpha-1 proteinase inhibitor at regular schedules is a specific therapy for individuals with alpha-1 antitrypsin deficiency (AATD) with pulmonary involvement. PMID:28752465 obsolete antispastic agents true Treatment with a drug used in the treatment of Parkinson's disease. 2019-01-22T17:52:48Z CHEBI:48407 NCIT:C38149 anti-Parkinson agent therapy antiparkinson agent treatment antiparkinson drug treatment antiparkinsonian agent therapy antiparkisonian agent treatment antiparkisonian drug treatment treatment with anti-Parkinson drug treatment with antiparkinson drug antiparkinson agent therapy Use of a substance used to treat or prevent parasitic infections. 2019-01-22T17:53:06Z CHEBI:35442 NCIT:C276 antiparasitic drug therapy antiparasitics therapy antiparisitics drug treatment treatment with anti-parasitic agent treatment with anti-parasitic medication treatment with antiparasitic agent treatment with antiparasitic drug treatment with antiparasitic medication antiparasititic agent therapy A therapy capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms. 2019-01-22T17:53:16Z CHEBI:35480 NCIT:C241 Analgesics therapy analgesic drug therapy analgesic medication therapy analgesic pharmacotherapeutic agent therapy treatment with analgesic analgesic agent therapy Treatment with a mood-stimulating drug used primarily in the treatment of affective disorders and related conditions. 2019-01-22T17:53:33Z CHEBI:35469 antidepressant drug therapy antidepressants treatment thymoanaleptics treatment thymoleptic agent therapy thymoleptic drug treatment therapy thymoleptics drug therapy treatment with antidepressant antidepressant agent therapy Use of a substance that attaches to and blocks cell receptors. 2019-01-22T17:54:06Z CHEBI:48706 NCIT:C69308 treatment with antagonist receptor antagonist therapy Use of any agent that can alter adrenal gland functions. 2019-01-22T17:54:15Z treatment with adrenal modifier treatment with adrenal modifying agent treatment with adrenal modifying drug treatment with adrenal modifying medication adrenal hormone modifying therapy adrenal-modifying, hormonal agent therapy Treatment with a drug that alleviates anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting the clarity of consciousness or neurologic conditions. 2019-01-22T17:54:43Z CHEBI:35474 anti-anxiety agent therapy anti-anxiety drug treatment anxiolytic agent drug treatment minor tranquiliser therapy minor tranquilizer treatment minor tranquilizing agent treatment minor tranquilizing drug therapy treatment with anxiolytic treatment with anxiolytic drug anxiolytic agent therapy Pharmaceutical Anti-gout Preparations such as colchicine, allopurinol, probenecid, and sulfinpyrazone contain natural or synthetic agents against gout, a condition characterized by increased uric acid accumulation. Anti-gout agents may reduce inflammation, stimulate elimination of uric acid, or increase production of uric acid. (NCI04) 2019-01-22T17:55:18Z CHEBI:35841 CHEBI:35845 NCIT:C29733 anti-gout agent therapy anti-gout combination medicine therapy anti-gout drug therapy anti-gout preparation therapy antigout agent therapy antigout combination medicine therapy antigout drug therapy antigout medication therapy antigout preparation therapy antigout therapy gout suppressant agent treatment treatment with anti-gout drug treatment with anti-gout medication treatment with antigout agent treatment with antigout drug treatment with antigout medication treatment with gout suppressant agent treatment with gout suppressant drug treatment with gout suppressant medication treatment with uricosuric drug uricosuric agent therapy Pharmaceutical Anti-gout Preparations such as colchicine, allopurinol, probenecid, and sulfinpyrazone contain natural or synthetic agents against gout, a condition characterized by increased uric acid accumulation. Anti-gout agents may reduce inflammation, stimulate elimination of uric acid, or increase production of uric acid. (NCI04) NCIT:C29733 Therapy using an agent that promotes the excretion of urine through its effects on kidney function 2019-01-22T17:55:27Z CHEBI:35498 NCIT:C448 diuretic agent drug treatment therapy diuretic drug therapy treatment with diuretic treatment with diuretic agent treatment with diuretic drug treatment with diuretic medication diuretic agent therapy Treatment with an agent that control agitated psychotic behavior, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. 2019-01-22T17:57:29Z CHEBI:35476 antipsychotic drug treatment antipsychotic therapy major tranquilizer drug treatment neuroleptic agent treatment neuroleptic therapies treatment with antipsychotic agent treatment with antipsychotic drug treatment with antipsychotic medication antipsychotic agent therapy Treatment with a drug used to prevent seizures or reduce their severity. 2019-01-22T17:57:37Z CHEBI:35623 NCIT:C264 anti-convulsant therapy anti-convulsive agent therapy anticonvulsant drug therapy anticonvulsive agent therapy antiepileptic therapy treatment with anticonvulsant treatment with anticonvulsant medication anticonvulsant agent therapy Treatment with a substance used in the prophylaxis or therapy of virus diseases. 2019-01-22T17:57:52Z CHEBI:36044 anti-viral drug therapy anti-virus drug treatment treatment with an anti-virus agent treatment with an anti-virus drug treatment with an anti-virus medication treatment with an antiviral agent treatment with an antiviral drug treatment with an antiviral medication treatment with antiviral drug antiviral agent therapy Use of a compound that has anti-inflammatory effects. 2019-01-22T17:58:04Z CHEBI:67079 anti-inflammatory agent treatment therapy anti-inflammatory medication therapy antiinflammatory agent therapy antiinflammatory drug therapy treatment with anti-inflammatory drug anti-inflammatory agent therapy A therapy utilizing a substance which produces loss of feeling or sensation. 2019-01-22T17:59:57Z CHEBI:38867 NCIT:C245 anaesthesia therapy anaesthetic medication therapy anesthesia therapy anesthetic drug therapy anesthetic medication therapy treatment with anaesthetic anesthetic agent therapy Treatment with medications to improve cognition and function for patients with dementia. 2019-01-22T18:00:43Z antidementia drug therapy antidementia medication treatment antidementia agent therapy Treatment with medications to improve cognition and function for patients with dementia. PMID:31517030 A grouping of agents that are used as antidotes, deterrents, or to counteract the effects of a toxic agents on the body. 2019-01-22T18:01:36Z antidote therapy rescue therapy therapeutic antidotes, deterrents, and toxicologic agent therapy Treatment with a drug used to prevent nausea or vomiting. 2019-01-22T18:01:53Z CHEBI:50919 NCIT:C267 anti-emetic agent therapy anti-emetic drug therapy anti-emetics therapy antiemetic drug therapy antiemetics medication treatment medication for nausea treatment medication for treatment of nausea treatment with antiemetic antiemetic therapy Use of a drug to prevent or treat fungal infections in humans or animals. 2019-01-22T18:02:00Z CHEBI:86327 anti-fungal drug therapy anti-fungal medication therapy antifungal treatment antifungals therapy treatment with an anti-fungal drug treatment with an anti-fungal medication treatment with an antifungal drug treatment with an antifungal medication treatment with an antifungal therapy treatment with antifungal drug pharmaceutical fungicide therapy anti-fungal agent therapy Any drug that works to lower abnormally high glucose (sugar) levels in the blood, which are characteristic of the endocrine system disorder known as diabetes mellitus. 2019-01-22T18:11:18Z blood glucose regulator drug treatment Treatment with an agent that regulates blood glucose levels. blood glucose regulator therapy Use of a drug that acts on blood and blood-forming organs and those that affect the hemostatic system. 2019-01-22T18:11:44Z CHEBI:50248 blood modifier treatment therapy blood modifying agent treatment hematologic agent treatment therapy treatment with hematologic agent treatment with hematologic drug treatment with hematologic medication hematologic agent therapy Treatment with a drug that promotes coagulation. 2019-01-22T18:11:58Z coagulant treatment therapy promotion of coagulation treatment with coagulant coagulant agent therapy Use of an agent that prevents blood clotting. 2019-01-22T18:12:06Z CHEBI:50249 anticoagulant agent treatment anticoagulant drug treatment treatment with anticoagulant anticoagulant agent therapy Treatment with an agent that stimulates formation of blood cells. 2019-01-22T18:12:20Z blood formation agent therapy Use of a drug which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system. 2019-01-22T18:12:39Z CHEBI:50427 platelet aggregation inhibitor agent treatment treatment with platelet aggregation antagonist treatment with platelet aggregation blocker treatment with platelet aggregation inhibitor platelet aggregation inhibitor therapy Use of a drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. 2019-01-22T18:13:06Z CHEBI:35554 NCIT:C78274 agent affecting cardiovascular system therapy cardiovascular agent drug treatment cardiovascular drug treatment therapy cardiovascular system agent therapy cardiovascular system drug therapy treatment with cardiovascular agent treatment with cardiovascular drug treatment with cardiovascular medication treatment with cardiovascular therapy treatment with heart agent treatment with heart drug treatment with heart medication cardiovascular agent therapy Treatment with a drug that acts on an alpha-adrenergic receptor. 2019-01-22T18:14:42Z CHEBI:48539 a-adrenergic agent therapy a-adrenergic drug therapy a-adrenergic receptor agent therapy a-adrenergic receptor drug therapy alpha adrenergic drug therapy alpha adrenergic receptor agent therapy alpha adrenergic receptor drug treatment alpha adrenergics drug therapy alpha-adrenergic agent treatment alpha-adrenergic drug treatment therapy alpha-adrenergic modifier therapy alpha-adrenergic modifying agent therapy alpha-adrenergic receptor agent therapy alpha-adrenergic receptor drug therapy alpha-adrenergic receptor drug treatment treatment with alpha adrenergic agent treatment with alpha adrenergic drug treatment with alpha adrenergic medication treatment with alpha-adrenergic agent treatment with alpha-adrenergic drug treatment with alpha-adrenergic medication treatment with alpha-adrenergic receptor agent treatment with alpha-adrenergic receptor drug treatment with alpha-adrenergic receptor medication alpha adrenergic agent therapy Treatment with an agent that selectively binds to and activates alpha-adrenergic receptors. 2019-01-22T18:15:26Z CHEBI:48539 a-adrenergic agonist drug treatment a-adrenergic agonist therapy a-adrenergic receptor agonist therapy alpha adrenergic agonist agent drug treatment alpha adrenergic agonist drug therapy alpha adrenergic agonist treatment alpha adrenergic receptor agonist therapy alpha adrentergic receptor agonist agent therapy alpha-adrenergic receptor agonist drug therapy alpha-adrenergic receptor agonist treatment alpha-adrenoceptor agonist agent therapy alpha-adrenoceptor agonist drug therapy alpha-adrenoceptor agonist therapy treatment with alpha-adrenergic agonist alpha adrenergic agonist therapy Treatment with an agent that binds to but does not activate alpha-adrenergic receptors thereby blocking the actions of endogenous or exogenous alpha-adrenergic agonists. 2019-01-22T18:15:59Z CHEBI:37890 a-adrenergic antagonist agent therapy a-adrenergic antagonist therapy a-adrenergic receptor antagonist drug treatment alpha adrenergic antagonist drug therapy alpha blocker therapy alpha-adrenergic antagonist agent treatment alpha-adrenergic antagonist drug therapy alpha-adrenergic antagonist drug treatment alpha-adrenergic antagonist medication therapy alpha-adrenergic blockader therapy alpha-adrenergic blocker therapy alpha-adrenergic blocking agent therapy alpha-adrenergic receptor antagonist agent therapy alpha-adrenergic receptor antagonist drug therapy alpha-adrenergic receptor blockader therapy alpha-adrenergic receptor blocker therapy alpha-adrenoceptor antagonist therapy treatment with alpha-adrenergic antagonist treatment with alpha-adrenergic antagonist drug treatment with alpha-adrenergic antagonist medication alpha adrenergic antagonist therapy Treatment with a drug for prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres. 2019-01-22T18:17:04Z CHEBI:38070 NCIT:C47793 anti-arrhythmia agent therapy anti-arrhythmic agent therapy anti-arrhythmic drug treatment therapy anti-arrythmic agent therapy antiarrhythmic agent therapy antiarrhythmic drug therapy antiarrhythmic drug treatment treatment with anti-arrhythmia agent treatment with anti-arrhythmia drug treatment with anti-arrhythmia medication treatment with anti-arrhythmic agent treatment with anti-arrhythmic drug treatment with anti-arrhythmic medication treatment with anti-arrythmic drug treatment with antiarrhythmic agent treatment with antiarrhythmic drug treatment with antiarrhythmic medication antiarrythmic agent therapy Treatment with a drug that acts on beta-adrenergic receptors. 2019-01-22T18:17:27Z CHEBI:48540 b-adrenergic drug treatment beta adrenergic receptor agent treatment beta adrenergic receptor drug therapy beta-adrenergic agent treatment beta-adrenergic drug treatment beta-adrenergic modifier therapy beta-adrenergic modifying agent therapy beta-adrenergic modifying drug treatment beta-adrenergics therapy treatment with beta-adrenergic agent treatment with beta-adrenergic drug treatment with beta-adrenergic medication beta adrenergic agent therapy Treatment with an agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. 2019-01-22T18:17:55Z CHEBI:35530 b-adrenergic antagonist therapy b-adrenergic receptor antagonist therapy beta adrenergic antagonist agent treatment beta adrenergic antagonist drug treatment beta adrenergic receptor antagonist therapy beta-adrenergic antagonist agent treatment beta-adrenergic receptor antagonist drug treatment beta-adrenergic receptor antagonist therapy beta-adrenergic receptor blockader therapy beta-adrenoceptor antagonist therapy treatment with beta blocker agent treatment with beta blocker drug treatment with beta blocker medication treatment with beta-adrenergic antagonist treatment with beta-adrenergic antagonist agent treatment with beta-adrenergic antagonist drug treatment with beta-adrenergic antagonist medication beta-adrenergic antagonist therapy obsolete calcium channel blocker agent therapy true Therapy using an agent that reduces plasma lipids, such as cholesterol or low density lipoproteins (LDL), acting systemically or locally (intestines) to decrease fat digestion, absorption, production, and accumulation in the plasma and reducing pathogenic atherosclerosis and thrombosis. 2019-01-22T18:19:20Z NCIT:C29703 anti-lipemic therapy anti-lipidemic agent therapy antihyperlipemic agent therapy antihyperlipidaemic agent therapy antihyperlipidemic agent therapy antihyperlipidemic drug therapy antilipemic therapy antilipidemic agent therapy antilipidemic drug treatment therapy dyslipidemia agent therapy dyslipidemia drug treatment therapy dyslipidemic agent drug treatment dyslipidemic drug therapy dyslipidemic drugs therapy hypolipidemic agent therapy lipid-lowering agent therapy treatment with anti-lipidemic agent treatment with anti-lipidemic drug treatment with anti-lipidemic medication treatment with antilipemic drug treatment with antilipidemic agent treatment with antilipidemic medication treatment with dyslipidemic agent treatment with dyslipidemic drug treatment with dyslipidemic medication dyslipidemic agent therapy Treatment with Renin-angiotensin-aldosterone system (RAAS) inhibitors, a group of drugs that act by inhibiting the renin-angiotensin-aldosterone system and include angiotensin-converting enzyme (ACE) inhibitors, angiotensin-receptor blockers (ARBs), and direct renin inhibitors 2019-01-22T18:19:47Z Treatment with RAAS inhibitor renin-angiotensin-aldosterone system inhibitor therapy treatment with renin-angiotensin-aldosterone system inhibitor RAAS inhibitor therapy A therapy using a drug to cause dilation of the blood vessels. 2019-01-22T18:20:06Z CHEBI:35620 NCIT:C29707 vasodilating agent therapy vasodilating drug treatment therapy vasodilator agent therapy vasodilator drug therapies vasodilator drug therapy vasodilator drug treatment therapy vasodilator therapies vasodilator agent therapy A therapy using a drug to cause dilation of the blood vessels. CHEBI:35620 obsolete other cardiovascular agent therapy true Use of a drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors. 2019-01-22T18:22:25Z CHEBI:35481 non-narcotic analgesic agent therapy non-narcotic analgesic drug therapy non-narcotic analgesic medication treatement non-opioid analgesic agent therapy non-opioid analgesics drug therapy non-opioid analgesics medication therapy non-opioid analgesics medication treatment non-opioid analgesics therapy treatment with non-narcotic analgesic non-opioid analgesic therapy Use of a narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. 2019-01-22T18:22:42Z narcotic therapy CHEBI:35482 narcotic analgesic medication therapy narcotic analgesic medication treatment narcotic analgesic therapy opioid analgesic drug therapy opioid analgesic medication therapy opioid analgesic medication treatment opioid analgesics opioid therapy treatment with opioid analgesic opioid analgesic agent therapy Treatment with any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. 2019-01-22T18:24:45Z CHEBI:36333 local anaesthesia therapy local anaesthetic medication therapy local anaesthetics therapy local anesthesia therapy local anesthesia treatment local anesthetic agent therapy local anesthetics therapy treatment with local anaesthetic epidural therapy spinal block therapy topical anesthesia therapy topical anesthetic therapy local anaesthetic agent therapy An antibacterial substance with aminoglycoside structure. 2019-01-22T18:25:15Z CHEBI:47779 aminoglycoside drug therapy aminoglycoside drug treatment aminoglycosides therapy aminoglycoside agent therapy An antibacterial substance with aminoglycoside structure. Use of a class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. 2019-01-22T18:25:44Z CHEBI:23066 cephalosporin antibacterial agent therapy cephalosporin beta-lactam therapy cephalosporin drug therapy cephalosporin drug treatment cephalosporin therapies cephalosporin treatment cephalosporins therapy treatment with cephalosporin agent treatment with cephalosporin antibacterial drug treatment with cephalosporin antibacterial medication treatment with cephalosporin antibiotic drug treatment with cephalosporin antibiotic medication Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. treatment with cephalosporin drug treatment with cephalosporin medication cephalosporin agent therapy Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. CHEBI:23066 Use of an antibacterial substance with penicillin structure. 2019-01-22T18:26:03Z CHEBI:17334 penicillin antibacterial therapy penicillin antibacterial treatment penicillin beta-lactam therapy penicillin drug therapy penicillin drug treatment penicillin treatment treatment with a penicillin agent treatment with a penicillin drug treatment with a penicillin medication treatment with a penicillin therapy treatment with penicillin antibacterial drug treatment with penicillin antibacterial medication treatment with penicillin antibiotic agent treatment with penicillin antibiotic drug treatment with penicillin antibiotic medication treatment with penicillin antibiotic therapy penicillin agent therapy obsolete other beta-lactams true Use of a drug with a macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. 2019-01-22T18:26:31Z macrolides CHEBI:25105 Treatment with a macrolide antibacterial agent Treatment with a macrolide antibacterial drug Treatment with a macrolide antibacterial medication Treatment with a macrolide antibiotic agent Treatment with a macrolide antibiotic drug Treatment with a macrolide antibiotic medication macrolide antibacterial drug therapy macrolide antibacterial therapy macrolide drug therapy macrolide drug treatment macrolide antibacterial agent therapy Use of an organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. 2019-01-22T18:26:50Z quinolones CHEBI:86324 quinolone antibacterial therapy quinolone antibiotic agent treatment treatment with quinolone antibacterial agent treatment with quinolone antibacterial drug treatment with quinolone antibacterial medication treatment with quinolone antibiotic agent treatment with quinolone antibiotic drug treatment with quinolone antibiotic medication quinolone antibacterial agent therapy Use of a class of sulfonamides whose members generally have bacteriostatic antibiotic properties. 2019-01-22T18:27:30Z sulfonamides therapy CHEBI:87228 sulfonamide antibacterial drug therapy sulfonamide antibacterial therapy sulfonamide antibiotic therapy sulfonamide drug therapy sulfonamide drug treatment treatment with a sulfonamide antibacterial drug treatment with a sulfonamide antibacterial medication treatment with a sulfonamide antibiotic agent treatment with a sulfonamide antibiotic drug treatment with a sulfonamide antibiotic medication treatment with a sulfonamide antibiotic therapy sulfonamide antibacterial agent therapy Treatment with a broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. 2019-01-22T18:28:05Z CHEBI:27902 tetracycline antibiotic therapy tetracycline drug therapy tetracycline drug treatment treatment with a tetracycline antibacterial agent treatment with a tetracycline antibacterial drug treatment with a tetracycline antibacterial medication treatment with a tetracycline antibacterial therapy treatment with a tetracycline antibiotic agent treatment with a tetracycline antibiotic drug treatment with a tetracycline antibiotic medication treatment with a tetracycline antibiotic therapy tetracycline therapy obsolete other antibacterial agents true Treatment with a drug that can regulate intracellular calcium levels. 2019-01-22T18:28:49Z CHEBI:38808 calcium channel modifier drug therapy treatment with calcium channel modifying agent treatment with calcium channel modifying medication treatment with calcium channel modulator calcium channel modifying agent therapy Treatment with a substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems. 2019-01-22T18:29:21Z CHEBI:51374 GABA augmenting therapy gamma-aminobutyric acid drug therapy gamma-aminobutyric acid modulating agent therapy treatment with GABA agent treatment with GABA drug treatment with GABA medication treatment with gamma-aminobutyric acid augmenting agent treatment with gamma-aminobutyric acid augmenting drug treatment with gamma-aminobutyric acid augmenting medication GABA augmenting agent therapy Treatment with an agent which decreases glutamate. 2019-01-22T18:29:56Z glutamate reducing agent therapy Use of a drug that inhibits sodium influx through cell membranes. 2019-01-22T18:30:15Z CHEBI:38633 Na+ channel blocker therapy Na+ channel inhibitor drug therapy sodium channel blocker drug therapy sodium channel inhibitor drug therapy treatment with Na+ channel inhibitor treatment with sodium channel antagonist treatment with sodium channel blocker treatment with sodium channel inhibitor sodium channel inhibitor therapy obsolete anticonvulsants, other true They are a group of drugs that block the normal breakdown of acetylcholine (ACh) into acetate and choline and thereby increase both the levels and duration of actions of acetylcholine found in the central and peripheral nervous system. 2019-01-22T18:32:56Z CHEBI:37733 cholinesterase inhibitor drug treatment cholinesterase inhibitor medication therapy treatment with EC 3.1.1.8 (cholinesterase) inhibitor Neurogenerative diseases such as Alzheimer disease, Parkinson disease, and Lewy body dementia are indications for cholinesterase inhibitor therapy. cholinesteriase inhibitor therapy They are a group of drugs that block the normal breakdown of acetylcholine (ACh) into acetate and choline and thereby increase both the levels and duration of actions of acetylcholine found in the central and peripheral nervous system. PMID:31335056 Neurogenerative diseases such as Alzheimer disease, Parkinson disease, and Lewy body dementia are indications for cholinesterase inhibitor therapy. PMID:31335056 Treatment with an agent which modifies glutamate. 2019-01-22T18:33:33Z glutamate modulator therapy glutamate pathway modifying drug treatment glutamatergic drug therapy glutamatergic drug treatment glutamatergic pathway modifying agent therapy obsolete antidementia agents, other true A drug that acts as an inhibitor that interferes with the action of monoamine oxidase (EC 1.4.3.4). 2019-01-22T18:36:08Z CHEBI:38623 NCIT:C667 MAO drug therapy MAO drug treatment MAO inhibitor therapy MAOI therapy inhibitors of MAO therapy inhibitors of monoamine oxidase therapy treatment with EC 1.4.3.4 (monoamine oxidase) inhibitor Any substance that inhibits monoamine oxidase (MAO), an enzyme that catalyzes the oxidative deamination of monoamines and plays a role in the inactivation of neurotransmitters. monoamine oxidase inhibitor therapy MAO inhibitor therapy MAOI therapy Any substance that inhibits monoamine oxidase (MAO), an enzyme that catalyzes the oxidative deamination of monoamines and plays a role in the inactivation of neurotransmitters. NCIT:C667 Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) and norepinephrine by inhibiting their reuptake into the presynaptic cell. 2019-01-22T18:40:17Z OMIT:0001323 SNRI agent therapy SNRI drug therapy SNRI drug treatment serotonin and noradrenaline reuptake inhibitor agent therapy serotonin and noradrenaline reuptake inhibitor drug therapy serotonin and noradrenaline reuptake inhibitor drug treatment serotonin and norepinephrine reuptake inhibitor therapy serotonin-noradrenaline reuptake inhibitor agent therapy serotonin-noradrenaline reuptake inhibitor drug treatment serotonin-norepinephrine reuptake inhibitor drug treatment serotonin-norepinephrine reuptake inhibitor agent therapy Treatment with mood-stimulating agents which contain a tricyclic structure and are used primarily in the treatment of affective disorders and related conditions. 2019-01-22T18:41:18Z NCIT:C94727 tricyclic antidepressant drug therapy tricyclic antidepressant drug treatment tricyclic antidepressant agent therapy obsolete antidepressants, other true Treatment with a therapeutic substance used to counteract the toxic action(s) of a specified xenobiotic. 2019-01-22T18:41:49Z CHEBI:50247 antidote drug therapy antidote agent therapy Treatment with a therapeutic substance used to counteract the toxic action(s) of a specified xenobiotic. PMID:9079217 Medication given to prevent or deter a patient from using a substance. 2019-01-22T18:42:02Z abuse deterrent drug treatment abuse deterrent agent therapy An agent used to treat a toxicologic agent. 2019-01-22T18:42:18Z toxicologic drug therapy toxicologic agent therapy Treatment with a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. 2019-01-22T18:44:08Z CHEBI:24261 treatment with a glucocorticoid drug treatment with a glucocorticoid medication treatment with a glucocorticoid therapy glucocorticicoid agent therapy Treatment with a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. CHEBI:24261 Treatment with an anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. 2019-01-22T18:44:26Z CHEBI:35475 non-steroidal anti-inflammatory medication treatment treatment with NSAID drug treatment with NSAID medication treatment with NSAID therapy treatment with non-steroidal anti-inflammatory drug treatment with non-steroidal anti-inflammatory medication NSAID therapy Treatment with medications to alleviate symptoms and occurrence of migraine headaches. 2019-01-22T18:45:01Z anti migraine drug therapy anti-migraine drug therapy anti-migraine medication therapy migraine headache therapy migraine medication treatment migraine treatment standard migraine therapies treatment for migraine treatment of migraine treatment with antimigraine agent antimigraine agent therapy Treatment with medications to alleviate symptoms and occurrence of migraine headaches. Use of medication to treat migraine headache symptoms acutely. 2019-01-22T18:45:12Z abortive anti migraine medication therapy abortive anti-migraine drug therapy abortive migraine headache treatment abortive migraine medication therapy abortive migraine treatment abortive therapy for migraine headache abortive treatment of migraine standard migraine abortive therapies symptomatic treatment of migraine treatment with abortive antimigraine agent abortive antimigraine agent therapy Use of medication to treat migraine headache symptoms acutely. Use of medication to decrease the occurrence of migraine headaches. 2019-01-22T18:45:30Z prophylactic migraine headache treatment prophylactic migraine therapy prophylactic migraine treatment prophylactic treament of migraine headache prophylactic treatment of migraine treatment with prophylactic antimigraine agent prophylactic antimigraine agent therapy Use of medication to decrease the occurrence of migraine headaches. Medication given by mouth or by injection to treat myasthenia gravis. 2019-01-22T18:47:33Z anti-myasthenic drug therapy antimyasthenic drug therapy antimyasthenic medication therapy antimyasthenic agent therapy Treatment with a drug to activate the parasympathetic nervous system (PSNS). They can act as direct agonists of acetylcholine receptors (ACh) or indirect agonists of ACh. While direct agonists act by binding directly to muscarinic or nicotinic ACh receptors, indirect agonists prolong the action of endogenous acetylcholine by inhibiting acetylcholinesterase. 2019-01-22T18:47:49Z cholinomimetic agents therapy cholinomimetic drug therapy cholinomimetic medication therapy parasympathomimetic agent therapy parasympathomimetic drug therapy parasympathomimetic drug treatment parasympathomimetic medication therapy treatment with cholinomimetic agent treatment with cholinomimetic drug treatment with cholinomimetic medication treatment with parasympathomimetic agent treatment with parasympathomimetic drug treatment with parasympathomimetic medication Direct agonists of ACh are used topically in ophthalmology to induce miosis, while indirect agonists are used to treat, e.g., postoperative ileus or urinary retention and myasthenia gravis. parasympathomimetic therapy Use of a treat or prevent infections caused by Mycobacteria, a genus of actinobacteria. 2019-01-22T18:48:12Z CHEBI:64912 antimycobacterial drug treatment antimycobacterials therapy antimycobacterium therapy treatment with an anti-mycobacterial agent treatment with an anti-mycobacterial drug treatment with an anti-mycobacterial medication treatment with an anti-mycobacterial therapy treatment with an antimycobacterial agent treatment with an antimycobacterial drug treatment with an antimycobacterial medication treatment with antimycobacterial drug antimycobacterial agent therapy Use of a substance that kills or slows the growth of Mycobacterium tuberculosis and is used in the treatment of tuberculosis. 2019-01-22T18:49:27Z CHEBI:33231 antitubercular drug therapy antitubercular drug treatment antituberculosis agent therapy treatment with an anti-tubercular agent treatment with an anti-tubercular drug treatment with an anti-tubercular medication treatment with an anti-tubercular therapy treatment with an antitubercular agent treatment with an antitubercular drug treatment with an antitubercular medication treatment with antitubercular agent tuberculostatic agent therapy antitubercular agent therapy Use of a substance that suppresses Mycobacterium leprae, ameliorates the clinical manifestations of leprosy, and/or reduces the incidence and severity of leprous reactions. 2019-01-22T18:49:45Z CHEBI:35816 leprostatic drug treatment treatment with a leprostatic agent treatment with a leprostatic drug treatment with a leprostatic medication treatment with a leprostatic therapy treatment with leprostatic drug leprostatic agent therapy An antineoplastic agent that replaces hydrogen atom(s) in nucleophilic moieties with alky radical(s), hindering proper function. Alkylating agents exhibit cytotoxic effects through the alkylation of DNA, resulting in strand cross-linking, ultimately inhibiting DNA replication and cancer cell growth. 2019-01-22T18:50:33Z CHEBI:22333 NCIT:C1590 NCIT:C223 alkylating drug therapy anti-neoplastic alkylating agent therapy antineoplastic alkylating agent therapy treatment with alkylating agent treatment with alkylating drug treatment with alkylating medication Highly reactive chemical that introduces alkyl radicals into biologically active molecules and thereby prevents their proper functioning. It could be used as an antineoplastic agent, but it might be very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. It could also be used as a component of poison gases. alkylating agent therapy An antineoplastic agent that replaces hydrogen atom(s) in nucleophilic moieties with alky radical(s), hindering proper function. Alkylating agents exhibit cytotoxic effects through the alkylation of DNA, resulting in strand cross-linking, ultimately inhibiting DNA replication and cancer cell growth. NCIT:C1590 Highly reactive chemical that introduces alkyl radicals into biologically active molecules and thereby prevents their proper functioning. It could be used as an antineoplastic agent, but it might be very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. It could also be used as a component of poison gases. CHEBI:22333 Use of an agent or endogenous substance that inhibits the formation of capillaries from existing blood vessels. 2019-01-22T18:50:46Z CHEBI:48422 NCIT:C1742 angiogenesis antagonist therapy angiogenesis blocker therapy anti-angiogenic agent therapy antiangiogenesis agent therapy antiangiogenic agent drug treatment treatment with angiogenesis antagonist agent treatment with angiogenesis antagonist drug treatment with angiogenesis antagonist medication treatment with angiogenesis blocker agent treatment with angiogenesis blocker drug treatment with angiogenesis blocker medication treatment with angiogenesis inhibitor treatment with angiogenesis inhibitor agent treatment with angiogenesis inhibitor drug treatment with angiogenesis inhibitor medication treatment with anti-angiogenic agent treatment with anti-angiogenic drug treatment with anti-angiogenic medication treatment with antiangiogenic agent treatment with antiangiogenic drug treatment with antiangiogenic medication angiostatic agent therapy antiangiogenic agent therapy obsolete antiestrogen agent therapy true Treatment of cancer that utilizes antimetabolite substances to disrupt DNA, RNA, or protein synthesis. 2019-01-22T18:51:33Z NCIT:C15183 anti-metabolite agent drug treatment antimetabolite agent drug treatment antimetabolite cancer drug antimetabolite cancer medication antimetabolites therapy cancer drug antimetabolite treatment with anti-metabolite agent treatment with anti-metabolite drug treatment with anti-metabolite medication treatment with antimetabolite agent treatment with antimetabolite drug treatment with antimetabolite medication antimetabolite agent therapy Treatment of cancer that utilizes antimetabolite substances to disrupt DNA, RNA, or protein synthesis. NCIT:C15183 Treatment with an EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor which interferes with the action of aromatase (EC 1.14.14.14) and so reduces production of estrogenic steroid hormones. 2019-01-22T18:54:45Z CHEBI:50790 aromatase inhibitor drug therapy aromatase inhibitor drug treatment treatment with EC 1.14.14.14 (aromatase) inhibitor treatment with aromatase inhibitor agent treatment with aromatase inhibitor drug treatment with aromatase inhibitor medication treatment with estrogen synthetase inhibitor agent treatment with estrogen synthetase inhibitor drug treatment with estrogen synthetase inhibitor medication treatment with estrogen synthetase inhibitor therapy treatment with oestrogen synthetase inhibitor agent treatment with oestrogen synthetase inhibitor drug treatment with oestrogen synthetase inhibitor medication aromatase inhibitor agent therapy A treatment that uses drugs to target specific genes and proteins that are involved in the growth and survival of cancer cells. 2019-01-22T18:55:15Z antineoplastic molecular target inhibitor drug treatment cancer targeted inhibitor drug treatment cancer targeted inhibitor therapy targeted cancer drug therapy targeted cancer therapy treatment with targeted cancer drug treatment with targeted cancer medication treatment with targeted cancer therapy antineoplastic molecular target inhibitor agent therapy Treatment with a biological agent (monoclonal antibody) that target factors responsible for deregulated cell proliferation as in cancer. 2019-01-22T18:55:45Z NCIT:C15490 antineoplastic monoclonal antibodies therapy antineoplastic monoclonal antibody drug treatment antineoplastic monoclonal antibody agent therapy Use of any of a group of agents that includes retinol (Vitamin A) and related compounds with potential antineoplastic and/or chemopreventive activities. 2019-01-22T18:56:30Z NCIT:C804 retinoic acid agent therapy retinoic acid drug therapy retinoid drug therapy retinoid drug treatment treatment with retinoic acid agent treatment with retinoic acid drug treatment with retinoic acid medication treatment with retinoic acid therapy treatment with retinoid agent treatment with retinoid drug treatment with retinoid medication treatment with retinoid therapy A retinoic acid agent binds to and/or activates specific nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs), thereby modulating transcription of genes responsible for cell differentiation and proliferation. A retinoic acid agent may exhibit immunomodulatory and anti-inflammatory properties and may inhibit ornithine decarboxylase, resulting in a decrease in polyamine synthesis and keratinization. retinoid agent therapy Substance intended to kill parasitic worms (helminths). 2019-01-22T18:57:26Z CHEBI:35443 anthelminitic agent drug therapy anthelmintic drug therapy anthelmintic drug treatment antihelminthics vermifuge therapy vermicide therapy anthelmintic agent therapy Substance intended to kill parasitic worms (helminths). CHEBI:35443 Treatment with an antimicrobial drug which is used to treat or prevent protozoal infections. 2019-01-22T18:57:54Z CHEBI:35820 antiprotozoal drug treatment antiprotozoals therapy treatment with an antiprotozoal agent treatment with an antiprotozoal drug treatment with an antiprotozoal medication treatment with antiprotozoal drug protozoan drug treatment antiprotozoal agent therapy An agent used to as a treament of ectoparasitic infestations. 2019-01-22T18:58:53Z CHEBI:38956 ectoparasiticide therapy ectoparasiticide agent therapy An agent used to as a treament of ectoparasitic infestations. Treatment with an antiviral drug used for treatment of cytomegalovirus infection. 2019-01-22T18:59:18Z Anti-CMV agent therapy anti-CMV medication reatment anti-cmv drug therapy anti-cmv therapy anti-cytomegalovirus drug therapy anti-cytomegalovirus drug treatment anti-cytomegalovirus medication treatment antiviral treatment of cytomegalovirus therapy cytomegalovirus drug treatment therapy anti-cytomegalovirus agent therapy Treatment with an antiviral drug used for treatment of cytomegalovirus infection. PMID:21827432 Treatment with a drug which can have different modes of action but which tend to be less likely than first generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements. 2019-01-22T19:00:47Z CHEBI:65191 atypical antipsychotic agent treatment atypical antipsychotic drug treatment second generation antipsychotic agent therapy second generation antipsychotic drug treatment treatment with atypical antipsychotic treatment with second generation antipsychotic atypical antipsychotic agent therapy Treatment with a drug which can have different modes of action but which tend to be more likely than second generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements; such body movements can become permanent even after treatment has ceased. 2019-01-22T19:01:06Z CHEBI:65190 conventional antipsychotic drug treatment first generation antipsychotic agent treatment first generation antipsychotic drug treatment treatment with conventional antipsychotic treatment with first generation antipsychotic typical antipsychotic agent therapy typical antipsychotic drug treatment typical antipsychotic therapy conventional antipsychotic agent therapy Treatment with an agent that suppresses muscle spasms. 2019-01-22T19:02:05Z CHEBI:53784 anti-spasticity agent therapy antispasmodic agent therapy antispasmodic drug therapy antispastic agent therapy antispastic drug treatment antispasticity agent drug treatment antispasticity drug therapy treatmeant with antispasticity drug treatmeant with antispasticity medication treatment with a antispasmodic drug treatment with a antispasmodic medication treatment with a antispasmodic therapy treatment with antispasticity agent antispasticity agent therapy Use of a drug for the treatment and prophylaxis of infection with hepatitis virus(es). 2019-01-22T20:15:16Z anti-hepatitis agent therapy anti-hepatitis drug therapy anti-hepatitis drug treatment antihepatitis drug therapy antihepatitis drug treatment treatment with anti-hepatitis drug treatment with anti-hepatitis medication treatment with antihepatitis medication antihepatitis agent therapy Use of any drug that counters herpes. 2019-01-22T20:15:33Z anti-herpes agent therapy anti-herpes drug therapy anti-herpes medication therapy antiherpetic agent drug therapy antiherpetic agent drug treatment treatment with anti-herpes agent treatment with anti-herpes drug treatment with antiherpetic agent treatment with antiherpetic drug treatment with antiherpetic medication antiherpetic agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus. 2019-01-22T20:16:07Z CHEBI:64946 NCIT:C1660 anti-HIV drug treatment treatment with anti-HIV agent treatment with anti-HIV drug treatment with anti-human immunodeficiency virus agent treatment with anti-human immunodeficiency virus drug treatment with anti-human immunodeficiency virus medication anti-HIV agent therapy Treatment with a drug which interferes with the binding, fusion and entry of an HIV virion to a human cell. By blocking this step in HIV's replication cycle, such agents slow the progression from HIV infection to AIDS. 2019-01-22T20:18:25Z CHEBI:59886 anti-HIV theraoym fusion inhibitor drug treatment anti-HIV therapy, fusion inhibitor drug treatment with HIV fusion inhibitor treatment with HIV fusion inhibitor agent treatment with HIV fusion inhibitor drug treatment with HIV fusion inhibitor medication treatment with HIV fusion inhibitor therapy anti-HIV therapy, fusion inhibitor Treatment with a substance structurally unlike a nucleoside molecule that is capable of inhibiting the function of a reverse transcriptase. These compounds do not bind to the active site of the polymerase but in a less conserved pocket near the active site, causing a distortion in the shape of the active site and resulting in inhibition of enzymatic function, chain termination, and inhibition of viral replication. 2019-01-22T20:18:58Z NCIT:C97453 anti-HIV non-nucleoside reverse transcriptase inhibitor drug therapy anti-HIV non-nucleoside reverse transcriptase inhibitor drug treatment treatment with anti-HIV therapy, non-nucleoside reverse transcriptase inhibitor agent treatment with anti-HIV therapy, non-nucleoside reverse transcriptase inhibitor drug treatment with anti-HIV therapy, non-nucleoside reverse transcriptase inhibitor medication non-nucleoside reverse transcriptase inhibitor therapy Treatment with nucleoside reverse transcriptase inhibitors (NRTIs) which block reverse transcriptase (an HIV enzyme). 2019-01-22T20:20:58Z NRTI drug therapy anti-HIV nucleoside and nucleotide reverse transcriptase inhibitor drug treatment treatment with NRTI agent treatment with NRTI drug treatment with NRTI medication treatment with nucleoside and nucleotide reverse transcriptase inhibitor medication treatment with nucleoside-nucleotide reverse transcriptase inhibitor drug treatment with nucleoside-nucleotide reverse transcriptase inhibitor medication treatment with nucleoside/nucleotide reverse transcriptase inhibitor drug treatment with nucleoside/nucleotide reverse transcriptase inhibitor medication nucleoside and nucleotide reverse transcriptase inhibitor therapy Use of an inhibitor of HIV protease, an enzyme required for production of proteins needed for viral assembly. 2019-01-22T20:21:25Z CHEBI:35660 NCIT:C97366 HIV protease inhibitor drug therapy HIV protease inhibitor drug treatment treatment with HIV protease inhibitor treatment with HIV protease inhibitor agent treatment with HIV protease inhibitor drug treatment with HIV protease inhibitor medication HIV protease inhibitor therapy Treatment with a drug used for the treatment and prophylaxis of infection with influenza viruses. 2019-01-22T20:21:48Z anti-flu medication therapy anti-influenza drug therapy anti-influenza drug treatment treatment with anti-influenza drug treatment with anti-influenza medication anti-influenza agent therapy obsolete anxiolytics, other true Treatment with an antidepressant that can be used to treat anxiety. 2019-01-22T20:32:25Z antidepressant anxiolytics Treatment with used to treat bipolar disorders or mania associated with other affective disorders. 2019-01-22T20:33:05Z CHEBI:35477 antimanic agent drug treatment antimanic agent treatment therapy bipolar agent drug therapy bipolar agent drug treatment bipolar disorder agent therapy treatment with antimanic agent treatment with antimanic drug treatment with antimanic medication antimanic agent therapy Treatment with any agent that treats or prevents diabetes or diabetes symptoms. 2019-01-22T20:33:31Z anti-diabetic therapy antidiabetic agent drug treatment antidiabetic therapy antidiabetic agent therapy Treatment with any drug or agent taken that maintains ando/or regulates blood glucose levels. 2019-01-22T20:33:43Z glycemic agent drug therapy glycemic regulation agent therapy glycemic regulation drug treatment glycemic regulator agent therapy glycemic agent therapy A synthetic or animal-derived form of insulin used in the treatment of diabetes mellitus. Therapeutic insulin is formulated to be short-, intermediate- and long-acting in order to individualize an insulin regimen according to individual differences in glucose and insulin metabolism. Therapeutic insulin may be derived from porcine, bovine or recombinant sources. Endogenous human insulin, a pancreatic hormone composed of two polypeptide chains, is important for the normal metabolism of carbohydrates, proteins and fats and has anabolic effects on many types of tissues. 2019-01-22T20:33:51Z NCIT:C581 insulin drug treatment insulin therapy therapeutic insulin preparations treatment therapeutic insulin therapy insulin treatment A synthetic or animal-derived form of insulin used in the treatment of diabetes mellitus. Therapeutic insulin is formulated to be short-, intermediate- and long-acting in order to individualize an insulin regimen according to individual differences in glucose and insulin metabolism. Therapeutic insulin may be derived from porcine, bovine or recombinant sources. Endogenous human insulin, a pancreatic hormone composed of two polypeptide chains, is important for the normal metabolism of carbohydrates, proteins and fats and has anabolic effects on many types of tissues. NCIT:C581 Treatment with drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. 2019-01-22T20:34:31Z CHEBI:35470 CNS agent therapy CNS drug therapy treatment with central nervous system drug central nervous system agent therapy CNS agent therapy CNS drug therapy Treatment with a class of central nervous system stimulants based on the structure of the parent amphetamine 1-phenylpropan-2-amine. 2019-01-22T20:35:07Z CHEBI:35338 NCIT:C62006 amphetamine drug intake amphetamine drug therapy amphetamines therapy treatment with amphetamine agent treatment with amphetamine drug treatment with amphetamine medication treatment with amphetamines amphetamine agent therapy Use of non-stimulant (non-amphetamine) medication for treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-01-22T20:35:24Z non-amphetamine ADHD agent therapy non-amphetamine ADHD drug therapy non-stimulant ADHD treatment non-stimulant Attention Deficient Hyperactivity Disorder agent therapy non-stimulant ADHD agent therapy Use of non-stimulant (non-amphetamine) medication for treatment of Attention Deficit Hyperactivity Disorder (ADHD). obsolete non-amphetamines, other true Any agent or drug used to treat oral diseases. 2019-01-22T20:35:53Z dental and oral agent therapy Use of a drug to treat or prevent skin disorders or for the routine care of skin. 2019-01-22T20:36:09Z CHEBI:50177 dermatologic agent therapy dermatologic drug treatment treatment with dermatolic drug treatment with dermatolic medication treatment with dermatolical drug treatment with dermatolical medication treatment with dermatologic drug dermatological agent therapy obsolete enzyme replacements and modifier agent therapy true Use of a drug for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion. 2019-01-22T20:36:38Z CHEBI:55324 gastrointestinal agent treatment gastrointestinal drug treatment gastrointestinal drug treatment therapy treatment with gastrointestinal drug treatment with gastrointestinal medication gastrointestinal agent therapy Treatment to regulate muscle contractions in the gastrointestinal tract. 2019-01-22T20:37:00Z gastrointestinal anti-spasmodic agent therapy gastrointestinal antispasmodic agent therapy gastrointestinal antispasmodic drug treatment gastrointestinal antispasmodic treatment therapy gastrointestinal antispasmodics agent therapy H2-receptor antagonists are the drugs that selectively bind to but do not activate histamine H2 receptors, thereby blocking the actions of endogenous histamine. 2019-01-22T20:37:14Z CHEBI:37961 H2 blocker treatment therapy H2 blocking agent treatment therapy H2 receptor antagonist treatment therapy H2 receptor blockader treatment H2-receptor blocker therapy Histamine2 antagonist therapy histamine H2 receptor antagonist therapy histamine H2 receptor antagonist treatment histamine2 blocking agent therapy H2-receptor antagonist agent therapy H2-receptor antagonists are the drugs that selectively bind to but do not activate histamine H2 receptors, thereby blocking the actions of endogenous histamine. CHEBI:37961 Treatment with any agent that helps treat irritable bowel syndrome. 2019-01-22T20:37:54Z irritable bowel syndrome agent therapy Treatment with medications that coat the ulcerated surfaces of gastrointestinal lining and are used mainly for peptic ulcer disease. 2019-01-22T20:38:16Z gastrointestinal protectant drug treatment gastrointestinal protectant treatment therapy gastroprotectant gastrointestinal protectant agent therapy Any one of the substituted benzimidazole compounds with anti-ulcer activity. A proton pump inhibitor is orally administered in the neutrally charged, inactive form and, upon entering the acidic environment of the parietal cell, gets protonated and converted into its active form. The active form will covalently and irreversibly bind to the proton pump, the H+/K+-ATPase, located on the surface of parietal cells. This leads to an inhibition of the transport of hydrogen ions, in exchange for potassium ions, into the gastric lumen and results in an inhibition of gastric acid secretion. 2019-01-22T20:38:35Z NCIT:C29723 PPI agent therapy PPI drug therapy PPI treatment therapy proton pump inhibitor drug treatment proton pump inhibitor treatment therapy proton pump inhibitor agent therapy Any one of the substituted benzimidazole compounds with anti-ulcer activity. A proton pump inhibitor is orally administered in the neutrally charged, inactive form and, upon entering the acidic environment of the parietal cell, gets protonated and converted into its active form. The active form will covalently and irreversibly bind to the proton pump, the H+/K+-ATPase, located on the surface of parietal cells. This leads to an inhibition of the transport of hydrogen ions, in exchange for potassium ions, into the gastric lumen and results in an inhibition of gastric acid secretion. NCIT:C29723 PPI agent therapy PPI drug therapy PPI treatment therapy obsolete gastrointestinal agents, other true Use of a drug to treat conditions of the reproductive organs and excretory system or urinary tract. 2019-01-22T20:39:18Z treatment with genitourinary agent treatment with genitourinary drug treatment with genitourinary medication genitourinary agent therapy Treatment to inhibit involuntary detrusor muscle contractions. 2019-01-22T20:39:46Z urinary antispasmodic agent therapy Treatment with agent to increase urine flow in patients with an enlarged prostate. 2019-01-22T20:40:09Z benign prostate hypertrophy agent therapy Treatment with agents used to reduce the absorption of dietary phosphate 2019-01-22T20:40:24Z phosphate binders agent therapy obsolete genitourinary agents, other true Treatments that are anti-inflammatory and immunosuppressive. 2019-01-22T20:42:45Z glucocorticoids/ mineralocorticoids therapy Treatment with an agent or medication that regulates hormones released by the pituitary. 2019-01-22T20:44:06Z treatment with pituitary modifier treatment with pituitary modifying agent treatment with pituitary modifying drug treatment with pituitary modifying medication pituitary-modifying, hormonal agent therapy Treatment with an agent regulating protaglandins. 2019-01-22T20:45:21Z treatment with prostaglandin modifier treatment with prostaglandin modifying agent treatment with prostaglandin modifying drug treatment with prostaglandin modifying medication prostaglandin-modifying, hormonal agent therapy Treatment with any agent or medication that modifies androgen, estrogens, and/or progestogens. 2019-01-22T20:46:02Z sex hormone modifying drug treatment gonadal steroid modifying agent therapy gonadocorticoid modifying agent therapy sex hormone modifying agent therapy Use of any agent that can alter hormone levels or modulate hormone effects. 2019-01-22T20:49:54Z NCIT:C147908 hormone modifiers hormone modifying agent hormone modifying drug hormone modifying drugs hormone therapies hormone therapy hormone therapy agents hormone therapy drugs treatment with hormone modifiers hormone modifying therapy Treatment with an agent or medication that regulates hormones released by the thyroid. 2019-01-22T20:51:04Z treatment with thyroid modifier treatment with thyroid modifying agent treatment with thyroid modifying drug treatment with thyroid modifying medication thyroid-modifying hormonal agent therapy Use of a compound which stimulates anabolism and inhibits catabolism. Anabolic agents stimulate the development of muscle mass, strength, and power. 2019-01-22T20:51:34Z CHEBI:36413 anabolic agent therapy anabolic steroid modifying drug treatment treatment with anabolic steroid anabolic steroid modifying agent therapy Treatment with an agent to modify androgen action. 2019-01-22T20:51:44Z treatment with androgen agent treatment with androgen drug treatment with androgen medication treatment with androgen modifying agent treatment with androgen modifying drug androgen modifying agent therapy A drug which acts to modulates estrogenic activity in the body, either by modulating the amount of estrogen or by modulating the activity of whatever estrogen is present. 2019-01-22T20:52:07Z CHEBI:50739 estrogen modifying drug therapy estrogen modifying medication therapy oestrogen modifying agent therapy oestrogen modifying drug therapy treatment with estrogen receptor modulator treatment with estrogent modifying medication treatment with oestrogen modifying medication estrogen modifying agent therapy Treatment with an agent to modify progestin action. 2019-01-22T20:52:15Z progestin modifying drug treatment treatment with progestin modifier treatment with progestin modifying agent treatment with progestin modifying drug treatment with progestin modifying medication progestin modifying agent therapy Treatment with an agent to that selectively modifies estrogen receptor action. 2019-01-22T20:52:46Z selective-estrogen receptor modifying agent therapy Use of a drug to treat hyperparathyroidism by reducing the excessive production of parathyroid hormones. 2019-01-22T20:53:28Z CHEBI:50827 antiparathyroid agent therapy treatment with antiparathyroid drug treatment with antiparathyroid medication treatment with parathyroid-suppressant agent treatment with parathyroid-suppressant drug treatment with parathyroid-suppressant medication parathyroid-suppressant hormone therapy Use of a compound which increases or activates the biosynthesis or actions of androgens. 2019-01-22T20:54:46Z treatment with androgen agonist treatment with androgen stimulant androgen stimulant agent therapy Use of a compound which inhibits or antagonizes the biosynthesis or actions of androgens. 2019-01-22T20:55:10Z CHEBI:35497 treatment with androgen antagonist treatment with androgen blocker treatment with androgen suppressant agent androgen suppressant hormone agent therapy Treatment with an agent or medication that stimulates hormones released by the thyroid. 2019-01-22T20:59:15Z treatment with thyroid agonist treatment with thyroid stimulating agent treatment with thyroid stimulating drug treatment with thyroid stimulating medication treatment with thyroid-stimulating agent thyroid-stimulating hormonal agent therapy Use of a drug to treat hyperthyroidism by reducing the excessive production of thyroid hormones. 2019-01-22T20:59:33Z CHEBI:50671 anti-thyroid drug treatment treatment with anti-thyroid agent treatment with antithyroid agent treatment with antithyroid drug treatment with antithyroid medication antithyroid agent therapy Use of a drug that induces, enhances, restores or suppresses the host's immune system, or an agent that utilizes or is derived from a component of the immune system. 2019-01-22T21:00:01Z CHEBI:50846 NCIT:C308 immune factor therapy immune mediator treatment therapy immune modulator therapy immune regulator therapy immunological agent treatment therapy immunomodulating agent treatment therapy immunomodulator treatment therapy immunomodulatory agent treatment therapy immunotherapeutic agent treatment therapy immunotherapy agent immunotherapy treatment treatment with immunological agent treatment with immunological drug treatment with immunological medication treatment with immunomodifying agent treatment with immunomodifying drug treatment with immunomodifying medication treatment with immunomodulator immunological agent therapy Use of a substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. 2019-01-22T21:00:13Z CHEBI:50847 immunoactivator treatment therapy immunoadjuvant treatment therapy immunologic adjuvant treatment therapy immunological adjuvant treatment therapy immunopotentiator treatment therapy immunostimulant treatment therapy treatment with immune stimulant treatment with immunoactivator treatment with immunoadjuvant treatment with immunological adjuvant A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. immune stimulant agent therapy A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. CHEBI:50847 Use of an agent that suppresses immune function by one of several mechanisms of action. 2019-01-22T21:00:25Z CHEBI:35705 NCIT:C574 immune suppressant agent treatment immunosuppressant agent therapy immunosuppressant treatment therapy immunosuppressive agent treatment therapy immunosuppressor agent therapy treatment immunosuppressant treatment with immune suppressant treatment with immunosuppressive treatment with immunosuppressive agent Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. immune suppressant agent therapy Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. CHEBI:35705 Treatment with antibodies to a disease to provide a temporary immunity. 2019-01-22T21:00:40Z passive immunizing agent therapy The drug treatment of inflammatory bowel disease (IBD), which may include the use of anti-inflammatory agents and agents that reduce the symptoms associated with IBD. 2019-01-22T21:01:33Z PMID:21857074 anti-IBD drug treatment therapy anti-inflammatory bowel disease drug treatment anti-inflammatory bowel disease therapy inflammatory bowel disease agent therapy The drug treatment of inflammatory bowel disease (IBD), which may include the use of anti-inflammatory agents and agents that reduce the symptoms associated with IBD. PMID:21857074 The salts or esters of salicylic acids, or salicylate esters of an organic acid. Some of these have analgesic, antipyretic, and anti-inflammatory activities by inhibiting prostaglandin synthesis. 2019-01-22T21:02:35Z CHEBI:30762 salicylate agent therapy The salts or esters of salicylic acids, or salicylate esters of an organic acid. Some of these have analgesic, antipyretic, and anti-inflammatory activities by inhibiting prostaglandin synthesis. Treatment with drug or agent to treat or prevent deformities or abnormalities of the bone caused by a metabolic disorder. 2019-01-22T21:04:21Z metabolic bone disease drug treatment metabolic bone disease agent therapy Use of a drug to treat eye conditions or eye diseases. 2019-01-22T21:04:40Z CHEBI:66981 ophthalmic drug treatment ophthalmics drug treatment ophthalmologicals therapy ophthalmology agent therapy ophthalmology agent treatment therapy treatment with ophthalmic agent treatment with ophthalmic drug treatment with ophthalmic medication treatment with ophthalmology drug ophthalmic agent therapy Treatment with medication delivered directly to the eye to treat allergies or allergy symptoms. 2019-01-22T21:04:55Z ophthalmic anti-allergy agent therapy Use of a drug which can be used to prevent or alleviate glaucoma, a disease in which the optic nerve is damaged, resulting in progressive, irreversible loss of vision. 2019-01-22T21:05:20Z CHEBI:39456 ophthalmic antiglaucoma agent therapy treatment with anti-glaucoma agent treatment with anti-glaucoma medication treatment with antiglaucoma agent treatment with antiglaucoma drug treatment with antiglaucoma medication antiglaucoma agent therapy Treatment with an agent or medication formulated to be applied in the eyes, to reduce pain or to treat inflammation, especially used after eye surgery to relieve pain. 2019-01-22T21:05:47Z ophthalmic anti-inflammatory agent therapy Treatment with an agent applied directly to the eye to treat elevated intraocular pressure (IOP) via regulating prostaglandin and prostamide. 2019-01-22T21:06:19Z ophthalmic prostaglandin and prostamide agent therapy obsolete ophthalmic agents, other true Treatment with a substance intended for administration either on the outer ear or into the auditory canal. 2019-01-22T21:08:34Z NCIT:C69040 NCIT:C69040 treatment with otic medication otic agent therapy An agent that exerts a physiologic effect on any anatomic entity that is part of the respiratory tract and airways. 2019-01-22T21:08:56Z NCIT:C78273 agent affecting respiratory system treatment respiratory tract agent treatment respiratory tract drug treatment therapy treatment with respiratory tract agent treatment with respiratory tract medication respiratory tract agent therapy An agent that exerts a physiologic effect on any anatomic entity that is part of the respiratory tract and airways. NCIT:C78273 Use of drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. 2019-01-22T21:09:06Z CHEBI:37956 antihistamine drug treatment antihistimine drug therapy histamine receptor blocker drug treatment histamine receptor blocker therapy treatment with antihistamine treatment with histamine antagonist treatment with histamine blocker antihistamine agent therapy Treatment with an inhaled agent that reduces inflammation and mucus in the airways that carry air to the lungs. 2019-01-22T21:09:38Z inhaled corticosteroid drug treatment inhaled corticosteroid agent therapy Use of a drug designed to prevent leukotriene synthesis or activity by blocking binding at the receptor level. 2019-01-22T21:09:53Z CHEBI:49159 antileukotriene drug treatment treatment with antileukotriene agent treatment with antileukotriene medication treatment with leukotriene antagonist treatment with leukotriene blocker antileukotriene agent therapy Use of an agent that causes an increase in the expansion of a bronchus or bronchial tubes. 2019-01-22T21:10:11Z CHEBI:35523 NCIT:C319 bronchodilator agent treatment bronchodilator drug treatment broncholytic agent therapy treatment with bronchodilator treatment with bronchodilator agent bronchodilator therapy Treatment with an agent that blocks the effect of acetylcholine in airways and nasal passages to keep the airways from constricting during asthma and allergy-related brathing issues. 2019-01-22T21:10:37Z anticholinergic bronchodilator drug treatment anticholinergic bronchodilator agent therapy Treatment with a phosphodiesterase (PDE) inhibitor that decreases mean pulmonary arterial pressure. 2019-01-22T21:11:08Z phosphodiesterase inhibitor bronchodilator drug treatment phosphodiesterase inhibitor bronchodilator agent therapy Treatment with an agent for reversible airway obstruction in diseases such as asthma and COPD. These agents produce bronchodilation by stimulating beta2 adrenergic receptors on airway smooth muscle. 2019-01-22T21:11:37Z adrenergic bronchiodilator agent therapy adrenergic bronchiodilator agent treatment adrenergic bronchiodilator drug therapy sympathomimetic bronchodilator drug therapy treatment with adrenergic bronchiodilator agent sympathomimetic bronchodilator agent therapy Treatment with an agent that block mast cell degranulation, stabilizing the cell and thereby preventing the release of histamine and other factors thereby preventing or regulating allergic disorders. 2019-01-22T21:12:02Z NCIT:C29714 mast cell stabiliser agent therapy mast cell stabiliser drug treatment mast cell stabilizer drug treatment mast cell stabilizer agent therapy Treatment with an agent that decreases pulmonary hypertension. 2019-01-22T21:12:15Z pulmonary antihypertensive drug treatment pulmonary antihypertensive agent therapy obsolete respiratory tract agents, other true Treatment with a central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. 2019-01-22T21:14:36Z CHEBI:35717 NCIT:C29756 hypnotic agent therapy hypnotic drug therapy hypnotics agent therapy sedative agent drug therapy sedative agent drug treatment sedative and hypnotic drug treatment sedative drug therapy sedative drug treatment sedative treatment therapy sedative-hypnotic drug treatment sedatives and hypnotic drug therapy sedatives/hypnotic drug treatment treatment with sedative sedatives and hypnotic agent therapy Treatment with a central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. CHEBI:35717 Use of a drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. 2019-01-22T21:14:48Z CHEBI:51371 NCIT:C29696 muscle relaxant agent therapy skeletal muscle relaxant drug treatment treatment with muscle relaxant skeletal muscle relaxant agent therapy Use of a substance for the prophylaxis or therapy of infectious diseases. 2019-04-10T19:56:29Z CHEBI:35441 anti-infective drug therapy treatment with anti-infective agent treatment with anti-infective drug treatment with anti-infective medication treatment with antiinfective agent treatment with antiinfective drug treatment with antiinfective medication anti-infective agent therapy Removal and examination of tissue, cells, or fluids from head for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z head biopsy biopsy of head Removal and examination of tissue, cells, or fluids from abdomen for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z abdomen biopsy biopsy of abdomen Removal and examination of tissue, cells, or fluids from adipose for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z adipose tissue biopsy biopsy of adipose tissue Removal and examination of tissue, cells, or fluids from adrenal cortex for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z adrenal cortex biopsy biopsy of adrenal cortex Removal and examination of tissue, cells, or fluids from adrenal gland for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z adrenal gland biopsy biopsy of adrenal gland Removal and examination of tissue, cells, or fluids from anal canal for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z anal canal biopsy biopsy of anal canal Removal and examination of tissue, cells, or fluids from anus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z NCIT:C51586 anus biopsy anal biopsy Removal and examination of tissue, cells, or fluids from aorta for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z aorta biopsy biopsy of aorta Removal and examination of tissue, cells, or fluids from the uterus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z body of uterus biopsy uterine biopsy Removal and examination of tissue, cells, or fluids from the calcified bone for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z biopsy of the bone bone element biopsy calcified bone biopsy Removal and examination of tissue, cells, or fluids from bone marrow for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z bone marrow biopsy biopsy of bone marrow Removal and examination of tissue, cells, or fluids from bone tissue for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z bone tissue biopsy biopsy of bone tissue Removal and examination of tissue, cells, or fluids from brain for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z brain biopsy biopsy of brain Removal and examination of tissue, cells, or fluids from brainstem for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z brainstem biopsy biopsy of brainstem Removal and examination of tissue, cells, or fluids from breast for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z breast biopsy biopsy of breast Removal and examination of tissue, cells, or fluids from bronchus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z bronchus biopsy bronchial biopsy Removal and examination of tissue, cells, or fluids from caecum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z caecum biopsy biopsy of caecum Removal and examination of tissue, cells, or fluids from cardiac ventricle for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z cardiac ventricle biopsy biopsy of cardiac ventricle Removal and examination of tissue, cells, or fluids from cerebellum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z cerebellum biopsy biopsy of cerebellum Removal and examination of tissue, cells, or fluids from cerebral cortex for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z cerebral cortex biopsy biopsy of cerebral cortex Removal and examination of tissue, cells, or fluids from chest wall for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z chest wall biopsy biopsy of chest wall Removal and examination of tissue, cells, or fluids from chordate pharynx for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z chordate pharynx biopsy biopsy of chordate pharynx Removal and examination of tissue, cells, or fluids from choroid plexus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z choroid plexus biopsy biopsy of choroid plexus Removal and examination of tissue, cells, or fluids from cochlea for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z cochlea biopsy biopsy of cochlea Removal and examination of tissue, cells, or fluids from colon for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z colon biopsy biopsy of colon Removal and examination of tissue, cells, or fluids from colorectum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z colorectum biopsy biopsy of colorectum Removal and examination of tissue, cells, or fluids from dermis for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z dermis biopsy biopsy of dermis Removal and examination of tissue, cells, or fluids from diaphragm for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z diaphragm biopsy biopsy of diaphragm Removal and examination of tissue, cells, or fluids from the thalamus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z dorsal plus ventral thalamus biopsy biopsy of thalamus Removal and examination of tissue, cells, or fluids from duodenum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z duodenum biopsy biopsy of duodenum Removal and examination of tissue, cells, or fluids from endocardium for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z endocardium biopsy biopsy of endocardium Removal and examination of tissue, cells, or fluids from endocrine pancreas for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z endocrine pancreas biopsy biopsy of endocrine pancreas Removal and examination of tissue, cells, or fluids from endometrium for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z endometrium biopsy biopsy of endometrium Removal and examination of tissue, cells, or fluids from esophagus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z esophagus biopsy biopsy of esophagus Removal and examination of tissue, cells, or fluids from eye for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z eye biopsy biopsy of eye Removal and examination of tissue, cells, or fluids from fallopian tube for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z fallopian tube biopsy biopsy of fallopian tube Removal and examination of tissue, cells, or fluids from frontal lobe for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z frontal lobe biopsy biopsy of frontal lobe Removal and examination of tissue, cells, or fluids from gallbladder for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z gallbladder biopsy biopsy of gallbladder Removal and examination of tissue, cells, or fluids from genitourinary system for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z genitourinary system biopsy biopsy of genitourinary system Removal and examination of tissue, cells, or fluids from gonad for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z gonad biopsy biopsy of gonad Removal and examination of tissue, cells, or fluids from heart for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z heart biopsy biopsy of heart Removal and examination of tissue, cells, or fluids from hypopharynx for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z hypopharynx biopsy biopsy of hypopharynx Removal and examination of tissue, cells, or fluids from hypothalamus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z hypothalamus biopsy biopsy of hypothalamus Removal and examination of tissue, cells, or fluids from intestine for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z intestine biopsy biopsy of intestine Removal and examination of tissue, cells, or fluids from the jaw bone for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z jaw skeleton biopsy biopsy of jaw bone Removal and examination of tissue, cells, or fluids from lacrimal apparatus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lacrimal apparatus biopsy biopsy of lacrimal apparatus Removal and examination of tissue, cells, or fluids from large intestine for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z large intestine biopsy biopsy of large intestine Removal and examination of tissue, cells, or fluids from larynx for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z larynx biopsy biopsy of larynx Removal and examination of tissue, cells, or fluids from limb for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z limb biopsy biopsy of limb Removal and examination of tissue, cells, or fluids from lip for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lip biopsy biopsy of lip Removal and examination of tissue, cells, or fluids from liver for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z liver biopsy biopsy of liver Removal and examination of tissue, cells, or fluids from lower respiratory tract for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lower respiratory tract biopsy biopsy of lower respiratory tract Removal and examination of tissue, cells, or fluids from lower urinary tract for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lower urinary tract biopsy biopsy of lower urinary tract Removal and examination of tissue, cells, or fluids from the lumbar spine for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lumbar region of vertebral column biopsy lumbar spine biopsy biopsy of lumbar spine Removal and examination of tissue, cells, or fluids from lung for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lung biopsy biopsy of lung Removal and examination of tissue, cells, or fluids from lymph node for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lymph node biopsy biopsy of lymph node Removal and examination of tissue, cells, or fluids from the lymphatic system for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z lymphatic part of lymphoid system biopsy biopsy of lymphatic system Removal and examination of tissue, cells, or fluids from the vulva for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z mammalian vulva biopsy vulva biopsy vulval biopsy biopsy of vulva Removal and examination of tissue, cells, or fluids from medulla oblongata for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z medulla oblongata biopsy biopsy of medulla oblongata Removal and examination of tissue, cells, or fluids from mouth for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z biopsy of oral cavity mouth biopsy biopsy of mouth obsolete biopsy of muscle true Removal and examination of tissue, cells, or fluids from muscle tissue for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z muscle biopsy muscle tissue biopsy biopsy of muscle tissue Removal and examination of tissue, cells, or fluids from nasolacrimal duct for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z nasolacrimal duct biopsy biopsy of nasolacrimal duct Removal and examination of tissue, cells, or fluids from nasopharynx for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z nasopharynx biopsy biopsy of nasopharynx Removal and examination of tissue, cells, or fluids from neck for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z neck biopsy biopsy of neck Removal and examination of tissue, cells, or fluids from ovary for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z ovary biopsy biopsy of ovary Removal and examination of tissue, cells, or fluids from pancreas for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z pancreas biopsy biopsy of pancreas Removal and examination of tissue, cells, or fluids from penis for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z penis biopsy biopsy of penis Removal and examination of tissue, cells, or fluids from perianal skin for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z perianal skin biopsy biopsy of perianal skin Removal and examination of tissue, cells, or fluids from peritoneum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z peritoneum biopsy biopsy of peritoneum Removal and examination of tissue, cells, or fluids from pituitary gland for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z pituitary gland biopsy biopsy of pituitary gland Removal and examination of tissue, cells, or fluids from pleura for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z pleura biopsy biopsy of pleura Removal and examination of tissue, cells, or fluids from rectum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z rectum biopsy biopsy of rectum Removal and examination of tissue, cells, or fluids from retina for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z retina biopsy biopsy of retina Removal and examination of tissue, cells, or fluids from the salivary gland for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z saliva-secreting gland biopsy salivary gland biopsy biopsy of salivary gland Removal and examination of tissue, cells, or fluids from scrotum for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z scrotum biopsy biopsy of scrotum Removal and examination of tissue, cells, or fluids from sebaceous gland for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z sebaceous gland biopsy biopsy of sebaceous gland Removal and examination of tissue, cells, or fluids from small intestine for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z small intestine biopsy biopsy of small intestine Removal and examination of tissue, cells, or fluids from spinal cord for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z spinal cord biopsy biopsy of spinal cord Removal and examination of tissue, cells, or fluids from spleen for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z spleen biopsy biopsy of spleen Removal and examination of tissue, cells, or fluids from stomach for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z stomach biopsy biopsy of stomach Removal and examination of tissue, cells, or fluids from subglottis for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z subglottis biopsy biopsy of subglottis Removal and examination of tissue, cells, or fluids from submandibular gland for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z submandibular gland biopsy biopsy of submandibular gland Removal and examination of tissue, cells, or fluids from testis for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z testis biopsy biopsy of testis Removal and examination of tissue, cells, or fluids from thymus for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z thymus biopsy biopsy of thymus Removal and examination of tissue, cells, or fluids from thyroid gland for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z thyroid gland biopsy biopsy of thyroid gland Removal and examination of tissue, cells, or fluids from tongue for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z tongue biopsy biopsy of tongue Removal and examination of tissue, cells, or fluids from tonsil for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z tonsil biopsy biopsy of tonsil Removal and examination of tissue, cells, or fluids from trachea for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z trachea biopsy biopsy of trachea Removal and examination of tissue, cells, or fluids from upper digestive tract for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z upper digestive tract biopsy biopsy of upper digestive tract Removal and examination of tissue, cells, or fluids from upper respiratory tract for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z upper respiratory tract biopsy biopsy of upper respiratory tract Removal and examination of tissue, cells, or fluids from ureter for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z ureter biopsy biopsy of ureter Removal and examination of tissue, cells, or fluids from urethra for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z urethra biopsy biopsy of urethra Removal and examination of tissue, cells, or fluids from the bladder for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z urinary bladder biopsy biopsy of bladder Removal and examination of tissue, cells, or fluids from uterine cervix for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z uterine cervix biopsy biopsy of cervix Removal and examination of tissue, cells, or fluids from vagina for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z vagina biopsy biopsy of vagina Removal and examination of tissue, cells, or fluids from the appendix for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z vermiform appendix biopsy biopsy of appendix Removal and examination of tissue, cells, or fluids from the skin for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z skin biopsy zone of skin biopsy biopsy of skin Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. 2019-04-26T17:25:14Z NCIT:C16809 MRI scan for therapeutics NMRI clinical magnetic resonance imaging procedure medical magnetic resonance imaging procedure nuclear magnetic resonance imaging for medical therapy therapeutic MRI magnetic resonance imaging procedure Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. NCIT:C16809 MRI scan for therapeutics NMRI therapeutic MRI A medical examination performed using of magnetic resonance imaging to image the head. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z Nuclear magnetic resonance imaging of the head head MRI head magnetic resonance imaging MRI of the head A medical examination performed using of magnetic resonance imaging to image the abdomen. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z Nuclear magnetic resonance imaging of the abdomen abdomen MRI abdomen magnetic resonance imaging abdominal MRI MRI of the abdomen A medical examination performed using of magnetic resonance imaging to image the brain. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z Nuclear magnetic resonance imaging of the brain brain MRI brain magnetic resonance imaging MRI of the brain A medical examination performed using of magnetic resonance imaging to image the chest. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z Nuclear magnetic resonance imaging of the chest chest MRI chest magnetic resonance imaging MRI of the chest Radiation therapy in which high-energy beams are delivered to a body part and/or tumor from outside of the body. 2019-04-26T19:28:21Z EBRT external beam RT external beam radiotherapeutics external beam radiotherapy external-beam radiation External radiation therapy external beam radiation therapy EBRT external beam RT A type of radiation therapy in which radioactive material is placed inside the body, into a tumor or body cavity. 2019-04-26T19:28:57Z NCIT:C15195 Brachytherapy Internal radiation brachytherapy internal radiation radiation brachytherapy internal radiation therapy A type of radiation therapy in which radioactive material is placed inside the body, into a tumor or body cavity. NCIT:C15195 A medical examination performed using of magnetic resonance imaging to image the breast. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z Nuclear magnetic resonance imaging of the breast breast MRI breast magnetic resonance imaging MRI of the breast Use of an organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. 2019-08-29T18:00:40Z beta-lactams therapy CHEBI:27933 beta-lactam antibacterial drug therapy beta-lactam antibacterial drug treatment beta-lactam antibiotic agent therapy treatment with a beta-lactam antibacterial drug treatment with a beta-lactam antibacterial medication treatment with a beta-lactam antibacterial therapy treatment with a beta-lactam antibiotic agent treatment with a beta-lactam antibiotic drug treatment with a beta-lactam antibiotic medication treatment with a beta-lactam antibiotic therapy beta-lactam antibacterial agent therapy Treatment with a pharmaceutical agent that inhibits the movement of calcium across through calcium channels in the cell membrane, preventing or decreasing the amount of calcium able to enter the cell. These drugs are used for their chronotropic, antihypertensive and vasodilatory effects. 2019-09-27T19:41:29Z CHEBI:38215 NCIT:C333 Ca2+ channel antagonist therapy Ca2+ channel blocker therapy calcium channel antagonist drug therapy calcium channel antagonist therapy calcium channel blocker drug therapy treatment with calcium channel blocker treatment with calcium channel blocker drug treatment with calcium channel blocker medication treatment with calcium channel blocking drug treatment with calcium channel blocking medication One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. calcium channel blocking agent therapy Ca2+ channel antagonist therapy Ca2+ channel blocker therapy One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. CHEBI:38215 Treatment with a drug that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. 2019-10-01T19:23:17Z CHEBI:60643 N-methyl-D-aspartate receptor antagonist therapy NMDA receptor antagonist drug treatment NMDA receptor antagonist treatment NMDA receptor blocker therapy treatment with NMDA blockade drug treatment with NMDA blockade medication treatment with NMDA blockade therapy treatment with NMDA blockers treatment with NMDA receptor antagonist They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. NMDA receptor antagonist therapy They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. CHEBI:60643 Use of medication for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-10-02T15:59:55Z ADHD drug therapy ADHD drug treatment Attention Deficit Hyperactivity Disorder drug therapy Attention Deficit Hyperactivity Disorder drug treatment drug therapy for ADHD ADHD agent therapy Use of medication for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). Use of stimulant medication (usually amphetamines) for treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-10-02T16:01:46Z stimulant ADHD drug treatment stimulant Attention Deficit Hyperactivity Disorder agent therapy stimulant Attention Deficit Hyperactivity Disorder drug treatment stimulant drug therapy for ADHD stimulant drug treatment for ADHD stimulant ADHD agent therapy Use of stimulant medication (usually amphetamines) for treatment of Attention Deficit Hyperactivity Disorder (ADHD). Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. 2019-10-02T18:41:07Z CHEBI:50949 NCIT:C94725 SSRI drug therapy SSRI drug treatment selective serotonin reuptake inhibitor drug therapy selective serotonin reuptake inhibitor drug treatment treatment with SSRI treatment with SSRI agent treatment with selective serotonin reuptake inhibitor agent treatment with selective serotonin reuptake inhibitor drug treatment with selective serotonin reuptake inhibitor medication treatment with serotonin uptake inhibitor Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. selective serotonin reuptake inhibitor therapy Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. NCIT:C94725 Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. NCIT:C94725 Glycoprotein growth factors produced by monocytes, macrophages, or activated lymphocytes that stimulate the proliferation of bone marrow cells and differentiation of stem cells into colonies of granulocytes, monocytes, or macrophages. These substances act in either paracrine or autocrine fashion on marrow cells, appear to act synergistically in complex and poorly understood ways. Each appears to exert actions on several lines of progenitor cells and to influence end cell function. Treatment with colony-stimulating factors (CSF) can help the blood-forming tissue recover from the effects of chemotherapy and radiation therapy. These factors include interleukin-3 (IL-3), granulocyte colony-stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). 2019-10-08T17:41:54Z NCIT:C387 CSF agent therapy recombinant colony stimulating factor drug therapy recombinant colony-stimulating factor treatment recombinant hematopoietic colony-stimulating factor drug treatment colony stimulating factor agent therapy Glycoprotein growth factors produced by monocytes, macrophages, or activated lymphocytes that stimulate the proliferation of bone marrow cells and differentiation of stem cells into colonies of granulocytes, monocytes, or macrophages. These substances act in either paracrine or autocrine fashion on marrow cells, appear to act synergistically in complex and poorly understood ways. Each appears to exert actions on several lines of progenitor cells and to influence end cell function. Treatment with colony-stimulating factors (CSF) can help the blood-forming tissue recover from the effects of chemotherapy and radiation therapy. These factors include interleukin-3 (IL-3), granulocyte colony-stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). NCIT:C387 CSF agent therapy Treatment with an agent that stimulate the proliferation of bone marrow cells and differentiation of stem cells into colonies of granulocytes. 2019-10-08T18:06:31Z NCIT:C1287 G-CSF treatment granulocyte-colony stimulating factor treatment therapy recombinant colony-stimulating factor 3 treatment therapy recombinant granulocyte colony stimulating factor agent therapy recombinant granulocyte colony-stimulating factor drug treatment rhG-CSF therapy granulocyte colony stimulating factor agent therapy G-CSF treatment rhG-CSF therapy Treatment with agents or medications which modulate the bone marrow's production of red blood cells. 2019-10-08T18:37:29Z erythropoietin modulating treatment erythropoietin regulating agent therapy Use of a recombinant therapeutic agent which is chemically identical to or similar to the endogenous glycoprotein erythropoietin (Epo). Epo promotes the differentiation and maturation of hematopoietic progenitors into erythrocytes; is a mitogen and a chemoattractant for endothelial cells; stimulates activated and differentiated B-cells and enhances B-cell immunoglobulin production and proliferation; and is hypoxia-inducible. 2019-10-08T18:38:34Z erythrocyte colony stimulating factor agent therapy erythropoietin therapy CHEBI:81579 NCIT:C477 ESA therapy hematopoietin treatment therapy recombinant EPO treatment recombinant erythropoietin drug therapy recombinant erythropoietin treatment treatment with erythropoietin stimulating agent treatment with erythropoietin stimulating medication erythropoietin stimulating agent therapy ESA therapy recombinant EPO treatment Use of a drug that inhibits erythropoietin, a glycoprotein hormone that controls erythropoiesis (red blood cell production). 2019-10-08T18:49:31Z CHEBI:91025 EPO inhibitor agent therapy EPO inhibitor drug treatment erythropoietin inhibitor drug treatment treatment with erythropoietin inhibitor erythropoietin inhibitor therapy EPO inhibitor agent therapy EPO inhibitor drug treatment A drug that prevents fibrinolysis or lysis of a blood clot or thrombus. 2019-10-08T19:21:34Z CHEBI:48675 antifibrinolytic drug treatment antifibrinolytic agent therapy A drug that prevents fibrinolysis or lysis of a blood clot or thrombus. CHEBI:48675 A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function. 2019-10-08T19:26:15Z CHEBI:4450 NCIT:C61701 1-(3-mercaptopropionic acid)-8-D-arginine-vasopressin, 1-deamino-8-D-arginine vasopressin drug treatment 1-deamino-8-D-arginine vasopressin agent therapy 1-desamino-8-D-arginine vasopressin agent therapy DDAVP agent therapy desmopresina agent therapy desmopressin drug treatment desmopressine agent therapy desmopressinum agent therapy desmopressin agent therapy A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function. CHEBI:4450 The surgical removal (cutting out) of part or all of a structure or organ. 2019-12-27T17:21:50Z excision NCIT:C15232 abscission surgical removal surgical excision Surgical removal (cutting out or off) without replacement of all of a body part or structure. 2019-12-27T17:45:26Z resection surgical resection Taking or cutting out solid matter from a body part. The solid matter contained in the definition may be an abnormal byproduct of a biological function or a foreign body. It may be embedded in a body part, or in the lumen of a tubular body part. The solid matter may or may not have been previously broken into pieces. 2020-01-02T19:00:34Z extirpation surgical extirpation Taking or cutting out solid matter from a body part. The solid matter contained in the definition may be an abnormal byproduct of a biological function or a foreign body. It may be embedded in a body part, or in the lumen of a tubular body part. The solid matter may or may not have been previously broken into pieces. ICD-10-PCS obsolete surgical enucleation true A surgical procedure that places something in the human body. 2020-01-06T18:21:08Z NCIT:C51982 implantation A surgical procedure that places something in the human body. NCIT:C51982 The removal of material from the surface of an object by vaporization, chipping, or other erosive process. 2020-01-06T19:26:24Z NCIT:C20985 ablation therapy The removal of material from the surface of an object by vaporization, chipping, or other erosive process. Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation. 2020-01-06T19:30:40Z NCIT:C111241 photoablation therapy laser ablation therapy Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation. NCIT:C111241 Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by chemical means. 2020-01-06T19:35:01Z NCIT:C111157 chemical ablation Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by chemical means. NCIT:C111157 The use of extreme cold to damage or destroy a body part, pathway, or function. The procedure is performed using small cryogenic probes during surgery, and has recently been applied to solitary sporadic renal tumor lesions. 2020-01-06T19:45:30Z NCIT:C15215 cryoablation therapy cryosurgical ablation therapy cryosurgery The use of extreme cold to damage or destroy a body part, pathway, or function. The procedure is performed using small cryogenic probes during surgery, and has recently been applied to solitary sporadic renal tumor lesions. NCIT:C15215 Thermal ablation refers to the destruction of tissue by extreme hyperthermia or hypothermia. 2020-01-06T19:50:11Z NCIT:C15670 thermal ablation therapy Thermal ablation refers to the destruction of tissue by extreme hyperthermia or hypothermia. NCIT:C15670 The management of pain by interventional procedures, pharmacotherapy, physical therapy, psychological counseling, or complementary and alternative medical therapies designed to treat or alleviate pain. 2020-01-08T17:26:31Z pain therapy pain management Hydrotherapy is the external or internal use of water in any of its forms (water, ice, steam) for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. 2020-01-08T17:32:42Z OMIT:0008013 PMID:24926444 hydropathy hydrotherapy treatment water therapy water cure hydrotherapy Hydrotherapy is the external or internal use of water in any of its forms (water, ice, steam) for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. PMID:24926444 Thermal hydrotherapy uses external or internal use of water in any of its forms (water, ice, steam) at temperatures above or below room temperature for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. 2020-01-08T17:39:29Z hydro-thermal therapy hydrothermal therapy thermal water therapy bathing in thermal waters thermal hydrotherapy Washing out a hollow organ (especially the stomach) by flushing with a fluid. 2020-01-08T17:42:19Z NCIT:C38068 OMIT:0008013 lavage therapeutic irrigation Washing out a hollow organ (especially the stomach) by flushing with a fluid. NCIT:C38068 Therapy where a substantial part of the body is immersed in warm water to produce a variety of therapeutic effects. 2020-01-08T18:05:56Z hot bath therapy warm water bath therapy hyperthermic immersion therapy warm water shower therapy warm water immersion therapy Therapy where a substantial part of the body is immersed in warm water to produce a variety of therapeutic effects. PMID:24926444 Therapy where a substantial part of the body is immersed in cold water to produce a variety of therapeutic effects. 2020-01-08T18:06:06Z CWI therapy ice bath therapy cold water immersion therapy CWI therapy A form of treatment where a limb or significant portion of the body is immersed in hot water immediately followed by the immersion into cold water. This procedure is repeated several times. 2020-01-08T18:06:31Z contrast water therapy Therapy occuring in a pool or bath which is a low-impact activity and takes the pressure off your bones, joints, and muscles. 2020-01-08T18:07:42Z aquatic exercise therapy A minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. 2020-01-08T19:03:16Z NCIT:C51969 breast duct lavage A minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. NCIT:C51969 Washing out the bronchi and alveoli by flushing with a fluid. 2020-01-08T19:03:33Z NCIT:C51913 bronchoaveolar lavage Washing out the bronchi and alveoli by flushing with a fluid. NCIT:C51913 A minimally invasive procedure that permits sampling of peritoneal fluid for cytopathologic analysis. 2020-01-08T19:03:46Z NCIT:C159340 peritoneal washing peritoneal lavage A minimally invasive procedure that permits sampling of peritoneal fluid for cytopathologic analysis. NCIT:C159340 The process in which the nasal cavity is washed to flush out mucus and debrise from the nose and sinuses with water or saline. 2020-01-08T19:04:02Z nasal irrigation nasal washing nasal lavage Avoid the administration or use of therapeutic procedure. http://orcid.org/0000-0001-7941-2961 2020-01-12T20:39:14Z avoid therapeutic procedure avoiding therapeutic procedure therapeutic procedure avoidance Avoid the administration or use of diagnostic procedure. http://orcid.org/0000-0001-7941-2961 2020-01-12T20:39:14Z avoid diagnostic procedure avoiding diagnostic procedure diagnostic procedure avoidance Avoid the administration or use of preventative therapy. http://orcid.org/0000-0001-7941-2961 2020-01-12T20:39:14Z avoid preventative therapy avoiding preventative therapy preventative therapy avoidance The implantation of a piece of mechanical or electronic equipment that is useful for prevention, diagnosis, monitoring, or treatment of disease or other conditions. 2020-01-20T14:58:18Z ERO:0001092 NCIT:C16830 implantation of a medical device insertion of a medical device insertion of a therapeutic device therapeutic device implantation medical instrument implantation medical machine implantation medical device implantation Implantation of a battery-powered device that is placed under the skin (typically in the left upper chest) with electrode wires that lead into the heart (typically lodging in the apex or septum of the right ventricle). The device can detect abnormal heart rhythms and deliver low-energy or high-energy shocks to interrupt malignant arrhythmia and thereby prevent sudden death. 2020-01-20T16:54:00Z NCIt:C93238 UMLS_CUI:C0162589 ICD placement automated implantable cardioverter defibrillator placement implantable cardioverter-defibrillator implantation implantable cardioverter-defibrillator placement ICD placement The resection or complete surgical removal of a nerve. 2020-01-20T17:09:07Z surgical denervation Left cardiac sympathetic denervation (LCSD) is a surgical antiadrenergic intervention with a strong antiarrhythmic effect. LCSD consists in the removal of the left thoracic sympathetic chain and paravertebral ganglia from T1 to T4. 2020-01-20T17:11:04Z PMID:30972341 LCSD left cardiac sympathetic denervation Left cardiac sympathetic denervation (LCSD) is a surgical antiadrenergic intervention with a strong antiarrhythmic effect. LCSD consists in the removal of the left thoracic sympathetic chain and paravertebral ganglia from T1 to T4. PMID:30972341 LCSD Any procedure relating to the branch of medicine dealing with the correction of deformities of bones or muscles. 2020-01-20T17:50:35Z MeSH:D019637 orthopaedic procedure orthopedic procedure Assessment by a surgeon who focuses on the preservation, investigation and restoration of the form and function of the extremities, spine and associated structures by medical, surgical and physical means. This specialist is involved with the care of patients whose musculoskeletal problems include congenital deformities, trauma, infections, tumors, metabolic disturbances of the musculoskeletal system, deformities, injuries and degenerative diseases of the spine, hands, feet, knee, hip, shoulder and elbow in children and adults. An orthopaedic surgeon is also concerned with primary and secondary muscular problems and the effects of central or peripheral nervous system lesions of the musculoskeletal system. 2020-01-20T17:50:52Z consultation with orthopedic surgeon orthopaedic consult orthopedic consult orthopedic surgeon consultation orthopedic surgeon referral orthopedist consultation referral to orthopedic surgeon referral to orthopedist orthopedic surgeon evaluation Assessment by a surgeon who focuses on the preservation, investigation and restoration of the form and function of the extremities, spine and associated structures by medical, surgical and physical means. This specialist is involved with the care of patients whose musculoskeletal problems include congenital deformities, trauma, infections, tumors, metabolic disturbances of the musculoskeletal system, deformities, injuries and degenerative diseases of the spine, hands, feet, knee, hip, shoulder and elbow in children and adults. An orthopaedic surgeon is also concerned with primary and secondary muscular problems and the effects of central or peripheral nervous system lesions of the musculoskeletal system. abms.org Any surgical procedure conducted on the skeletal system. 2020-01-20T17:51:02Z NCIT:C16186 orthopedic surgical procedure orthopedics surgery skeletal system surgical procedure orthopedic surgery obsolete orthopedic consultation true Orthotic services provide prescription insoles, braces, splints, callipers, footwear, spinal jackets and helmets which help people recover from or avoid injury, or live with lifelong conditions. 2020-01-20T18:01:00Z orthotic services The recommendation of the use of an orthosis or multiple orthoses, which are externally applied device used to modify the structural and functional characteristics of the neuromuscular and skeletal system. 2020-01-20T18:02:48Z PMID:26835739 orthoses usage orthotic device usage The recommendation of the use of an orthosis or multiple orthoses, which are externally applied device used to modify the structural and functional characteristics of the neuromuscular and skeletal system. PMID:26835739 A procedure where a healthcare provider, who was not previously involved in a patient's treatment, reviews a patient's medical history, examines the patient, and makes recommendations as to care and treatment. 2020-01-20T18:30:15Z medical professional consultation medical professional examination An appraisal or evaluation of a patient's condition by a clinician that is based on a physical exam, medical history, and the patient's account of symptoms. medical professional evaluation An appraisal or evaluation of a patient's condition by a clinician that is based on a physical exam, medical history, and the patient's account of symptoms. PMID:19567008 NCIT:C25305 Increase in the longest dimension of a bone to correct anatomical deficiencies, congenital, traumatic, or as a result of disease. The lengthening is not restricted to long bones. The usual surgical methods are internal fixation and distraction. 2020-01-21T19:47:30Z MeSH:D001852 OMIT:0003210 limb lengthening procedure leg lengthening bone lengthening procedure Increase in the longest dimension of a bone to correct anatomical deficiencies, congenital, traumatic, or as a result of disease. The lengthening is not restricted to long bones. The usual surgical methods are internal fixation and distraction. MeSH:D001852 A bone fixation technique using an external fixator for lengthening limbs, correcting pseudarthroses and other deformities, and assisting the healing of otherwise hopeless traumatic or pathological fractures and infections, such as chronic osteomyelitis. 2020-01-21T19:52:10Z MeSH:D018889 Ilizarov technique Ilizarov procedure A bone fixation technique using an external fixator for lengthening limbs, correcting pseudarthroses and other deformities, and assisting the healing of otherwise hopeless traumatic or pathological fractures and infections, such as chronic osteomyelitis. MeSH:D018889 Bone lengthening by gradual mechanical distraction. An external fixation device produces the distraction across the bone plate. The technique was originally applied to long bones but in recent years the method has been adapted for use with mandibular implants in maxillofacial surgery. 2020-01-21T20:01:15Z MeSH:D019857 distraction osteogenesis Bone lengthening by gradual mechanical distraction. An external fixation device produces the distraction across the bone plate. The technique was originally applied to long bones but in recent years the method has been adapted for use with mandibular implants in maxillofacial surgery. MeSH:D019857 A measurement performed in a clinical setting using clinician's observations and instrument data to inform patient care and research. 2020-01-21T20:29:43Z CMO:0000000 PMID:2647562 clinical measurement clinical assessment A measurement performed in a clinical setting using clinician's observations and instrument data to inform patient care and research. PMID:2647562 An assessment of body temperature. 2020-01-21T20:35:51Z 2023-04-11T12:00:00Z CMO:0000015 NCBIBook:NBK331 body temperature measurement The act of assessing an individual's current temperature, heart rate, respiratory rate, pulse oxygenation, and blood pressure. 2020-01-21T20:43:33Z NCIT:C49672 VSTEST vital signs assessment vital signs measurement The act of assessing an individual's current temperature, heart rate, respiratory rate, pulse oxygenation, and blood pressure. NCIT:C49672 VSTEST An assessment of the number of heartbeats per unit time, usually expressed as beats per minute. 2020-01-21T20:47:05Z CMO:0000002 NCIT:C49677 HR measurement heart rate assessment heart rate measurement HR measurement Assessment and recording of arterial pulses in any of a number of locations. The observer should note its intensity, rate, rhythm, and if any blood vessel tenderness, tortuosity, or nodularity exists. 2020-01-21T20:59:19Z NCBIBook:NBK350 pulse assessment The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute. 2020-01-21T21:04:00Z CMO:0000289 NCIT:C49678 respiratory rate assessment The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute. NCIT:C49678 Procedure to evaluate the structure and/or function of the cardiovascular system. http://orcid.org/0000-0001-7941-2961 2020-01-21T21:09:50Z CMO:0000001 NCIT:C100084 cardiovascular diagnostic procedure cardiovascular system diagnostic procedure diagnostic procedure of cardiovascular system Measurement of the pressure on the walls of the vessels as blood moves around the body. Systolic blood pressure is the pressure when the heart beats – while the heart muscle is contracting (squeezing) and pumping oxygen-rich blood into the blood vessels. Diastolic blood pressure is the pressure on the blood vessels when the heart muscle relaxes. The diastolic pressure is always lower than the systolic pressure. 2020-01-21T21:13:22Z CMO:0000003 NCBIBook:NBK279251 blood pressure assessment blood pressure monitoring blood pressure measurement Monitoring blood pressure with a sphygmomanometer and a stethoscope to hear blood flow. 2020-01-22T15:29:56Z MMO:0000055 NCIT:C69318 PMID:20937442 VSO:0000001 ausculatory sphygmomanometer blood pressure measurement auscultatory blood pressure measurement process auscultatory blood pressure monitoring Although the auscultatory method using mercury sphygmomanometer is regarded as the ‘gold standard’ for office blood pressure measurement, widespread implementation of the ban in use of mercury sphygmomanometers continues to diminish the role of this technique. auscultatory blood pressure measurement Although the auscultatory method using mercury sphygmomanometer is regarded as the ‘gold standard’ for office blood pressure measurement, widespread implementation of the ban in use of mercury sphygmomanometers continues to diminish the role of this technique. PMID:20937442 A blood pressure measurement using a sphygmomanometer and an electronic pressure sensor (transducer) that detects blood flow by the presence of oscillations in the cuff pressure. 2020-01-22T20:49:15Z NCIT:C69319 PMID:20937442 VSO:0000026 oscillometric blood pressure measurement A method for monitoring blood pressure without requiring instruments introduced into the body. 2020-01-22T21:01:49Z NCIT:C69319 PMID:20937442 VSO:0000024 non-invasive blood presure measurement noninvasive blood pressure measurement An intra-arterial method of monitoring blood pressure. 2020-01-22T21:18:39Z VSO:0000023 invasive blood pressure measurement All manners of treatment to bring respiratory system back to its normal state. http://orcid.org/0000-0001-7941-2961 2020-01-23T15:55:17Z NCIT:C15322 respiratory system therapeutic procedure respiratory therapy therapeutic procedure of respiratory system A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. 2020-01-23T15:56:57Z MeSH:D058109 airway management A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. PMID:18675024 Removal of an endotracheal tube from the patient. 2020-01-23T16:07:45Z MeSH:D060666 NCIT:C50819 airway extubation tracheal extubation endotracheal extubation Removal of an endotracheal tube from the patient. MeSH:D060666 A procedure involving placement of a tube into the trachea through the mouth or nose in order to provide a patient with oxygen and anesthesia. 2020-01-23T16:16:19Z MeSH:D007442 NCIT:C116648 airway intubation intratracheal intubation tracheal intubation endotracheal intubation A procedure involving placement of a tube into the trachea through the mouth or nose in order to provide a patient with oxygen and anesthesia. MeSH:D007442 Any method of artificial breathing that employs mechanical or non-mechanical means to force the air into and out of the lungs. Artificial respiration or ventilation is used in individuals who have stopped breathing or have respiratory insufficiency to increase their intake of oxygen (O2) and excretion of carbon dioxide (CO2). 2020-01-23T16:34:17Z artificial ventilation mechanical ventilation artificial respiration Surgical formation of an opening into the trachea through the neck, or the opening so created. http://orcid.org/0000-0001-7941-2961 2020-01-23T16:48:07Z MeSH:D014140 PMID:32644550 trach tracheotomy Tracheostomy and tracheotomy are sometimes used interchangeably, but tracheotomy is simply a surgical incision of the trachea. tracheostomy A manual method for maintaining oxygenation using a mask. 2020-01-23T17:41:09Z bag-mask ventilation mask ventilation Techniques for administering artificial respiration without the need for intratracheal intubation. 2020-01-23T17:52:50Z MeSH:D063087 non-invasive ventilation noninvasive ventilation Techniques for administering artificial respiration without the need for intratracheal intubation. MeSH:D063087 Ventilatory support system using frequencies from 60-900 cycles/min or more. Three types of systems have been distinguished on the basis of rates, volumes, and the system used. 2020-01-23T17:57:32Z MeSH:D006612 high frequency oscillation ventilation high frequency positive pressure ventilation high-frequency ventilation Ventilatory support system using frequencies from 60-900 cycles/min or more. Three types of systems have been distinguished on the basis of rates, volumes, and the system used. MeSH:D006612 A technique of mechanical ventilation in which the lungs are insufflated with an oxygenated perfluorochemical liquid rather than an oxygen-containing gas mixture. 2020-01-23T18:01:24Z MeSH:D021061 liquid-assisted ventilation liquid ventilation A technique of mechanical ventilation in which the lungs are insufflated with an oxygenated perfluorochemical liquid rather than an oxygen-containing gas mixture. PMID:22043370 A method of mechanical ventilation in which pressure is maintained to increase the volume of gas remaining in the lungs at the end of expiration, thus reducing the shunting of blood through the lungs and improving gas exchange. 2020-01-23T18:06:14Z MeSH:D011175 positive control ventilation positive controlled respiration positive end expiratory pressure technique positive pressure respiration positive pressure ventilation positive-controlled ventilation positive-pressure respiration positive-pressure ventilation positive controlled ventilation A method of mechanical ventilation in which pressure is maintained to increase the volume of gas remaining in the lungs at the end of expiration, thus reducing the shunting of blood through the lungs and improving gas exchange. MeSH:D011175 Assisted ventilation by applying intermittent subatmospheric pressure around the thorax, abdomen, or airway and periodically expand the chest wall and inflate the lungs. 2020-01-23T18:22:46Z iron lung ventilation portalung ventilation MeSH:D015919 negative-pressure ventilation negative-pressure respiration obsolete bilevel positive airway pressure ventilation true A form of non-invasive mechanical pressure support ventilation that uses a continuous positive airway pressure level to support spontaneous breathing activity. 2020-01-23T18:31:36Z MeSH:D045422 NCIT:C124040 CPAP ventilation nCPAP ventilation nasal continuous positive airway pressure ventilation continuous positive airway pressure ventilation A form of non-invasive mechanical pressure support ventilation that uses a continuous positive airway pressure level to support spontaneous breathing activity. NCIT:C124040 CPAP ventilation nCPAP ventilation A rehabilitation therapy for removal of copious mucus secretion from the lung of patients with diseases. The patient's head is placed in a downward incline (so the trachea is inferior to the affected area) for 15 to 20 minute sessions. 2020-01-23T19:45:07Z MeSH:D015916 postural respiratory drainage pulmonary postural drainage postural drainage A respiratory support system used to remove mucus and clear airway by oscillating pressure on the chest. 2020-01-23T20:18:02Z MeSH:D035641 external chest wall oscillation high-frequency chest compression high-frequency chest wall oscillation chest wall oscillation A respiratory support system used to remove mucus and clear airway by oscillating pressure on the chest. MeSH:D035641 Application of a life support system that circulates the blood through an oxygenating system, which may consist of a pump, a membrane oxygenator, and a heat exchanger. 2020-01-23T20:23:16Z MeSH:D015199 ECLS treatment ECMO treatment extracorporeal life support extracorporeal membrane oxygenation Application of a life support system that circulates the blood through an oxygenating system, which may consist of a pump, a membrane oxygenator, and a heat exchanger. MeSH:D015199 ECLS treatment ECMO treatment Chest physical therapy (CPT or Chest PT) is an airway clearance technique (ACT) to drain the lungs, and may include percussion (clapping), vibration, deep breathing, and huffing or coughing. 2020-01-23T20:32:18Z CPT Chest PT chest physical therapy chest physiotherapy The insertion of a cannula or tube into a hollow body organ. 2020-01-23T20:44:41Z ERO:0001108 MeSH:D007440 NCIT:C37981 intubation procedure The insertion of a cannula or tube into a hollow body organ. NCIT:C37981 The removal of a previously inserted tube from a hollow organ or passageway, often from the airway. 2020-01-23T20:48:40Z NCIT:C50819 extubation procedure The removal of a previously inserted tube from a hollow organ or passageway, often from the airway. NCIT:C50819 Use of medical ultrasonography in pregnancy where sound waves are used to create a real-time visual image of the developing fetus in the uterus. Imaging can include the mother's ovaries and uterus as well. 2020-01-24T19:29:52Z fetal ultrasound obstetric sonography obstetric ultrasonography obstetric ultrasound prenatal ultrasound procedure fetal ultrasonography A clinical recommendation to avoid or refrain from certain behaviors in order to maintain health or ameliorate symptoms. 2020-01-29T17:35:05Z behavior avoidance for therapeutic purposes cognitive and behavioral intervention avoidance A direct assessment of a patient's condition by a clinical health professional that is based on a physical exam, medical history, and the patient's account of symptoms. 2020-03-04T17:09:05Z NCIT:C25305 clinical examination medical examination examination by physician examination by clinical professional A direct assessment of a patient's condition by a clinical health professional that is based on a physical exam, medical history, and the patient's account of symptoms. PMID:19567008 A systemic evaluation of the body and its functions using visual inspection, palpation, percussion and auscultation. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. 2020-03-04T17:45:04Z physical examination A systemic evaluation of the body and its functions using visual inspection, palpation, percussion and auscultation. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. NCIT:C20989 A test or diagnostic examination to assess the health status of the mother and well being of the fetus. 2021-02-11T22:00:54Z NCIT:C92714 antenatal examination prenatal examination Testing of fetal DNA during pregnancy to determine if the fetus has chromosomal aberrations, fetal aneuploidy, or other detectable genetic disorders. 2020-03-17T18:55:32Z fetal genetic testing foetal genetic screening prenatal genetic screening prenatal genetic testing A genetic test to whether a healthy person harbors a recessive mutation in one of their copies of a gene or genes. 2020-03-17T20:04:20Z carrier screening genetic carrier screening A test that analyzes small fragments of DNA that are circulating in a pregnant woman’s blood to determine the risk that the fetus will be born with genetic abnormalities. 2020-03-17T20:22:26Z NIPT cell free fetal DNA testing noninvasive prenatal screening noninvasive prenatal testing NIPT obsolete prenatal molecular genetic testing true A diverse set of techniques used to identify the molecular basis of genetic disease. Examples of molecular genetic tests include: genotyping to detect specific pathogenic variants; sequencing of a gene to detect pathogenic variants; amplification or hybridization methods (e.g., qPCR, array CGH, MLPA) to detect copy number variants involving one or more genes; methylation-specific techniques to detect epigenetic changes that influence gene expression; and exome and genome sequencing. 2020-03-18T19:19:07Z molecular genetic testing A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. 2020-03-19T19:24:04Z NCIT:C52009 amniocentisis A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. NCIT:C52009 Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. 2020-03-19T19:39:48Z surgical aspiration procedure Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. NCIT:C15631 A prenatal test in which a sample of chorionic villi is removed from the placenta for testing. The sample can be taken through the cervix (transcervical) or the abdominal wall (transabdominal). Mayo Clinic http://orcid.org/0000-0001-7941-2961 2022-06-23T20:39:14Z 2020-03-19T19:51:26Z NCIT:C92755 CVS chorionic villus biopsy The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects. chorionic villus sampling CVS The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects. NCIT:C92755 A procedure conducted during pregnancy for the presence of Gardnerella vaginalis, Ureaplasma urealyticum, Mycoplasma hominis, Mobiluncus, Prevotella and anaerobic bacteria. 2020-03-19T20:17:55Z NCIT:C92740 BV testing bacterial vaginosis screening BV testing A test for the presence of fetal fibronectin in the cervico-vaginal area that is used to predict preterm birth. 2020-03-19T20:22:14Z NCIT:C92786 FBNCTFT fFN testing fetal fibronectin assessment fetal fibronectin testing A test for the presence of fetal fibronectin in the cervico-vaginal area that is used to predict preterm birth. NCIT:C92786 FBNCTFT fFN testing Screening with a swab from the vaginal and rectal areas in late pregnancy to test for the presence of Group B streptococcal infection. 2020-03-19T20:47:28Z NCIT:C92805 GBS beta-hemolytic strep culture screening broup B Beta-hemolytic streptococcus screening group B strep screening prenatal group B streptococcus screening Screening with a swab from the vaginal and rectal areas in late pregnancy to test for the presence of Group B streptococcal infection. NCIT:C92805 GBS An ultrasonic examination of the fetus in the late first trimester to measure the clear space at the back of the fetal neck to assess risk of genetic or cardiac abnormalities. 2020-03-19T21:03:16Z NCIT:C92837 NT testing nuchal translucency ultrasound screening ultrasonographic nuchal translucency exam nuchal translucency screening An ultrasonic examination of the fetus in the late first trimester to measure the clear space at the back of the fetal neck to assess risk of genetic or cardiac abnormalities. NCIT:C92837 NT testing A screening measurement in which the maternal blood levels of alpha-fetoprotein, unconjugated estriol, human chorionic gonadotrophin and Inhibin A are calculated. These are then evaluated in relation to the mother's age, weight and fetal gestational age. 2020-03-19T21:11:02Z NCIT:C92865 quad screen quadruple marker testing quad test assessment A screening measurement in which the maternal blood levels of alpha-fetoprotein, unconjugated estriol, human chorionic gonadotrophin and Inhibin A are calculated. These are then evaluated in relation to the mother's age, weight and fetal gestational age. NCIT:C92865 A determination of the number of eosinophil in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C64550 EOS cell count eosinophil count test eosinophil count EOS cell count A determination of the number of granulocyte in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C96654 granulocyte count test polymorphonuclear leukocyte count granulocyte count A determination of the number of basophil in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C64470 basophil cell count basophil count test total basophil count basophil count A determination of the number of lymphocyte in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C51949 lymphocyte count test lymphocyte count A procedure by which biological material is obtained from a subject for testing, diagnostic, treatment, or research purposes. 2020-03-27T15:53:08Z NCIT:C70700 clinical specimen collection clinical biospecimen collection obsolete swab-based biospecimen collection true Measuring a person's own body temperature usually at home using any of a number of types of thermometers. 2020-03-29T18:25:39Z self-reported temperature measurement at home temperature measurement self-reported fever measurement self body temperature measurement A characteristic that can be objectively measured and serves as an indicator for the inflammatory response. It could be used to indicate the normal inflammatory processes, pathogenic processes, state of health or disease, the risk for disease development and/or prognosis, or responsiveness to a particular therapeutic intervention. 2020-03-29T18:32:41Z inflammatory biomarker measurement inflammatory biomarker assessment Assay based assessment of a serum sample for detection and concentration (mg/L) C-reactive protein. 2020-03-29T18:33:44Z CRP measurement C-reactive protein (CRP) measurement is a measurement of the level of C-reactive protein in the blood. Levels are known to rise in response to inflammation, CRP is therefore used as a clinical measure of inflammation. The measurement is used in the process of clinical diagnosis as high levels of CRP are associated with cardiovascular disease, diabetes and hypertension and in some cancers. C-reactive protein biomarker assessment Assay based assessment of a serum sample for detection and concentration (mg/L) C-reactive protein. PMID:11238291 CRP measurement C-reactive protein (CRP) measurement is a measurement of the level of C-reactive protein in the blood. Levels are known to rise in response to inflammation, CRP is therefore used as a clinical measure of inflammation. The measurement is used in the process of clinical diagnosis as high levels of CRP are associated with cardiovascular disease, diabetes and hypertension and in some cancers. EFO:0004458 Detection of circultating interleukin-6, which stimulates the inflammatory and auto-immune processes in many diseases. 2020-03-29T18:44:31Z IL-6 level assessment IL-6 measurement A quantification of interleukin-6, a pro-inflammatory and anti-inflammatory cytokine. interleukin-6 biomarker measurement IL-6 level assessment IL-6 measurement A quantification of interleukin-6, a pro-inflammatory and anti-inflammatory cytokine. EFO:0004810 A chemokine that can be objectively measured and serves as an indicator for the inflammatory response. 2020-03-30T15:51:58Z cytokine biomarker measurement Cytokines are small, nonstructural proteins, including interleukins, chemokines, interferons, and tumor necrosis factors, which have a multitude of pleiotropic effects in various organs [1]. They are released in a number of paracrine, autocrine, or endocrine pathways and have been implicated in a variety of infections and immune system-affecting disorders by both proinflammatory and anti-inflammatory mechanisms. Macrophages and T lymphocytes (T-cells) are the primary producers of cytokines which may have predominantly pro-inflammatory (inflammation-promoting)(IL-1alpha, IL-1beta, IL-2, IL-6, Il-8, IL-12, TNF-alpha, IFN-gamma) or anti-inflammatory (inflammation-suppressive)(IL-4, IL-5, IL-10, TGF-beta) abilities. cytokine biomarker assessment Cytokines are small, nonstructural proteins, including interleukins, chemokines, interferons, and tumor necrosis factors, which have a multitude of pleiotropic effects in various organs [1]. They are released in a number of paracrine, autocrine, or endocrine pathways and have been implicated in a variety of infections and immune system-affecting disorders by both proinflammatory and anti-inflammatory mechanisms. PMID:28487810 Macrophages and T lymphocytes (T-cells) are the primary producers of cytokines which may have predominantly pro-inflammatory (inflammation-promoting)(IL-1alpha, IL-1beta, IL-2, IL-6, Il-8, IL-12, TNF-alpha, IFN-gamma) or anti-inflammatory (inflammation-suppressive)(IL-4, IL-5, IL-10, TGF-beta) abilities. PMID:24962838 Detection of interleukin-1 beta levels, an IL-1 cytokine family protein, secreted by macrophages and a mediator of inflammatory response. 2020-03-30T16:03:54Z IL-1 beta assessment interleukin-1 beta biomarker measurement Detection of interleukin-1 alpha, a mediator of the inflammatory response. 2020-03-30T16:05:46Z IL-1 alpha assessment IL-1 alpha testing interleukin-1 alpha biomarker measurement Detection of interleukin-2, a mediator of inflammatory response. 2020-03-30T16:08:32Z IL-2 level assessment IL-2 testing interleukin-2 biomarker measurement Detection of interleukin-8 levels, a mediator of inflammatory response. 2020-03-30T16:09:36Z IL-8 level assessment IL-8 testing interleukin-8 biomarker measurement Detection of interleukin-12 levels, an inflammatory cytokine. 2020-03-30T16:24:01Z IL-12 assessment IL-12 level testing interleukin-12 biomarker measurement Detection of TNF-alpha levels, a cytokine involved in systemic inflammation. 2020-03-30T16:28:04Z TNF-alpha assessment TNF-alpha level testing tumor necrosis factor-alpha biomarker measurement Detection of interferon-gamma, a cytokine that indicates an inflammatory response. 2020-03-30T16:31:18Z INF-gamma assessment INF-gamma levels testing interferon-gamma biomarker measurement Detection of interleukin-4, a cytokine identified as an inflammation suppressant. 2020-03-30T18:59:24Z IL-4 measurement IL-4 testing IL4 assessment interleukin-4 biomarker measurement Detection of interleukin-5, a cytokine identified as an inflammation suppressant. 2020-03-30T19:04:15Z IL-5 measurement IL-5 testing IL5 assessment interleukin-5 biomarker measurement Detection of interleukin-10, a cytokine identified as an inflammation suppressant. 2020-03-30T19:05:58Z IL-10 measurement IL-10 testing IL10 assessment Interleukin-10 biomarker measurement Detection of tumor necrosis factor-beta (TNF-beta), a cytokine identified as an inflammation suppressant. 2020-03-30T19:07:19Z TNF-beta measurement TNF-beta testing TNFbeta assessment tumor necrosis factor-beta biomarker measurement Detection of serum levels of amyloid A (SAA) in response to inflammation. 2020-03-30T19:37:28Z SAA biomarker measurement serum amyloid A biomarker assessment A clinical laboratory procedure designed for the quantification of an organic or inorganic chemical within a biological specimen required for diagnostics or monitoring of treatments. 2020-03-30T19:49:21Z NCIT:C49237 clincal chemistry test clinical chemistry measurement testing clinical chemistry testing clinical chemistry assessment A quantitative measurement for assessing the amount of glucose present in a blood sample. 2020-03-30T19:58:59Z NCIT:C92744 blood glucose measurement blood glucose testing blood surgar testing blood glucose assessment A quantitative measurement for assessing the amount of glucose present in a blood sample. NCIT:C92744 Glucose Plasma Concentration (GPC) measurement is an essential diagnostic modality for different types of carbohydrate metabolism derangements including diabetes mellitus. 2020-03-30T20:02:19Z NCIT:C41376 plasma glucose measurement Glucose Plasma Concentration (GPC) measurement is an essential diagnostic modality for different types of carbohydrate metabolism derangements including diabetes mellitus. The disordered carbohydrate metabolism that underlies diabetes manifests as hyperglycemia. Plasma glucose concentrations in healthy individuals vary with age. Normal fasting plasma glucose intervals (in the morning after an overnight fast) in children are 3.3 - 5.6 mmol/L (60-100 mg/dL); adult range - 4.1- 5.9 mmol/L (74-106 mg/dL). GPCs are approximately 11% higher than whole blood if the hematocrit is normal. Glucose concentrations in heparinized plasma are reported to be 5% lower than in serum. plasma glucose assessment Glucose Plasma Concentration (GPC) measurement is an essential diagnostic modality for different types of carbohydrate metabolism derangements including diabetes mellitus. The disordered carbohydrate metabolism that underlies diabetes manifests as hyperglycemia. Plasma glucose concentrations in healthy individuals vary with age. Normal fasting plasma glucose intervals (in the morning after an overnight fast) in children are 3.3 - 5.6 mmol/L (60-100 mg/dL); adult range - 4.1- 5.9 mmol/L (74-106 mg/dL). GPCs are approximately 11% higher than whole blood if the hematocrit is normal. Glucose concentrations in heparinized plasma are reported to be 5% lower than in serum. NCIT:C41376 A quantitative measurement of the amount of glucose present in a sample of blood, obtained from a source that has abstained from nutrition, typically at least 8 hours prior to the sample collection time. 2020-03-30T20:05:54Z NCIT:C80400 FBS measurement fasting blood glucose measurement fasting blood sugar measurement testing fasting blood glucose assessment A quantitative measurement of the amount of glucose present in a sample of blood, obtained from a source that has abstained from nutrition, typically at least 8 hours prior to the sample collection time. NCIT:C80400 A technique to collect sputum by inhaling hypertonic saline through an oxygen mask in order to induce sputum. 2020-03-30T20:17:26Z induced sputum collection A technique to collect sputum by inhaling hypertonic saline through an oxygen mask in order to induce sputum. PMID:32171389 A method of examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. 2020-03-30T20:32:28Z NCIT:C17204 CAT scan CT CT scan computerized axial tomography computed tomography procedure A method of examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. NCIT:C17204 Use of a drug that lower the level of glucose in the blood. 2020-03-31T00:42:37Z CHEBI:35526 hypoglycaemic drug therapy treatment with hypoglycemic agent treatment with hypoglycemic drug treatment with hypoglycemic medication hypoglycemic drug therapy Treatment of retroviral infections with medications that target the virus directly, limiting the ability of infected cells to produce new virus particles. 2020-03-31T00:49:23Z NCIT:C94631 ART anti-retroviral therapy treatment with an anti-retroviral medication treatment with an antiretroviral drug treatment with an antiretroviral medication antiretroviral therapy Treatment of retroviral infections with medications that target the virus directly, limiting the ability of infected cells to produce new virus particles. NCIT:C94631 The process of gathering information regarding a person's medical history. 2020-03-31T00:59:49Z patient assessment NCIT:C146918 medical history collection medical history taking The process of gathering information regarding a person's medical history. NCIT:C146918 Determination if a patient's background or demographic characteristics makes the patient susceptible to disease. 2020-03-31T01:03:49Z patient demographic characteristics assessment Determination if patient's travel history may impact current health. 2020-03-31T01:05:10Z patient travel risk assessment A questionnaire designed to determine if patient's travel history may impact current health. 2020-03-31T01:05:32Z patient travel risk questionnaire Determination if the patient may have been exposed to something which would impact the health of the patient. 2020-03-31T01:11:38Z patient environmental exposure assessment A test that measures the amount of oxygen and carbon dioxide in the blood. It may also be used to determine the pH of the blood. 2020-03-31T19:11:20Z NCIT:C71252 blood gas measurement testing blood gas test arterial blood gas measurement pH and blood gas measurements are used to detect and monitor ventilation, oxygenation, and acid-base disturbances. blood gas assessment pH and blood gas measurements are used to detect and monitor ventilation, oxygenation, and acid-base disturbances. PMID:33371 The determination of the unmeasured anions (those other than the chloride and bicarbonate anions) present in a sample. 2020-03-31T19:16:41Z NCIT:C74685 anion gap measurement testing anion gap assessment The determination of the unmeasured anions (those other than the chloride and bicarbonate anions) present in a sample. NCIT:C74685 A quantitative measurement of the amount of calcium present in a sample, usually serum or urine. 2020-03-31T19:19:43Z NCIT:C64488 calcium measurement calcium assessment A quantitative measurement of the amount of an electrolyte present in urine or serum. 2020-03-31T19:32:42Z NCIT:C74946 electrolyte measurement electrolyte assessment A quantitative measurement of the amount of an electrolyte present in serum. 2020-03-31T19:33:45Z electrolytes- serum testing serum electrolyte measurement serum electrolyte assessment A quantitative measurement of the amount of an electrolyte present in urine. 2020-03-31T19:34:22Z electrolytes- urine testing urine eletrolyte measurement urine eletrolyte assessment Any laboratory procedure for growing microorganisms. 2020-03-31T20:08:52Z NCIT:C25300 microbial culture procedure Any laboratory procedure for growing microorganisms. NCIT:C25300 A type of mechanical ventilation using endotracheal intubation. 2020-03-31T20:23:41Z invasive ventilation A time-triggered, pressure-limited, inverse-ratio mode of ventilation that provides continuous distending airway pressure with intermittent release phases 2020-04-01T20:00:59Z APRV airway pressure release ventilation A time-triggered, pressure-limited, inverse-ratio mode of ventilation that provides continuous distending airway pressure with intermittent release phases PMID:29641221 APRV A technique that detects a particular nucleic acid sequence in order to identify a pathogen (organism or virus) in blood, tissue, urine, or other bodily fluids. 2020-04-02T20:59:07Z NAT clinical nucleic acid testing nucleic acid testing pathogen nucleic acid testing clinical nucleic acid testing for pathogens NAT A tecnique that uses an amplification of nucleic acids to detect a pathogen. Some amplification methods include polymerase chain reaction (PCR), strand displacement assay (SDA), or transcription mediated assay (TMA) to detect a virus, bacteria or other pathogen. 2020-04-02T21:17:28Z NCIT:C20055 NAAT nucleic acid amplification procedure Any of various amplification and detection strategies applied to detection of virus contamination in donor blood. Specifically designed to detect recently infected individuals during the latency period before seroconversion. nucleic acid amplification testing NAAT Any of various amplification and detection strategies applied to detection of virus contamination in donor blood. Specifically designed to detect recently infected individuals during the latency period before seroconversion. NCIT:C20055 A type of nucleic acid amplification test in which sample DNA is exposed to a single temperature in the presence of multiple sets of primers and a polymerase with replication and high strand displacement activity. This test negates the need for thermal cyclers and may be a low cost alternative to PCR. 2020-04-02T21:43:07Z NCIT:C102661 loop-mediated isothermal amplification procedure loop-mediated isothermal amplification testing A type of nucleic acid amplification test in which sample DNA is exposed to a single temperature in the presence of multiple sets of primers and a polymerase with replication and high strand displacement activity. This test negates the need for thermal cyclers and may be a low cost alternative to PCR. NCIT:C102661 A technique that detects a particular DNA sequence in order to identify a pathogen (organism or virus) in blood, tissue, urine, or other bodily fluids. 2020-04-03T00:29:00Z DNA detection examination DNA detection procedure DNA detection testing DNA detection kit testing clinical DNA detection testing A technique that detects a particular RNA sequence in order to identify a pathogen (organism or virus) in blood, tissue, urine, or other bodily fluids. 2020-04-03T00:30:09Z RNA detection examination RNA detection procedure RNA detection testing RNA detection kit testing clinical RNA detection testing A clinical assay that amplifies and quantifies a specific DNA molecule based on in tissue, blood, sputum, urine, or any other bodily fluid to detect the presence of a pathogen. It enables both detection and quantification of one or more specific sequences in a DNA sample. 2020-04-03T00:38:02Z NCIT:C51962 OBI:0000893 clinical qPCR testing clinical real-time RT-PCR procedure real-time PCR procedure for clinical use clinical real-time PCR testing A method to measure very small amounts of RNA transcripts as cDNA targets from tissue, blood, sputum or other body fluids. 2020-04-03T00:47:00Z NCIT:C28408 OBI:0000911 clinical quantitative RT-PCR procedure clinical quantitative RT-PCR testing clinical quantitative reverse transcription PCR procedure clinical quantitative reverse transcription PCR testing A procedure producing an image on a radiosensitive surface by x-ray radiation that has penetrated and passed through a structure in order to diagnose or treat a patient. 2020-04-07T15:49:43Z NCIT:C38101 NCIT:C60727 X-ray imaging procedure radiogram imaging procedure radiographic imaging procedure radiographic procedure radiography radiography imaging procedure radiograph imaging procedure The process of taking a thorough history and physical exam to determine if a patient has been exposed to an infectious disease. Close attention is paid to travel history, environmental exposures, and vaccination history. 2020-04-07T18:27:36Z infectious disease testing infectious disease screening The administration of oxygen to an individual, usually to aid in respiration by means of a mask. 2020-04-07T19:00:52Z oxygen support therapy with mask supplemental oxygen therapy with mask The administration of oxygen to an individual, usually to aid in respiration by means of a nasal cannula. 2020-04-07T19:01:10Z oxygen support therapy with nasal cannula supplemental oxygen therapy with nasal cannula Therapy using a substance used in the treatment of hypotension. A vasopressor agent increases reduced blood pressure. 2020-04-07T19:23:15Z CHEBI:137431 NCIT:C126567 antihypotensive agent drug therapy treatment with antihypotensive agent treatment with antihypotensive drug treatment with antihypotensive medication treatment with vasopressor agent treatment with vasopressor medication vasopressor support therapy vasopressor agent therapy Treatments that substitute for the blood-filtering function of the kidneys. 2020-04-07T19:42:23Z MeSH:D017582 NCIT:C126400 RRT kidney replacement therapy It includes dialysis (hemodialysis or peritoneal dialysis), hemofiltration, and hemodiafiltration. Kidney transplant may also be considered a renal replacement therapy. renal replacement therapy RRT A procedure to remove toxic substances from the blood that is used in patients with end-stage chronic kidney disease or acute kidney failure. This includes hemodialysis and peritoneal dialysis. 2020-04-07T19:57:22Z NCIT:C15221 dialysis renal dialysis A therapeutic procedure used in patients with kidney failure. It involves the extracorporeal removal of harmful wastes and fluids from the blood using a dialysis machine. Following the dialysis, the blood is returned to the body. 2020-04-07T20:03:50Z NCIT:C15248 hemodialysis A therapeutic procedure used in patients with kidney failure. It involves the extracorporeal removal of harmful wastes and fluids from the blood using a dialysis machine. Following the dialysis, the blood is returned to the body. NCIT:C15248 A form of dialysis that uses the peritoneum as a membrane across which the infused diasylate exchanges nutrients for waste products that are removed when the fluid is exchanged. 2020-04-07T20:04:03Z NCIT:C15297 peritoneal dialysis A form of dialysis that uses the peritoneum as a membrane across which the infused diasylate exchanges nutrients for waste products that are removed when the fluid is exchanged. NCIT:C15297 A laboratory procedure that tests the function of an endocrine organ and measures the amount of a hormone present in a sample. 2020-04-07T20:40:24Z NCIT:C74971 endocrine testing A laboratory procedure that tests the function of an endocrine organ and measures the amount of a hormone present in a sample. NCIT:C74971 The determination of the amount of protein present in the sample. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:51:38Z NCIT:C64430 protein assessment protein test protein measurement The determination of the amount of procalcitonin (human) present in the sample. http://orcid.org/0000-0001-7941-2961 2020-04-07T21:30:45Z 2020-04-07T21:30:45Z NCIT:C103430 procalcitonin (human) assessment procalcitonin (human) test procalcitonin level measurement procalcitonin level testing procalcitonin testing A substance produced in response to bacterial infections and tissue injury. procalcitonin assessment The determination of the amount of D-dimer (human) present in the sample. http://orcid.org/0000-0001-7941-2961 2020-04-07T21:37:45Z NCIT:C82621 D dimer level testing D-dimer (human) assessment D-dimer (human) test D-dimer measurement fibrin degradation fragment testing fragment D-dimer testing A quantification of a fibrin degradation product in blood used in the diagnosis of thrombosis. D-dimer assessment A quantitative measurement of the amount of phosphate present in a sample of serum. 2020-04-07T21:53:04Z NCIT:C61028 serum phosphate measurement serum phosphorus measurement serum phosphate assessment A quantitative measurement of the amount of phosphate present in a sample of serum. NCIT:C61028 Testing blood serum for the presence of specifc antibody or antibodies to a specific antigen. Often used when an infection is suspected. 2020-04-08T14:34:24Z serology assay serology testing A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way. (BioTech Life Science Dictionary) 2020-04-08T14:51:34Z NCIT:C16553 OBI:0000661 enzyme linked immunosorbent assay testing enzyme-linked immunosorbent assay clinical ELISA testing A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way. (BioTech Life Science Dictionary) NCIT:C16553 A type of lateral flow assay that qualitatively detect IgG and IgM antibodies of an infectious disease within human serum, plasma or whole blood in vitro. 2020-04-08T15:03:41Z rapid IgM-IgG testing rapid IgM-IgG combined antibody testing A procedure using a paper-based platform for the detection and quantification of analytes in complex mixtures, where the sample is placed on a test device for clinical use. 2020-04-08T15:06:47Z LFA testing lateral flow immuno assay lateral flow immunoassay clinical lateral flow assay testing A procedure using a paper-based platform for the detection and quantification of analytes in complex mixtures, where the sample is placed on a test device for clinical use. PMID:27365041 LFA testing Any of several immunoassay methods that use an enzyme covalently linked to an antigen or antibody as a label and are typically used for diagnostics or disease progression. 2020-04-08T15:17:14Z NCIT:C17455 clinical immunoassay Immunofluorescence staining used in a pathology or clinical lab to diagnose diseases of the skin, kidney, heart, cilia and other organ systems. 2020-04-08T15:46:23Z clinical immunofluorescence assay testing A technique for analyzing or identifying proteins immobilized on a filter by complementary reaction with specific antibodies. 2020-04-08T15:46:38Z NCIT:C17638 OBI:0001978 clinical Western blot assay clinical immunoblot assay testing A technique for analyzing or identifying proteins immobilized on a filter by complementary reaction with specific antibodies. NCIT:C17638 The measurement of the ratio of oxygenated hemoglobin to total hemoglobin in the blood. 2020-04-08T18:45:55Z NCIT:C60832 oxygen saturation measurement The measurement of the ratio of oxygenated hemoglobin to total hemoglobin in the blood. NCIT:C60832 A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin. 2020-04-08T18:54:34Z NCIT:C38085 pulse ox measurement pulse oximetry A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin. NCIT:C38085 A therapy of replenishing bodily fluids lost through sweating, bleeding, fluid shifts or other pathological processes, such as sepsis. 2020-04-08T19:29:53Z fluid resuscitation therapy fluid replacement therapy Prone positioning improves ventilation-perfusion matching (transferring delivered oxygen into the bloodstream more efficiently) and keeps alveolar units open and evenly distributed at end-expiration (improving gas exchange and preventing ventilator-induced lung injury). 2020-04-08T19:45:40Z ventilation with proning Prone positioning improves ventilation-perfusion matching (transferring delivered oxygen into the bloodstream more efficiently) and keeps alveolar units open and evenly distributed at end-expiration (improving gas exchange and preventing ventilator-induced lung injury). A procedure of surgical placement of a catheter, which lumen is usually occupied by a trocar, into the central vein (internal jugular, subclavian, and femoral often used) or veins, to provide vascular access for measurement of hemodynamic variables that cannot be measured accurately by noninvasive means. It also can be used to deliver medications that were too potent or too toxic to be administered through peripheral access, for parenteral nutrition delivery; and for placing wires and pulmonary artery catheters. Central veins are usually cannulated percutaneously. The procedure is associated with many adverse events and has to be performed or supervised by an experienced physician. 2020-04-08T20:12:41Z NCIT:C40972 central line insertion central line placement central venous access catheter insertion central venous line insertion cvc insertion central venous cannula insertion A procedure of surgical placement of a catheter, which lumen is usually occupied by a trocar, into the central vein (internal jugular, subclavian, and femoral often used) or veins, to provide vascular access for measurement of hemodynamic variables that cannot be measured accurately by noninvasive means. It also can be used to deliver medications that were too potent or too toxic to be administered through peripheral access, for parenteral nutrition delivery; and for placing wires and pulmonary artery catheters. Central veins are usually cannulated percutaneously. The procedure is associated with many adverse events and has to be performed or supervised by an experienced physician. NCIT:C40972 A thin catheter inserted into an artery to monitor blood pressure directly and obtain blood samples. 2020-04-08T20:20:40Z a-line insertion art-line placement arterial line placement arterial catheter line insertion Allows delivery of positive-pressure ventilation with a tight-fitting nasal or facial mask that is attached to a continuous positive airway pressure (CPAP) or a bilevel positive airway pressure (BiPAP) machine. 2020-04-27T20:57:00Z NIPPV non-invasive positive pressure ventilation noninvasive positve-pressure ventilation NIPPV Nutrition intervention for nutrition counseling is a supportive process, characterized by a collaborative counselor–patient/client relationship to establish food, nutrition and physical activity priorities, goals, and individualized action plans that acknowledge and foster responsibility for self-care to treat an existing condition and promote health. 2020-04-28T16:03:29Z dietary counseling nutritional counseling nutrition counseling Nutrition intervention for nutrition counseling is a supportive process, characterized by a collaborative counselor–patient/client relationship to establish food, nutrition and physical activity priorities, goals, and individualized action plans that acknowledge and foster responsibility for self-care to treat an existing condition and promote health. Reference: Academy of Nutrition and Dietetics. Nutrition Terminology Reference Manual (eNCPT): Dietetics Language for Nutrition Care 2014, Nutrition Intervention/Terms and Definitions/Nutrition Counseling (C), page-064, http://ncpt.webauthor.com An in-depth evaluation of an individual's food and nutrient intake, lifestyle, and medical history designed to help the individual either maintain their health status or attain a healthier status. 2020-04-28T16:12:44Z NCIT:C15286 dietary assessment nutritional assessment nutrition assessment An in-depth evaluation of an individual's food and nutrient intake, lifestyle, and medical history designed to help the individual either maintain their health status or attain a healthier status. NCIT:C15286 A therapy utilizing an inhaled substance that produces loss of consciousness. 2020-05-26T16:13:05Z anesthetic gas therapy gas anesthetic drug therapy inhalation anaesthetic drug therapy inhalation anaesthetic medication therapy inhalation anesthesia treatment inhalation anesthetic drug therapy inhalation anesthetic medication therapy inhalation anesthetic treatment inhalation anesthetic utilization treatment with inhalation anaesthetic inhalation anesthetic therapy A therapy utilizing an intravenous substance that produces loss of consciousness. 2020-05-26T18:19:32Z IV anaesthetic agent therapy IV anesthetic agent therapy i.v. anesthetic agent therapy i.v. anesthetic drug therapy i.v. anesthetic drug treatment i.v. anesthetic medication therapy intravenous anaesthetic agent therapy intravenous anesthesia treatment intravenous anesthetic drug therapy intravenous anesthetic medication therapy treatment with intravenous anaesthetic intravenous anesthetic therapy Treatment with an agent that causes a superficial loss of sensation in conjunctiva, mucous membranes, or skin, produced by direct application of local anesthetic solutions, ointments, gels or sprays. 2020-05-26T18:25:03Z topical anaesthetic agent therapy topical anaesthetic drug treatment topical anesthesia treatment topical anesthetic drug therapy topical anesthetic medication treatment treatment with topical anaesthetic topical anesthetic therapy Treatment with an agent that causes a superficial loss of sensation in conjunctiva, mucous membranes, or skin, produced by direct application of local anesthetic solutions, ointments, gels or sprays. PMID:26702198 Use of an agent that modulates the physiologic angiogenesis process. 2020-05-26T19:04:03Z CHEBI:50926 angiogenesis modulating drug treatment angiogenesis modulating medication therapy treatment with angiogenesis modulating agent angiogenesic modulating agent therapy Use of an agent that induces or stimulates the physiologic angiogenesis process. 2020-05-26T19:05:59Z CHEBI:50927 angiogenesis inducing drug treatment angiogenesis inducing medication therapy treatment with http://purl.obolibrary.org/obo/CHEBI_50927 angiogenesis inducing agent therapy Use of a compound that promotes the growth of new blood vessels from pre-existing vessels. 2020-05-26T19:22:45Z CHEBI:72571 pro-angiogenic drug treatment pro-angiogenic medication therapy pro-angiogenic medication treatment proangiogenic agent therapy treatment with pro-angiogenic agent pro-angiogenic agent therapy A therapy used to neutralize stomach acidity. 2020-05-26T19:41:56Z CHEBI:65265 antacid drug therapy antacid medication therapy treatment with antacid antacid agent therapy A therapy used to treat or ameliorate peptic ulcer or irritation of the gastrointestinal tract. 2020-05-26T20:00:43Z CHEBI:49201 anti-ulcer medication treatment treatment with anti-ulcer agent treatment with anti-ulcer drug treatment with anti-ulcer medication anti-ulcer agent therapy Treatment of allergic reactions with medications. 2020-05-26T20:23:47Z CHEBI:50857 allergy drug therapy allergy drug treatment allergy medication therapy anti-allergic drug therapy anti-allergic drug treatment anti-allergic medication therapy anti-allergic medication treatment treatment with allergy medication treatment with an allergy drug treatment with anti-allergic agent allergy agent therapy Usage of a drug to treat asthma. 2020-05-26T20:37:22Z CHEBI:49167 anti-asthma drug therapy anti-asthma drug treatment asthma medication therapy drug treatment of asthma treatment with anti-asthmatic drug anti-asthmatic agent therapy Treatment with a drug which acts to reduce estrogenic activity in the body, either by reducing the amount of estrogen or by reducing the activity of whatever estrogen is present. 2020-05-26T21:17:28Z CHEBI:50751 anti-estrogen drug therapy anti-estrogen medication treatment anti-oestrogen agent therapy treatment with anti-estrogen agent treatment with anti-estrogen drug treatment with anti-estrogen medication treatment with anti-oestrogen medication treatment with antiestrogen medication treatment with antioestrogen medication treatment with estrogen antagonist anti-estrogen agent therapy Use of a compound which can be used to treat or alleviate the symptoms of dyskinesia. 2020-05-27T14:13:29Z CHEBI:66956 anti-dyskinesia agent therapy anti-dyskinesia medication therapy anti-dyskinetic drug therapy anti-dyskinetic medication therapy antidyskinesia drug therapy antidyskinetic drug therapy antidyskinetic medication therapy treatment with an anti-dyskinesia drug treatment with an antidyskinetic drug treatment with anti-dyskinesia medication treatment with anti-dyskinetic drug treatment with anti-dyskinetic medication treatment with antidyskinesia agent treatment with antidyskinesia drug treatment with antidyskinesia medication treatment with antidyskinetic medication antidyskinesia agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the herpes simplex virus. 2020-05-28T13:49:36Z CHEBI:64952 Treatment of HSV with drug Treatment of HSV with medication Treatment of herpes simplex virus with medication Treatment with anti-HSV drug Treatment with anti-HSV medication Treatment with anti-herpes simplex virus drug Treatment with anti-herpes simplex virus medication anti-HSV drug therapy anti-HSV drug treatment anti-HSV medication therapy anti-herpes simplex virus agent therapy anti-herpes simplex virus drug therapy anti-herpes simplex virus drug treatment anti-herpes simplex virus medication therapy treatment with anti-HSV agent anti-HSV agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the herpes simplex virus-1. 2020-05-28T14:07:27Z CHEBI:64953 anti-herpes simplex virus 1 drug therapy anti-herpes simplex virus 1 medication treatment treatment for HSV-1 with medication treatment with anti-HSV-1 agent treatment with anti-HSV-1 drug treatment with anti-HSV-1 medication anti-HSV-1 agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the herpes simplex virus-2. 2020-05-28T14:07:27Z 2020-05-28T14:20:29Z CHEBI:64954 anti-herpes simplex virus 2 drug therapy anti-herpes simplex virus 2 medication treatment treatment for HSV-2 with medication treatment with anti-HSV-2 agent treatment with anti-HSV-2 drug treatment with anti-HSV-2 medication anti-HSV-2 agent therapy Use of a natural or synthetic analog of the hormones secreted by the adrenal gland as a type of anti-inflammatory treatment. 2020-05-28T15:10:35Z CHEBI:50858 corticosteroid treatment treatment with corticosteroid agent treatment with corticosteroid drug treatment with corticosteroid medication treatment with corticosteroid therapy corticosteroid injection treatment oral corticosteroid drug treatment corticosteroid agent therapy Treatment to induce vomiting and nausea usually administered in emergency situations after ingestion of a toxin. 2020-05-28T18:31:36Z CHEBI:149552 emetic drug therapy emetic medication therapy treatment with an emetic drug treatment with an emetic medication treatment with an emetic therapy treatment with emetic emetic therapy Treatment with a drug to alleviate rheumatoid arthritis and its symptoms. 2020-05-28T18:46:29Z CHEBI:35842 anti-rheumatic agent therapy anti-rheumatic drug therapy anti-rheumatic medication therapy antirheumatic drug treatment antirheumatic medication therapy treatment with anti-rheumatic agent treatment with anti-rheumatic drug treatment with anti-rheumatic medication treatment with antirheumatic agent treatment with antirheumatic drug treatment with antirheumatic medication antirheumatic agent therapy Treatment with an agent that modifies a particular molecular pathway. 2020-05-28T19:11:27Z CHEBI:52206 treatment with biochemical role molecular pathway modifying agent therapy Use of an inhibitor that interferes with the action of enzyme acetylcholinesterase, which helps breaking down of acetylcholine into choline and acetic acid 2020-05-28T19:16:31Z AChE inhibitor drug treatment AChE inhibitor medication treatment acetylcholinesterase inhibitor agent therapy acetylcholinesterase inhibitor drug therapy treatment with EC 3.1.1.7 (acetylcholinesterase) inhibitor acetylcholinesterase inhibitor therapy Treatment that uses drugs to stop the growth of cancer cells, either by killing the cells or by stopping them from dividing. Chemotherapy may be given by mouth, injection, or infusion, or on the skin, depending on the type and stage of the cancer being treated. It may be given alone or with other treatments, such as surgery, radiation therapy, or biologic therapy. 2020-05-29T20:29:34Z anti-neoplastic chemotherapy antineoplastic chemotherapy NCRO:0000233 cancer chemotherapeutic agent treatment cytotoxic antineoplastic agent therapy cytotoxic antineoplastic medication therapy cytotoxic cancer treatment treatment with cancer chemotherapeutic agent treatment with cancer chemotherapeutic drug treatment with cancer chemotherapeutic medication Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. cancer chemotherapy Treatment that uses drugs to stop the growth of cancer cells, either by killing the cells or by stopping them from dividing. Chemotherapy may be given by mouth, injection, or infusion, or on the skin, depending on the type and stage of the cancer being treated. It may be given alone or with other treatments, such as surgery, radiation therapy, or biologic therapy. Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. NCIT:C15632 The use of synthetic or naturally-occurring chemicals for the treatment of diseases. 2020-06-02T13:10:41Z NCIT:C15632 OGMS:0000113 chemotherapeutic agent treatment chemotherapeutic drug treatment treatment with a chemotherapeutic agent treatment with a chemotherapeutic drug treatment with a chemotherapeutic medication Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. chemotherapy The use of synthetic or naturally-occurring chemicals for the treatment of diseases. NCIT:C15632 Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. NCIT:C15632 A therapy using a compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. 2020-06-02T18:44:24Z CHEBI:23924 enzyme inhibitor drug treatment enzyme inhibitor medication treatment treatment with enzyme inhibitor treatment with enzyme inhibitor agent treatment with enzyme inhibitor drug treatment with enzyme inhibitor medication treatment with enzyme inhibitor therapy enzyme inhibitor agent therapy Use of a drug which increases blood glucose level. 2020-06-02T20:39:40Z CHEBI:76916 treatment with hyperglycemic agent treatment with hyperglycemic drug treatment with hyperglycemic medication hyperglycemic agent therapy Treatment with a cardiovascular drug that prevents atherogenesis, the accumulation of lipid-containing plaques on the innermost layers of the arteries. 2020-06-03T14:37:54Z CHEBI:50855 anti-atherogenic agent therapy treatment with anti-atherogenic agent treatment with anti-atherogenic drug treatment with anti-atherogenic medication treatment with anti-atherogenic therapy treatment with antiatherogenic agent treatment with antiatherogenic drug treatment with antiatherogenic medication antiatherogenic drug therapy Treatment with a cardiovascular drug that prevents atherosclerosis, a disease in which the inside of an artery narrows due to the build-up of plaque. 2020-06-03T14:51:06Z CHEBI:145947 anti-atherosclerotic agent therapy treatment with anti-atherosclerosis drug treatment with anti-atherosclerosis medication treatment with anti-atherosclerosis therapy treatment with anti-atherosclerotic agent treatment with anti-atherosclerotic drug treatment with anti-atherosclerotic medication treatment with antiatherosclerotic agent treatment with antiatherosclerotic drug treatment with antiatherosclerotic medication antiatherosclerotic drug therapy Use of a drug that inhibits angiotensin-converting enzyme (ACE), an enzyme that catalyzes the conversion of angiotensin I to angiotensin II. Inhibition of ACE results in a reduction in angiotensin II and angiotensin II-induced aldosterone secretion, causing vasodilation and natriuresis. 2020-06-04T17:31:19Z CHEBI:147289 NCIT:C247 Treatment with ACE inhibitor Treatment with angiotensin-converting enzyme inhibitor angiotensin-converting enzyme inhibitor therapy ACE inhibitor therapy Treatment with a class of agents that act by selectively inhibiting angiotensin II receptor activation in the renin-angiotensin-aldosterone system. 2020-06-04T17:31:52Z CHEBI:61016 NCIT:C66930 ARB therapy treatment with ARB treatment with angiotensin II receptor antagonist treatment with angiotensin II receptor blocker treatment with angiotensin receptor antagonist A pharmaceutical agent that selectively inhibits angiotensin II receptor activation in the renin-angiotensin-aldosterone system reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. It is primarily used for the reduction of proteinuria and the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. Angiotensin II receptor antagonists bind to and block the activation of angiotensin II type 1 (AT1) receptors, thereby reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. Although this class of agents is also used in diabetic nephropathy (kidney damage due to diabetes) and congestive heart failure, it is primarily used for the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. angiotensin receptor blocker therapy A pharmaceutical agent that selectively inhibits angiotensin II receptor activation in the renin-angiotensin-aldosterone system reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. It is primarily used for the reduction of proteinuria and the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. NCIT:C66930 Angiotensin II receptor antagonists bind to and block the activation of angiotensin II type 1 (AT1) receptors, thereby reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. Although this class of agents is also used in diabetic nephropathy (kidney damage due to diabetes) and congestive heart failure, it is primarily used for the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. NCIT:C66930 Treatment with a group of pharmaceutical drugs used primarily in treatment of essential hypertension. These drugs inhibit the first and rate-limiting step of the renin–angiotensin–aldosterone system, namely the conversion of angiotensinogen to angiotensin I. 2020-06-04T17:32:06Z renin inhibitor therapy Use of a drug that inhibits angiotensin-converting enzyme (ACE) 1, an enzyme that catalyzes the conversion of angiotensin I to angiotensin II. 2020-06-04T18:03:38Z CHEBI:35457 Treatment with ACE-1 inhibitor Treatment with ACE1 inhibitor angiotensin-converting enzyme-1 inhibitor therapy peptidyl-dipeptidase A inhibitor therapy treatment with EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor treatment with angiotensin I-converting enzyme inhibitor ACE1 inhibitor therapy Use of a drug that inhibits angiotensin-converting enzyme (ACE) 2, an enzyme that catalyzes the conversion of angiotensin I to angiotensin II. 2020-06-04T18:17:34Z Treatment with ACE-2 inhibitor angiotensin-converting enzyme-2 inhibitor therapy treatment with EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor treatment with hACE2 inhibitor ACE2 inhibitor therapy Use of a drug that selectively binds to and inhibits metabotropic glutamate receptors. 2020-06-05T20:18:05Z CHEBI:63963 treatment with mGluR antagonist treatment with metabotropic glutamate receptor antagonist treatment with metabotropic glutamate receptor blockade treatment with metabotropic glutamate receptor blocker metabotropic glutamate receptor antagonist therapy Use of a drug that modulates the action of N-methyl-D-aspartate (NMDA) receptors. 2020-06-08T17:47:39Z Treatment with NMDA receptor modulator NMDA receptor modulator agent therapy Treatment with an agent which regulates AMPA recepter signaling. 2020-06-08T17:48:19Z AMPA-targeting agent therapy Use of a drug that selectively binds to and regulates metabotropic glutamate receptors (mGluR). 2020-06-08T17:48:54Z treatment with mGluR modulator treatment with metabotropic glutamate receptor modulator metabotropic glutamate receptor–targeting agent therapy Use of a drug that activates the action of N-methyl-D-aspartate (NMDA) receptors. 2020-06-08T18:14:26Z CHEBI:64571 treatment with NMDA receptor agonist NMDA receptor agonist therapy Use of a drug that selectively binds to and activates AMPA receptors. 2020-06-09T13:52:30Z CHEBI:64102 treatment with AMPA receptor agonist AMPA receptor agonist therapy Use of a drug that selectively binds to and inhibits AMPA receptors. 2020-06-09T13:52:48Z CHEBI:71014 treatment with AMPA receptor antagonist treatment with AMPA receptor blockade treatment with AMPA receptor blocker AMPA receptor antagonist therapy Treatment with an agent that is used to prevent or inhibit diarrhea. 2020-06-09T15:32:19Z CHEBI:55323 anti-diarrheal agent therapy antidiarrhoeal agent therapy treatment with anti-diarrheal drug treatment with antidiarrheal agent treatment with antidiarrheal medication treatment with antidiarrhoeal drug antidiarrheal agent therapy A procedure where a medical specialtist healthcare provider, who was not previously involved in a patient's treatment, reviews a patient's medical history, examines the patient, and makes recommendations as to care and treatment. 2020-07-01T18:18:19Z specialty medical professional consultation specialty medical professional evaluation medical specialist evaluation An assessment by an allergist-immunologist who diagnoses and manages disorders involving immune system conditions such as asthma, anaphylaxis, rhinitis and eczema as well as adverse reactions to drugs, foods and insect stings. An allergist-immunologist also manages immune deficiency diseases and problems related to autoimmune disease, organ transplantation or malignancies of the immune system. 2020-07-01T18:29:08Z allergy and immunologist consultation allergy and immunologist doctor consultation allergy and immunologist doctor evaluation allergy and immunologist evaluation allergy and immunology specialist consultation consultation with allergy and immunologist referral to allergist and immunologist allergist consultation allergist doctor consultation allergist doctor evaluation allergist evaluation consultation with allergist evaluation by an immunologist immunologist evaluation allergy and immunology specialist evaluation An assessment by an allergist-immunologist who diagnoses and manages disorders involving immune system conditions such as asthma, anaphylaxis, rhinitis and eczema as well as adverse reactions to drugs, foods and insect stings. An allergist-immunologist also manages immune deficiency diseases and problems related to autoimmune disease, organ transplantation or malignancies of the immune system. ABMS.org An assessment by a physician who provides anesthesia for patients undergoing surgical, obstetric, diagnostic or therapeutic procedures while monitoring the patient's condition and supporting vital organ functions. The anesthesiologist also diagnoses and treats acute, chronic and/or cancer pain as well as provides resuscitation and medical management for patients with critical illnesses and severe injuries. 2020-07-01T18:42:19Z NCIT:C93067 anesthesiologist consultation anesthesiologist evaluation anesthesiology doctor consultation anesthesiology doctor evaluation anesthesiology specialist consultation consultation with anesthesiologist referral to anesthesiologist anesthesiology specialist evaluation An assessment by a physician who provides anesthesia for patients undergoing surgical, obstetric, diagnostic or therapeutic procedures while monitoring the patient's condition and supporting vital organ functions. The anesthesiologist also diagnoses and treats acute, chronic and/or cancer pain as well as provides resuscitation and medical management for patients with critical illnesses and severe injuries. abms.org An evaluation by an anesthesiologist who specializes in Pediatric Anesthesiology. This specialist provides anesthesia for neonates, infants, children and adolescents undergoing surgical, diagnostic or therapeutic procedures as well as appropriate pre- and post-operative care, advanced life support, and acute pain management. 2020-07-01T18:48:51Z consultation with pediatric anesthesiologist pediatric anesthesiologist consultation pediatric anesthesiologist evaluation pediatric anesthesiology specialist consultation pediatric anesthesiology specialist evaluation An assessment by a colon and rectal surgeon who diagnoses and treats various diseases of the small intestine, colon, rectum, anal canal and perianal area including the organs and tissues related with primary intestinal diseases (liver, urinary and female reproductive system). This specialist treats conditions such as hemorrhoids, fissures (painful tears in the anal lining), abscesses and fistulas (infections located around the anus and rectum). A colon and rectal surgeon diagnoses and treats problems of the intestine and colon such as cancer, polyps (precancerous growths) and inflammatory conditions. 2020-07-01T19:08:36Z colon and rectal surgeon consultation colon and rectal surgeon evaluation colon and rectal surgery specialist consultation colorectal surgeon consultation colorectal surgeon evaluation consultation with colon and rectal surgeon consultation with colon and rectal surgery specialist consultation with colorectal surgeon referral to a colon and rectal surgeon referral to colorectal surgeon colon and rectal surgery specialist evaluation An assessment by a colon and rectal surgeon who diagnoses and treats various diseases of the small intestine, colon, rectum, anal canal and perianal area including the organs and tissues related with primary intestinal diseases (liver, urinary and female reproductive system). This specialist treats conditions such as hemorrhoids, fissures (painful tears in the anal lining), abscesses and fistulas (infections located around the anus and rectum). A colon and rectal surgeon diagnoses and treats problems of the intestine and colon such as cancer, polyps (precancerous growths) and inflammatory conditions. abms.org An assessment by a physician with training and expertise in the diagnosis and medical/surgical management of diseases of the skin, hair and nails, and mucous membranes. 2020-07-01T19:12:58Z consultation with a dermatologist dermatologist consultation dermatologist evaluation dermatology specialist consultation referral to a dermatologist dermatology specialist evaluation An assessment by a physician with training and expertise in the diagnosis and medical/surgical management of diseases of the skin, hair and nails, and mucous membranes. abms.org An assessment by a physician who specializes in immediate decision making and action necessary to prevent death or any further disability both in the pre-hospital setting by directing emergency medical technicians and in the emergency department. This specialist provides immediate recognition, evaluation, care, stabilization and disposition of a generally diversified population of adult and pediatric patients in response to acute illness and injury. 2020-07-01T19:23:12Z assessment by emergency medicine specialist emergency medicine specialist assessment emergency room doctor evaluation emergency medicine specialist evaluation An assessment by a physician who specializes in immediate decision making and action necessary to prevent death or any further disability both in the pre-hospital setting by directing emergency medical technicians and in the emergency department. This specialist provides immediate recognition, evaluation, care, stabilization and disposition of a generally diversified population of adult and pediatric patients in response to acute illness and injury. abms.org An assessment by a physician who provides front-line health care that is accessible, high quality, comprehensive and continuous over time for people of all ages, life stages, backgrounds and conditions. The specialists care for individuals and for entire families, from birth through the end of life, including a broad range of preventive care; healthy lifestyle counseling; mental health care; care of acute illnesses; management of chronic diseases, including patients with multi-morbidity. When needed, they also provide referral and coordination of care with other specialists. 2020-07-01T19:39:31Z consultation with family medicine specialist family medicine specialist consultation family medicine specialist evaluation An assessment by a physician who provides front-line health care that is accessible, high quality, comprehensive and continuous over time for people of all ages, life stages, backgrounds and conditions. The specialists care for individuals and for entire families, from birth through the end of life, including a broad range of preventive care; healthy lifestyle counseling; mental health care; care of acute illnesses; management of chronic diseases, including patients with multi-morbidity. When needed, they also provide referral and coordination of care with other specialists. abms.org An assessment by a physician with special knowledge of the aging process and special skills in the diagnostic, therapeutic, preventive and rehabilitative aspects of illness in the elderly. This specialist cares for geriatric patients in the patient’s home, the office, long-term care settings such as nursing homes, and the hospital. 2020-07-01T19:52:16Z assessment by geriatric medicine specialist consultation with geriatric medicine specialist evaluation by geriatric medicine specialist geriatric medicine specialist consultation referral to geriatric medicine specialist geriatric medicine specialist evaluation An assessment by a physician with special knowledge of the aging process and special skills in the diagnostic, therapeutic, preventive and rehabilitative aspects of illness in the elderly. This specialist cares for geriatric patients in the patient’s home, the office, long-term care settings such as nursing homes, and the hospital. abms.org An assessment by a physician who specializes in Hospice and Palliative Medicine who provides care to prevent and relieve the suffering experienced by patients with life-limiting illnesses. This specialist works with an interdisciplinary hospice or palliative care team to optimize quality of life while addressing the physical, psychological, social and spiritual needs of both patient and family. 2020-07-01T19:53:31Z consultation with hospice and palliative medicine specialist hospice and palliative medicine specialist consultation referral to hospice and palliative medicine specialist assessment by palliative care specialist consultation with palliative care specialist evaluation by palliative care specialist palliative care specialist consultation palliative care specialist evaluation palliative care specialist referral referral to palliative care specialist hospice and palliative medicine specialist evaluation An assessment by a physician who diagnoses and treats patients experiencing problems with acute or chronic pain, or pain related to cancer, in both hospital and outpatient settings and coordinates care needs with other specialists. 2020-07-01T19:56:48Z assessment by pain medicine specialist consultation with pain medicine specialist evaluation by pain medicine specialist pain medicine specialist consultation referral to a pain medicine specialist pain medicine specialist evaluation An assessment by a physician who diagnoses and treats patients experiencing problems with acute or chronic pain, or pain related to cancer, in both hospital and outpatient settings and coordinates care needs with other specialists. abms.org An assesment a specialist focuses on preventing, diagnosing, and treating injuries related to participating in sports and/or exercise. In addition to the study of those fields that focus on prevention, diagnosis, treatment, and management of injuries, Sports Medicine specialists also deal with illnesses and diseases that might have effects on health and physical performance. 2020-07-01T19:59:07Z consultation with sports medicine specialist referral to a sports medicine specialist sports medicine specialist consultation sports medicine specialist evaluation An assesment a specialist focuses on preventing, diagnosing, and treating injuries related to participating in sports and/or exercise. In addition to the study of those fields that focus on prevention, diagnosis, treatment, and management of injuries, Sports Medicine specialists also deal with illnesses and diseases that might have effects on health and physical performance. abms.org An assessment with a specialist who has expertise in the diagnosis and management of clinical conditions that occur during sleep, that disturb sleep, or that are affected by disturbances in the wake-sleep cycle. This specialist is skilled in the analysis and interpretation of comprehensive polysomnography, and well versed in emerging research and management of a sleep laboratory. 2020-07-01T20:01:47Z assessment by sleep medicine specialist assessment by sleep specialist consultation with sleep medicine specialist consultation with sleep specialist evaluation by sleep medicine specialist evaluation by sleep specialist referral to sleep medicine specialist referral to sleep specialist sleep medicine specialist consultation sleep specialist assessment sleep specialist consultation sleep specialist evaluation sleep specialist referral sleep study evaluation sleep medicine specialist evaluation An assessment with a specialist who has expertise in the diagnosis and management of clinical conditions that occur during sleep, that disturb sleep, or that are affected by disturbances in the wake-sleep cycle. This specialist is skilled in the analysis and interpretation of comprehensive polysomnography, and well versed in emerging research and management of a sleep laboratory. abms.org An assessment by a personal physician who provides long-term, comprehensive care in the office and in the hospital, managing both common and complex illnesses of adolescents, adults and the elderly. Internists are trained in the diagnosis and treatment of cancer, infections and diseases affecting the heart, blood, kidneys, joints and the digestive, respiratory and vascular systems. Internists are also trained in the essentials of primary care internal medicine, which incorporates an understanding of disease prevention, wellness, substance abuse, mental health and effective treatment of common problems of the eyes, ears, skin, nervous system and reproductive organs. 2020-07-01T20:07:16Z consultation with internal medicine specialist consultation with internist internal medicine specialist consultation internist consultation internist evaluation referral to an internal medicine specialist referral to an internist internal medicine specialist evaluation An assessment by a personal physician who provides long-term, comprehensive care in the office and in the hospital, managing both common and complex illnesses of adolescents, adults and the elderly. Internists are trained in the diagnosis and treatment of cancer, infections and diseases affecting the heart, blood, kidneys, joints and the digestive, respiratory and vascular systems. Internists are also trained in the essentials of primary care internal medicine, which incorporates an understanding of disease prevention, wellness, substance abuse, mental health and effective treatment of common problems of the eyes, ears, skin, nervous system and reproductive organs. abms.org An assessment with a multidisciplinary health care specialist trained in the unique physical, psychological and social characteristics of adolescents, their health care problems and needs. 2020-07-01T20:13:15Z adolescent medicine specialist consultation adolescent medicine specialist evaluation assessment by adolescent medicine specialist consultation with adolescent medicine specialist evaluation by adolescent medicine specialist referral to adolescent medicine specialist adolescent medicine specialist evaluation An assessment with a multidisciplinary health care specialist trained in the unique physical, psychological and social characteristics of adolescents, their health care problems and needs. abms.org An assessment by an internist who specializes in diseases of the heart and blood vessels and manages complex cardiac conditions, such as heart attacks and life-threatening, abnormal heartbeat rhythms. 2020-07-01T20:16:52Z assessment by cardiologist cardiologist consultation cardiologist evaluation cardiologist referral cardiovascular disease internist consultation cardiovascular disease internist evaluation consultation with cardiologist consultation with cardiovascular disease internist consultation with internal medicine cardiovascular disease specialist evaluation by cardiologist internal medicine cardiovascular disease specialist consultation referral to cardiologist referral to cardiovascular disease internist cardiologist evaluation An assessment by an internist who specializes in diseases of the heart and blood vessels and manages complex cardiac conditions, such as heart attacks and life-threatening, abnormal heartbeat rhythms. abms.org An assessment by a specialist who specializes in intricate technical procedures to evaluate heart rhythms and determine appropriate treatment. 2020-07-01T20:30:10Z consultation with clinical cardiac electrophysiologist consultation with clinical cardiac electrophysiology specialist internal medicine clinical cardiac electrophysiologist consultation internal medicine clinical cardiac electrophysiology specialist consultation internal medicine clinical cardiac electrophysiology specialist evaluation referral to a clinical electrophysiologist clinical cardiac electrophysiologist evaluation An assessment by a specialist who specializes in intricate technical procedures to evaluate heart rhythms and determine appropriate treatment. abms.org An assessment with an internist trained in critical care medicine who has expertise in the diagnosis, treatment and support of critically ill and injured patients, particularly trauma victims and patients with multiple organ dysfunction. 2020-07-01T20:35:47Z consultation with critical care medicine internist consultation with internal medicine critical care medicine specialist internal medicine critical care medicine consultation internal medicine critical care medicine evaluation referral to critical care internist critical care medicine internist evaluation An assessment with an internist who specializes in the diagnosis and management of disorders of hormones and their actions, metabolic disorders, and neoplasia of the endocrine glands. This specialist cares for patients with diabetes mellitus, thyroid disorders, disorders of calcium and bone, hyperlipidemia, obesity and nutritional disorders, pituitary disorders, reproductive and gonadal disorders, adrenal diseases, and endocrine hypertension. 2020-07-01T20:43:06Z consultation with endocrinologist consultation with endocrinology, diabetes and metabolism specialist endocrinologist consultation endocrinology, diabetes and metabolism specialist consultation endocrinology, diabetes and metabolism specialist evaluation referral to endocrinologist endocrinologist evaluation An assessment with an internist who specializes in the diagnosis and management of disorders of hormones and their actions, metabolic disorders, and neoplasia of the endocrine glands. This specialist cares for patients with diabetes mellitus, thyroid disorders, disorders of calcium and bone, hyperlipidemia, obesity and nutritional disorders, pituitary disorders, reproductive and gonadal disorders, adrenal diseases, and endocrine hypertension. abms.org An evaluation with an internist who specializes in diagnosis and treatment of diseases of the digestive organs including the stomach, bowels, liver and gallbladder. This specialist treats conditions such as abdominal pain, ulcers, diarrhea, cancer and jaundice and performs complex diagnostic and therapeutic procedures using endoscopes to visualize internal organs. 2020-07-01T20:46:33Z consultation with gastroenterologist consultation with gastroenterology specialist gastroenterologist consultation gastroenterology specialist evaluation referral to gastroenterologist gastroenterologist evaluation An evaluation with an internist who specializes in diagnosis and treatment of diseases of the digestive organs including the stomach, bowels, liver and gallbladder. This specialist treats conditions such as abdominal pain, ulcers, diarrhea, cancer and jaundice and performs complex diagnostic and therapeutic procedures using endoscopes to visualize internal organs. abms.org An assessment by an internist with additional training who specializes in diseases of the blood, spleen and lymph. This specialist treats conditions such as anemia, clotting disorders, sickle cell disease, hemophilia, leukemia and lymphoma. 2020-07-01T21:00:28Z consultation with hematologist hematologist consultation hematology specialist consultation hematology specialist evaluation referral to hematologist hematologist evaluation An assessment by an internist with additional training who specializes in diseases of the blood, spleen and lymph. This specialist treats conditions such as anemia, clotting disorders, sickle cell disease, hemophilia, leukemia and lymphoma. abms.org An assessment by an internist who deals with infectious diseases of all types and in all organ systems. Infectious disease specialists may also have expertise in preventive medicine and travel medicine. 2020-07-02T17:10:50Z consultation with infectious disease specialist infectious disease specialist consultation infectious disease specialist evaluation referral to infectious disease internist infectious disease internist evaluation An assessment by an internist who deals with infectious diseases of all types and in all organ systems. Infectious disease specialists may also have expertise in preventive medicine and travel medicine. abms.org An assessment by an internist who specializes in the diagnosis and treatment of all types of cancer and other benign and malignant tumors. This specialist decides on and administers therapy for these malignancies, as well as consults with surgeons and radiotherapists on other treatments for cancer. 2020-07-02T17:50:50Z consultation with medical oncologist consultation with medical oncology internist medical oncologist consultation medical oncology internist consultation medical oncology internist evaluation referral to oncologist medical oncologist evaluation An assessment by an internist who specializes in the diagnosis and treatment of all types of cancer and other benign and malignant tumors. This specialist decides on and administers therapy for these malignancies, as well as consults with surgeons and radiotherapists on other treatments for cancer. abms.org An assessment by an internist who treats disorders of the kidney, high blood pressure, fluid and mineral balance, and dialysis of body wastes when the kidneys do not function. This specialist consults with surgeons about kidney transplantation. 2020-07-02T18:23:18Z consultation with nephrologist consultation with nephrology internist nephrologist consultation nephrology internist consultation nephrology internist evaluation referral to nephrologist nephrologist evaluation An assessment by an internist who treats disorders of the kidney, high blood pressure, fluid and mineral balance, and dialysis of body wastes when the kidneys do not function. This specialist consults with surgeons about kidney transplantation. abms.org An assessment by an internist who treats diseases of the lungs and airways. The specialist diagnoses and treats cancer, pneumonia, pleurisy, asthma, occupational and environmental diseases, bronchitis, sleep disorders, emphysema and other complex disorders of the lungs. 2020-07-02T18:32:06Z consultation with pulmonary disease internist consultation with pulmonary disease specialist consultation with pulmonologist pulmonary disease internist consultation pulmonary disease internist evaluation pulmonologist consultation referral to pulmonologist pulmonologist evaluation An assessment by an internist who treats diseases of the lungs and airways. The specialist diagnoses and treats cancer, pneumonia, pleurisy, asthma, occupational and environmental diseases, bronchitis, sleep disorders, emphysema and other complex disorders of the lungs. abms.org An assessment by an internist who treats diseases of joints, muscle, bones and tendons. This specialist diagnoses and treats arthritis, back pain, muscle strains, common athletic injuries and collagen diseases. 2020-07-02T19:00:04Z consultation with rheumatologist consultation with rheumatology internist referral to rhematologist rheumatologist consultation rheumatology internist consultation rheumatology internist evaluation rheumatology specialist consultation rheumatology specialist evaluation rheumatologist evaluation An assessment by an internist who treats diseases of joints, muscle, bones and tendons. This specialist diagnoses and treats arthritis, back pain, muscle strains, common athletic injuries and collagen diseases. abms.org An assessment with a specialist who directs and interprets a wide range of specialized, laboratory biochemical genetic analyses relevant to the diagnosis and management of inherited metabolic disorders. The specialist acts as a consultant regarding laboratory diagnosis on a broad range of inborn errors of metabolism. 2020-07-02T20:14:07Z clinical biochemical geneticist consultation consultation with clinical biochemical geneticist referral to a clinical biochemical geneticist clinical biochemical geneticist evaluation An assessment with a specialist who directs and interprets a wide range of specialized, laboratory biochemical genetic analyses relevant to the diagnosis and management of inherited metabolic disorders. The specialist acts as a consultant regarding laboratory diagnosis on a broad range of inborn errors of metabolism. abms.org An assessment with a specialist who provides comprehensive diagnostic, management, therapeutic, and counseling services for individuals and families at risk for clinical disorders with a genetic basis. The specialist is trained to evaluate individuals of all ages for hereditary conditions. 2020-07-02T20:16:59Z clinical geneticist consultation clinical geneticist evaluation clinical genetics and genomics specialist consultation consultation with clinical geneticist consultation with clinical genetics and genomics specialist referral to a clinical geneticist clinical genetics and genomics specialist evaluation An assessment with a specialist who provides comprehensive diagnostic, management, therapeutic, and counseling services for individuals and families at risk for clinical disorders with a genetic basis. The specialist is trained to evaluate individuals of all ages for hereditary conditions. abms.org An assessment or consultation by a diplomate certified in Laboratory Genetics and Genomics who directs and interprets both clinical cytogenetic and molecular genetic analyses relevant to the diagnosis and management of human genetic disease. This specialist acts as a consultant in laboratory diagnoses for a broad range of molecular and chromosomal-based disorders, including both inherited and acquired conditions. 2020-07-02T20:29:00Z clinical laboratory geneticist evaluation An assessment or consultation by a diplomate certified in Laboratory Genetics and Genomics who directs and interprets both clinical cytogenetic and molecular genetic analyses relevant to the diagnosis and management of human genetic disease. This specialist acts as a consultant in laboratory diagnoses for a broad range of molecular and chromosomal-based disorders, including both inherited and acquired conditions. abms.org An assessment by this specialist provides care for adult and pediatric patients in the treatment of pain or pathological processes that may modify the function or activity of the central nervous system (e.g., brain, hypophysis, and spinal cord), the peripheral nervous system (e.g., cranial, spinal, and peripheral nerves), the autonomic nervous system, the supporting structures of these systems (e.g., meninges, skull & skull base, and vertebral column), and their vascular supply (e.g., intracranial, extracranial, and spinal vasculature). 2020-07-08T15:24:04Z NCIT:C17722 consultation with neurological surgeon consultation with neurological surgery specialist consultation with neurosurgeon neurological surgeon consultation neurological surgeon evaluation neurological surgery specialist consultation neurosurgeon consultation neurosurgeon evaluation referral to neurosurgeon neurological surgery specialist evaluation An assessment by this specialist provides care for adult and pediatric patients in the treatment of pain or pathological processes that may modify the function or activity of the central nervous system (e.g., brain, hypophysis, and spinal cord), the peripheral nervous system (e.g., cranial, spinal, and peripheral nerves), the autonomic nervous system, the supporting structures of these systems (e.g., meninges, skull & skull base, and vertebral column), and their vascular supply (e.g., intracranial, extracranial, and spinal vasculature). abms.org An evaluation by a specialist that uses molecular tracers (usually labeled with radioactive atoms) for diagnosis and therapy. 2020-07-08T17:46:13Z consultation with nuclear medicine specialist nuclear medicine specialist consultation referral to nuclear medicine specialist These labeled tracers are most often used to produce images that provide information about organ function, as well as cellular function on a molecular level (molecular imaging). Molecular imaging can be combined with anatomical imaging by using specialized cameras. The most common diagnostic applications of Nuclear Medicine include the early detection of coronary artery disease, cancer diagnosis and staging and the evaluation of the effect of cancer treatment. The fusion of molecular and anatomical information increases diagnostic accuracy and changes medical management. Radioactive materials are also used to treat a variety of health problems, including thyroid disorders and cancer. nuclear medicine specialist evaluation An evaluation by a specialist that uses molecular tracers (usually labeled with radioactive atoms) for diagnosis and therapy. abms.org These labeled tracers are most often used to produce images that provide information about organ function, as well as cellular function on a molecular level (molecular imaging). Molecular imaging can be combined with anatomical imaging by using specialized cameras. The most common diagnostic applications of Nuclear Medicine include the early detection of coronary artery disease, cancer diagnosis and staging and the evaluation of the effect of cancer treatment. The fusion of molecular and anatomical information increases diagnostic accuracy and changes medical management. Radioactive materials are also used to treat a variety of health problems, including thyroid disorders and cancer. abms.org An evaluation with a specialist who focuses on the health of women before, during and after childbearing years, diagnosing and treating conditions of the reproductive system and associated disorders. 2020-07-08T17:53:55Z OB/GYN specialist consultation OB/GYN specialist evaluation consultation OB/GYN specialist consultation obstetrician/gynecologist consultation with obstetrics and gynecology specialist obstetrician/gynecologist consultation obstetrician/gynecologist evaluation obstetrics and gynecology specialist consultation obstetrics/gynecology specialist consultation obstetrics/gynecology specialist evaluation referral to OB/GYN specialist obstetrics and gynecology specialist evaluation An evaluation with a specialist who focuses on the health of women before, during and after childbearing years, diagnosing and treating conditions of the reproductive system and associated disorders. abms.org An evaluation by a specialist focused on the medical and surgical care of the eyes. Ophthalmologists are the only physicians medically trained to manage the complete range of the eye and vision care. They can prescribe glasses and contact lenses, dispense medications, diagnose and treat eye conditions and diseases and perform surgeries. 2020-07-08T20:14:31Z consultation with ophthalmologist ophthalmologist consultation ophthalmologist referral ophthalmology specialist consultation ophthalmology specialist evaluation referral to ophthalmologist referral to ophthalmology specialist referral to optometrist ophthalmologist evaluation An evaluation by a specialist focused on the medical and surgical care of the eyes. Ophthalmologists are the only physicians medically trained to manage the complete range of the eye and vision care. They can prescribe glasses and contact lenses, dispense medications, diagnose and treat eye conditions and diseases and perform surgeries. abms.org An evaluation by a specialist who has expertise in the surgical and medical care for all structures of the musculoskeletal system directly affected by participation in sporting activity. This specialist is proficient in areas including conditioning, training and fitness, athletic performance and the impact of dietary supplements, pharmaceuticals, and nutrition on performance and health, coordination of care within the team setting utilizing other health care professionals, field evaluation and management, soft tissue biomechanics and injury healing and repair. Knowledge and understanding of the principles and techniques of rehabilitation, athletic equipment and orthotic devices enables the specialist to prevent and manage athletic injuries. 2020-07-08T20:31:50Z consultation with sports medicine orthopedic surgeon referral to sports medicine orthopedic surgeon referral to sports medicine orthopedist sports medicine orthopedic surgeon consultation sports medicine orthopedic surgeon evaluation sports medicine orthopedist consultation sports medicine orthopedist referral sports medicine orthopedist evaluation An evaluation by a specialist who has expertise in the surgical and medical care for all structures of the musculoskeletal system directly affected by participation in sporting activity. This specialist is proficient in areas including conditioning, training and fitness, athletic performance and the impact of dietary supplements, pharmaceuticals, and nutrition on performance and health, coordination of care within the team setting utilizing other health care professionals, field evaluation and management, soft tissue biomechanics and injury healing and repair. Knowledge and understanding of the principles and techniques of rehabilitation, athletic equipment and orthotic devices enables the specialist to prevent and manage athletic injuries. abms.org An assessment by a specialist with expertise in the surgical, medical and rehabilitative care of patients with diseases, injuries, and disorders affecting the hand, wrist and forearm. 2020-07-08T20:34:54Z consultation with hand surgeon consultation with orthopedic hand surgeon hand surgeon consultation referral to hand surgeon referral to orthopedic hand surgeon Common conditions treated by a hand surgeon include carpal tunnel syndrome, trigger fingers, ganglia (lumps), sports injuries to the hand and wrist, and hand injuries involving cut tendons, nerves and arteries. Hand Surgeons may be General Surgeons, Orthopedic Surgeons or Plastic Surgeons who have received additional training in this area. hand surgeon evaluation An assessment by a specialist with expertise in the surgical, medical and rehabilitative care of patients with diseases, injuries, and disorders affecting the hand, wrist and forearm. abms.org Common conditions treated by a hand surgeon include carpal tunnel syndrome, trigger fingers, ganglia (lumps), sports injuries to the hand and wrist, and hand injuries involving cut tendons, nerves and arteries. Hand Surgeons may be General Surgeons, Orthopedic Surgeons or Plastic Surgeons who have received additional training in this area. abms.org An assessment by a specialist who provides medical and/or surgical therapy or prevention of diseases, allergies, neoplasms, deformities, disorders and/or injuries of the ears, nose, sinuses, throat, respiratory and upper alimentary systems, face, jaws and the other head and neck systems. 2020-07-09T16:10:20Z consultation by otolaryngology specialist consultation with head and neck surgeon consultation with otolaryngologist evaluation by otolaryngologist head and neck surgeon consultation head and neck surgeon evaluation head and neck surgeon referral otolaryngologist consultation otolaryngologist referral otolaryngology specialist consultation otolaryngology specialist evaluation otolaryngology specialist referral otorhinolaryngologist evaluation referral to head and neck surgeon referral to otolaryngologist Head and neck oncology, facial plastic and reconstructive surgery and the treatment of disorders of hearing and voice are fundamental areas of expertise. otolaryngologist evaluation An assessment by a specialist who provides medical and/or surgical therapy or prevention of diseases, allergies, neoplasms, deformities, disorders and/or injuries of the ears, nose, sinuses, throat, respiratory and upper alimentary systems, face, jaws and the other head and neck systems. abms.org Head and neck oncology, facial plastic and reconstructive surgery and the treatment of disorders of hearing and voice are fundamental areas of expertise. abms.org An assessment by a specialist concerned with the physical, emotional, and social health of children from birth to young adulthood. 2020-07-09T17:48:27Z evaluation by pediatrician pediatrician consultation Pediatric care encompasses a broad spectrum of health services ranging from preventive health care to the diagnosis and treatment of acute and chronic diseases. Pediatricians understand the many factors that affect the growth and development of children. They understand that children are not simply small adults. Children change rapidly, and they must be approached with an appreciation for their stage of physical and mental development. pediatrician evaluation An assessment by a specialist concerned with the physical, emotional, and social health of children from birth to young adulthood. abms.org Pediatric care encompasses a broad spectrum of health services ranging from preventive health care to the diagnosis and treatment of acute and chronic diseases. Pediatricians understand the many factors that affect the growth and development of children. They understand that children are not simply small adults. Children change rapidly, and they must be approached with an appreciation for their stage of physical and mental development. abms.org An evaluation with a specialist who possesses special skills, training and experience to foster understanding and promotion of optimal development of children and families through research, education, clinical care and advocacy efforts. This physician assists in the prevention, diagnosis and management of developmental difficulties and problematic behaviors in children and in the family dysfunctions that compromise children’s development. 2020-07-09T18:05:01Z consultation with developmental-behavior pediatrician developmental-behavior pediatrician consultation developmental-behavior pediatrician referral referral to developmental-behavior pediatrician developmental-behavior pediatrician evaluation An evaluation with a specialist who possesses special skills, training and experience to foster understanding and promotion of optimal development of children and families through research, education, clinical care and advocacy efforts. This physician assists in the prevention, diagnosis and management of developmental difficulties and problematic behaviors in children and in the family dysfunctions that compromise children’s development. abms.org An evaluation by a specialist who provides expert care to infants, children and adolescents who have diseases that result from an abnormality in the endocrine glands (glands which secrete hormones). These diseases include diabetes mellitus, growth failure, unusual size for age, early or late pubertal development, birth defects, the genital region and disorders of the thyroid, the adrenal and pituitary glands. 2020-07-09T18:48:58Z assessment by pediatric endocrinologist consultation with pediatric endocrinologist evaluation by pediatric endocrinologist pediatric endocrinologist consultation pediatric endocrinologist referral referral to pediatric endocrinologist pediatric endocrinologist evalutation An evaluation by a specialist who provides expert care to infants, children and adolescents who have diseases that result from an abnormality in the endocrine glands (glands which secrete hormones). These diseases include diabetes mellitus, growth failure, unusual size for age, early or late pubertal development, birth defects, the genital region and disorders of the thyroid, the adrenal and pituitary glands. abms.org Evaluation by a specialist who provides comprehensive care to patients with cardiovascular problems. This specialist is skilled in selecting, performing, and evaluating the structural and functional assessment of the heart and blood vessels, and the clinical evaluation of cardiovascular disease. 2020-07-09T18:54:16Z assessment by pediatric cardiologist consultation with pediatric cardiologist evaluation by pediatric cardiologist pediatric cardiologist consultation pediatric cardiologist referral referral to pediatric cardiologist pediatric cardiologist evaluation Evaluation by a specialist who provides comprehensive care to patients with cardiovascular problems. This specialist is skilled in selecting, performing, and evaluating the structural and functional assessment of the heart and blood vessels, and the clinical evaluation of cardiovascular disease. abms.org Assessment by a specialist who treats patients with disorders or disabilities in the muscles, bones, and nervous system, including neck or back pain, sports and work injuries, stroke, brain injury, spinal cord injury, spasticity, and any other disability or disorder that affects function. 2020-07-09T19:45:07Z assessment by physiatrist assessment by physical medicine and rehabilitation specialist consultation by physiatrist consultation with physical medicine and rehabilitation specialist evaluation by physical medicine and rehabilitation specialist physiatrist assessment physiatrist consultation physiatrist referral physical medicine and rehabilitation specialist assessment physical medicine and rehabilitation specialist consultation physical medicine and rehabilitation specialist evaluation physical medicine and rehabilitation specialist referral referral to physiatrist Treatment modalities by a physiatrist may include medications, injections, therapeutic exercise, electrodiagnosis, and any equipment required for daily activities. physiatrist evaluation Assessment by a specialist who treats patients with disorders or disabilities in the muscles, bones, and nervous system, including neck or back pain, sports and work injuries, stroke, brain injury, spinal cord injury, spasticity, and any other disability or disorder that affects function. abms.org Treatment modalities by a physiatrist may include medications, injections, therapeutic exercise, electrodiagnosis, and any equipment required for daily activities. abms.org An assessment with a specialist who focuses on the repair, reconstruction or replacement of physical defects of form or function involving the skin, musculoskeletal system, craniomaxillofacial structures, hand, extremities, breast and trunk and external genitalia or cosmetic enhancement of these areas of the body. 2020-07-09T19:54:01Z consultation with plastic surgeon evaluation by plastic surgeon plastic surgeon assessment plastic surgeon consultation plastic surgeon referral plastic surgeon evaluation An assessment with a specialist who focuses on the repair, reconstruction or replacement of physical defects of form or function involving the skin, musculoskeletal system, craniomaxillofacial structures, hand, extremities, breast and trunk and external genitalia or cosmetic enhancement of these areas of the body. abms.org Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders. 2020-07-09T20:37:35Z assessment by psychiatrist consult with psychiatrist evaluation by psychiatrist psychiatrist assessment psychiatrist consultation psychiatrist referral referral to psychiatrist psychiatrist evaluation Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders. abms.org Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders in children and adolescence. 2020-07-09T20:41:16Z assessment by child and adolescent psychiatrist assessment by child psychiatrist child and adolescent psychiatrist assessment child and adolescent psychiatrist consultation child and adolescent psychiatrist referral child psychiatrist assessment child psychiatrist evaluation child psychiatrist referral consultation with child and adolescent psychiatrist consultation with child psychiatrist evaluation by child and adolescent psychiatrist referral to child and adolescent psychiatrist referral to child psychiatrist child and adolescent psychiatrist evaluation Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders in children and adolescence. abms.org An evaluation a specialist who treats all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures. 2020-07-10T16:33:00Z consultation with neurologist neurologist assessment neurologist consultation neurologist referral referral to neurologist neurologist evaluation An evaluation a specialist who treats all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures. abms.org Evaluation with a specialist who diagnose and treat all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures in infants, children, and adolescents. They also have special competence in genetic and metabolic problems, malformation, retardation and other neurodevelopmental problems of childhood. 2020-07-10T18:35:13Z assessment by pediatric neurologist child neurologist assessment child neurologist consultation consultation with child neurologist consultation with pediatric neurologist evaluation by child neurologist pediatric neurologist assessment pediatric neurologist consultation pediatric neurologist evaluation referral to child neurologist referral to pediatric neurologist child neurologist evaluation Evaluation with a specialist who diagnose and treat all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures in infants, children, and adolescents. They also have special competence in genetic and metabolic problems, malformation, retardation and other neurodevelopmental problems of childhood. abms.org Evaluation by a specialist who uses imaging methodologies to diagnose and manage patients and provide therapeutic options. 2020-07-10T19:06:21Z assessment by radiologist evaluation by radiologist radiologist assessment radiologist evaluation Evaluation by a specialist who uses imaging methodologies to diagnose and manage patients and provide therapeutic options. abms.org Evaluation by an expert in the diagnosis and care of patients with diseases and disorders affecting the abdomen, digestive tract, endocrine system, breast, skin and blood vessels. A general surgeon is also trained in the treatment of patients who are injured or critically ill, and in the care of pediatric and cancer patients. General surgeons are skilled in the use of minimally invasive techniques and endoscopies. 2020-07-10T19:33:25Z assessment by general surgeon consultation with general surgeon evaluation by general surgeon general surgeon assessment general surgeon consultation general surgeon evaluation general surgeon evaluation Evaluation by an expert in the diagnosis and care of patients with diseases and disorders affecting the abdomen, digestive tract, endocrine system, breast, skin and blood vessels. A general surgeon is also trained in the treatment of patients who are injured or critically ill, and in the care of pediatric and cancer patients. General surgeons are skilled in the use of minimally invasive techniques and endoscopies. abms.org An evaluation by a specialist who performs preoperative, operative, and postoperative management of patients with disorders of the arterial, venous and lymphatic systems, excluding vessels of the brain and the heart. 2020-07-10T19:54:59Z assessment by vascular surgeon evaluation by vascular surgeon referral by vascular surgeon vascular surgeon assessment vascular surgeon consultation vascular surgeon referral vascular surgeon evaluation Evaluation by a specialist who focuses on the operative, perioperative, and surgical critical care of patients with acquired and congenital pathologic conditions within the chest. 2020-07-10T20:40:44Z assessment by thoracic and cardiac surgeon assessment by thoracic surgeon consultation with thoracic and cardiac surgeon consultation with thoracic surgeon evaluation by thoracic and cardiac surgeon evaluation by thoracic surgeon referral to thoracic and cardiac surgeon referral to thoracic surgeon thoracic and cardiac surgeon assessment thoracic and cardiac surgeon consultation thoracic and cardiac surgeon referral thoracic surgeon assessment thoracic surgeon evaluation thoracic surgeon referral thoracic and cardiac surgeon evaluation Evaluation by a specialist who focuses on the operative, perioperative, and surgical critical care of patients with acquired and congenital pathologic conditions within the chest. abms.org An evaluation by a specialist that focuses on diagnosing and treating disorders of the urinary tracts of males and females, and on the reproductive system of males. This specialist manages non-surgical problems such as urinary tract infections and benign prostatic hyperplasia, as well as surgical problems such as the surgical management of cancers, the correction of congenital abnormalities, and correcting stress incontinence. 2020-07-10T20:44:20Z assessment by genitourinary surgeon assessment by urologist consultation with genitourinary surgeon consultation with urologist evaluation by genitourinary surgeon evaluation by urologist genitourinary surgeon consultation genitourinary surgeon evaluation referral to genitourinary surgeon referral to urologist urologist assessment urologist consultation urologist referral urologist evaluation An evaluation by a specialist that focuses on diagnosing and treating disorders of the urinary tracts of males and females, and on the reproductive system of males. This specialist manages non-surgical problems such as urinary tract infections and benign prostatic hyperplasia, as well as surgical problems such as the surgical management of cancers, the correction of congenital abnormalities, and correcting stress incontinence. abms.org Evaluation by a physician who specializes in the evaluation and treatment of of the brain. 2020-07-13T17:01:27Z psychiatry and neurology specialist evaluation Assessment by a specialist who has expertise in the diagnosis and preoperative, operative, and postoperative management of patient care. 2020-07-13T17:57:48Z surgeon evaluation Assessment by a specialist who has expertise in the diagnosis and preoperative, operative, and postoperative management of patient care. abms.org A procedure, also known as sonohysterography or saline infusion sonography, using a minimally invasive ultrasound technique to view the inside of the uterus. Sterile saline is injected into the endometrial cavity thereby distending the endometrial cavity, providing good visualization of the anatomic structures within. 2020-07-16T14:18:41Z NCIT:C38066 diagnostic hysterosonography medical hysterosonography sonohysterography saline infusion sonography hysterosonography A procedure, also known as sonohysterography or saline infusion sonography, using a minimally invasive ultrasound technique to view the inside of the uterus. Sterile saline is injected into the endometrial cavity thereby distending the endometrial cavity, providing good visualization of the anatomic structures within. NCIT:C38066 An invasive procedure in which sound waves (called ultrasound) are bounced off of vascular tissues from within the vessel and the echoes produce a picture (sonogram). 2020-07-16T14:31:24Z NCIT:C99535 IVUS diagnostic intravascular ultrasound intravascular sonography intravascular ultrasound medical intravascular ultrasonography intravascular ultrasonography An invasive procedure in which sound waves (called ultrasound) are bounced off of vascular tissues from within the vessel and the echoes produce a picture (sonogram). NCIT:C99535 IVUS A technique in which sound waves are sent out by an ultrasound probe that has been inserted in the vagina and a computer uses the ultrasound echoes to create an image of the female genital tract. The test can be performed to evaluate women with infertility problems, abnormal bleeding, sources of unexplained pain, congenital malformations of the uterus and ovaries, and possible tumors and infection. 2020-07-16T14:38:38Z NCIT:C17644 TVS TVU diagnostic transvaginal ultrasound medical transvaginal sonography transvaginal sonography transvaginal ultrasound transvaginal ultrasound examination transvaginal ultrasonography A technique in which sound waves are sent out by an ultrasound probe that has been inserted in the vagina and a computer uses the ultrasound echoes to create an image of the female genital tract. The test can be performed to evaluate women with infertility problems, abnormal bleeding, sources of unexplained pain, congenital malformations of the uterus and ovaries, and possible tumors and infection. NCIT:C17644 TVS TVU A procedure that uses sound waves to create a video image of the pelvic organs and tissues. A small, lubricated probe placed into the rectum releases sound waves, which create echoes as they enter a pelvic organ. The echoes that bounce back are sent to a computer that translates the pattern of echoes into a picture of the specific organ under examination. This procedure is most often used to evaluate the prostate gland. 2020-07-16T14:46:48Z NCIT:C18315 ERUS TRUS diagnostic transrectal ultrasound endorectal sonography endorectal ultrasound endorectal ultrsonography medical transrectal ultrasound transrectal sonography transrectal ultrasound transrectal ultrasound examination transrectal ultrasonography A procedure that uses sound waves to create a video image of the pelvic organs and tissues. A small, lubricated probe placed into the rectum releases sound waves, which create echoes as they enter a pelvic organ. The echoes that bounce back are sent to a computer that translates the pattern of echoes into a picture of the specific organ under examination. This procedure is most often used to evaluate the prostate gland. NCIT:C18315 ERUS TRUS A procedure where a allied health care provider who was not previously involved in a patient's treatment, reviews a patient's medical history, examines the patient, and makes recommendations as to care and treatment. This is care provided by health care practitioners who are distinct providers from dentistry, nursing, medicine, and pharmacy health care professionals. 2020-10-06T17:59:44Z allied health clnicians support allied health practitioner consultation allied health practitioner evaluation allied health professional consultation assessment by allied health professional consulationat with allied health professional consultation with allied health practitioner evaluation by allied health professional evaluation managed by allied health professional support by allied health clinicians allied health professional evaluation An initial evaluation or assessment by a health professional trained to help people who are ill or disabled learn to manage their daily activities. 2020-10-06T19:51:46Z OT assessment OT consult OT eval OT evaluation OT treatment assessment by occupational therapist evaluation by occupational therapist managed by occupational therapist occupational therapist assessment occupational therapist consultation occupational therapist management occupational therapist treatment treatment by OT treatment by occupational therapist occupational therapist evaluation OT assessment OT consult OT eval OT evaluation OT treatment treatment by OT An initial assessment by a professional who works to prevent, assess, diagnose, and treat speech, language, social communication, congnitive-communication, and swallowing disorders. 2020-10-08T15:24:36Z assessment with speech therapist consult with speech therapist evaluation by speech and language therapist speech and language pathologist evaluation speech and language therapist evaluation speech therapist assessment speech therapist consultation speech therapist evaluation speech-language pathologist assessment speech-language pathologist examination speech/language pathologist evaluation speech/language therapist evaluation speech-language pathologist evaluation An initial assessment by a professional who works to prevent, assess, diagnose, and treat speech, language, social communication, congnitive-communication, and swallowing disorders. asha.org A first assessment by a trained non-medical health professional who specializes in the identification, testing, habilitation and rehabilitation of hearing loss and other auditory and balance disorders. Particularly, an audiologist may be involved in diagnostic and screening procedures to determine hearing deficits, as well as in assessment of amplification devices and instruction in their care, training in speechreading, and may serve as consultant to government and industry on issues concerning environmental, noise-induced hearing loss. 2020-10-08T20:20:40Z NCIT:C51804 assessment by audiologist audilogic assessment audiologic evaluation audiology evaluation audiology examination evaluation by audiologist treatment by audiologist audiologist evaluation A therapy derived from fibric acid that lowers serum LDL cholesterol levels by activating peroxisome proliferator activated receptor alpha (PPARa). 2020-11-17T21:12:47Z NCIT:C98150 fibrate dyslipidemic agent therapy fibrate antilipidemic agent therapy Therapy using a highly charged polymeric agent to bind bile acids in the gastrointestinal tract and prevent their reabsorption from the gut. The bound bile acids are excreted with the feces and plasma cholesterol is converted to bile acid to reestablish normal bile acid levels, resulting in a lowering of plasma cholesterol concentrations. 2020-11-17T21:21:54Z bile-acid sequestrant agent therapy bile-acid sequestrant therapy treatment with bile-acid sequestrant bile acid sequestrant therapy Therapy that inhibits HMG-CoA reductase inhibitor. 2020-11-17T21:37:04Z hydroxymethylglutaryl-CoA reductase inhibitor therapy statin agent therapy treatment with EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor treatment with statins HMG-CoA reductase inhibitor therapy Treatment with an agent that works through, or mimics, the action of niacin. 2020-11-17T21:45:22Z CHEBI:15940 NCIT:C98151 niacin-based antilipidemic agent niacin agent therapy treatment with niacin An antilipidemic agent that works through, or mimics, the action of niacin to increase HDL-C levels by blocking hepatic uptake of apolipoprotein A-1 and decreasing HDL clearance. The use of free niacin is limited by its side effects of skin flushing (i.e., redness, itching, burning, and paresthesias) nicotinic acid agent therapy An antilipidemic agent that works through, or mimics, the action of niacin to increase HDL-C levels by blocking hepatic uptake of apolipoprotein A-1 and decreasing HDL clearance. The use of free niacin is limited by its side effects of skin flushing (i.e., redness, itching, burning, and paresthesias) NCIT:C98151 Treatment with a diuretic agent that produces diuresis without increasing potassium excretion. 2020-11-18T16:10:36Z NCIT:C49186 treatment with potassium-sparing diuretic Potassium sparing diuretics are generally either aldosterone antagonists and thus prevent the aldosterone-mediated promotion of sodium and water retention, or are epithelial sodium channel blockers and prevent the exchange of potassium for sodium in the distal convoluted tubule. These agents cause diuresis without increasing potassium secretion and thus do not cause hypokalemia. potassium-sparing diuretic agent therapy Potassium sparing diuretics are generally either aldosterone antagonists and thus prevent the aldosterone-mediated promotion of sodium and water retention, or are epithelial sodium channel blockers and prevent the exchange of potassium for sodium in the distal convoluted tubule. These agents cause diuresis without increasing potassium secretion and thus do not cause hypokalemia. NCIT:C49186 Treatment with a benzothiadiazide derivative or other thiazide-like agent with diuretic and anti-hypertensive activity. 2020-11-18T16:16:04Z NCIT:C49185 treatment with thiazide diuretic agent Thiazide diuretics inhibit the sodium-chloride transporter in the distal tubule in the kidneys, thereby suppressing sodium and chloride reabsorption from the distal convoluted tubules (DCT) and increasing the excretion of sodium, chloride, potassium and water. In addition, thiazide diuretics decrease excretion of calcium and uric acid. These agents cause vasodilation possibly by activating calcium-activated potassium channels in vascular smooth muscle and inhibiting various carbonic anhydrases in vascular tissue. thiazide diuretic agent therapy Thiazide diuretics inhibit the sodium-chloride transporter in the distal tubule in the kidneys, thereby suppressing sodium and chloride reabsorption from the distal convoluted tubules (DCT) and increasing the excretion of sodium, chloride, potassium and water. In addition, thiazide diuretics decrease excretion of calcium and uric acid. These agents cause vasodilation possibly by activating calcium-activated potassium channels in vascular smooth muscle and inhibiting various carbonic anhydrases in vascular tissue. NCIT:C49185 Treatment with sulfonamide urea derivatives with antihyperglycemic activity. 2020-11-18T16:22:03Z NCIT:C97936 sulfonylurea antidiabetic agent therapy treatment with sulfonylurea treatment with sulfonylurea agent Sulphonylurea antidiabetic agents bind to sulfonylurea receptor type 1 (SUR1), the subunit of ATP-sensitive inwardly-rectifier potassium (IKATP) channels on the membranes of pancreatic beta cells, thereby blocking the inward current flow (influx) of positively charged K+ ions into the cell. This results in tonic membrane depolarization, and induces a calcium ion influx through voltage-sensitive calcium channels; increased intracellular calcium ion levels trigger exocytosis of insulin-containing granules. This eventually induces secretion of insulin. The IKATP channels found in pancreatic islets are complexes of four IKATP 6.2 and four SUR1 subunits. In addition, some sulfonylureas of larger molecular size may increase the sensitivity of peripheral tissues to insulin mediated through peroxisome proliferator-activated receptor gamma (PPARgamma). sulfonylurea agent therapy Sulphonylurea antidiabetic agents bind to sulfonylurea receptor type 1 (SUR1), the subunit of ATP-sensitive inwardly-rectifier potassium (IKATP) channels on the membranes of pancreatic beta cells, thereby blocking the inward current flow (influx) of positively charged K+ ions into the cell. This results in tonic membrane depolarization, and induces a calcium ion influx through voltage-sensitive calcium channels; increased intracellular calcium ion levels trigger exocytosis of insulin-containing granules. This eventually induces secretion of insulin. The IKATP channels found in pancreatic islets are complexes of four IKATP 6.2 and four SUR1 subunits. In addition, some sulfonylureas of larger molecular size may increase the sensitivity of peripheral tissues to insulin mediated through peroxisome proliferator-activated receptor gamma (PPARgamma). NCIT:C97936 Treatment with estrogens or estrogen/progesterone after menopause or ovariectomy to prevent pathological effects of decreased estrogen production. 2020-11-19T16:03:14Z MHT menopausal hormone replacement therapy postmenopausal hormone therapy menopausal hormone therapy Treatment with estrogens or estrogen/progesterone after menopause or ovariectomy to prevent pathological effects of decreased estrogen production. NCIT:C15599 Techniques for analysis of chromosomal and subchromosomal properties and structures, such as those to diagnose, classify, screen for, or manage genetic diseases and abnormalities. 2020-11-19T19:13:57Z NCIT:C18280 cytogenetic study cytogenetic testing cytogenetic analysis Techniques for analysis of chromosomal and subchromosomal properties and structures, such as those to diagnose, classify, screen for, or manage genetic diseases and abnormalities. NCIT:C18280 A test to detect chromosomal breakage or aberrations (breaks, gaps, rearrangements, radials, exchanges, endoreduplications) in peripheral blood cells after culture with a T-cell mitogen and a DNA clastogenic (cross-linking) agent, such as diepoxybutane (DEB) or mitomycin C (MMC). 2020-11-19T19:24:16Z Chromosome Breakage Analysis (DEB/MMC) DEB/MMC testing chromosomal breakage testing induced chormosomal breakage testing chromosomal breakage analysis A test to detect chromosomal breakage or aberrations (breaks, gaps, rearrangements, radials, exchanges, endoreduplications) in peripheral blood cells after culture with a T-cell mitogen and a DNA clastogenic (cross-linking) agent, such as diepoxybutane (DEB) or mitomycin C (MMC). PMID:25006279 Transfer of multipotent hematopoietic stem cells, usually derived from bone marrow, peripheral blood, or umbilical cord blood into the body. 2020-11-19T19:56:02Z HPSCT HSCT hematopoietic stem cell transplantation HPSCT HSCT The transplantation of fecal bacteria, via enema, colonoscopy, or other method, from a healthy individual to a recipient. 2020-11-19T20:03:04Z FMT fecal material transplantation fecal transplantation stool transplantation fecal microbiota transplantation The transplantation of fecal bacteria, via enema, colonoscopy, or other method, from a healthy individual to a recipient. NCIT:C118643 FMT The removal of T-cells from the donor's hematopoietic stem cell specimen prior to its transfusion into the recipient. 2020-11-19T20:07:15Z NCIT:C116468 T cell-depleted hematopoietic stem cell transplantation The removal of T-cells from the donor's hematopoietic stem cell specimen prior to its transfusion into the recipient. NCIT:C116468 Administration of high doses of chemotherapy or radiation therapy, as well as immunosuppressive therapy, to a transplant recipient prior to a bone marrow or hematopoietic stem cell transplant. Conditioning destroys the patient's abnormal blood cells or cancer, as well as slows the patient's immune response against the donor bone marrow (graft rejection). 2020-11-19T20:12:40Z NCIT:C64468 conditioning regimen transplant conditioning Administration of high doses of chemotherapy or radiation therapy, as well as immunosuppressive therapy, to a transplant recipient prior to a bone marrow or hematopoietic stem cell transplant. Conditioning destroys the patient's abnormal blood cells or cancer, as well as slows the patient's immune response against the donor bone marrow (graft rejection). NCIT:C64468 The systematic collection, analysis, and interpretation of health data on an ongoing basis. 2020-11-19T20:25:20Z NCIT:C15719 clinical surveilance The systematic collection, analysis, and interpretation of health data on an ongoing basis. NCIT:C15719 Removal of a small amount of liquid bone marrow through a needle. 2020-11-19T20:31:02Z bone marrow aspiration procedure bone marrow aspiration The pathologic analysis of samples of bone marrow obtained by bone marrow biopsy and bone marrow aspiration. 2020-11-19T20:33:41Z bone marrow testing bone marrow monitoring bone marrow examination The determination of the amount of degree, quality or condition of cells present in a sample. 2020-11-19T20:39:47Z NCIT:C111153 cellularity grade measurement cellularity indexing cellularity measurement The determination of the amount of degree, quality or condition of cells present in a sample. NCIT:C111153 The sampling and analysis of non-solid biological tissue often through rapid and non-invasive methods, which allows the assessment in real-time of the evolving landscape of cancer. 2020-11-19T20:45:40Z solid tumor monitoring liquid biopsy The sampling and analysis of non-solid biological tissue often through rapid and non-invasive methods, which allows the assessment in real-time of the evolving landscape of cancer. PMID:32580740 The injection of whole blood or a blood component directly into the bloodstream. 2020-11-19T20:58:55Z transfusion NCIT:C15192 OGMS:0000145 transfusion of blood products blood component transfusion blood transfusion The injection of whole blood or a blood component directly into the bloodstream. NCIT:C15192 Any form of treatment that is introduced into the body via a blood vessel, a muscle, or the spinal cord. 2020-11-19T21:01:00Z NCIT:C15388 infusion infusion procedure Any form of treatment that is introduced into the body via a blood vessel, a muscle, or the spinal cord. NCIT:C15388 Avoid sexual intercourse without the use of precautions to prevent conception or the transmission of sexually transmitted diseases. 2020-11-19T21:20:20Z avoid unprotected sexual intercourse Vaccination against human papillomavirus infection. 2020-11-19T21:22:47Z VO:0000667 HPV vaccination human papillomavirus vaccination Addition of vitamin B12 to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of vitamin B12 supplementation of vitamin B12 vitamin B12 supplemental intake vitamin B12 supplementation Addition of B vitamin to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2022-08-25T09:00:01Z B vitamin supplemental intake dietary supplementation of B vitamin supplementation of B vitamin B vitamin supplementation Intake of nutrients intravenously. 2020-11-30T16:40:53Z parenteral nutrition intake Intake of nutrients intravenously as well as enterically. 2020-11-30T16:43:26Z partial parenteral nutrition intake Intravenous nutrition intake administered via vein access in a limb. 2020-11-30T16:45:00Z PPN intake peripheral parenteral nutrition intake Intravenous nutrition administration via the central vein. 2020-11-30T16:46:01Z CVN intake central venous nutrition intake A recommendation to alter dietary intake where 30% or less of the calories come from fat. 2020-11-30T17:13:24Z NCBIBook:NBK553097 low fat diet intake Recommendation of a specific diet to adhere to prevent, relieve, or alleviate symptoms. 2020-11-30T17:15:20Z prescriptive dietary intake A recommendation to alter a standard diet from 2-3 large meals per day to many frequent smaller meals throughout the day. 2020-11-30T17:19:06Z frequent small meals recommendation small meal size recommendation A recommendation to maintain a vegetarian diet for health reasons. 2020-11-30T17:26:23Z vegetarian diet intake prescriptive vegetarian diet intake Dietary recommendation to closely control the amount of carbohydrates consumed. 2020-11-30T17:38:43Z NCBIBook:NBK537084 Very low-carbohydrate (< 10% carbohydrates) or 20-50 gm/day Low-carbohydrate (<26% carbohydrates) or less than < 130 gm/day Moderate-carbohydrate (26%-44%) High-carbohydrate (45% or greater) carbohydrate controlled diet intake Very low-carbohydrate (< 10% carbohydrates) or 20-50 gm/day Low-carbohydrate (<26% carbohydrates) or less than < 130 gm/day Moderate-carbohydrate (26%-44%) High-carbohydrate (45% or greater) NCBIBook:NBK537084 A dietary recommendation to restrict the amount of carbohydrates consumed. 2020-11-30T17:41:20Z carbohydrate restrictive diet intake low carbohydrate diet intake carbohydrate-restricted diet intake A recommendation to consume food low in purine content. 2020-11-30T17:50:25Z low intake of purine-rich diet low intake of purine-rich food purine restrictive diet intake low purine diet intake A recommendation to adhere to Dietary Approaches to Stop Hypertension (DASH) diet. The diet promotes consumption of vegetables and fruits, lean meat and dairy products, and the inclusion of micronutrients and the reduction of sodium in the diet to about 1500 mg/day. 2020-11-30T18:26:25Z dietary approaches to stop hypertension diet intake DASH diet intake A recommendation to adhere to Dietary Approaches to Stop Hypertension (DASH) diet. The diet promotes consumption of vegetables and fruits, lean meat and dairy products, and the inclusion of micronutrients and the reduction of sodium in the diet to about 1500 mg/day. NCBIBook:NBK482514 Exclusively feeding an infant formula in efforts to prevent allergic reactions, intolerances, or communication of diseases (i.e. HIV) through feeding human milk. 2020-11-30T18:51:35Z EFF exclusive formula feeding Exclusively feeding an infant formula in efforts to prevent allergic reactions, intolerances, or communication of diseases (i.e. HIV) through feeding human milk. PMID:23711175 EFF A diet low in poorly absorbed, fermentable, short chain carbohydrates including fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) intended to reduce bloating, abdominal pain, excessive flatus and altered bowel habit. 2020-11-30T19:48:31Z low FODMAP diet intake A diet low in poorly absorbed, fermentable, short chain carbohydrates including fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) intended to reduce bloating, abdominal pain, excessive flatus and altered bowel habit. PMID:28244669 Addition of iron to the diet by taking ferrous sulfate supplements. 2020-12-07T19:35:36Z slow release iron supplementation ferrous sulfate supplementation The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. 2019-01-15T19:35:59Z NCIT:C74954 LFT liver function assessment liver function testing The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. NCIT:C74954 LFT Treatment with growth hormone or analog. 2021-02-09T14:02:34Z GH replacement therapy HGH replacement therapy growth hormone therapy hGH replacement therapy hGH treatment human growth hormone therapy somatotropin replacement therapy human growth hormone replacement therapy Any procedure associated with female reproductive organs in their pregnant and non-pregnant states. 2021-02-09T19:21:56Z OB/GYN procedure obstetrics and gynecology procedure Any examination performed to assess if a female is gravid (pregnant). 2021-02-09T20:02:47Z NCIT:C92949 pregnancy test A quantitative measurement of the amount of human chorionic gonadotropin present in urine or serum. 2021-02-09T20:20:44Z human chorionic gonadotropin measurement HCG measurement A quantitative measurement of the amount of human chorionic gonadotropin present in a sample of serum. 2021-02-09T20:22:47Z NCIT:C73495 blood HCG pregancy test serum HCG pregnancy measurement serum human chorionic gonadotropin measurement serum HCG measurement A quantitative measurement of the amount of human chorionic gonadotropin present in a sample of serum. NCIT:C73495 A quantitative measurement of the amount of human chorionic gonadotropin present in a sample of urine. 2021-02-09T20:24:57Z urine HCG pregancy test urine HCG pregnancy measurement urine human chorionic gonadotropin measurement urine HCG measurement The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory. 2021-02-09T20:32:13Z NCIT:C47868 blood chemistry test blood chemistry measurement The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory. NCIT:C47868 A quantitative measurement of a particular substance present in a sample of serum. 2021-02-09T20:41:32Z NCIT:C61014 serum chemistry measurement A quantitative measurement of a particular substance present in a sample of serum. NCIT:C61014 A quantitative measurement of a particular substance present in a sample of urine. 2021-02-09T21:22:57Z NCIT:C61044 urine chemistry measurement A quantitative measurement of a particular substance present in a sample of urine. NCIT:C61044 A systemic evaluation of the breast using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2961 2021-02-10T14:39:14Z breast examination NCIT:C70552 breast exam clinical breast exam examination of breast physical examination of breast An exam of the breast performed by a health care provider to check for lumps or other changes. [ NCI ] clinical breast examination An exam of the breast performed by a health care provider to check for lumps or other changes. [ NCI ] NCIT:C70552 Procedure where the individual examines their own breasts for lumps and other changes. 2021-02-09T21:37:22Z NCIT:C70551 breast self-exam breast self-surveillance breast self-examination Procedure where the individual examines their own breasts for lumps and other changes. NCIT:C70551 A systemic evaluation of the abdomen using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2961 2021-02-10T14:39:14Z NCIT:C167415 abdomen exam examination of abdomen examination of the abdomen physical examination of abdomen abdominal examination A systemic evaluation of the pelvic region of trunk using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2961 2021-02-10T14:39:14Z NCIT:C38104 examination of pelvic region of trunk examination of pelvis pelvic exam pelvic region of trunk exam pelvis examination physical examination of pelvic region of trunk pelvic examination A measurement generally defined as the distance in centimeters from the pubic bone to the top of the uterus to determine fetal growth. 2021-02-09T22:00:43Z NCIT:C154876 fundal height measurement Determination of the uterine size by ultrasound or other measurement. 2021-02-09T22:03:45Z uterine size measurement Determination of the uterine size by ultrasound or other measurement. PMID:16212222 The act of observing and recording the fetal heart rate for determining the baseline values or other abnormal findings. 2021-02-10T19:36:36Z NCIT:C92929 fetal heart monitoring fetal heart rate measurement fetal heart rate monitoring The act of observing and recording the fetal heart rate for determining the baseline values or other abnormal findings. NCIT:C92929 obsolete fetal Doppler monitoring true A technique that utilizes a wire attached to the fetal scalp to monitor fetal heart rate. The wire detects fetal cardiac electrical activity to determine the baseline fetal heart rate and variability. 2021-02-10T19:51:21Z NCIT:C114083 FSE fetal scalp electrode monitoring internal fetal heart rate monitoring A technique that utilizes a wire attached to the fetal scalp to monitor fetal heart rate. The wire detects fetal cardiac electrical activity to determine the baseline fetal heart rate and variability. NCIT:C114083 FSE Recommendation for specific nutrients, vitamin supplementation, and food avoidance while pregnant. 2021-02-10T20:05:20Z pregnancy diet intake recommendation pregnancy diet intake A clinical recommendation to avoid or refrain from excessively hot environments in order to maintain health or ameliorate symptoms. 2021-02-10T21:19:31Z avoid excessive heat A recommendation to avoid infection with toxoplasmosis especially when pregnant due to serious risk of passing the infection on to the baby. 2021-02-10T21:19:55Z Cats play an important role in the spread of toxoplasmosis. They become infected by eating infected rodents, birds, or other small animals. The parasite is then passed in the cat’s feces. Kittens and cats can shed millions of parasites in their feces for as long as 3 weeks after infection. Mature cats are less likely to shed Toxoplasma if they have been previously infected. Cats and kittens prefer litter boxes, garden soils, and sandboxes for elimination, and you may be exposed unintentionally by touching your mouth after changing a litter box, or after gardening without gloves. Fruits and vegetables may have contact with contaminated soil or water also, and you can be infected by eating fruits and vegetables if they are not cooked, washed, or peeled. Risk is most profound by a pregnant mother passing toxoplasmosis to their infant. Infected infants do not have symptoms at birth but can develop serious symptoms later in life, such as blindness or mental disability. avoid toxoplasmosis exposure Cats play an important role in the spread of toxoplasmosis. They become infected by eating infected rodents, birds, or other small animals. The parasite is then passed in the cat’s feces. Kittens and cats can shed millions of parasites in their feces for as long as 3 weeks after infection. Mature cats are less likely to shed Toxoplasma if they have been previously infected. Cats and kittens prefer litter boxes, garden soils, and sandboxes for elimination, and you may be exposed unintentionally by touching your mouth after changing a litter box, or after gardening without gloves. Fruits and vegetables may have contact with contaminated soil or water also, and you can be infected by eating fruits and vegetables if they are not cooked, washed, or peeled. Risk is most profound by a pregnant mother passing toxoplasmosis to their infant. Infected infants do not have symptoms at birth but can develop serious symptoms later in life, such as blindness or mental disability. Clinical recommendation to avoid strenuous exercise that may increase heart rate and temperature. 2021-02-10T21:22:05Z abstain from excessive exercise avoid strenuous physical work avoid excessive exercise A clinical recommendation to avoid or refrain from lifting heavy items in order to maintain health or ameliorate symptoms. 2021-02-10T21:22:33Z avoid heavy lifting activities Limit activities where a great deal of balance may be required to prevent issues or help the wellbeing of a patient. 2021-02-10T21:23:13Z avoid acitivities requiring balance avoid destabilizing activities Education by care providers about nutrition, health issues, and resources for prenatal and postnatal care. 2021-02-12T20:01:45Z prenatal education counseling birth class recommendation pregnancy education counseling obsolete urine protein assessment true A measurement of the amount of sugar (glucose) in a urine sample. 2021-02-12T20:44:57Z urine glucose assessment urine glucose monitoring urine glucose testing urine glucose measurement Testing for sexually transmitted disease syphilis. Syphilis is a contagious bacterial infection caused by the spirochete Treponema pallidum. 2021-02-12T20:56:40Z syphylis testing syphilis screening Testing to determine whether a patient has sufficient antibodies to be protected from rubella virus or to verify infection. 2021-02-12T21:04:52Z rubella testing rubella antibody titer testing Testing to diagnose primary VZV infection (varicella) as well as reactivation (herpes zoster). 2021-02-12T21:26:02Z VZV testing chickenpox testing varicella-zoster virus testing varicella testing Screening for hepatitis B antibodies to determine if a patient has immunity to hepatitis B. 2021-02-12T21:29:21Z hep B antibody titer testing hep B testing hepatitis B testing hepatitis B assessement Testing to detect hepatitis B viral antigens and an active hepatitis B infection. 2021-02-12T21:32:40Z HBsAg testing hepatitis B surface antigen testing Testing a patient for the antibodies to the human immunodeficiency virus (HIV). 2021-02-12T21:40:46Z HIV testing HIV screening Testing to determine if the patient has a chlamydia bacterial infection. 2021-02-12T21:51:15Z chlamydia screening Testing for the sexually transmitted disease gonorrhea. 2021-02-12T21:54:20Z gonorrhea testing Screening for hepatitis C antibodies to determine if a patient has immunity to hepatitis C. 2021-02-12T21:55:19Z hep C testing hepatitis C screening Collecting of blood for clinical use. http://orcid.org/0000-0001-7941-2961 2021-02-15T12:00:00Z blood collection collection of blood specimen blood specimen collection Collecting of bile for clinical use. http://orcid.org/0000-0001-7941-2961 2021-02-15T12:00:00Z bile collection collection of bile specimen bile specimen collection A procedure to tell what a patient's blood type and cell surface markers are. 2021-02-16T15:17:39Z blood typing procedure A procedured performed to determine the antigens patient's red blood cells (RBCs) that correspond to the four main blood groups: A, B, O, and AB. 2021-02-16T15:25:11Z ABO blood type testing ABO blood typing procedure Testing to determine whether the protien Rhesus (Rh) factor is present on patient's red blood cells. If the protein is present, the patient is said to be Rh positive. If the protein is not present, the patient is Rh negative. 2021-02-16T15:34:20Z Rh factor blood testing Rhesus factor blood testing Rh factor blood typing procedure A quantitative measurement of the amount of hemoglobin present in a sample. 2021-02-16T20:10:36Z NCIT:C64848 HGB measurement hemoglobin measurement A quantitative measurement of the amount of hemoglobin present in a sample. NCIT:C64848 A determination of the number of reticulocyte in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C51947 reticulocyte count test reticulocyte count A quantitative measurement of the amount of iron in serum. 2021-02-16T20:19:31Z serum iron measurement A quantitative measurement determining the amount of ferritin in serum as an indicator of iron metabolism. 2021-02-16T20:21:40Z serum ferritin level measurement serum ferritin measurement The determination of the saturation of iron binding sites on serum transferrin proteins. 2021-02-16T20:30:55Z iron-binding capacity assessment NCIT:C74718 IBCT TIBC total iron binding content measurement total iron binding capacity measurement The determination of the saturation of iron binding sites on serum transferrin proteins. NCIT:C74718 IBCT TIBC A measurement of size, shape, number, or other parameter of blood cells in order to diagnose or treat a patient. 2021-02-16T20:40:24Z blood cell measurement A determination of the structure of erythrocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z NCIT:C92296 RBC morphology measurement erythrocyte morphology assessment red blood cell morphology measurement erythrocyte morphology measurement A procedure taking a thin layer of blood smeared on a glass microscope slide and stained to allow blood cells to be examined with a microscope. 2021-02-16T20:44:14Z blood film test peripheral blood film test peripheral blood smear blood smear test A quantitative measurement of the amount of creatinine present in a sample of serum. 2021-02-16T20:56:49Z NCIT:C61023 Serves to assist in the evaluation of renal function. serum creatinine measurement A quantitative measurement of the amount of creatinine present in a sample of serum. NCIT:C61023 Serves to assist in the evaluation of renal function. PMID:29763080 The determination of the amount of thyroid stimulating hormone present in blood. http://orcid.org/0000-0001-7941-2961 2021-02-16T21:03:38Z TSH level test blood thyroid stimulating hormone test thyroid stimulating hormone blood assessment thyroid-stimulating hormone test Determination of thyroxine (T4) levels in the blood as an indicator of thyroid health. 2021-02-16T21:05:40Z T4 level test thyroxine level test T4 thyroid hormone test Determination of triiodothyronine (T3) levels in blood as an indicator of thyroid health. 2021-02-16T21:05:52Z T3 level test triiodothyronine level test T3 thyroid hormone test A measure of a patient's ability to clot, and how long it takes to clot. 2021-02-16T21:13:53Z NCIT:C62662 coagulation study blood coagulation test A measurement of the length of time that it takes for clotting to occur when reagents are added to a plasma specimen. The test is partial due to the absence of tissue factor (Factor III) from the reaction mixture. 2021-02-16T21:14:12Z NCIT:C38462 APTT test PTT test activated partial thromboplastin time test partial thromboplastin time test The determination of the ratio of the prothrombin time in a subject's specimen compared to a control sample. The measurement may be expressed as a ratio or percentage. 2021-02-16T21:19:29Z NCIT:C170591 PT/INR measurement PTAC measurement prothrombin time actual/control measurement prothrombin time/international normalized ratio measurement The determination of the ratio of the prothrombin time in a subject's specimen compared to a control sample. The measurement may be expressed as a ratio or percentage. NCIT:C170591 A measurement of the time it takes a plasma sample to clot after adding the active enzyme thrombin. 2021-02-16T21:23:02Z NCIT:C80365 TCT measurement TT measurment thrombin clotting time measurement thrombin time measurement A measurement of the time it takes a plasma sample to clot after adding the active enzyme thrombin. NCIT:C80365 The determination of the amount of alanine aminotransferase (human) present in the sample. http://orcid.org/0000-0001-7941-2961 2021-02-16T21:34:21Z NCIT:C64433 ALT test GPT test SGPT test alanine aminotransferase (human) assessment alanine aminotransferase (human) test alanine transaminase measurement serum glutamic-pyruvic transaminase test Alanine aminotransferase is an enzyme produced mainly in the liver. When serum activity is measured, it provides a marker of hepatic disease. alanine transaminase test Alanine aminotransferase is an enzyme produced mainly in the liver. When serum activity is measured, it provides a marker of hepatic disease. PMID:1992953 The determination of the amount of aspartate aminotransferase (human) present in the sample. http://orcid.org/0000-0001-7941-2961 2021-02-16T21:38:44Z NCIT:C64467 AST blood test SGOT test aspartate aminotransferase (human) assessment aspartate aminotransferase (human) test aspartate aminotransferase blood test serum glutamic oxaloacetic transaminase test Alanine aminotransferase (ALT), aspartate aminotransferase (AST) and gamma-glutamyl transferase (GGT) are enzymes measured in serum or plasma to investigate liver disease. aspartate aminotransferase measurement Alanine aminotransferase (ALT), aspartate aminotransferase (AST) and gamma-glutamyl transferase (GGT) are enzymes measured in serum or plasma to investigate liver disease. PMID:24072574 The determination of the amount of gamma-glutamyltranspeptidase present in the sample. http://orcid.org/0000-0001-7941-2961 2021-02-16T21:42:40Z NCIT:C64847 GGT test GTP test gamma-GT test gamma-glutamyltranspeptidase assessment gamma-glutamyltranspeptidase test Determination of gamma-glutamyl transferase (GGT) present in the sample as a measurement of liver function. gamma glutamyl transpeptidase measurement Determination of gamma-glutamyl transferase (GGT) present in the sample as a measurement of liver function. PMID:24072574 The determination of the amount of albumin (human) present in the sample. http://orcid.org/0000-0001-7941-2961 2021-02-16T21:45:46Z NCIT:C64431 ALB level test albumin (human) assessment albumin (human) test albumin assessment albumin level measurement albumin test albumin measurement The determination of the amount of alkaline phosphatase present in the sample. http://orcid.org/0000-0001-7941-2961 2021-02-16T21:50:44Z NCIT:C64432 ALP measurement alk phos test alkaline phosphatase assessment alkaline phosphatase test alkaline phosphatase measurement The measurement of the total amount of bilirubin present in a particular substrate. The substrate most often tested is blood, but other fluids extracted from the body may be used periodically depending on the purpose of the test. 2021-02-16T21:52:27Z NCIT:C38037 BILI measurement total bilirubin level measurement total bilirubin measurement The measurement of the total amount of bilirubin present in a particular substrate. The substrate most often tested is blood, but other fluids extracted from the body may be used periodically depending on the purpose of the test. NCIT:C38037 The determination of the amount of lactate dehydrogenase present in the sample. 2021-02-17T14:57:21Z NCIT:C64855 LDH measurement lactate dehydrogenase measurement The determination of the amount of 5'-nucleotidase present in the sample. http://orcid.org/0000-0001-7941-2961 2021-02-17T15:01:15Z NCIT:C79437 5 prime nucleotidase measurement 5'- nucleotidase measurement 5'-nucleotidase assessment 5'-nucleotidase test 5'-nucleotidase measurement The measurement of bilirubin present in a particular sample. 2021-02-17T15:06:51Z bilirubin measurement A measurement of the unconjugated or non-water-soluble bilirubin in a biological specimen. 2021-02-17T15:07:19Z NCIT:C64483 indirect bilirubin measurement A quantitative measurement of total protein present in the sample, usually serum or urine. 2021-02-17T15:16:41Z NCIT:C64858 total protein measurement The determination of the amount of protein present in urine. http://orcid.org/0000-0001-7941-2961 2021-02-17T15:25:01Z NCIT:C74760 protein urine assessment urine protein assessment urine protein test urine protein testing urine protein measurement The measurement of the total protein present in a urine sample that was collected over a period of 24 hours. 2021-02-17T16:13:50Z NCIT:C135567 24 hour urine for total protein 24-hour urine protein test 24-hour urine collection The measurement of the total protein present in a urine sample that was collected over a period of 24 hours. NCIT:C135567 A quantitative measurement of the total amount of protein present in a sample of serum. 2021-02-17T16:23:27Z NCIT:C61033 serum total protein measurement A quantitative measurement of the total amount of protein present in a sample of serum. NCIT:C61033 The determination of the amount of haptoglobin present in the sample. 2021-02-17T17:02:35Z NCIT:C74740 haptog measurement haptoglobin assessment haptoglobin protein measurement haptoglobin test haptoglobin measurement Determination of the types of normal or abnormal types of hemoglobin in the blood. Some types of hemoglobin are associated with sickle cell disease or anemia. 2021-02-17T19:58:00Z Hb ELP Hb electrophoresis measurement hemoglobin evaluation hemoglobin fractionation hemoglobinopathy evaluation sickle cell screen hemoglobin electrophoresis test Determination of serum levels of pregnancy-associated plasma protein A (PAPP-A). Maternal levels of PAPP-A increase throughout the pregnancy. Low levels during pregnancy are associated with Down syndrome and trisomy 18. 2021-02-17T20:59:28Z pregnancy-associated plasma protein A test serum PAPP-A measurement A test that involves administration of a know quantity of glucose as a means of screening for glucose intolerance or diabetes mellitus. Typically a baseline (fasting plasma or serum glucose) is drawn prior to the administration of the glucose bolus. Serial plasma glucose levels are obtained (e.g. 30min, 1hr, 2hr, 3hr) and a plot of plasma glucose versus time is created. Comparison of these values against standardized results can be used in establishing the diagnosis of glucose intolerance or diabetes mellitus. 2021-02-17T21:38:54Z NCIT:C45946 glucose tolerance test A test that involves administration of a know quantity of glucose as a means of screening for glucose intolerance or diabetes mellitus. Typically a baseline (fasting plasma or serum glucose) is drawn prior to the administration of the glucose bolus. Serial plasma glucose levels are obtained (e.g. 30min, 1hr, 2hr, 3hr) and a plot of plasma glucose versus time is created. Comparison of these values against standardized results can be used in establishing the diagnosis of glucose intolerance or diabetes mellitus. NCIT:C45946 A test or diagnostic examination to assess the health status and well being of the fetus. 2021-02-18T14:38:59Z fetal assessment fetal exam foetal examination fetal examination A test or diagnostic examination to assess the health status and well being of the fetus. NCIT:C92714 A series of maneuvers to determine the position and presenting part of the fetus with respect to the maternal pelvic canal in preparation for labor and the birth process. 2021-02-18T14:53:47Z NCIT:C92737 fetal presentation assessment fetal position assessment assessment of fetal presentation A series of maneuvers to determine the position and presenting part of the fetus with respect to the maternal pelvic canal in preparation for labor and the birth process. NCIT:C92737 The use of pharmacological and/or mechanical methods to initiate labor, including spontaneous rupture of membranes without contractions. Examples of methods include: artificial rupture of membranes, balloons, oxytocin, prostaglandin, laminaria, or other cervical ripening agents. (adapted from reVITALize) 2021-02-18T15:06:07Z NCIT:C92814 induction of labor labor induction The use of pharmacological and/or mechanical methods to initiate labor, including spontaneous rupture of membranes without contractions. Examples of methods include: artificial rupture of membranes, balloons, oxytocin, prostaglandin, laminaria, or other cervical ripening agents. (adapted from reVITALize) NCIT:C92814 obsolete fetal Doppler velocimetry true A method to assess fetal oxygenation status during labor and delivery using a noninvasive reflectance pulse oximeter. 2021-02-18T15:16:22Z fetal pulse oximetry A method to assess fetal oxygenation status during labor and delivery using a noninvasive reflectance pulse oximeter. NCIT:C92794 The determination of the amount of protein present in blood. http://orcid.org/0000-0001-7941-2961 2021-02-17T15:25:01Z blood protein test protein blood assessment protein measurement in blood A systemic evaluation of the abdomen using visual inspection, palpation, and percussion during pregnancy to determine the health of the mother and fetus. 2021-05-27T15:12:17Z abdominal examination during pregnancy pregnant abdomen examination obstetric abdominal examination A quantitative measurement of the amount of human chorionic gonadotropin present in urine or serum for the purpose of determining whether the patient is pregnant. 2021-05-27T19:38:10Z HCG pregnancy test pregnancy HCG test A systemic evaluation of the cervix during pregnancy to determine dilation and effacement of the cervix, cervical position and consistancy, and fetal position. 2021-06-07T18:34:00Z cervical exam while pregnant obstetric examination of the cervix. pregnant cervical exam obstetric cervical examination An evaluation of the breast using visual inspection, palpation, and percussion for the specific purpose of identifying breast changes which may be cancer. 2021-06-07T18:51:49Z cancer breast exam cancer screening breast examination A test that evaluates of the sensitivity of a person's sense of hearing and is used to determine a person's hearing sensitivity at different frequencies. 2021-06-07T21:03:43Z hearing assessment hearing exam hearing test hearing examination The determination of the amount of albumin (human) present in the sample in order to assess the liver's function. 2021-06-08T14:05:06Z albumin test for liver function assessment liver function albumin test albumin test for liver function The determination of the amount of 5'-nucleotidase present in the sample to assess liver function. 2021-06-08T14:17:21Z 5'-nucleotidase test for liver function assessment liver function 5'-nucleotidase measurement liver function 5'-nucleotidase test 5'-nucleotidase measurement for liver function The determination of the amount of alkaline phosphatase present in the sample for assessment of liver function. 2021-06-08T14:20:25Z alkaline phosphatase measurement for liver function assessment liver function alk phos test liver function alkaline phosphatase measurement alkaline phosphatase measurement for liver function A quantitative measurement of the amount of calcium present in a sample, usually serum or urine for the assessment of liver function. 2021-06-08T14:23:54Z calcium test for liver function assessement liver function calcium test calcium assessment for liver function The determination of the amount of lactate dehydrogenase present in the sample to assess liver function. 2021-06-08T14:34:11Z lactate dehydrogenase measurement for liver assessment The measurement of the total amount of bilirubin present in a particular substrate in order to assess liver function. The substrate most often tested is blood, but other fluids extracted from the body may be used periodically depending on the purpose of the test. 2021-06-08T14:47:38Z total bilirubin measurement for assessment of liver function A measurement of the unconjugated or non-water-soluble bilirubin in a biological specimen to assess liver function. 2021-06-08T15:31:21Z indirect bilirubin measurement for assessment of liver function The use of operant conditioning, including rewards and punishments, in helping a person create an atmosphere where he or she does not contribute to painful stimuli. 2021-08-05T17:18:12Z NCIT:C15184 behavior conditioning therapy behavioral modification behavioral treatment behavioural intervention behavioural modification behavioral intervention The use of operant conditioning, including rewards and punishments, in helping a person create an atmosphere where he or she does not contribute to painful stimuli. NCIT:C15184 A type of psychotherapy utilized to treat different forms of mental disorders.The treatment involves the identification of unhelpful or destructive patterns of thinking and behaviors and the subsequent replacement with behaviors that are beneficial and constructive. 2021-08-05T17:53:44Z NCIT:C64345 cognitive therapy cognitive behavior therapy A type of psychotherapy utilized to treat different forms of mental disorders.The treatment involves the identification of unhelpful or destructive patterns of thinking and behaviors and the subsequent replacement with behaviors that are beneficial and constructive. NCIT:C64345 The use of operant conditioning to alter a person's dietary choices and behaviors. 2021-08-05T17:56:02Z NCIT:C67021 behavioral dietary intervention The use of operant conditioning to alter a person's dietary choices and behaviors. NCIT:C67021 A surgical procedure that leads to the removal of body part or body fluid. 2021-08-05T19:16:15Z surgical removal procedure A laboratory procedure that evaluates the kidney function. 2021-08-06T18:59:22Z NCIT:C74972 renal function test kidney function testing A laboratory procedure that evaluates the kidney function. NCIT:C74972 A measurement of the volume of fluid filtered from the renal glomerular capillaries into the Bowman's capsule per unit time. 2021-08-09T13:28:29Z GFR test glomerular filtration rate test GFR test An estimated rate of glomerular filtration is calculated from blood creatinine test, age, body size and gender. 2021-08-09T15:51:41Z eGFR test estimated glomerular filtration rate calculation Removal of hard deposits made of minerals and salts also called 'kidney stones' or 'renal calculi' by any of a number of methods. 2021-08-09T16:22:26Z kidney stone removal renal calculi removal Removal of hard deposits made of minerals and salts also called 'stones' or 'calculi' by any of a number of methods. Stones can be found in the kidney, gallbladder, urethra, salivary gland or other ducts. 2021-08-09T16:46:18Z stone removal calculi removal A procedure to break a stone into small particles that can be more easily cleared from the body. 2021-08-09T17:17:19Z NCIT:C51994 lithotripsy A procedure to break a stone into small particles that can be more easily cleared from the body. NCIT:C51994 A treatment to remove kidney snotes by sending ultrasonic energy/shock waves directly to the stone. 2021-08-09T17:20:00Z kidney lithotripsy renal lithotripsy A scope is inserted in the urinary tract to locate the stone. Using an optical fiber, laser light is directly emitted to the stone causing stone fragmentation. 2021-08-09T17:21:56Z laser lithotripsy Using a lithotripter to aim sound waves directly at stones through the body, the shock waves break down stones or calculi which are then able to pass. 2021-08-09T17:22:14Z ESWL extracorporeal shock-wave lithotripsy shock wave lithotripsy shock-wave lithotripsy extracorporeal shock wave lithotripsy ESWL A small cut is made through the patient's back and a nephroscope is inserted to locate and remove the kidney stone. 2021-08-09T18:17:54Z percutaneous nephrolithotomy obsolete ureteroscopy true A ureteroscope is inserted into the ureter and a wire basket inserted through the tube to remove the stone(s). In addition, a laser or other mechanical device can be used to break up the stone(s). 2021-08-09T18:26:36Z ureteroscopic stone removal Treatment with an antimetabolite that affects the metabolism and utilization of purines. 2021-08-09T19:15:23Z NCIT:C1556 purine inhibitor agent therapy purine antagonist agent therapy A procedure that displays the electrical activity of the heart. 2021-08-09T19:19:35Z NCIT:C38053 ECG EKG electrocardiogram procedure electrocardiography A procedure that displays the electrical activity of the heart. NCIT:C38053 ECG EKG Treatment with acetylsalicylic acid. It is often a treatment for pain, fever, inflammation or to reduce risk of heart attack. 2021-08-10T14:35:53Z acetylsalicylic acid therapy treatment with aspirin aspirin therapy Treatment with an inhibitor that inteferes with the action of alpha-glucosidase. 2021-08-10T14:39:44Z CHEBI:67239 alpha-glucosidase inhibitor therapy Treatment with one of a group of heterocyclic compounds with a core structure containing a benzene ring fused to a diazepine ring. It is often used to treat anxiety. 2021-08-10T14:58:25Z CHEBI:22720 benzodiazepine agent therapy Treatment with a pharmaceutical agent that inhibits T-type calcium channels. 2021-08-10T15:05:39Z T-type calcium channel antagonist therapy T-type calcium channel blocking agent therapy Treatment with a pharmaceutical agent that inhibits L-type calcium channels. 2021-08-10T15:10:56Z L-type calcium channel antagonist therapy L-type calcium channel blocking agent therapy Treatment with a phosphodiesterase (PDE) inhibitor. 2021-08-10T15:15:41Z PDE inhibitor therapy phosphodiesterase inhibitor therapy An agent or drug used to reduce or control weight. 2021-08-10T18:20:00Z weight loss pharmacotherapy Treatment with an agent or drug to reduce or control weight in obese patients. 2021-08-10T18:21:20Z CHEBI:74518 anti-obesity agent therapy The management of pain by interventional procedures, pharmacotherapy, physical therapy, psychological counseling, or complementary and alternative medical therapies designed to treat or alleviate pain specifically for patients receiving palliative care treatment. 2021-08-11T14:13:00Z pain management for palliative care A measurement or assessment to determine if a patient's sleep is disrupted. 2021-08-11T14:52:56Z assessement for sleep disorders sleep assessment sleep disturbance screening assessment for sleep disturbance A questionnaire designed to determine sleep quality, daytime sleepiness, or other issues related to having restful sleep. 2021-08-11T14:56:38Z sleep assessment questionnaire Use of a portable device (actigraph) to study sleep-wake patterns and circadian rhythms by assessing movement. 2021-08-11T14:59:42Z actigraphy Use of a portable device (actigraph) to study sleep-wake patterns and circadian rhythms by assessing movement. PMID:26608435 A group of tests (usually central electroencephalogram (EEG) (C3 or C4), reference occipital EEG (O1 or O2), right and left electro-oculogram (EOG), mental or submental electromylogram (EMG), thoracic effort, abdominal effort, nasal and oral airflow, a microphone to record snoring, pulse oxygen saturation, EKG, and video recording to document body positions during sleep) taken during sleep. 2021-08-11T15:00:34Z NCIT:C114185 PSG polysomnography A group of tests (usually central electroencephalogram (EEG) (C3 or C4), reference occipital EEG (O1 or O2), right and left electro-oculogram (EOG), mental or submental electromylogram (EMG), thoracic effort, abdominal effort, nasal and oral airflow, a microphone to record snoring, pulse oxygen saturation, EKG, and video recording to document body positions during sleep) taken during sleep. PMID:26608435 PSG obsolete airway endoscopy true Insertion of a tube into a blocked passageway, such as a blood vessel, to keep it open. 2021-08-11T16:01:02Z stenting placement of a stent A tube-shaped medical device is inserted into the nasal passage to prevent obstruction of the airway. 2021-08-11T16:26:00Z placement of nasal stent placement of nasopharyngeal stent insertion of a nasopharyngeal stent An initial evaluation by a professional trained and qualified to provide nutritional services at individual, institutional and community levels in term of assessing nutritional needs. 2021-08-11T17:06:20Z NCIT:C28248 nutritionist evaluation dietician evaluation An initial evaluation by a trained and certified individual who applies knowledge of the concepts, principles, and practices of physical therapy for the treatment or prevention of physical disability or disease. 2021-08-11T17:11:32Z NCIT:C53422 physiotherapist evaluation physical therapist evaluation An initial assessment by a professional trained and qualified to perform technical work concerned with administering therapeutic and diagnostic respiratory care and life support to patients with cardiopulmonary deficiencies and abnormalities. 2021-08-11T17:34:31Z NCIT:C53425 respiratory therapist evaluation An initial assessment by a professionally trained person who is employed in the administration of charity, social service, and welfare. The assistance this professional provides helps disadvantaged individuals and families adjust themselves to the community. 2021-08-11T17:59:26Z NCIT:C28190 social worker evaluation A general assessment of the overall health of a newborn. 2021-08-11T19:22:27Z NCIT:C84749 newborn examination A general assessment of the overall health of a newborn. NCIT:C84749 The assessment of behavior in neonates. 2021-08-11T19:25:11Z NCIT:C81314 newborn behavior examination The assessment of behavior in neonates. NCIT:C81314 A test conducted at 1 minute and 5 minutes after birth to determine the overall health of the newborn. 2021-08-11T19:31:30Z NCIT:C81230 Apgar testing Any method used to elicit a fetal heart rate acceleration response during labor. 2021-08-11T19:47:14Z NCIT:C114084 intrapartum fetal stimulation Any method used to elicit a fetal heart rate acceleration response during labor. NCIT:C114084 Determination of the newborn's heart rate. 2021-08-11T20:53:10Z NCIT:C87103 newborn heart rate measurement A procedure during labor in which the occiput is manually rotated from posterior to anterior. 2021-08-11T20:56:18Z NCIT:C114133 manual fetal rotation A procedure during labor in which the occiput is manually rotated from posterior to anterior. NCIT:C114133 A manual method of maneuvering the fetus from outside the mother's abdomen to convert a breech into a cephalic presentation. 2021-08-11T20:58:11Z NCIT:C92776 external fetal rotation A manual method of maneuvering the fetus from outside the mother's abdomen to convert a breech into a cephalic presentation. NCIT:C92776 The treatment of communication disorders (speech disorders and language disorders), cognitive-communication disorders, voice disorders, and swallowing disorders. 2021-08-12T13:17:16Z NCIT:C159273 speech language therapy speech therapy The treatment of communication disorders (speech disorders and language disorders), cognitive-communication disorders, voice disorders, and swallowing disorders. NCIT:C159273 An initial assessment by a person who specializes in the study of mind and behavior or in the treatment of mental, emotional, and behavioral disorders. 2021-08-12T13:32:47Z NCIT:C28181 psychologist evaluation The neurophysiologic exploration of the electrical activity of the brain by the application of electrodes to the scalp. The resulting traces are known as an electroencephalogram (EEG). This test is used to assess brain damage, epilepsy and other problems. 2021-08-12T13:47:43Z NCIT:C38054 EEG electroencephalography The neurophysiologic exploration of the electrical activity of the brain by the application of electrodes to the scalp. The resulting traces are known as an electroencephalogram (EEG). This test is used to assess brain damage, epilepsy and other problems. NCIT:C38054 EEG Treatment with a synthetic enzyme or mixture of enzymes used to replace or supplement enzymes to treat enzyme deficiency. 2021-08-12T13:51:53Z NCIT:C29726 enzyme replacement or supplementation therapy Detection of phosphoethanolamine in urine. 2021-08-12T13:57:56Z urine phosphoethanolamine measurement The determination of the amount of bone specific alkaline phosphatase present in a sample. 2021-08-12T14:00:14Z NCIT:C92287 ALPBS test bone ALP measurement bone specific alkaline phosphatase measurement The determination of the amount of bone specific alkaline phosphatase present in a sample. NCIT:C92287 ALPBS test bone ALP measurement Measurement of alkaline phosphatase enzamatic activity in a biological sample. 2021-08-12T14:13:09Z alkaline phosphatase enzyme activity test The determination of the amount of inorganic pyrophosphate present in a sample. 2021-08-12T15:24:26Z NCIT:C161358 PPI measurement PPi measurement inorganic pyrophosphate measurement PPI measurement PPi measurement Open brain surgery to remove part of the brain causing seizures. 2021-08-12T15:36:25Z resective brain surgery Procedure to arouse the body or parts to increase functional activity. 2021-08-12T15:41:57Z stimulation procedure Placement of a stimulator electrode in the part of the brain causing seizures. 2021-08-12T15:44:05Z RNS responsive neurostimulation Stimulation of the nerves that are outside of the heart. 2021-08-12T15:47:24Z extracardiac nerve stimulation A procedure that uses a device to stimulate the vagus nerve with electrical impulses. 2021-08-12T19:05:29Z vagus nerve stimulation A neurosurgical procedure involving the placement of a medical device called a neurostimulator (sometimes referred to as a "brain pacemaker"), which sends electrical impulses, through implanted electrodes, to specific targets in the brain (brain nuclei) for the treatment of movement disorders, including Parkinson's disease, essential tremor, and dystonia.[1] and other conditions such as obsessive-compulsive disorder and epilepsy. 2021-08-12T19:24:31Z DBS deep brain stimulation A neurosurgical procedure involving the placement of a medical device called a neurostimulator (sometimes referred to as a "brain pacemaker"), which sends electrical impulses, through implanted electrodes, to specific targets in the brain (brain nuclei) for the treatment of movement disorders, including Parkinson's disease, essential tremor, and dystonia.[1] and other conditions such as obsessive-compulsive disorder and epilepsy. DBS The use of skin electrodes to pass a low intensity, pulsed electrical current through the scalp and into the brain. This procedure is used to treat a variety of illnesses including anxiety, depression, and chronic pain. 2021-08-12T19:29:07Z NCIT:C116561 cranial electrical stimulation An invasive procedure to stimulate the spinal cord to aid in the management of chronic, intractable pain of the trunk and/or limbs, including unilateral or bilateral pain. 2021-08-12T19:30:24Z spinal cord stimulation Any surgical procedure conducted on the nervous system. http://orcid.org/0000-0001-7941-2961 2021-08-12T19:44:10Z nervous system surgical procedure neurosurgery neurosurgical procedure surgical procedure on nervous system Surgery performed on any part of the brain. 2021-08-12T19:45:31Z NCIT:C154268 brain surgery Surgery performed on any part of the brain. NCIT:C154268 Surgical creation of an opening of the skull. 2021-08-12T19:47:17Z cranial surgery NCIT:C15214 craniotomy Surgical creation of an opening of the skull. NCIT:C15214 Treatment with a hormone that is naturally produced in the thyroid. When calcitonin given to patients with osteoporosis, calcitonin produces modest increases in bone mass because it slows the rate at which osteoclasts absorb bone. 2021-08-12T19:57:09Z calcitonin therapy calcitonin treatment Supportive therapy involves the teaching of such life skills as managing medication, learning to socialize, handling finances, and getting a job. 2021-08-12T20:10:44Z supportive care Therapeutic care designed to maintain the natural processes of the body and return to a more normal state of health. 2021-08-12T20:14:31Z physiological support therapy Therapeutic care designed to maintain the natural processes of the body and return to a more normal state of health. NCIT:C66895 Delivery of fluids to the body by any methods necessary. 2021-08-12T20:16:16Z hydration therapy Use of isotonic saline intravenously. 2021-08-12T20:16:36Z saline hydration Treatment with a set of compounds that allow osteoblasts (bone building cells) to work more effectively, improving bone mass. Bisphosphonates are used in the treatment of osteoporosis, Paget's disease of bone, and may be used to lower high calcium levels. 2021-08-12T20:21:07Z bisphosphonate agent therapy Bi-level positive airway pressure (or trade name BiPAP) delivers, by mask, two levels of pressure in response to patient flow. It is intended to support ventilation in a nonin-vasive way in spontaneously but insufficiently breathing patients in the home care environment. 2021-08-13T20:17:37Z BiPAP Two new ventilatory techniques with almost identical names have been developed for adults: BiPAP(trademark) and BIPAP. BiPAP is a trade name derived from 'bi-level positive airway pressure'. BiPAP delivers, by mask, two levels of pressure in response to patient flow. It is intended to support ventilation in a nonin-vasive way in spontaneously but insufficiently breathing patients in the home care environment. In contrast, BIPAP (biphasic positive airway pressure) is a mode of ventilation developed for full ventilatory support in intensive care settings with the use of an endotracheal tube. bi-level positive airway pressure ventilation Bi-level positive airway pressure (or trade name BiPAP) delivers, by mask, two levels of pressure in response to patient flow. It is intended to support ventilation in a nonin-vasive way in spontaneously but insufficiently breathing patients in the home care environment. PMID:11353935 BiPAP Two new ventilatory techniques with almost identical names have been developed for adults: BiPAP(trademark) and BIPAP. BiPAP is a trade name derived from 'bi-level positive airway pressure'. BiPAP delivers, by mask, two levels of pressure in response to patient flow. It is intended to support ventilation in a nonin-vasive way in spontaneously but insufficiently breathing patients in the home care environment. In contrast, BIPAP (biphasic positive airway pressure) is a mode of ventilation developed for full ventilatory support in intensive care settings with the use of an endotracheal tube. PMID:11353935 Biphasic positive airway pressure ventilation (BIPAP) is a mode of ventilation developed for full ventilatory support in intensive care settings with the use of an endotracheal tube. 2021-08-13T20:22:51Z BIPAP Recently two new ventilatory techniques with almost identical names have been developed for adults: BiPAP(trademark) and BIPAP. BiPAP is a trade name derived from 'bi-level positive airway pressure'. BiPAP delivers, by mask, two levels of pressure in response to patient flow. It is intended to support ventilation in a nonin-vasive way in spontaneously but insufficiently breathing patients in the home care environment. In contrast, BIPAP (biphasic positive airway pressure) is a mode of ventilation developed for full ventilatory support in intensive care settings with the use of an endotracheal tube. biphasic positive airway pressure ventilation Biphasic positive airway pressure ventilation (BIPAP) is a mode of ventilation developed for full ventilatory support in intensive care settings with the use of an endotracheal tube. PMID:11353935 BIPAP Recently two new ventilatory techniques with almost identical names have been developed for adults: BiPAP(trademark) and BIPAP. BiPAP is a trade name derived from 'bi-level positive airway pressure'. BiPAP delivers, by mask, two levels of pressure in response to patient flow. It is intended to support ventilation in a nonin-vasive way in spontaneously but insufficiently breathing patients in the home care environment. In contrast, BIPAP (biphasic positive airway pressure) is a mode of ventilation developed for full ventilatory support in intensive care settings with the use of an endotracheal tube. PMID:11353935 A procedure where filtering membrane is created for fluid to move out of the front chamber of the eye to underneath the superficial tissues around it (conjunctiva) and thus lowering the presure of the eye. 2023-02-24T17:30:45Z NPDS non-penetrating deep sclerectomy deep sclerectomy Canaloplasty is a modification of viscocanalostomy, in which an additional intracanalicular stent is inserted to maintain canal patency and enhance the circumferential flow. 2023-02-24T17:31:07Z canaloplasty A procedure that is a variation of a deep sclerectomy procedure. This procedure involves unroofing and dilation of the Schlemm’s canal without penetrating the trabecular meshwork or anterior chamber. A high-viscosity viscoelastic solution is injected to dilate the canal and create a passage from the canal to a scleral reservoir, thereby reducing intraocular pressure. 2023-02-24T17:34:27Z viscocanalostomy A procedure to reduce intraocular pressure by enhancing the natural aqueous outflow channels, while reducing outflow resistance located in the inner wall of the Schlemm's canal and the juxtacanalicular trabecular meshwork. 2023-02-24T17:51:12Z NPGS non-penetrating filtrating surgery non-penetrating glaucoma surgery The surgery creates an alternative pathway for fluid to leave the eye. A small channel, or 'bleb' is created to allow fluid to drain from the eye. 2023-02-24T17:54:23Z filtering sugery filtrating glaucoma surgery incisional glaucoma surgery glaucoma filtration surgery The construction of a passage between a cavity or hollow organ to the surface of the body often to help drain bodily fluid. 2023-02-27T18:00:04Z NCIT:C15290 construction of a stoma ostomy surgical procedure This technique surgically creates the patient’s anus within the sphincter muscle. 2023-02-27T21:28:55Z posterior sagittal anorectoplasty A diagnostic procedure to evaluate the structure and/or function of the eye and visual system. 2023-02-24T19:03:34Z ophthalmological diagnostic procedure ophthalmology diagnostic procedure ophthalmic diagnostic procedure A noninvasive imaging technique that provides high-resolution, cross-sectional images of the retina, retinal nerve fiber layer and the optic nerve head. 2023-02-24T19:20:56Z OCT optical coherence tomography A noninvasive imaging technique that provides high-resolution, cross-sectional images of the retina, retinal nerve fiber layer and the optic nerve head. PMID:23429598 An examination of the anterior chamber of the eye with a lens that is placed against the eye as a part of a slit-lamp examination. 2023-02-24T19:25:28Z slit-lamp gonioscopy gonioscopy A test to assess the ability to focus on and discern objects, colors, depth, etc. 2023-02-24T19:28:40Z NCIT:C156778 vision screening vision test vision assessment Assessment of the parameters of eye movement, including horizontal and vertical rotations of the eye, opening or closing of the eyes in response to stimuli, pupil response to light, and blink reflex. 2023-02-24T19:31:14Z NCIT:C162707 eye movement assessment eye movement measurement A test performed by an ophthalmologist or optometrist assessing vision and ability to focus on and discern objects, as well as other tests and examinations pertaining to the eyes. 2023-02-24T19:35:05Z NCIT:C38060 slit-lamp examination A method in which pressure is applied to the surface of the cornea in order to flatten a prespecified area of the membrane, which is used to calculate intraocular pressure. 2023-02-24T19:38:54Z IOP measurement intraocular pressure measurement tonometry A method in which a constant pressure is applied to the surface of the cornea in order to flatten a prespecified area of the membrane, which is used to calculate intraocular pressure. 2023-02-24T19:40:23Z NCIT:C120682 applanation tonometry A method in which a probe is bounced off of the surface of the cornea, creating an induction current that is used to calculate intraocular pressure. 2023-02-24T19:41:43Z NCIT:C120703 rebound tonometry The surgeon makes small incisions in the abdomen in order to insert an endoscope into the body. The endoscope can either clear the blockage, or remove the portion of intestines without nerves. The healthy portions of intestines are then reconnected in order to allow stool to pass through. 2023-02-27T21:33:53Z TERPT transanal endorectal pull-through procedure pull-through procedure A techniqhe which positions the neorectum accurately inside the sphincter complex without dividing any of these muscles. 2023-02-27T21:48:16Z LAARP laparoscopic-assisted anorectoplasty Procedure to evaluate the structure and/or function of a particular by part or system. 2023-03-29T20:10:49Z diagnostic procedure by body location diagnostic procedure by site The use of computed tomography to produce images of structures of a particular body site. 2023-03-30T17:40:25Z computed tomography procedure by body location CT by site A specimen collection from a particular body site used for diagnostic purposes. 2023-03-30T17:56:49Z biopsy by body location clinical biopsy by site A procedure to take off or remove part or entire nail. 2023-03-31T14:53:59Z nail removal removal of nail Reduction in the thickness and length of the nail. Often used to remove thickened nails due to fungal infection. 2023-03-31T14:54:13Z nail debridement Debridement can be done by filing or drilling or other methods. debridement of nail Removal or elimination of a portion of skin for therapeutic use. 2023-03-31T15:11:49Z removal of skin Removal of dead (necrotic) or infected skin to help a wound heal. 2023-03-31T18:20:39Z debridement of skin Removing slough from a wound. 2023-03-31T18:20:54Z removal of slough from skin desloughing of skin Addition of a softening or soothing agent to the skin. 2023-03-31T19:02:52Z use of emollient emollient application to skin use of skin emollients application of emollient to skin Determination of shape of body or body parts. This may be used to assess symmetry, number, size, and shape of a patient's body or body parts. 2023-04-13T16:06:37Z body shape assessment Determination of shape, symmetry, and/or size of face. 2023-04-13T16:10:13Z facial morphology assessment Determination of shape, symmetry, and/or size of head. 2023-04-13T16:11:14Z head morphology assessment The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. 2019-04-26T20:04:29Z NCIT:C17958 Functional MRI fMRI functional magnetic resonance imaging procedure The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. NCIT:C17958 Functional MRI fMRI Gene therapy involves the use of nucleic acids (DNA or RNA) for the treatment, cure or prevention of human disorders. 2019-05-07T16:28:50Z NCIT:C15238 SCDO:0001344 DNA therapy gene therapies gene transfer procedure genetic therapy gene therapy Gene therapy involves the use of nucleic acids (DNA or RNA) for the treatment, cure or prevention of human disorders. PMID:24106209 The goal of immunotherapy is to induce anti-disease (usually tumor) responses by reprogramming and augmenting immune surveillance, and reducing immune suppression. 2019-05-07T16:32:45Z NCIT:C15262 OGMS:0000114 immune therapy immunologically directed therapy immunotherapy procedure The goal of immunotherapy is to induce anti-disease (usually tumor) responses by reprogramming and augmenting immune surveillance, and reducing immune suppression. PMID:29242097 Treatment with a drug that deters or encourages the cessation of drinking alcohol. 2019-05-15T16:33:57Z alcohol deterrent drug treatment alcohol deterrent agent therapy Treatment with a drug that deters smoking or encourages the cessation of smoking tobacco. 2019-05-15T16:44:49Z smoking cessation drug treatment smoking cessation agent therapy An agent that binds to but does not activate an opioid receptor thereby blocking the actions of endogenous or exogenous opioid receptor agonists. 2019-05-15T16:45:09Z CHEBI:60605 NCIT:C681 opiate antagonist agent therapy opioid antagonist drug treatment opioid antagonist agent therapy An agent that binds to but does not activate an opioid receptor thereby blocking the actions of endogenous or exogenous opioid receptor agonists. CHEBI:60605 obsolete hematopoeitic cell count true A determination of the number of erythrocyte in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C51946 erythrocyte count test red blood cell count red cell count erythrocyte count A determination of the number of platelet in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C51951 platelet count test thrombocyte count platelet count A determination of the number of neutrophil in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z neutrophil count test neutrophil count A determination of the number of leukocyte in a blood sample. http://orcid.org/0000-0001-7941-2961 2019-05-16T18:20:55Z NCIT:C51948 WBC leukocyte count test white blood cell count leukocyte count WBC Measuring the body or its parts. 2023-04-13T16:22:35Z body measurement Measuring the distance around (circumference) a patient's waist. 2023-04-13T16:49:17Z waist measurement A measurement of circumference around the hip. 2023-04-13T16:49:27Z hip measurement A recommendation of abstaining or avoiding any medical action that might normally be clinically prescribed. 2019-06-12T14:22:47Z avoid medical action recommendation avoidance of a medical action medical action avoidance Avoid the administration or use of aerobic exercise therapy. http://orcid.org/0000-0001-7941-2961 2019-05-19T20:39:14Z avoid aerobic exercise therapy avoiding aerobic exercise therapy aerobic exercise therapy avoidance Inoculating an individual with either killed or live agents to prevent contraction of a disease. 2019-06-14T15:47:12Z EFO:0004292 IDOMAL:0001040 NCIT:C15258 VO:0000002 vaccination Inoculating an individual with either killed or live agents to prevent contraction of a disease. NCIT:C15258 Nutrition intake is the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. 2019-07-23T18:14:54Z nutrient consumption nutrient intake nutrition consumption nutritional intake take nourishment dietary intake eating food consumption food intake ingesting nutrition intake Nutrition intake is the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. Addition of vitamin supplement, prenatal to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z NCIT:C92860 antenatal supplementation antenatal vitamin supplement treatment antenatal vitamin treatment dietary supplementation of vitamin supplement, prenatal prenatal vitamin supplement treatment supplementation of vitamin supplement, prenatal supplementation with prenatal vitamin treatment with prenatal supplements vitamin supplement, prenatal supplemental intake A vitamin enriched supplement containing higher doses for specific nutrients such as folic acid, intended for women before, during and after pregnancy and also during their lactating phase. prenatal vitamin supplementation A vitamin enriched supplement containing higher doses for specific nutrients such as folic acid, intended for women before, during and after pregnancy and also during their lactating phase. NCIT:C92860 A therapy utilizing a substance that produces loss of consciousness. 2019-07-24T15:53:13Z CHEBI:38869 general anaesthetic agents therapy general anaesthetic medication therapy general anaesthetics therapy general anesthesia therapy general anesthesia treatment general anesthetic medication therapy general anesthetics therapy treatment with general anaesthetic general anesthetic agent therapy Use of a drug or therapy to treat or prevent microbial infections. 2019-07-24T16:13:47Z CHEBI:36043 antimicrobial drug treatment antimicrobial treatment treatment with an anti-microbial agent treatment with an anti-microbial drug treatment with an anti-microbial medication treatment with an antimicrobial agent treatment with an antimicrobial drug treatment with an antimicrobial medication treatment with antimicrobial drug antimicrobial agent therapy Use of a loosely defined grouping of drugs that have effects on psychological function. 2019-07-24T19:33:44Z CHEBI:35471 psychoactive agent therapy psychoactive drug treatment psychopharmaceutical therapy psychotropic agent drug therapy psychotropic drug treatment treatment with psychotropic drug psychotropic agent therapy obsolete tranquilizing agent therapy true A ratio determined by waist measurement divided by hip measurement. 2023-04-13T16:50:13Z waist to hip ratio measurement waist to hip ratio calculation Therapy using any agent that acts on an adrenergic receptor or affects adrenergic signal transduction. 2019-07-25T14:32:48Z CHEBI:37962 NCIT:C29747 adrenergic agent drug treatment treatment with adrenergic agent treatment with adrenergic drug treatment with adrenergic medication adrenergic drug therapy Treatment with an agent that selectively binds to and activates beta-adrenergic receptors. 2019-07-25T14:42:00Z CHEBI:35522 treatment with beta-adrenergic agonist treatment with beta-adrenergic agonist agent treatment with beta-adrenergic agonist drug treatment with beta-adrenergic agonist medication beta-adrenergic agonist therapy Determination of shape, symmetry, and/or size of face using a particular method. 2023-04-13T16:53:56Z facial morphology assessment by type The surgical removal (cutting out) of part or all of pharyngeal tonsil. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C51697 adenoid removal pharyngeal tonsil surgical removal removal of adenoids removal of nasopharyngeal tonsil removal of tonsil of Luschka removal of tonsilla pharyngealis adenoidectomy The surgical removal (cutting out) of part or all of adrenal gland. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z adrenal gland surgical removal adrenalectomy The surgical removal (cutting out) of part or all of tooth root. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z tooth root surgical removal apicoectomy The surgical removal (cutting out) of part or all of vermiform appendix. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C51687 appendicectomy appendix removal removal of appendix vermiform appendix surgical removal appendectomy The surgical removal (cutting out) of part or all of skeletal joint. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z removal of a joint skeletal joint surgical removal arthectomy The surgical removal (cutting out) of part or all of ear. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z ear surgical removal auriculectomy The surgical removal (cutting out) of part or all of synovial bursa. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z bursa removal removal of bursa synovial bursa surgical removal bursectomy The surgical removal (cutting out) of part or all of cardia of stomach. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z cardia of stomach surgical removal cardiectomy cardiectomy of stomach gastric cardiectomy The surgical removal (cutting out) of part or all of head. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z decapitation head surgical removal cephalectomy The surgical removal (cutting out) of part or all of uterine cervix. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z cervix removal removal of cervix uterine cervix surgical removal cervicectomy The surgical removal (cutting out) of part or all of gallbladder. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C51676 gallbladder surgical removal cholecystectomy The surgical removal (cutting out) of part or all of optic choroid. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z optic choroid surgical removal removal of choroid layer of they eye choroidectomy The surgical removal (cutting out) of part or all of clitoris. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z clitorectomy clitoris surgical removal clitoridectomy The surgical removal (cutting out) of part or all of colon. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C15209 colon surgical removal colectomy The surgical removal (cutting out) of part or all of cranium. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C51791 cranium surgical removal craniectomy The surgical removal (cutting out) of part or all of urinary bladder. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C15217 bladder removal removal of the bladder urinary bladder surgical removal Can mean the removal of the urinary bladder or the surgical removal of a cyst. cystectomy The surgical removal (cutting out) of part or all of bony vertebral centrum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z body of vertebrae removal bony vertebral centrum surgical removal corpus vertebra removal corpus vertebrae removal vertebral body removal vertebrectomy corpectomy The surgical removal (cutting out) of part or all of intervertebral disk. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C21009 intervertebral disk surgical removal removal of intervertebral disc removal of spinal disc discectomy The surgical removal (cutting out) of part or all of digestive tract diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z digestive tract diverticulum surgical removal digestive tract diverticulectomy The surgical removal (cutting out) of part or all of thyroid diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z thyroid diverticulum surgical removal thyroid diverticulectomy The surgical removal (cutting out) of part or all of hepatic diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z hepatic diverticulum surgical removal hepatic diverticulectomy The surgical removal (cutting out) of part or all of duodenum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z duodenum surgical removal enterectomy pancreas-sparing duodenectomy small bowel resection duodenectomy The surgical removal (cutting out) of part or all of sympathetic nerve trunk. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z sympathetic nerve trunk surgical removal endoscopic thoracic sympathectomy The surgical removal (cutting out) of part or all of esophagus. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z esophagus surgical removal oesophagectomy esophagectomy The surgical removal (cutting out) of part or all of stomach. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z stomach surgical removal gastrectomy The surgical removal (cutting out) of part or all of tongue. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z tongue surgical removal glossectomy The surgical removal (cutting out) of part or all of gonad. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z gonad surgical removal gonadectomy The surgical removal (cutting out) of part or all of liver. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z liver surgical removal hepatectomy The surgical removal (cutting out) of part or all of pituitary gland. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z hypophysis removal pituitary gland surgical removal hypophysectomy The surgical removal (cutting out) of part or all of uterus. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z uterus surgical removal hysterectomy The surgical removal (cutting out) of part or all of iris. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z iris surgical removal iridectomy The surgical removal (cutting out) of part or all of cornea. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z cornea surgical removal keratectomy The surgical removal (cutting out) of part or all of vertebra. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z vertebra surgical removal laminectomy The surgical removal (cutting out) of part or all of larynx. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z larynx surgical removal lymph node dissection laryngectomy The surgical removal (cutting out) of part or all of lymph node. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z lymph node surgical removal lymphadenectomy The surgical removal (cutting out) of part or all of breast. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z breast surgical removal mastectomy The surgical removal (cutting out) of part or all of kidney. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z kidney surgical removal nephrectomy The surgical removal (cutting out) of part or all of nerve. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z nerve surgical removal neurectomy The surgical removal (cutting out) of part or all of ovary. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z female gonad removal ovariectomy ovary surgical removal removal of female genitalia removal of female gonad removal of female reproductive system gonada removal of gonada of female oophorectomy The surgical removal (cutting out) of part or all of testis. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z castration orchidectomy removal of male genitalia gonad removal of testicles testis surgical removal orchiectomy The surgical removal (cutting out) of part or all of bone tissue. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z bone tissue surgical removal ostectomy The surgical removal (cutting out) of part or all of pancreas. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z pancreas surgical removal pancreatectomy The surgical removal (cutting out) of part or all of panniculus adiposus. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C51597 panniculus adiposus surgical removal abdominal panniculectomy The surgical removal (cutting out) of part or all of parathyroid gland. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z parathyroid gland surgical removal parathyroid removal parathyroidectomy The surgical removal (cutting out) of part or all of pineal body. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z pineal body surgical removal removal of pineal gland pinealectomy The surgical removal (cutting out) of part or all of lung. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z lung surgical removal pneumectomy pneumonectomy The surgical removal (cutting out) of part or all of skin of prepuce of penis. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z circumcision forskin removal skin of prepuce of penis surgical removal posthectomy The surgical removal (cutting out) of part or all of fallopian tube. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z fallopian tube surgical removal salpingectomy The surgical removal (cutting out) of part or all of spleen. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z spleen surgical removal splenectomy The surgical removal (cutting out) of part or all of synovial membrane of synovial joint. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z synovial membrane of synovial joint surgical removal synovectomy The surgical removal (cutting out) of part or all of thymus. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z thymus surgical removal thymectomy The surgical removal (cutting out) of part or all of thyroid gland. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z thyroid gland surgical removal thyroidectomy The surgical removal (cutting out) of part or all of palatine tonsil. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z palatine tonsil surgical removal tonsillectomy A surgical procedure aimed at lowering the intraocular pressure by producing an outflow of aqueous humour through a drainage passage created in the sclera between the anterior chamber and the subconjunctival space. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:12:12Z eye trabecular meshwork surgical removal The filtering procedure involves full thickness penetration of sclera to remove a small portion of the trabecular meshwork or surrounding tissue; it bypasses the natural outflow system by diverting aqueous humor from the anterior chamber into a subconjunctival reservoir with a filtering bleb on the eye. Antifibrotic agents, such as mitomycin-C and 5-fluorouracil, may be used intraoperatively and postoperatively to reduce scarring and prevent closure of the new channel. trabeculectomy The surgical removal (cutting out) of part or all of vagina. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z vagina surgical removal vaginectomy The surgical removal (cutting out) of part or all of vas deferens. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z vas deferens surgical removal vasectomy The surgical removal (cutting out) of part or all of vitreous humor. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z vitreous humor surgical removal vitrectomy The surgical removal (cutting out) of part or all of mammalian vulva. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z mammalian vulva surgical removal vulvectomy The surgical removal (cutting out) of part or all of penis. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z penis surgical removal penectomy The surgical removal (cutting out) of part or all of Pulmonary bulla. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Pulmonary bulla surgical removal bullectomy The surgical removal (cutting out) of part or all of Hallux valgus. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C96171 Hallux valgus surgical removal bunion removal removal of bunion bunionectomy Computer aided analysis of 3D facial images to detect abnormal facial phenotypes that assist in diagnosis, treatment monitoring and surgical planning. 2023-04-13T16:54:13Z '3D facial assessment' three dimensional facial analysis three dimensional facial assessment 3D facial analysis Computer aided analysis of 3D facial images to detect abnormal facial phenotypes that assist in diagnosis, treatment monitoring and surgical planning. PMID:34108542 Surgical removal of an abnormal pouch of the lining of the small intestine (bowel). http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Meckel diverticulum surgical removal Meckel's diverticulectomy The surgical removal (cutting out) of part or all of Cardiac diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Cardiac diverticulum surgical removal cardiac diverticulectomy The surgical removal (cutting out) of part or all of Esophageal diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Esophageal diverticulum surgical removal esophageal diverticulectomy The surgical removal (cutting out) of part or all of Gastric diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Gastric diverticulum surgical removal gastric diverticulectomy The surgical removal (cutting out) of part or all of Renal diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Renal diverticulum surgical removal renal diverticulectomy The surgical removal (cutting out) of part or all of Bladder diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Bladder diverticulum surgical removal bladder diverticulectomy The surgical removal (cutting out) of part or all of Urethral diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Urethral diverticulum surgical removal uethral diverticulectomy The surgical removal (cutting out) of part or all of Fibrous cardiac diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Fibrous cardiac diverticulum surgical removal fibrous cardiac diverticulectomy The surgical removal (cutting out) of part or all of Muscular cardiac diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Muscular cardiac diverticulum surgical removal muscular cardiac diverticulectomy The surgical removal (cutting out) of part or all of Spinal meningeal diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Spinal meningeal diverticulum surgical removal spinal meningeal diverticulectomy The surgical removal (cutting out) of part or all of Coronary sinus diverticulum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Coronary sinus diverticulum surgical removal coronary sinus diverticulectomy The surgical removal (cutting out) of part or all of Thromboembolism. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Thromboembolism surgical removal thromboembolectomy The surgical removal (cutting out) of part or all of Pulmonary embolism. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Pulmonary embolism surgical removal pulmonary embolectomy The surgical removal (cutting out) of part or all of Arterial calcification. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C52002 Arterial calcification surgical removal endarterectomy The surgical removal (cutting out) of part or all of Neoplasm of the breast. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C15755 Neoplasm of the breast surgical removal breast segmental resection breast wide local lumpectomy of breast excision partial mastectomy tylectomy Surgery to remove abnormal tissue or cancer from the breast and a small amount of normal tissue around it. It is a type of breast-sparing surgery. NCIT:C15755 lumpectomy The surgical removal (cutting out) of part or all of Uterine leiomyoma. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z NCIT:C51645 Uterine leiomyoma surgical removal fiboroidectomy removal of uterine fibroids myomectomy The surgical removal (cutting out) of part or all of Arterial thrombosis. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Arterial thrombosis surgical removal arterial thrombosis The surgical removal (cutting out) of part or all of Venous thrombosis. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Venous thrombosis surgical removal venous thrombosis The surgical removal (cutting out) of part or all of Abnormal thrombosis. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Abnormal thrombosis surgical removal removal of thrombosis thrombosis removal thrombosis The surgical removal (cutting out) of part or all of Neoplasm. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z cancer surgery NCIT:C157740 Neoplasm surgical removal cancer removal removal of tumor tumor removal tumorectomy The surgical removal (cutting out) of part or all of gland. http://orcid.org/0000-0001-7941-2961 2022-03-23T20:39:14Z gland surgical removal adenectomy obsolete kidney ct true A medical requirement or recommendation of avoiding or preventing abnormal physiologic state. 2020-09-15T11:00:00Z avoid physiologic state recommendation prevent physiologic state avoidance prevent physiologic state recommendation prevention of abnormal physiologic state A medical requirement or recommendation of avoiding or preventing Ketosis. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Ketosis avoidance avoid Ketosis recommendation ketosis prevention recommendation A medical requirement or recommendation of avoiding or preventing Diabetes mellitus. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Diabetes mellitus avoidance avoid Diabetes mellitus recommendation Diabetes mellitus prevention recommendation A medical requirement or recommendation of avoiding or preventing Fever. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Fever avoidance avoid Fever recommendation fever prevention recommendation Recommendation to avoid triggers known to cause seizures or take medicine to avoid seizures. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Seizure avoidance avoid Seizure recommendation seizure prevention recommendation A medical requirement or recommendation of avoiding or preventing Hypotension. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Hypotension avoidance avoid Hypotension recommendation hypotension prevention recommendation A medical requirement or recommendation of avoiding or preventing Hyperglycemia. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Hyperglycemia avoidance avoid Hyperglycemia recommendation hyperglycemia prevention recommendation A medical requirement or recommendation of avoiding or preventing Weight loss. http://orcid.org/0000-0001-7941-2961 2020-09-15T11:00:00Z Weight loss avoidance avoid Weight loss recommendation weight loss avoidance recommendation Removal and examination of tissue, cells, or fluids from kidney for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z kidney biopsy biopsy of kidney The use of computed tomography to produce images of structures of the kidney. http://orcid.org/0000-0001-7941-3010 2020-06-09T20:39:14Z CAT scan of kidney CT of kidney kidney CAT scan kidney CT examination kidney computed tomography kidney computerized axial tomography renal CAT scan renal CT kidney CT Addition of potassium atom to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-17T02:36:00Z dietary supplementation of potassium dietary supplementation of potassium atom potassium atom supplemental intake supplementation of potassium supplementation of potassium atom potassium supplementation Treatment with any agent that lowers cholesterol. http://orcid.org/0000-0001-7941-2961 2020-11-17T11:00:00Z antihypercholesterolemic agent therapy cholesterol inhibitor therapy hypocholesteremic agent therapy treatment with anticholesteremic drug anticholesteric agent therapy Therapy with an agent that inhibits the function of the sodium-potassium-chloride (Na+, K+, Cl-) cotransporter system in the thick ascending limb of the loop of Henle, thereby inhibiting the reabsorption of sodium, potassium, and chloride ions. This leads to an increase in the excretion of sodium, potassium, chloride, calcium, magnesium, ammonium and water. http://orcid.org/0000-0001-7941-2961 2020-11-17T11:00:00Z treatment with loop diuretic loop diuretic agent therapy Avoid the administration or use of blood transfusion. http://orcid.org/0000-0001-7941-2961 2020-11-19T20:39:14Z avoid blood transfusion avoiding blood transfusion blood transfusion avoidance Avoid the administration or use of radiograph imaging procedure. http://orcid.org/0000-0001-7941-2961 2020-11-19T20:39:14Z avoid radiograph imaging procedure avoiding radiograph imaging procedure radiograph imaging procedure avoidance Addition of folic acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of folic acid folic acid supplemental intake supplementation of folic acid folic acid supplementation Addition of vitamin (role) to a diet for adequate and complete nutrition. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of vitamin (role) supplementation of vitamin (role) supplementation with a vitamin vitamin (role) supplemental intake vitamin supplementation Addition of nicotinic acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of nicotinic acid niacin supplementation nicotinic acid supplemental intake supplementation of nicotinic acid nicotinic acid supplementation Addition of pyridoxine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of pyridoxine pyridoxine supplemental intake supplementation of pyridoxine pyridoxine supplementation obsolete dietary purine intake avoidance true Addition of ascorbic acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z ascorbic acid supplemental intake dietary supplementation of ascorbic acid supplementation of ascorbic acid ascorbic acid supplementation Addition of sodium pyruvate to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of sodium pyruvate sodium pyruvate supplemental intake supplementation of sodium pyruvate sodium pyruvate supplementation Addition of fat-soluble vitamin (role) to a diet for adequate and complete nutrition. http://orcid.org/0000-0001-7941-2961 2022-09-07T09:00:01Z dietary supplementation of fat-soluble vitamin (role) fat soluble vitamin supplementation fat-soluble vitamin (role) supplemental intake supplementation of fat-soluble vitamin (role) supplementation with fat-soluble vitamin fat-soluble vitamin supplementation Addition of S-adenosyl-L-methionine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z S-adenosyl-L-methionine supplemental intake SAM-e supplementation dietary supplementation of S-adenosyl-L-methionine supplementation of S-adenosyl-L-methionine S-adenosyl methionine supplementation Addition of isoleucine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of isoleucine isoleucine supplemental intake supplementation of isoleucine isoleucine supplementation Addition of valine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of valine supplementation of valine valine supplemental intake valine supplementation Addition of calcium atom to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z calcium atom supplemental intake dietary supplementation of calcium atom supplementation of calcium atom supplementation with calcium calcium supplementation Addition of calcium carbonate to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z calcium carbonate supplemental intake dietary supplementation of calcium carbonate supplementation of calcium carbonate calcium carbonate supplementation Addition of glucose to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of glucose glucose supplemental intake supplementation of glucose glucose supplementation Addition of docosahexaenoic acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z DHA supplementtion dietary supplementation of docosahexaenoic acid docosahexaenoic acid supplemental intake supplementation of docosahexaenoic acid supplementation with DHA docosahexaenoic acid supplementation Addition of omega-3 fatty acid to the diet for complete nutrition. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of omega-3 fatty acid eicosapentaenoic acid supplementation omega-3 fatty acid supplemental intake supplementation of omega-3 fatty acid omega-3 fatty acid supplementation Addition of lutein to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of lutein lutein supplemental intake supplementation of lutein lutein supplementation Addition of ribose to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of ribose ribose supplemental intake supplementation of ribose ribose supplementation Addition of fluoride to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of fluoride fluoride supplemental intake supplementation of fluoride fluoride supplementation Addition of dietary supplement, fibre to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplement, fibre supplemental intake dietary supplementation of dietary supplement, fibre supplementation of dietary supplement, fibre supplementation with soluble fiber soluble fiber supplementation Addition of fish oil to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-23T09:00:01Z dietary supplementation of fish oil fish oil supplemental intake supplementation of fish oil fish oil supplementation Addition of magnesium atom to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2020-11-30T09:00:01Z dietary supplementation of magnesium atom magnesium atom supplemental intake magnesium supplemental intake supplementation of magnesium supplementation of magnesium atom magnesium supplementation A systemic evaluation of the head using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2961 2021-02-10T14:39:14Z examination of head head exam physical examination of head head examination A systemic evaluation of the neck using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2979 2021-02-10T14:39:14Z examination of neck neck exam physical examination of neck neck examination A systemic evaluation of the chest using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-3010 2021-02-10T14:39:14Z chest exam examination of chest physical examination of chest chest examination A systemic evaluation of the uterus using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2961 2021-02-10T14:39:14Z examination of uterus physical examination of uterus uterus exam uterus examination A systemic evaluation of the uterine cervix using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2979 2021-02-10T14:39:14Z examination of the cervix examination of uterine cervix physical examination of uterine cervix uterine cervix exam cervical examination A systemic evaluation of the eye using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2961 2021-02-10T14:39:14Z examination of eye eye exam physical examination of eye eye examination A systemic evaluation of the multicellular organism using visual inspection, palpation, and percussion. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. http://orcid.org/0000-0001-7941-2979 2021-02-10T14:39:14Z examination of multicellular organism examination of whole body multicellular organism exam physical examination of multicellular organism whole body exam whole body examination A medical requirement or recommendation of avoiding the consumption of fish steak (raw). http://orcid.org/0000-0001-7941-2961 2021-02-10T11:00:00Z avoid fish steak (raw) intake avoiding dietary fish steak (raw) intake fish steak (raw) consumption avoidance fish steak (raw) restricted diet intake fish steak (raw) restriction raw fish intake avoidance A medical requirement or recommendation of avoiding the consumption of cow milk (raw). http://orcid.org/0000-0001-7941-2961 2021-02-10T11:00:00Z avoid cow milk (raw) intake avoiding dietary cow milk (raw) intake cow milk (raw) consumption avoidance cow milk (raw) restricted diet intake cow milk (raw) restriction raw milk intake avoidance unpasturised milk intake avoidance unpasturized milk intake avoidance Collection biological material from within the endocervix with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2021-02-15T20:39:14Z endocervical swab swab collection of endocervix endocervical swab collection Collecting of sputum for clinical use. http://orcid.org/0000-0001-7941-2961 2021-02-15T12:00:00Z collection of sputum specimen sputum collection sputum specimen collection Collecting of urine for clinical use. http://orcid.org/0000-0001-7941-2974 2021-02-15T12:00:00Z collection of urine specimen urine collection urine specimen collection Collecting of semen for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z collection of semen specimen semen collection sperm collection semen specimen collection Collecting of amniotic fluid for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z amniotic fluid collection collection of amniotic fluid specimen amniotic fluid specimen collection Collecting of pus for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z collection of pus specimen pus collection pus specimen collection Collecting of mucus for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z collection of mucus specimen mucus collection mucus specimen collection Collecting of respiratory system mucus for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z collection of respiratory system mucus specimen respiratory system mucus collection respiratory system mucus specimen collection Collecting of nasal mucus for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z collection of nasal mucus specimen nasal mucus collection nasal mucus specimen collection Collecting of bodily fluid for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z bodily fluid collection collection of bodily fluid specimen bodily fluid specimen collection Collecting of cerebrospinal fluid for clinical use. http://orcid.org/0000-0001-7941-2978 2021-02-15T12:00:00Z cerebral spinal fluid collection cerebrospinal fluid collection collection of cerebrospinal fluid specimen cerebrospinal fluid specimen collection The use of ultrasound to produce images of structures in the venous blood vessel. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of venous blood vessel ultrasonography of venous blood vessel venous blood vessel diagnostic sonography venous blood vessel medical ultrasound venous blood vessel sonography venous blood vessel ultrasound examination venous blood vessel ultrasound imaging procedure venous blood vessel ultrasound procedure venous sonography venous ultrasonography The use of ultrasound to produce images of structures in the testis. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of testis testis diagnostic sonography testis medical ultrasound testis sonography testis ultrasound examination testis ultrasound imaging procedure testis ultrasound procedure ultrasonography of testis testicular ultrasonography The determination of the amount of insulin hormone present in the sample. http://orcid.org/0000-0001-7941-2961 2021-03-19T21:42:40Z insulin hormone assessment insulin hormone test insulin level assessment insulin measurement The determination of the amount of albumin (human) present in urine. http://orcid.org/0000-0001-7941-2961 2021-03-19T15:25:01Z albumin (human) urine assessment urine albumin (human) test urine albumin measurement The determination of the amount of protein present in blood serum. http://orcid.org/0000-0001-7941-2961 2021-03-19T15:25:01Z blood serum protein test protein blood serum assessment serum protein measurement The surgical transfer of some or all of a(n) liver from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2022-10-06T20:39:14Z NCIT:C15271 liver transplantation surgical procedure transplantation of liver liver transplantation Treatment with drug or agent that regulates potassium channels. http://orcid.org/0000-0001-7941-2961 2021-08-10T11:00:00Z K-channel modulator therapy treatment with potassium channel modulator potassium channel modulator agent therapy Treatment with a drug or agent that inhibits potassium channels. http://orcid.org/0000-0001-7941-2961 2021-08-10T11:00:00Z K-channel antagonist therapy K-channel inhibitor therapy potassium channel antagonist therapy treatment with potassium channel blocker potassium channel blocker agent therapy Treatment with a drug or agent that inhibits xanthine oxidase. http://orcid.org/0000-0001-7941-2961 2021-08-10T11:00:00Z treatment with EC 1.17.3.2 (xanthine oxidase) inhibitor xanthine oxidase inhibitor agent therapy Treatment with a drug or agent that inhibits purinergic P2 receptor. http://orcid.org/0000-0001-7941-2961 2021-08-10T11:00:00Z P2 antagonist therapy treatment with purinergic receptor P2 antagonist purinergic receptor P2 antagonist agent therapy Treatment with a drug or agent that inhibits P2Y12 receptor. http://orcid.org/0000-0001-7941-2961 2021-08-10T11:00:00Z ADP receptor inhibitor therapy purinergic PY12 antagonist therapy treatment with P2Y12 receptor antagonist P2Y12 receptor antagonist agent therapy The determination of the amount of alkaline phosphatase present in blood serum. http://orcid.org/0000-0001-7941-2961 2021-08-12T15:25:01Z alkaline phosphatase blood serum assessment blood serum alkaline phosphatase test serum Alk phos measurement serum alkaline phosphatase measurement Inspection of skeletal joint using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of skeletal joint skeletal joint endoscope arthroscopy Inspection of lung using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z airway endoscopy endoscopy of lung lung endoscope bronchoscopy Inspection of colon using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z colon endoscope endoscopy of colon colonoscopy Inspection of urinary bladder using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of urinary bladder urinary bladder endoscope cystoscopy Inspection of small intestine using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of small intestine small intestine endoscope enterosccopy Inspection of uterus using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of uterus uterus endoscope hysteroscopy Inspection of abdomen using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z abdomen endoscope endoscopy of abdomen laparoscopy Inspection of larynx using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of larynx larynx endoscope laryngoscopy Inspection of mediastinum using an endoscope. 2022-03-16T20:39:14Z endoscopy of mediastinum mediastinum endoscope mediastinoscopy Inspection of sigmoid colon using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of sigmoid colon sigmoid colon endoscope sigmoidoscopy Inspection of pleural cavity using an endoscope. 2022-03-16T13:39:34Z endoscopy of pleural cavity pleural cavity endoscope thoracoscopy Inspection of upper digestive tract using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z EGD OGD endoscopy of upper digestive tract oesophagogastroduodenoscopy upper GI endoscopy upper digestive tract endoscope upper endoscopy upper gastrointestinal endoscopy esophagogastroduodenoscopy Inspection of ureter using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of ureter ureter endoscope ureteroscopy Inspection of lower digestive tract using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of lower digestive tract lower digestive tract endoscope proctoscopy Inspection of rectum using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of rectum rectum endoscope rectoscopy Inspection of anus using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z anus endoscope endoscopy of anus anoscopy Inspection of ear using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z ear endoscope endoscopy of ear otoscopy Inspection of fallopian tube using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of fallopian tube fallopian tube endoscope falloscopy Inspection of esophagus using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of esophagus esophagus endoscope oesophagoscopy esophagoscopy Inspection of brain using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z brain endoscope endoscopy of brain neuroendoscopy Inspection of tracheobronchial tree using an endoscope. http://orcid.org/0000-0001-7941-2961 2022-03-16T20:39:14Z endoscopy of tracheobronchial tree tracheobronchial tree endoscope tracheobronchoscopy The use of any device, marker, or other means for the purpose of detecting the presence Neoplasm of the breast, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Neoplasm of the breast screening screening for breast cancer The use of any device, marker, or other means for the purpose of detecting the presence Venous thrombosis, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z Venous thrombosis screening screening for venous thrombosis The use of any device, marker, or other means for the purpose of detecting the presence Colorectal polyposis, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Colorectal polyposis screening screening for colorectal polyps The use of any device, marker, or other means for the purpose of detecting the presence Intestinal polyp, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Intestinal polyp screening screening for intestinal polyps The use of any device, marker, or other means for the purpose of detecting the presence Ureteral polyp, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Ureteral polyp screening screening for uterine polyps The use of any device, marker, or other means for the purpose of detecting the presence Cervical polyp, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Cervical polyp screening screening for cervical polyps The use of any device, marker, or other means for the purpose of detecting the presence Small intestinal polyp, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Small intestinal polyp screening screening for small intestinal polyps The use of any device, marker, or other means for the purpose of detecting the presence Multiple gastric polyps, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Multiple gastric polyps screening screening for gastric polyps The use of any device, marker, or other means for the purpose of detecting the presence Hepatoblastoma, usually in asymptomatic individuals. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Hepatoblastoma screening screening for hepatoblastoma Visualization of a particular body system, organ, or cell type using a variety of imaging techniques for use in screening, diagnosis, surgical procedures or therapy. 2023-02-21T18:01:42Z clinical imaging procedure by system The surgical removal (cutting out) of part or all of colorectal polyps. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Colorectal polyposis surgical removal colonic polypectomy colorectal polypectomy The surgical removal (cutting out) of part or all of Intestinal polyp. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Intestinal polyp surgical removal intestinal polypectomy The surgical removal (cutting out) of part or all of Ureteral polyp. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Ureteral polyp surgical removal ureterine polypectomy The surgical removal (cutting out) of part or all of Cervical polyp. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Cervical polyp surgical removal cervical polypectomy The surgical removal (cutting out) of part or all of Small intestinal polyp. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Small intestinal polyp surgical removal small intestinal polypectomy The surgical removal (cutting out) of part or all of Osteoma. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Osteoma surgical removal surgical removal of Osteoma The surgical removal (cutting out) of part or all of Multiple gastric polyps. http://orcid.org/0000-0001-7941-2961 2022-03-24T20:39:14Z Multiple gastric polyps surgical removal gastric polypectomy The surgical removal (cutting out) of part or all of lens of camera-type eye. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z lens of camera-type eye surgical removal removal of lens The surgical removal (cutting out) of part or all of colorectum. http://orcid.org/0000-0001-7941-2961 2020-06-23T20:39:14Z colorectum surgical removal proctocolectomy The determination of the amount of alpha-fetoprotein present in blood serum. http://orcid.org/0000-0001-7941-2961 2022-03-28T15:25:01Z alpha-fetoprotein (human) blood serum assessment alpha-fetoprotein serum measurement blood serum alpha-fetoprotein (human) test serum alpha-fetoprotein test serum alpha-fetoprotein measurement Use of a chemical compound that binds tightly to metal ions. Often used to remove toxic metals from the body. http://orcid.org/0000-0001-7941-2961 2022-03-30T11:00:00Z treatment with chelator chelator agent therapy Treatrment with an agent that binds excess amounts of copper to keep it from accumulating in some parts of the body, particularly the liver. http://orcid.org/0000-0001-7941-2961 2022-03-30T11:00:00Z treatment with copper chelator copper chelator agent therapy Use of a compound which binds tightly to iron molecules. http://orcid.org/0000-0001-7941-2961 2022-03-30T11:00:00Z treatment with iron chelator iron chelator agent therapy Treatment with a sequestering agent that can envelop multiple ions at a time. http://orcid.org/0000-0001-7941-2961 2022-03-30T11:00:00Z treatment with sequestrant sequestrant agent therapy The determination of the amount of beta-carotene present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z b-carotene measurement beta carotene assessment beta-carotene assessment beta-carotene measurement beta-carotene test beta carotene measurement The determination of the amount of creatine present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z creatine assessment creatine test creatine measurement The determination of the amount of N-phosphocreatine present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z N-phosphocreatine assessment N-phosphocreatine test phosphocreatine measurement The determination of the amount of folic acid present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z folic acid assessment folic acid test folic acid measurement The determination of the amount of carnitine present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z carnitine assessment carnitine test carnitine measurement The determination of the amount of choline present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z choline assessment choline test choline measurement The determination of the amount of glycerylphosphorylcholine present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z glycerylphosphorylcholine assessment glycerylphosphorylcholine test glycerylphosphorylcholine measurement The determination of the amount of phosphocholines present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z phosphocholines assessment phosphocholines test phosphocholine measurement The determination of the amount of pyridoxal 5'-phosphate present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z pyridoxal 5'-phosphate assessment pyridoxal 5'-phosphate test pyridoxal 5'-phosphate measurement The determination of the amount of chemical entity present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z chemical entity assessment chemical entity test chemical measurement The determination of the amount of vitamin A present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin A assessment vitamin A test vitamin A measurement The determination of the amount of B vitamin present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z B vitamin assessment B vitamin test vitamin B measurement The determination of the amount of vitamin B complex present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin B complex assessment vitamin B complex test vitamin B complex measurement The determination of the amount of vitamin B1 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z thiamin measurement vitamin B1 assessment vitamin B1 test vitamin B1 measurement The determination of the amount of vitamin B2 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z riboflavin measurement vitamin B2 assessment vitamin B2 test vitamin B2 measurement The determination of the amount of vitamin B3 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z niacin measurement vitamin B3 assessment vitamin B3 test vitamin B3 measurement The determination of the amount of vitamin B5 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin B5 assessment vitamin B5 test vitamin B5 measurement The determination of the amount of vitamin B6 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin B6 assessment vitamin B6 test vitamin B6 measurement The determination of the amount of vitamin B7 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin B7 assessment vitamin B7 test vitamin B7 measurement The determination of the amount of vitamin B9 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin B9 assessment vitamin B9 test vitamin B9 measurement The determination of the amount of vitamin B12 present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin B12 assessment vitamin B12 test vitamin B12 measurement The determination of the amount of vitamin D present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin D assessment vitamin D test vitamin D measurement The determination of the amount of vitamin C present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin C assessment vitamin C test vitamin C measurement The determination of the amount of vitamin E present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin E assessment vitamin E test vitamin E measurement The determination of the amount of vitamin K present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z vitamin K assessment vitamin K test vitamin K measurement The determination of the amount of folates present in the sample. http://orcid.org/0000-0001-7941-2961 2022-05-04T13:40:00Z folates assessment folates test folate measurement Use of an imaging test that uses small amounts of radiation to produce pictures of pelvic region of trunk. http://orcid.org/0000-0001-7941-2961 2022-05-09T20:39:14Z X-ray of the pelvis pelvic radiogram procedure pelvic region of trunk X-ray procedure pelvic region of trunk radiogram procedure pelvis radiograph radiograph of pelvic region of trunk radiograph of pelvis radiography of pelvic region of trunk pelvic radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of skull. http://orcid.org/0000-0001-7941-2961 2022-05-09T20:39:14Z X-ray of the skull radiograph of skull radiography of skull skull X-ray procedure skull radiogram procedure skull radiograph procedure Addition of cholic acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2022-08-25T09:00:01Z cholic acid supplemental intake dietary supplementation of cholic acid supplementation of cholic acid cholic acid supplementation Addition of vitamin K to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2022-08-25T09:00:01Z dietary supplementation of vitamin K supplementation of vitamin K vitamin K supplemental intake vitamin K supplementation Addition of vitamin E to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2022-08-25T09:00:01Z dietary supplementation of vitamin E supplementation of vitamin E vitamin E supplemental intake vitamin E supplementation Addition of vitamin A to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2022-09-07T09:00:01Z dietary supplementation of vitamin A supplementation of vitamin A vitamin A supplemental intake vitamin A supplementation A medical imaging technique used to visualize the inside, or lumen, of blood vessels and organs of the body, with particular interest in the arteries, veins, and the heart chambers. 2023-02-21T18:03:45Z arteriography angiography A medical imaging technique used to visualize the inside, or lumen, of blood vessels and organs of the body, with particular interest in the arteries, veins, and the heart chambers. Addition of water-soluble vitamin (role) to a diet for adequate and complete nutrition. http://orcid.org/0000-0001-7941-2961 2022-09-07T09:00:01Z dietary supplementation of water-soluble vitamin (role) supplementation of water-soluble vitamin (role) water soluble vitamin supplementation water-soluble vitamin (role) supplemental intake water-soluble supplementation Addition of macronutrient to a diet for adequate and complete nutrition. http://orcid.org/0000-0001-7941-2961 2022-09-07T09:00:01Z dietary supplementation of macronutrient macronutrient supplemental intake supplementation of macronutrient macronutrient supplementation Addition of micronutrient to a diet for adequate and complete nutrition. http://orcid.org/0000-0001-7941-2961 2022-09-07T09:00:01Z dietary supplementation of micronutrient micronutrient supplemental intake supplementation of micronutrient micronutrient supplementation The surgical transfer of some or all of a(n) face from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2022-10-06T20:39:14Z transplantation of face face transplantation The surgical transfer of a whole pair of lungs from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2022-10-06T10:00:01Z transplantation of whole pair of lungs double lung transplant The surgical transfer of some or all of a(n) lobe of lung from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2022-10-06T20:39:14Z transplantation of lobe of lung partial lung transplantation Transplantation of some or all of the liver, small intestine, and other abdominal organs (for example, the stomach and pancreas) at the same time. http://orcid.org/0000-0001-7941-2961 2022-10-06T20:39:14Z transplantation of digestive system multivisceral transplantation Addition of selenium atom to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2022-11-01T09:00:01Z PMID:27171069 dietary supplementation of selenium atom selenium atom supplemental intake supplementation of selenium atom Food supplementation with selenium should be carried out in a careful and controlled way, to avoid causing the opposite effect than intended, because selenium is one of the most toxic elements in relatively small quantities being at the same time an essential micronutrient with an important biological role. The range between the necessary quantity of selenium and toxic dose is very narrow. PMID:27171069 selenium supplementation A medical requirement or recommendation of avoiding the consumption of selenium atom. http://orcid.org/0000-0001-7941-2961 2022-11-01T09:00:01Z PMID:27171069 avoid selenium atom intake avoiding dietary selenium atom intake selenium atom consumption avoidance selenium atom restricted diet intake selenium atom restriction Food supplementation with selenium should be carried out in a careful and controlled way, to avoid causing the opposite effect than intended, because selenium is one of the most toxic elements in relatively small quantities being at the same time an essential micronutrient with an important biological role. The range between the necessary quantity of selenium and toxic dose is very narrow. PMID:27171069 dietary selenium atom intake avoidance A specimen collection from a patient that is used for diagnostic purposes. 2022-12-08T20:39:14Z OBI:0002650 diagnostic biopsy clinical biopsy Use of computed tomography assisted biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002652 A needle biopsy guided by real-time computed tomography (CT) scan images. OBI:0002652 clinical computed tomography assisted biopsy Use of core needle biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002656 A biopsy that uses a hollow tube to collect a core of tissue. OBI:0002656 clinical core needle biopsy Use of fine needle aspiration biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002655 A biopsy that uses a thin needle to extract cells. OBI:0002655 clinical fine needle aspiration biopsy Use of image guided biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002651 A biopsy which uses an imaging procedure to guide a needle biopsy. OBI:0002651 clinical image guided biopsy Use of needle biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002654 A biopsy that uses a hollow needle to extract cells. OBI:0002654 clinical needle biopsy Use of surgical biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002657 A biopsy involving a surgical incision into an organism to access the biopsy material. OBI:0002657 clinical surgical biopsy Use of ultrasound-guided needle biopsy to removal and examination of tissue, cells, or fluids from a patient purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2022-12-08T20:39:14Z OBI:0002653 An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. OBI:0002653 clinical ultrasound-guided needle biopsy A surgery that fixes or mends coronary artery. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z coronary artery surgical repair surgical repair of coronary artery A surgery that fixes or mends cardiac valve. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z cardiac valve surgical repair heart valve repair A surgery that fixes or mends tricuspid valve. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z tricuspid valve surgical repair surgical repair of tricuspid valve A surgery that fixes or mends pulmonary valve. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z pulmonary valve surgical repair surgical repair of pulmonary valve A surgery that fixes or mends aorta. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z aorta surgical repair surgical repair of aorta A surgery that fixes or mends endocrine gland. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z endocrine gland surgical repair surgical repair of endocrine gland A surgery that fixes or mends fallopian tube. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z fallopian tube surgical repair surgical repair of fallopian tube A surgery that fixes or mends pancreas. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z pancreas surgical repair surgical repair of pancreas A surgery that fixes or mends eye. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z eye surgical repair surgical repair of eye A surgery that fixes or mends digestive tract. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z digestive tract surgical repair surgical repair of digestive tract A surgery that fixes or mends ligament. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z ligament surgical repair surgical repair of ligament A surgery that fixes or mends vertebra. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z vertebra surgical repair surgical repair of vertebra A surgery that fixes or mends bone tissue. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z bone tissue surgical repair surgical repair of bone tissue A medically necessary surgery performed to restore function and conventional appearance of ear. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z ear surgical plastic reconstruction surgical plastic reconstruction of ear A medically necessary surgery performed to restore function and conventional appearance of cranium. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z cranium surgical plastic reconstruction cranioplasty A medically necessary surgery performed to restore function and conventional appearance of face. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z face surgical plastic reconstruction surgical plastic reconstruction of face A medically necessary surgery performed to restore function and conventional appearance of manus. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z manus surgical plastic reconstruction reconstructive plastic surgery of hand hand reconstructive plastic surgery A medically necessary surgery performed to restore function and conventional appearance of nasal septum. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z nasal septum surgical plastic reconstruction septoplasty A medically necessary surgery performed to restore function and conventional appearance of bronchus. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z bronchus surgical plastic reconstruction bronchoplasty A medically necessary surgery performed to restore function and conventional appearance of iris. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-07-14T20:39:14Z gonioplasty iris surgical plastic reconstruction iridoplasty can be performed despite corneal clouding, whereas iridotomy cannot iridoplasty A surgery that fixes or mends cardiovascular system. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z cardiovascular system surgical repair surgical repair of cardiovascular system A treatment that helps someone feel better, grow stronger, etc., especially after an illness. 2023-04-13T17:54:15Z therapy A surgery that fixes or mends pericardium. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z pericardium surgical repair surgical repair of pericardium A surgery that fixes or mends artery. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z artery surgical repair surgical repair of artery A surgery that fixes or mends vein. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z vein surgical repair surgical repair of vein A medical examination performed using of magnetic resonance imaging to image the placenta. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the placenta placenta MRI placenta magnetic resonance imaging MRI of the placenta A medical examination performed using of magnetic resonance imaging to image the heart. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the heart heart MRI heart magnetic resonance imaging cardiac MRI A medical examination performed using of magnetic resonance imaging to image the vertebral column. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z MRI of the spinal column Nuclear magnetic resonance imaging of the vertebral column spinal column MRI vertebral column MRI vertebral column magnetic resonance imaging MRI of the vertebral column A medical examination performed using of magnetic resonance imaging to image the kidney. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the kidney kidney MRI kidney magnetic resonance imaging MRI of the kidney A medical examination performed using of magnetic resonance imaging to image the liver. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the liver liver MRI liver magnetic resonance imaging MRI of the liver A medical examination performed using of magnetic resonance imaging to image the whole body. 2023-02-10T20:39:14Z MRI of whole body total body magnetic resonance imaging total body MRI A medical examination performed using of magnetic resonance imaging to image the cervical region of vertebral column. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z MRI of cervical spine Nuclear magnetic resonance imaging of the cervical region of vertebral column cervical region of vertebral column MRI cervical region of vertebral column magnetic resonance imaging cervical spine MRI A medical examination performed using of magnetic resonance imaging to image the adrenal gland. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the adrenal gland adrenal gland MRI adrenal gland magnetic resonance imaging MRI of the adrenal gland A medical examination performed using of magnetic resonance imaging to image the pancreas. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the pancreas pancreas MRI pancreas magnetic resonance imaging MRI of the pancreas A medical examination performed using of magnetic resonance imaging to image the limb. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the limb limb MRI limb magnetic resonance imaging MRI of the limb The transfer of a whole organ from one body to another. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z NCIT:C122934 transplantation of whole organ whole organ transplantation An X-ray imaging technique that involves visualization of the pulmonary vasculature after fluoroscopy-guided catheter placement and injection of an iodinated contrast medium into the pulmonary circulation. 2023-02-21T18:31:55Z NCIT:C154789 X-ray of pulmonary vasculature contrast pulmonary angiography X-ray pulmonary angiography procedure An X-ray imaging technique that involves visualization of the pulmonary vasculature after fluoroscopy-guided catheter placement and injection of an iodinated contrast medium into the pulmonary circulation. NCIT:C154789 The X-ray examination of the blood vessels in and around the brain. 2023-02-21T18:40:16Z X-ray of brain blood vessels contrast cerebral angiography X-ray cerebral angiography procedure Use of an imaging test that uses small amounts of radiation to produce pictures of teeth. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z calcareous tooth X-ray procedure calcareous tooth radiogram procedure radiograph of calcareous tooth radiography of calcareous tooth dental radiography Imaging of small blood or lymphatic vessels less than 200 micrometers in diameter. 2023-02-21T18:58:06Z microangiography Radiography of small blood or lymphatic vessels of an organ less than 200 micrometers in diameter. 2023-02-21T18:59:46Z X-ray microangiography This test consists of injecting indocyanine green dye (ICG) through a peripheral intravenous line. The ICG subsequently binds to blood lipoproteins and travels to where there is blood flow. Using a near-infrared laser coupled with a camera, one can then visualize blood flow within 3–5 millimeters of the skin surface. 2023-02-21T19:02:21Z This technique can be used as a bedside diagnosis for frostbite fluorescent microangiography This test consists of injecting indocyanine green dye (ICG) through a peripheral intravenous line. The ICG subsequently binds to blood lipoproteins and travels to where there is blood flow. Using a near-infrared laser coupled with a camera, one can then visualize blood flow within 3–5 millimeters of the skin surface. PMID:36409932 The X-ray examination of the blood vessels of the heart. 2023-02-21T19:09:18Z X-ray of the blood vessel in the heart contrast coronary angiography X-ray coronary angiography procedure Use of a drug or agent that inhibits GABA signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with GABA antagonist GABA antagonist therapy Use of a small amount of radioactive chemical called a tracer that can aid in imaging a target organ. The tracer emits gamma rays which are detected by a gamma radiation camera and analyzed by a computer to form the image of the desired region. 2023-02-21T19:50:18Z NCIT:C62667 nuclear medicine scan radioimaging radionuclide imaging radionuclide scanning scintigraphy nuclear medicine imaging procedure Use of a drug or agent that does not act as agonist or antagonist but does affect GABA-ionophore complex signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with GABA modulator GABA modulator therapy Treatment with a drug or agent that modifies cholinergic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with cholinergic drug cholinergic agent therapy Treatment with drug or agent that activates cholinergic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with cholinergic agonist cholinergic agonist therapy Treatment with drug or agent to activate muscarinic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with muscarinic agonist muscarinic agonist therapy Use of a drug or agent that activates nicotinic acetylcholine receptor signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with nicotinic acetylcholine receptor agonist nicotinic acetylcholine receptor agonist therapy Treatment with a drug or agent that inhibits cholinergic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z anticholinergic agent therapy treatment with cholinergic antagonist cholinergic antagonist therapy Treatment with a drug or agent to inhibit muscarinic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with muscarinic antagonist muscarinic antagonist therapy Use of a drug or agent that inhibits nicotinic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with nicotinic antagonist nicotinic antagonist therapy Use of a drug or agent that modulates parasympatholytic signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z dopaminergic modifying agent therapy treatment with parasympatholytic parasympatholytic therapy Use of a drug or agent that modulates dopamine signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with dopaminergic agent dopaminergic agent therapy Use of a drug or agent that activates dopamine signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_51065 dopamine agonist therapy Use of a drug or agent that activates dopamine D1 receptor signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_131795 dopamine receptor D1 agonist therapy Use of a drug or agent that inhibits dopamine neurotransmitter reuptake. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with dopamine uptake inhibitor dopamine uptake inhibitor therapy Use of a drug or agent that inhibits dopamine signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with dopaminergic antagonist dopaminergic antagonist agent therapy Use of a drug or agent that modulates neurotransmitter signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with neurotransmitter agent neurotransmitter agent therapy Use of a drug or agent that activates GABA signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with GABA agonist GABA agonist agent therapy Treatment with a drug or agent that activates GABAA receptor signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_91016 GABAA receptor agonist therapy Treatment with a drug or agent that activates GABAB receptor signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_143001 GABAB receptor agonist therapy Treatment with a drug or agent that inhibits GABAA receptor signaling. http://orcid.org/0000-0001-7941-2961 2023-02-23T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_145515 GABAA receptor antagonist therapy The surgical removal (cutting out) of part or all of sclera. http://orcid.org/0000-0001-7941-2961 2023-02-24T20:39:14Z sclera surgical removal sclerectomy The surgical formation of an external opening from the colon through the abdominal wall. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z colostomy Surgical creation of an external opening into the anterior bladder wall. [ NCI ] http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z NCIT:C15218 cystostomy procedure The surgical formation of an external opening from the small intestines through the abdominal wall. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z NCIT:C52005 enterostomy A surgically created connection between the ureter and the skin, which drains urine from the ureter in individuals with urinary obstruction or other issues that prevent normal urination. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z NCIT:C15345 ureterostomy The creation of an artificial external opening into the stomach for nutritional support or gastric decompression. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z https://en.wikipedia.org/wiki/Gastrostomy placement of g-tube placement of gastrostomy-tube gastrostomy The surgical formation of an external opening from the duodenum through the abdominal wall. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z NCIT:C122593 duodenostomy The surgical formation of an external opening from the ileum through the abdominal wall. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z NCIT:C15257 ileostomy The surgical formation of an external opening from the jejunum through the abdominal wall. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z NCIT:C79978 placement of j-tube jejunostomy The surgical formation of an external opening from the kidney through the abdominal wall. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z nephrostomy An assessment and intervention to develop, recover, or maintain life activies or occupations. 2023-04-13T17:56:56Z occupational therapy A surgery that fixes or mends anorectum. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z anorectum surgical repair surgical repair of anorectum A surgery that fixes or mends large intestine. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z large intestine surgical repair surgical repair of large intestine A surgery that fixes or mends intestine. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z intestine surgical repair surgical repair of intestine A surgery that fixes or mends small intestine. http://orcid.org/0000-0001-7941-2961 2023-02-27T20:39:14Z small intestine surgical repair surgical repair of small intestine A determination of the structure of hematopoietic cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z hematopoietic cell morphology assessment hematopoietic cell morphology measurement A determination of the structure of lymphocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z lymphocyte morphology assessment lymphocyte morphology measurement A determination of the structure of reticulocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z reticulocyte morphology assessment reticulocyte morphology measurement A psychological intervention that applies empirical approaches based upon the principles of respondent and operant conditioning to change behavior of social significance. 2023-04-13T18:07:09Z ABA therapy behavioral engineering applied behavior analysis therapy A determination of the structure of granulocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z granulocyte morphology assessment granulocyte morphology measurement A determination of the structure of basophil. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z basophil morphology assessment basophil morphology measurement A determination of the structure of neutrophil. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z neutrophil morphology assessment neutrophil morphology measurement A determination of the structure of platelet. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z platelet morphology assessment platelet morphology measurement A determination of the structure of sperm. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z sperm morphology assessment sperm morphology measurement A determination of the structure of T cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z T cell morphology assessment T cell morphology measurement A determination of the structure of B cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z B cell morphology assessment B cell morphology measurement A determination of the number of sperm in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z sperm count test sperm count A determination of the number of helper T cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z helper T cell count test helper T cell count A determination of the number of T cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z T cell count test T cell count A determination of the number of B cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z B cell count test B cell count A determination of the number of natural killer cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z natural killer cell count test natural killer cell count A determination of the number of echinocyte in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z echinocyte count test burr cell count A determination of the number of plasma cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z plasma cell count test plasma cell count A determination of the number of dendritic cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z dendritic cell count test dendritic cell count A determination of the number of regulatory T cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z T reg cell count regulatory T cell count test regulatory T cell count A determination of the structure of natural killer cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z natural killer cell morphology assessment natural killer cell morphology measurement A determination of the structure of echinocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z echinocyte morphology assessment echinocyte morphology measurement A determination of the structure of Langerhans cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z Langerhans cell morphology assessment Langerhans cell morphology measurement A determination of the structure of mast cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z mast cell morphology assessment mast cell morphology measurement A determination of the structure of Schwann cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z Schwann cell morphology assessment Schwann cell morphology measurement A determination of the structure of myeloid cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z myeloid cell morphology assessment myeloid cell morphology measurement A determination of the structure of germ cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z germ cell morphology assessment germ cell morphology measurement A determination of the structure of glial cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z glial cell morphology assessment glial cell morphology measurement A determination of the structure of kidney glomerular epithelial cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z kidney glomerular epithelial cell morphology assessment kidney glomerular epithelial cell morphology measurement A determination of the structure of oocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z oocyte morphology assessment oocyte morphology measurement A determination of the structure of myeloid leukocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z myeloid leukocyte morphology assessment myeloid leukocyte morphology measurement A determination of the structure of bone marrow cell. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z bone marrow cell morphology assessment bone marrow cell morphology measurement Assessing and providing skills to eat better. Therapy is focused on tongue movements, chewing, swallowing, as well as other behaviors. 2023-04-13T18:37:03Z feeding therapy The use or insertion of a catheter which is a flexible tube inserted through a narrow opening into a body cavidy for removing fluid. 2023-08-29T19:47:50Z catheterization Treatment with a drug to inhibit or suppress adrenal hormone production. 2023-08-08T20:42:41Z adrenal function inhibitor therapy adrenal hormone suppression therapy adrenal hormone suppressant therapy A drug or agent therapy regimen that closely mimics the physiological diurnal cortisol secretion pattern, tailored to the patient's daily needs. 2023-08-09T15:46:50Z adrenal HRT adrenal hormone replacement therapy A drug or agent therapy regimen that closely mimics the physiological diurnal cortisol secretion pattern, tailored to the patient's daily needs. PMID:33707469 A procedure to drain the bladder and collect urine via a flexible tube. 2023-08-29T20:03:15Z bladder catheterization urinary catheterization A procedure that uses radio waves to create heat to destroy tissue. 2023-11-28T20:44:56Z RFA radiofrequency neurotomy radiofrequency ablation therapy RFA Procedure to evaluate the structure and/or function of the digestive system. http://orcid.org/0000-0001-7941-2961 2019-01-15T19:35:36Z digestive system diagnostic procedure digestive system testing diagnostic procedure of digestive system All manners of treatment to bring visual system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z visual system therapeutic procedure therapeutic procedure of visual system Procedure to evaluate the structure and/or function of the circulatory system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z circulatory system diagnostic procedure diagnostic procedure of circulatory system Procedure to evaluate the structure and/or function of the excretory system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z excretory system diagnostic procedure diagnostic procedure of excretory system Procedure to evaluate the structure and/or function of the exocrine system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z exocrine system diagnostic procedure diagnostic procedure of exocrine system Procedure to evaluate the structure and/or function of the genitourinary system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z genitourinary system diagnostic procedure diagnostic procedure of genitourinary system Procedure to evaluate the structure and/or function of the hematopoietic system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z hematopoietic system diagnostic procedure diagnostic procedure of hematopoietic system Procedure to evaluate the structure and/or function of the integumental system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z integumental system diagnostic procedure diagnostic procedure of integumental system Procedure to evaluate the structure and/or function of the skin of body. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z skin diagnostic procedure skin of body diagnostic procedure diagnostic procedure of skin Procedure to evaluate the structure and/or function of the musculoskeletal system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z musculoskeletal system diagnostic procedure diagnostic procedure of musculoskeletal system Procedure to evaluate the structure and/or function of the nervous system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z nervous system diagnostic procedure diagnostic procedure of nervous system Procedure to evaluate the structure and/or function of the reproductive system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z reproductive system diagnostic procedure diagnostic procedure of reproductive system Procedure to evaluate the structure and/or function of the respiratory system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z respiratory system diagnostic procedure diagnostic procedure of respiratory system All manners of treatment to bring digestive system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z digestive system therapeutic procedure therapeutic procedure of digestive system All manners of treatment to bring cardiovascular system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z cardiovascular system therapeutic procedure therapeutic procedure of cardiovascular system All manners of treatment to bring circulatory system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z circulatory system therapeutic procedure therapeutic procedure of circulatory system All manners of treatment to bring excretory system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z excretory system therapeutic procedure therapeutic procedure of excretory system All manners of treatment to bring exocrine system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z exocrine system therapeutic procedure therapeutic procedure of exocrine system All manners of treatment to bring genitourinary system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z genitourinary system therapeutic procedure therapeutic procedure of genitourinary system All manners of treatment to bring hematopoietic system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z hematopoietic system therapeutic procedure therapeutic procedure of hematopoietic system All manners of treatment to bring integumental system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z integumental system therapeutic procedure therapeutic procedure of integumental system All manners of treatment to bring skin of body back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z skin of body therapeutic procedure therapeutic procedure of skin of body All manners of treatment to bring musculoskeletal system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z musculoskeletal system therapeutic procedure therapeutic procedure of musculoskeletal system All manners of treatment to bring nervous system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z nervous system therapeutic procedure therapeutic procedure of nervous system All manners of treatment to bring reproductive system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z reproductive system therapeutic procedure therapeutic procedure of reproductive system Treatment with a drug that softens, separates, and causes desquamation of the cornified epithelium or horny layer of skin. http://orcid.org/0000-0001-7941-2961 2023-03-31T11:00:00Z treatment with keratolytic drug Keratolytic drugs are used to expose mycelia of infecting fungi or to treat corns, warts, and certain other skin diseases. keratolytic agent therapy All manners of treatment to bring vestibulo-auditory system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z vestibulo-auditory system therapeutic procedure therapeutic procedure of vestibulo-auditory system All manners of treatment to bring immune system back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z immune system therapeutic procedure therapeutic procedure of immune system All manners of treatment to bring organism substance back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z organism substance therapeutic procedure therapeutic procedure of organism substance All manners of treatment to bring amniotic fluid back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z amniotic fluid therapeutic procedure therapeutic procedure of amniotic fluid All manners of treatment to bring blood clot back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z blood clot therapeutic procedure therapeutic procedure of blood clot All manners of treatment to bring excreta back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z excreta therapeutic procedure therapeutic procedure of excreta All manners of treatment to bring feces back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z feces therapeutic procedure therapeutic procedure of feces All manners of treatment to bring urine back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z urine therapeutic procedure therapeutic procedure of urine All manners of treatment to bring interstitial fluid back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z interstitial fluid therapeutic procedure therapeutic procedure of interstitial fluid All manners of treatment to bring ocular refractive media back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z ocular refractive media therapeutic procedure therapeutic procedure of ocular refractive media All manners of treatment to bring aqueous humor of eyeball back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z aqueous humor of eyeball therapeutic procedure therapeutic procedure of aqueous humor of eyeball All manners of treatment to bring vitreous humor back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z vitreous humor therapeutic procedure therapeutic procedure of vitreous humor All manners of treatment to bring pus back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z pus therapeutic procedure therapeutic procedure of pus All manners of treatment to bring reproductive gland secretion back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z reproductive gland secretion therapeutic procedure therapeutic procedure of reproductive gland secretion All manners of treatment to bring female reproductive gland secretion back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z female reproductive gland secretion therapeutic procedure therapeutic procedure of female reproductive gland secretion All manners of treatment to bring male reproductive gland secretion back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z male reproductive gland secretion therapeutic procedure therapeutic procedure of male reproductive gland secretion All manners of treatment to bring respiratory system fluid/secretion back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z respiratory system fluid/secretion therapeutic procedure therapeutic procedure of respiratory system fluid/secretion All manners of treatment to bring sputum back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z sputum therapeutic procedure therapeutic procedure of sputum All manners of treatment to bring secretion of exocrine gland back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z secretion of exocrine gland therapeutic procedure therapeutic procedure of secretion of exocrine gland All manners of treatment to bring bile back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z bile therapeutic procedure therapeutic procedure of bile All manners of treatment to bring gastric juice back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z gastric juice therapeutic procedure therapeutic procedure of gastric juice All manners of treatment to bring organ back to its normal state. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z organ therapeutic procedure therapeutic procedure of organ Procedure to evaluate the structure and/or function of the visual system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z visual system diagnostic procedure diagnostic procedure of visual system Procedure to evaluate the structure and/or function of the vestibulo-auditory system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z auditory diagnostic procedure vestibulo-auditory system diagnostic procedure diagnostic procedure of auditory system Procedure to evaluate the structure and/or function of the immune system. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z immune system diagnostic procedure diagnostic procedure of immune system Procedure to evaluate the structure and/or function of the organism substance. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z body substance diagnostic procedure organism substance diagnostic procedure diagnostic procedure of body substance Procedure to evaluate the structure and/or function of the amniotic fluid. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z amniotic fluid diagnostic procedure diagnostic procedure of amniotic fluid Procedure to evaluate the structure and/or function of the blood clot. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z blood clot diagnostic procedure diagnostic procedure of blood clot Procedure to evaluate the structure and/or function of the excreta. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z excreta diagnostic procedure diagnostic procedure of excreted substance Procedure to evaluate the structure and/or function of the feces. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z feces diagnostic procedure diagnostic procedure of feces Procedure to evaluate the structure and/or function of the urine. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z urine diagnostic procedure diagnostic procedure of urine Procedure to evaluate the structure and/or function of the interstitial fluid. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z interstitial fluid diagnostic procedure diagnostic procedure of interstitial fluid Procedure to evaluate the structure and/or function of the ocular refractive media. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z ocular refractive media diagnostic procedure diagnostic procedure of ocular refractive media Procedure to evaluate the structure and/or function of the aqueous humor of eyeball. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z aqueous humor of eyeball diagnostic procedure diagnostic procedure of aqueous humor of eyeball Procedure to evaluate the structure and/or function of the vitreous humor. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z vitreous humor diagnostic procedure diagnostic procedure of vitreous humor Procedure to evaluate the structure and/or function of the pus. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z pus diagnostic procedure diagnostic procedure of pus Procedure to evaluate the structure and/or function of the reproductive gland secretion. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z reproductive gland secretion diagnostic procedure diagnostic procedure of reproductive gland secretion Procedure to evaluate the structure and/or function of the female reproductive gland secretion. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z female reproductive gland secretion diagnostic procedure diagnostic procedure of female reproductive gland secretion Procedure to evaluate the structure and/or function of the male reproductive gland secretion. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z male reproductive gland secretion diagnostic procedure diagnostic procedure of male reproductive gland secretion Procedure to evaluate the structure and/or function of the respiratory system fluid/secretion. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z respiratory system fluid/secretion diagnostic procedure diagnostic procedure of respiratory system fluid/secretion Procedure to evaluate the structure and/or function of the sputum. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z sputum diagnostic procedure diagnostic procedure of sputum Procedure to evaluate the structure and/or function of the secretion of exocrine gland. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z secretion of exocrine gland diagnostic procedure diagnostic procedure of exocrine gland secretion Procedure to evaluate the structure and/or function of the bile. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z bile diagnostic procedure diagnostic procedure of bile Procedure to evaluate the structure and/or function of the gastric juice. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z gastric juice diagnostic procedure diagnostic procedure of gastric juice Procedure to evaluate the structure and/or function of the semen. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z semen diagnostic procedure diagnostic procedure of semen Procedure to evaluate the structure and/or function of the organ. http://orcid.org/0000-0001-7941-2961 2023-03-30T20:39:14Z organ diagnostic procedure diagnostic procedure of organ The surgical removal (cutting out) of part or all of zone of skin. http://orcid.org/0000-0001-7941-2961 2023-03-31T20:39:14Z skin excision zone of skin surgical removal surgical skin removal Use of a drug or agent that inhibits farnesyltransferase. http://orcid.org/0000-0003-4830-7530 2023-05-15T11:00:00Z farnesyltransferase inhibitor treatment treatment with EC 2.5.1.58 (protein farnesyltransferase) inhibitor farnesyltransferase inhibitor agent therapy Use of a drug or agent that inhibits matrix metalloprotease inhibitor. http://orcid.org/0000-0001-7941-2961 2023-05-15T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_50664 MMP inhibitor agent therapy Treatment with a topical cream that is used to treat psoriasis. http://orcid.org/0000-0001-7941-2961 2023-05-15T11:00:00Z tazarotene agent therapy A therapeutic surgical procedure to treat gastroesophageal reflux disease and hiatus hernia. It involves the wrapping of the fundus of the stomach around the lower esophagus to strengthen the lower esophageal sphincter. 2023-11-28T21:09:28Z NCIT:C91834 Nissen fundoplication fundoplication A therapeutic surgical procedure to treat gastroesophageal reflux disease and hiatus hernia. It involves the wrapping of the fundus of the stomach around the lower esophagus to strengthen the lower esophageal sphincter. NCIT:C91834 Treatment with a diuretic to treat hypertension or edema. http://orcid.org/0000-0001-7941-2961 2023-05-15T11:00:00Z benzothiadiazine derivative therapy Treatment with thyroid hormone or drugs replicating thyroid hormone to maintain a normally functioning thyroid. http://orcid.org/0000-0001-7941-2961 2023-05-15T11:00:00Z treatment with thyroid hormone thyroid hormone therapy Treatment with a class of medicines inhibit sodium-glucose cotransporter-2. Drugs are used with diet and exercise to lower blood sugar in adults with type 2 diabetes. http://orcid.org/0000-0001-7941-2961 2023-05-15T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_73273 sodium-glucose cotransporter-2 inhibitor therapy Treatment with an activator to the somatostatin receptor. http://orcid.org/0000-0001-7941-2961 2023-05-15T11:00:00Z treatment with http://purl.obolibrary.org/obo/CHEBI_177023 somatostatin recepter agonist therapy A surgery to move a testical from growin to scrotum. The procedure permanently fixes the testical to the scrotum. 2023-11-28T21:42:56Z NCIT:C111066 PMID:32809739 SNOMEDCT_US:85419002 fixation of testes scrotal fixation of testes scrotal orchiopexy testicular fixation Orchiopexy corrects undescended testicles that have not dropped into the scrotum or testicular torsion where testicular blood supply twists and cuts off blood flow to the testicle. orchiopexy Magnetic resonance imaging of the developing fetus in utero. 2023-04-11T12:00:00Z fetal MRI A type of hematopoietic stem cell transplantation in which stem cells are obtained from a donor other than the recipient. 2023-04-11T12:00:00Z allogeneic hematopoietic stem cell transplantation Intravenous administration of Immune globulin antibodies) derived from the plasma of donors. 2023-04-11T12:00:00Z immunoglobulin infusion therapy A type of biologic therapy that is designed to inhibit the activity of IgE immunoglobulins. 2023-04-11T12:00:00Z IgE-targeting biologic therapy A type of biologic therapy that is designed to modulate helper 2 (Th2) T cell activity 2023-04-11T12:00:00Z Th2-targeting biologic therapy Therapeutic administration of an inhibitor of complement component 5. 2023-04-11T12:00:00Z complement 5 inhibitor therapy A molecular genetic produce to alter a target gene sequence with the intention of repairing or altering the activity of a gene product that is related to a disease. 2023-04-11T12:00:00Z gene editing therapy Administration of dietary glutamine. 2023-04-11T12:00:00Z glutamine supplementation Therapeutic administration of interferon alpha. 2023-04-11T12:00:00Z interferon alpha therapy Therapeutic administration of interferon gamma 2023-04-11T12:00:00Z interferon-gamma therapy Therapeutic administration of an inhibitor of interleukin 1 2023-04-11T12:00:00Z interleukin-1 receptor inhibitor therapy A medical requirement or recommendation of avoiding vaccination with live (ative) agents 2023-04-11T12:00:00Z live vaccine avoidance The infusion of thrombocytes directly into the bloodstream 2023-04-11T12:00:00Z platelet transfusion Therapeutic administration of an analog of somatostatin. 2023-04-11T12:00:00Z somatostatin analog therapy Ongoing clinical investigations targeted at the early identification or return of cancer. 2023-04-11T12:00:00Z surveillance for malignancies Therapeutic administration of an inhibitor of tumor necrosis factor. 2023-04-11T12:00:00Z tumor necrosis factor inhibitor therapy obsolete ophthalmological diagnostic procedure true Avoid the administration or use of serotonin-norepinephrine reuptake inhibitor agent therapy. http://orcid.org/0000-0001-7941-2961 2023-06-06T20:39:14Z avoid serotonin-norepinephrine reuptake inhibitor agent therapy avoiding serotonin-norepinephrine reuptake inhibitor agent therapy serotonin-norepinephrine reuptake inhibitor agent therapy avoidance Avoid the administration or use of antidepressant agent therapy. http://orcid.org/0000-0001-7941-2961 2023-06-06T20:39:14Z avoid antidepressant agent therapy avoiding antidepressant agent therapy antidepressant agent therapy avoidance A pharmaceutical substance that is biologically inactive, but it is metabolized by the body to produce a drug. http://orcid.org/0000-0001-7941-2961 2023-08-15T11:00:00Z treatment with prodrug prodrug therapy A drug or pharmaceutical agent tht is used to attempt to prevent or reverse neuronal damage, thereby retaining physiological function. http://orcid.org/0000-0001-7941-2961 2023-08-15T11:00:00Z treatment with neuroprotective agent neuroprotective agent therapy A drug or pharmaceutical agent tht is used to attempt to prevent or reverse neuronal damage, thereby retaining physiological function. ISBN:978-0-12-374203-2 A drug or pharmaceutical agent that is developed to treat a rare medical condition. http://orcid.org/0000-0001-7941-2961 2023-08-15T11:00:00Z orphan drug treatment treatment with orphan drug orphan drug therapy A drug or substance used as therapy to inhibit 4-hydroxyphenylpyruvate hydroxylase. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z 4-hydroxyphenylpyruvate hydroxylase inhibitor therapy treatment with EC 1.13.11.27 (4-hydroxyphenylpyruvate dioxygenase) inhibitor HPPD inhibitor therapy A drug or substance that inhibits the metabolism of tyrosine. 2023-08-21T16:57:48Z tyrosine metabolism inhibitor Any surgical procedure conducted on the digestive system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z digestive system surgical procedure surgical procedure on digestive system Any surgical procedure conducted on the alimentary part of gastrointestinal system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z alimentary part of gastrointestinal system surgical procedure surgical procedure on alimentary part of gastrointestinal system Gross motor therapy is designed to help individuals improve their use of large muscles and the coordination of the arms, legs, and the entire body. 2023-11-30T17:16:03Z gross motor skills therapy gross motor therapy Any surgical procedure conducted on the circulatory system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z circulatory system surgical procedure surgical procedure on circulatory system Any surgical procedure conducted on the genitourinary system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z genitourinary system surgical procedure surgical procedure on genitourinary system Any surgical procedure conducted on the musculoskeletal system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z musculoskeletal system surgical procedure surgical procedure on musculoskeletal system A determination of the number of blood cell in a blood sample. http://orcid.org/0000-0001-7941-2961 2023-11-01T20:39:14Z CBC blood cell count test complete blood cell count complete blood count full blood count blood cell count Any surgical procedure conducted on the pancreatic system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z pancreatic system surgical procedure surgical procedure on pancreatic system Any surgical procedure conducted on the renal collecting system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z renal collecting system surgical procedure surgical procedure on renal collecting system Any surgical procedure conducted on the reproductive system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z reproductive system surgical procedure surgical procedure on reproductive system Any surgical procedure conducted on the zone of skin. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z zone of skin surgical procedure skin surgery Any surgical procedure conducted on the respiratory system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z respiratory system surgical procedure surgical procedure on respiratory system Any surgical procedure conducted on the vascular system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z vascular system surgical procedure surgical procedure on vascular system Therapy aids in the development and use of the small muscles of the hands for tasks such as grasping objects, writing, cutting with scissors, shoe-tying, and fastening buttons. 2023-11-30T17:19:07Z fine motor skills therapy fine motor therapy A medical requirement or recommendation of avoiding cannabis consumption. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid cannabis consumption cessation of cannabis consumption cannabis consumption avoidance A medical requirement or recommendation of avoiding tobacco consumption. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid tobacco consumption cessation of tobacco consumption tobacco consumption avoidance A medical requirement or recommendation of avoiding smoking behavior. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid smoking behavior cessation of smoking behavior smoking behavior avoidance A medical requirement or recommendation of avoiding consumption of an addictive substance. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid consumption of an addictive substance cessation of consumption of an addictive substance consumption of an addictive substance avoidance A medical requirement or recommendation of avoiding agitation behavior. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid agitation behavior agitation avoidance A medical requirement or recommendation of avoiding fear/anxiety related behavior. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid fear/anxiety related behavior fear or anxiety avoidance A medical requirement or recommendation of avoiding sexual activity. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid sexual activity sexual activity avoidance A medical requirement or recommendation of avoiding copulation. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid copulation copulation avoidance A medical requirement or recommendation of avoiding stress related behavior. http://orcid.org/0000-0001-7941-2961 2020-01-28T11:00:00Z avoid stress related behavior stress avoidance Genetic testing of one or more cells removed from early embryos conceived by in vitro fertilization and transferring to the mother's uterus only those embryos determined not to have the pathogenic variant(s)/chromosome anomaly(ies) of concern. 2022-03-21T14:25:49Z PGD PGS PGT preimplantation genetic screening preimplation genetic diagnosis preimplantation genetic testing Genetic testing of one or more cells removed from early embryos conceived by in vitro fertilization and transferring to the mother's uterus only those embryos determined not to have the pathogenic variant(s)/chromosome anomaly(ies) of concern. NCBIBook:NBK5191 PGD PGS PGT A procedure that can determine the DNA sequence for all of the exons (protein coding region) in an individual. 2022-03-21T18:25:01Z NCIT:C101295 WES WXS exome sequencing whole exome sequencing Clinical Exome Sequencing is a test for identifying disease-causing DNA variants within the 1% of the genome which codes for proteins (exons) or flanks the regions which code for proteins (splice junctions). Sequence analysis of the exons of protein-coding genes in the genome typically performed by target enrichment or capture of exons followed by next-generation sequencing. clinical whole-exome sequencing WES WXS Clinical Exome Sequencing is a test for identifying disease-causing DNA variants within the 1% of the genome which codes for proteins (exons) or flanks the regions which code for proteins (splice junctions). Sequence analysis of the exons of protein-coding genes in the genome typically performed by target enrichment or capture of exons followed by next-generation sequencing. NCBIBook:NBK5191 The removal of the large intestine and rectum followed by making a pouch of the last part of the small intestine for solid material storage. The pouch is then sewn to the anus. 2022-03-28T15:44:07Z RPC-IPAA proctocolectomy with IPAA restorative proctocolectomy with ileal pouch-anal anastomosis proctocolectomy with ileal pouch anal anastomosis RPC-IPAA A procedure that can determine the DNA sequence for coding and non-coding regions in an individual. 2022-03-22T17:16:58Z WGS genome sequencing whole genome sequncing Sequence analysis of the genome including coding and noncoding regions typically performed by next-generation sequencing (NGS) of sheared genomic DNA. clinical whole genome sequencing WGS Sequence analysis of the genome including coding and noncoding regions typically performed by next-generation sequencing (NGS) of sheared genomic DNA. NCBIBook:NBK5191 Fetal echocardiography is a test that uses sound waves (ultrasound) to evaluate the structure and function of the fetus's heart. 2022-03-22T18:19:25Z fetal echo procedure fetal echocardiogram procedure prenatal echo procedure prenatal echocardiagraphy fetal echocardiography An application of diagnostic ultrasound used to detect moving blood cells or other moving structures and measure their direction and speed of movement. The Doppler effect is used to evaluate movement by measuring changes in frequency of the echoes reflected from moving structures. 2022-03-23T15:43:36Z Doppler ultrasonography The use of ultrasound on a pregnant person to produce images of structures in the kidney of the fetus. 2022-03-23T16:10:42Z fetal kidney ultrsonography fetal renal ultrasonography prenatal kidney ultrasonography prenatal renal sonography prenatal renal ultrasonography A surgical procedure where the whole colon is removed and the ileum is joined directly to the rectum. 2022-03-28T17:29:48Z colectomy with IRA colectomy with ileorectal anastomosis Surgical removal of part of the pancreas, duodenum, and distal part of the bile duct. Sometimes, the lower portion of the stomach and the gallbladder are also removed. This procedure is performed for pancreatic, ampullary, duodenal and distal bile duct cancers. 2022-03-28T17:35:35Z NCIT:C15356 Kausch-Whipple procedure Whipple procedure pancreaticoduodenectomy Surgical removal of part of the pancreas, duodenum, and distal part of the bile duct. Sometimes, the lower portion of the stomach and the gallbladder are also removed. This procedure is performed for pancreatic, ampullary, duodenal and distal bile duct cancers. NCIT:C15356 Infusion of red blood cells into a fetus through the umbilical code. 2022-03-28T19:32:20Z Foetal transfusion IUT fetal transfusion intrauterine transfusion percutaneous fetal transfusion percutaneous foetal transfusion intrauterine fetal transfusion Infusion of red blood cells into a fetus through the umbilical code. PMID:24903741 IUT Use of a drug or therapy that block neuromuscular transmission, causing paralysis of the affected skeletal muscles. 2022-03-28T21:04:52Z neuromuscular blocking agent therapy Treatment with a neuromuscular blocking agent and inhibitor of acetyl choline release at motor terminals. It can be used to treat certain ailments like cervical dystonia and sialorrhea. 2022-03-28T21:07:53Z botulinum toxin type B injection botulinum toxin type B therapy Treatment with Botulinum toxin, a neurotoxic protein which blocks release of acetylcholine at neuromuscular junctions causing muscle paralysis. This therapy has many therapeutic uses including chronic migraine, spastic disorders, cervical dystonia, and detrusor hyperactivity. 2022-03-29T16:24:35Z botox injection botox therapy botulinum toxin injection botulinum toxin therapy Treatment with Botulinum toxin, a neurotoxic protein which blocks release of acetylcholine at neuromuscular junctions causing muscle paralysis. This therapy has many therapeutic uses including chronic migraine, spastic disorders, cervical dystonia, and detrusor hyperactivity. PMID:32491319 Treatment with Botulinum toxin type A which can treat certain conditions. Currently it is used to smoothed wrinkles. It is also called Botox treatment. 2022-03-29T16:32:49Z botulinum toxin type A injection botulinum toxin type A therapy A set of tests or assessments to determine congnitive abilities of a patient. 2022-03-30T14:02:52Z cognitive tests cognitive assessment Evaluation for cognitive impairment by assessing the neuropsychological domains. 2022-03-30T14:05:42Z neuropsychological assessment Evaluation for cognitive impairment by assessing the neuropsychological domains. PMID:32310509 Evaluation of patient's cominucation involving naming, reading, writing, and repeating words. 2022-03-30T14:07:13Z language assessment Evaluation of patient's cominucation involving naming, reading, writing, and repeating words. PMID:32310509 Evaluation of organizing and planning ability, as well as working memory, mental flexibility, list-making, and execution of tasks. 2022-03-30T14:08:50Z executive function assessment Evaluation of organizing and planning ability, as well as working memory, mental flexibility, list-making, and execution of tasks. PMID:32310509 Evaluation of a patient's ability to analyze information, detect patterns, detect relationships, or problem solveing abilities on an intangible level. 2022-03-30T14:10:53Z abstract reasoning assessment Evaluation of a patient's ability to analyze information, detect patterns, detect relationships, or problem solveing abilities on an intangible level. PMID:32310509 Evaluation of short-term and long-term emory in a patient. 2022-03-30T14:12:36Z memory assessement Evaluation of short-term and long-term emory in a patient. PMID:32310509 Evaluation of a patient's concentration or attention to a prompt or test. 2022-03-30T14:14:33Z attention and concentration assessment Evaluation of a person’s ability to conceptualize and manipulate two- and three-dimensional objects. 2022-03-30T14:20:27Z visuospatial skill assessment Evaluation of a person’s ability to conceptualize and manipulate two- and three-dimensional objects. PMID:32310509 Surgical implantation of a device for the treatment of severe to profound sensorineural hearing loss. It works by transducing acoustic energy into an electrical signal, which is used to stimulate surviving spiral ganglion cells of the auditory nerve. 2022-03-31T20:40:42Z implantation of cochlear device implantation of cochlear prosthesis surgical introduction of cochlear implant cochlear device implantation Surgical implantation of a device for the treatment of severe to profound sensorineural hearing loss. It works by transducing acoustic energy into an electrical signal, which is used to stimulate surviving spiral ganglion cells of the auditory nerve. PMID:30931225 A procedure where a substance or object is inserted into the body. 2022-04-01T16:56:14Z introduction procedure A procedure to place an electrode in some part of the body for therapeutic purposes. 2022-04-01T17:01:07Z implantation of an electrode electrode implantation The surgical implantation of a central neural auditory prosthesis for treatment of profound sensorinerual hearing loss in patients who are not cochlear implant candidates due to a lack of anatomically intact cochlear nerves or implantable cochleae. 2022-04-01T18:27:27Z ABI auditory brainstem implantation The surgical implantation of a central neural auditory prosthesis for treatment of profound sensorinerual hearing loss in patients who are not cochlear implant candidates due to a lack of anatomically intact cochlear nerves or implantable cochleae. PMID:30931229 ABI Treatment to improve hearing. 2022-04-01T18:42:23Z auditory enhancement hearing therapy Use of hearing aids to improve hearing. 2022-04-01T18:54:14Z hearing aid usage Assessment and management of hearing loss. 2022-04-01T18:57:13Z adult audiologic rehabilitation aural rehab aural rehabilitation auditory rehabilitation Hearing therapy to help children born with hearing loss that have not learned to listen and talk. 2022-04-04T17:01:13Z child aural rehabilitation child hearing habilitation child audiologic habilitation A medical device inserted into the body to help control or monitor the heart and/or cardiovascular system. 2022-04-04T18:50:47Z CIED implantation cardiac implantable electronic device insertion implantation of a cardiac device cardiac device implantation Surgical insertion of an adjustable artificial electrical pulse generators into the body to interrogate and control the he pacing rate, the pulse width, and the voltage in order to a person's heart function. 2022-04-04T18:56:11Z pacemaker implantation Surgical insertion of an adjustable artificial electrical pulse generators into the body to interrogate and control the he pacing rate, the pulse width, and the voltage in order to a person's heart function. PMID:30252257 Insertion of a pacemaker that attaches one lead to the upper or lower heart chamber. 2022-04-04T19:14:01Z implantation of a single chamber pacemaker single chamber pacemaker implantation Insertion of a pacemaker that attaches one lead to the upper or lower heart chamber. PMID:32310471 The implantation of a pacemaker that uses two leads, one for the upper and one for lower chamber of the heart. 2022-04-04T19:17:56Z implantation of a dual-chamber pacemaker dual-chamber pacemaker implantation The implantation of a pacemaker that uses two leads, one for the upper and one for lower chamber of the heart. PMID:32310471 Surgical insertion of a pacemaker that is used in cardiac resynchronization therapy. 2022-04-04T19:23:18Z implantation of biventricular pacemaker biventricular pacemaker implantion Surgical insertion of a pacemaker that is used in cardiac resynchronization therapy. PMID:32310471 Expandable tubular metallic devices inserted into coronary arteries. 2022-04-04T19:41:08Z PCI coronary angioplasty with stent placement percutaneous coronary intervention coronary stent insertion PCI Insertion of a medical device that delivers fluids, such as nutrients and medications, into a patient's body in controlled amounts. 2022-04-04T20:03:04Z implantation of a fusion pump insertion of an infusion pump infusion pump implantation Insertion of a continuous subcutaneous insulin infusion to regulate insulin levels in a patient. 2022-04-05T15:10:49Z continuous subcutaneous insulin infusion pump implantation insulin pump implantation A therapy used in patients with type 1 diabetes mellitus (T1DM) to improve glucose control and/or reduce the risk of hypoglycaemia. 2022-04-05T15:31:40Z CSII therapy insulin pump infusion therapy insulin pump therapy continuous subcutaneous insulin infusion therapy A therapy used in patients with type 1 diabetes mellitus (T1DM) to improve glucose control and/or reduce the risk of hypoglycaemia. PMID:23760696 CSII therapy Use of a medical device that delivers fluids, such as nutrients and medications, into a patient's body in controlled amounts. 2022-04-05T16:48:06Z infusion pump therapy Surgical removal of the opacified lens and implantation of an artificial intraocular lens (IOL). 2022-04-05T18:10:41Z cataract extraction with IOL implantation cataract removal with intraocular lens insertion cataract surgery with artificial intraocular lens insertion cataract extraction with intraocular lens insertion Surgical incision into the eardrum to relieve pressure or drain fluid with placement of tympanostomy tubes to allow fluid to pass through the ear canal into the middle ear. 2022-04-05T18:39:00Z insertion of ear tubes myringotomy and tube placement myringotomy and insertion of tympanic ventilation tube myringotomy with placement of tympanostomy tube myringotomy and insertion of tympanic ventilation tube Surgical placement of a prosthetic device to replace a joint. 2022-04-05T19:13:44Z prosthetic arthoplasty implantation of joint prosthesis Surgical procedure to replace the weight-bearing surfaces of the knee joint. 2022-04-05T19:15:51Z total knee arthoplasty total knee replacement A reconstructive proceder that surgically replaces the hip joint with an artificial prosthesis. 2022-04-05T19:19:25Z total hip replacement hip replacement A reconstructive proceder that surgically replaces the hip joint with an artificial prosthesis. PMID:7725707 Placement of a intrauterine contraceptive device that prevents pregnancy. 2022-04-05T19:30:10Z IUD implantation insertion of IUD insertion of intrauterine contraceptive device insertion of IUD Surgical removal of a mass without cutting into or dissecting it. 2022-04-11T16:22:02Z surgical enucleation enucleation Surgical procedure that involves removal of the entire globe and its intraocular contents, with preservation of all other periorbital and orbital structures. 2022-04-11T16:28:25Z removal of the eye orbital enucleation enucleation of the eye Surgical removal of tumor cells without removing surrounding tissue or organs. 2022-04-11T16:30:19Z tumor enucleation enucleation of a tumor A procedure that uses very small amounts of radioactive materials to examine organ function and structure. 2022-05-10T17:12:49Z nuclear medicine radiation biology procedure radiology-nuclear medicine procedure nuclear medicine procedure A procedure that uses very small amounts of radioactive materials to examine organ function and structure. A direct appraisal of a patient's condition by a clinical specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T15:54:47Z medical specialist examination A direct assessment of a patient's condition by an immunologist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T15:56:27Z NCIT:C74803 examination by immunologist A direct assessment of a patient's condition by a dermatologist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T15:57:40Z dermatologist examination examination by dermatologist A direct assessment of a patient's condition by an emergency medicine specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T16:09:47Z ED examination ER examination emergency medicine specialist examination emergency department physician examination emergency room physician examination examination by emergency medicine specialst A direct assessment of a patient's condition by a family medicine specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T16:19:37Z examination by family medicine specialist A direct assessment of a patient's condition by a neurologist that is based on a physical exam, medical history, and the patient's account of symptoms.neurologist. 2022-05-02T16:30:32Z examination by a neurologist A direct assessment of a patient's condition by an obstetrics and gynecologist specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T17:30:59Z ob/gyn examination gynecologist examination obstetrics examination examination by ob/gyn specialist A direct appraisal of a patient's condition by a ophthalmologist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-02T17:43:19Z ophthalmologist examination examination by ophthalmologist A direct appraisal of a patient's condition by an otolaryngologist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T13:58:22Z examination by otolaryngologist A direct appraisal of a patient's condition by an orthopedic specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T15:44:47Z examination by orthopedist A direct appraisal of a patient's condition by a pediatric specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T15:45:49Z pediatric examination examination by pediatrician A direct appraisal of a patient's condition by a physical medicine and rehabilition specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T15:50:43Z examination by physical mediciane and rehabilitation specialist examination by physiatrist A test that involves the administration of intravenous contrast and X-ray imaging of the urinary tract. The iodinated contrast flows through the renal vasculature and filtered into the collecting system highlighting the anatomic structures on the X-ray image. 2022-05-10T18:02:12Z IVP intravenous urography intravenous pyelogram A test that involves the administration of intravenous contrast and X-ray imaging of the urinary tract. The iodinated contrast flows through the renal vasculature and filtered into the collecting system highlighting the anatomic structures on the X-ray image. PMID:32644460 IVP A direct appraisal of a patient's condition by a psychiatric specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T15:57:23Z psychiatric examination examination by psychiatrist A direct appraisal of a patient's condition by a urology specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T15:57:55Z examination by urologist A direct appraisal of a patient's condition by an allied health professional specialist that is based on a physical exam, medical history, and the patient's account of symptoms. 2022-05-03T16:13:07Z examination by allied health professional allied health professional examination The determination of the type and/or amount of vitamins in a sample. 2022-05-04T20:45:27Z vitamin measurement Delivery of a gamma-emitting radioisotope (a radionuclide) into the patient, normally through injection into the bloodstream and detected by gamma camera The radioisotope could be is a simple soluble dissolved ion, such as an isotope of gallium(III), or a marker radioisotope is attached to a specific ligand to create a radioligand targeting a place of interest in the body. 2022-05-10T18:09:15Z SPECT single-photon emission computed tomography Surgeical procedure to restore or replace physical defects of form or function. Physical defects could be a consequence of birth defects, trauma, or medical conditions. 2022-06-02T17:19:14Z surgery to repair surgical reconstruction surgical repair Elective surgeries to improve or correct patients body imperfections or appearance. These surgeries can address imperfections due to preference, congenital, acquired, illness, or traumatic or para-physiological events such as aging. 2022-06-13T16:08:56Z cosmetic plastic surgery Elective surgeries to improve or correct patients body imperfections or appearance. These surgeries can address imperfections due to preference, congenital, acquired, illness, or traumatic or para-physiological events such as aging. PMID:28194357 A procedure for increasing the size of the breast using a prosthetic implant. 2022-06-13T16:53:05Z augmentation mammoplasty breast implantation surgery breast augmentation surgery A surgical procedure to remove excess skin and fat from the abdomen. 2022-06-13T17:23:10Z tummy tuck abdominoplasty A surgical procedure to remove excess skin and fat from the abdomen. NCIT:C158024 A medically necessary surgery performed to restore function and conventional appearance of the body part. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. 2022-06-13T20:16:10Z reconstructive plastic surgery A surgical procedure that is performed for therapeutic or cosmetic reformation of tissue. 2022-06-13T20:26:49Z plastic surgery A medically necessary surgery performed to restore function and conventional appearance of lip. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-06-15T17:44:45Z lip surgical plastic reconstruction cheiloplasty A medically necessary surgery performed to restore function and conventional appearance of secondary palate. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-06-15T17:44:59Z secondary palate surgical plastic reconstruction palatorrhaphy A medically necessary surgery performed to restore function and conventional appearance of breast. The surgery can correct deformities created by birth defects, trauma or medical conditions and is performed by a plastic surgeon. http://orcid.org/0000-0001-7941-2961 2022-06-15T17:45:14Z breast surgical plastic reconstruction mammoplasty Surgery using incisional, excisional, or use of local/regional flaps to repair burned areas. 2022-06-15T17:47:00Z burn reconstructive surgery reconstructive burn surgery Surgery using incisional, excisional, or use of local/regional flaps to repair burned areas. PMID:15284153 Surgical reconstruction or replacement of all or part of a malformed, diseased, degenerated, or otherwise damaged joint. NCIT:C51691 http://orcid.org/0000-0001-7941-2961 2022-06-15T17:47:14Z NCIT:C51691 joint repair surgery skeletal joint surgical repair arthroplasty A surgery that fixes or mends knee joint. http://orcid.org/0000-0001-7941-2961 2022-06-15T17:47:24Z arthroplasty of knee knee joint surgical repair knee repair surgery knee arthroplasty A surgery that fixes or mends hip joint. http://orcid.org/0000-0001-7941-2961 2022-06-15T17:47:36Z arthroplasty of hip joint hip joint repair hip joint surgical repair hip arthroplasty Surgical replacement of part or all of a damaged knee joint with an artificial joint. 2022-06-15T18:05:58Z knee replacement surgery Surgical replacement of all parts of a damaged knee joint with an artificial joint. 2022-06-15T18:06:11Z total knee replacement surgery Surgical replacement of all parts of a damaged knee joint with an artificial joint. NCIT:C51565 The surgery to correct a torn knee ligament involves replacing the ligament with a piece of healthy tendon. 2022-06-15T18:16:25Z knee joint ligament repair repair of ligament of knee joint repair of knee ligament A procedure that delivers a single, highly concentrated dose of ionizing radiation from an external source to a small, precise target using 3-D computerized imaging to focus beams. There is no incision, but this technique distorts and destroys the DNA of tumor cells in a highly directed fashion. 2022-06-17T19:33:11Z SRS stereotactic radiosurgery A procedure that delivers a single, highly concentrated dose of ionizing radiation from an external source to a small, precise target using 3-D computerized imaging to focus beams. There is no incision, but this technique distorts and destroys the DNA of tumor cells in a highly directed fashion. SRS A type of stereotactic surgery that uses specialized equipment to focus approximately 200 beams of radiation on a tumor or other target with submillimeter accuracy. 2022-06-17T20:36:46Z Gamma Knife surgery stereotactic radiosurgery using Gamma Knife A type of sterotactic radiosurgery using photons to treat cancerous and noncancerous abnormalities via a linear accelerator (LINAC) machine. 2022-06-17T20:43:21Z stereotactic radiosurgery using LINAC stereotactic radiosurgery using Linear Accelerator External radiation therapy that is directed at a specific body part/tumor over a fractionated treatment schedule. 2022-06-17T20:48:57Z SRT stereotactic radiation therapy SRT A method of external beam radiotherapy (EBRT) that accurately delivers a high irradiation dose to an extracranial target in one or few treatment fractions 2022-06-20T18:56:35Z SBRT stereotactic body radiation therapy A method of external beam radiotherapy (EBRT) that accurately delivers a high irradiation dose to an extracranial target in one or few treatment fractions PMID:24052011 SBRT A type of stereotactic radiosurgery that uses prroton beams. 2022-06-20T19:49:50Z Proton beam radiosurgery stereotactic radiosurgery using proton beam therapy Treatment with zinc (typically a zinc salt, like zinc acetate or zinc sulfate) with an expected therapeutic benefit. 2022-08-18T18:20:16Z treatment with zinc zinc treatment Zinc therapy can induce metallothionein zinc therapy Use of a drug that inhibits Janus kinases. 2022-08-17T19:11:56Z JAK inhibitor therapy Janus kinase (JAK) Inhibitors are the latest drug class of disease-modifying medication to emerge for the treatment of rheumatoid arthritis (RA). They are a small molecule-targeted treatment and are the first oral option to compare favourably to existing biologic disease-modifying anti-rheumatic drugs (DMARDs). Janus kinase inhibitor therapy Janus kinase (JAK) Inhibitors are the latest drug class of disease-modifying medication to emerge for the treatment of rheumatoid arthritis (RA). They are a small molecule-targeted treatment and are the first oral option to compare favourably to existing biologic disease-modifying anti-rheumatic drugs (DMARDs). PMID:32982367 Treatment with a substance that inhibits GABA trasaminase. http://orcid.org/0000-0001-7941-2961 2022-08-18T11:00:00Z GABA transaminase inhibitor treatment with EC 2.6.1.19 (4-aminobutyrate--2-oxoglutarate transaminase) inhibitor GABA transaminase inhibitor agent therapy Use of a swab as the collection device to obtain clinical specimens. 2022-12-08T16:49:02Z clinical swab collection clinical biospecimen swab collection Assistance provided by clinicians and public health practitioners to enhance an individual and/or their family’s self-efficacy in managing one or more conditions. This assistance can include activities such as patient education, support for lifestyle modifications, and support to help individuals develop the skills needed for effective chronic disease management. 2023-01-05T18:53:29Z patient health-management support and education Assistance provided by clinicians and public health practitioners to enhance an individual and/or their family’s self-efficacy in managing one or more conditions. This assistance can include activities such as patient education, support for lifestyle modifications, and support to help individuals develop the skills needed for effective chronic disease management. Services and supports provided to babies and young children with developmental delays and disabilities and their families. These may include speech therapy, physical therapy, and other types of services based on the needs of the child and family. They can have a significant impact on a child’s ability to learn new skills and overcome challenges and can increase success in school and life. 2023-01-05T19:13:08Z NCIT:C159524 early intervention A range of targeted services and supports that are available to babies and young children with developmental delays or specific health conditions. [ NCI ] early intervention services Services and supports provided to babies and young children with developmental delays and disabilities and their families. These may include speech therapy, physical therapy, and other types of services based on the needs of the child and family. They can have a significant impact on a child’s ability to learn new skills and overcome challenges and can increase success in school and life. A range of targeted services and supports that are available to babies and young children with developmental delays or specific health conditions. [ NCI ] NCIT:C159524 An education and support system that addresses the comprehensive blend of clinical, educational, psychosocial, and behavioral aspects of care needed for daily self-management and provides the foundation to help all people with diabetes navigate their daily self-care with confidence and improved outcomes. 2023-01-05T19:25:22Z diabetes self-management support and education diabetes self health-management support and education An education and support system that addresses the comprehensive blend of clinical, educational, psychosocial, and behavioral aspects of care needed for daily self-management and provides the foundation to help all people with diabetes navigate their daily self-care with confidence and improved outcomes. PMID:32513817 A medical requirement or recommendation of avoiding the consumption of gluten. http://orcid.org/0000-0001-7941-2961 2019-07-11T09:00:01Z avoid gluten intake avoiding dietary gluten intake celiac dietary intake gluten consumption avoidance gluten restricted diet intake gluten restriction gluten-free dietary intake Intake may interfere with disease treatment, prolong the recovery phase, or cause complications. dietary gluten intake avoidance A medical requirement or recommendation of avoiding the consumption of liquid chemical food component. http://orcid.org/0000-0001-7941-2961 2019-07-11T09:00:01Z avoid liquid chemical food component intake avoiding dietary liquid chemical food component intake liquid chemical food component consumption avoidance liquid chemical food component restricted diet intake liquid chemical food component restriction dietary liquid chemical food component intake avoidance A medical requirement or recommendation of avoiding the consumption of protein extract, concentrate or isolate. http://orcid.org/0000-0001-7941-2961 2019-11-13T02:36:00Z avoid protein extract, concentrate or isolate intake avoiding dietary protein extract, concentrate or isolate intake protein extract, concentrate or isolate consumption avoidance protein extract, concentrate or isolate restricted diet intake protein extract, concentrate or isolate restriction protein intake avoidance A medical requirement or recommendation of avoiding the consumption of fat or oil. http://orcid.org/0000-0001-7941-2961 2019-11-13T02:36:00Z avoid fat or oil intake avoiding dietary fat or oil intake fat or oil consumption avoidance fat or oil restricted diet intake fat or oil restriction dietary fat or oil intake avoidance Addition of amino-acid betaine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-07-11T09:00:01Z amino-acid betaine supplemental intake dietary supplementation of amino-acid betaine supplementation of amino-acid betaine supplementation with betaine betaine supplementation Addition of folates to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-07-11T09:00:01Z dietary supplementation of folates folates supplemental intake supplementation of folates supplementation with folate folate supplementation Addition of carnitine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T02:36:00Z carnitine supplemental intake dietary supplementation of carnitine supplementation of carnitine carnitine supplementation Addition of methionine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T02:36:00Z dietary supplementation of methionine methionine supplemental intake supplementation of methionine methionine supplementation Addition of creatine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z creatine supplemental intake dietary supplementation of creatine supplementation of creatine creatine supplementation Addition of arginine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z arginine supplemental intake dietary supplementation of arginine supplementation of arginine arginine supplementation Addition of biotins to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z biotins supplemental intake dietary supplementation of biotins supplementation of biotins biotin supplementation Addition of chenodeoxycholic acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z chenodeoxycholic acid supplemental intake dietary supplementation of chenodeoxycholic acid supplementation of chenodeoxycholic acid chenodeoxycholic acid supplementation Addition of coenzyme Q10 to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z coenzyme Q10 supplemental intake dietary supplementation of coenzyme Q10 supplementation of coenzyme Q10 coenzyme Q10 supplementation Addition of glycine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of glycine glycine supplemental intake supplementation of glycine glycine supplementation Addition of N-acetyl-L-cysteine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z N-acetyl-L-cysteine supplemental intake dietary supplementation of N-acetyl-L-cysteine supplementation of N-acetyl-L-cysteine N-acetyl-L-cysteine supplementation Addition of ornithine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of ornithine ornithine supplemental intake supplementation of ornithine ornithine supplementation Addition of riboflavin to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of riboflavin riboflavin supplemental intake supplementation of riboflavin riboflavin supplementation Addition of vitamin B6 to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of vitamin B6 supplementation of vitamin B6 vitamin B6 supplemental intake vitamin B6 supplementation Addition of citrulline to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z citrulline supplemental intake dietary supplementation of citrulline supplementation of citrulline citrulline supplementation Addition of vitamin B1 to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of vitamin B1 supplementation of vitamin B1 vitamin B1 supplemental intake vitamin B1 supplementation Addition of amino acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z NCIT:C15509 amino acid supplemental intake dietary supplementation of amino acid supplementation of amino acid A concentrated dietary supplement for injection containing the essential amino acids leucine, isoleucine, lysine, valine, phenylalanine, histidine, threonine, methionine and tryptophan as well as the non-essential amino acids alanine, arginine, glycine, proline, serine and tyrosine, with potential anabolic and anti-catabolic activities. Upon dilution and intravenous infusion of the amino acid nutritional supplement, the amino acids serve as protein building blocks, promote protein synthesis in muscle cells and prevent protein breakdown. NCIT:C15509 amino acid supplementation Addition of L-serine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z L-serine supplemental intake dietary supplementation of L-serine supplementation of L-serine serine supplementation Addition of uridine to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of uridine supplementation of uridine uridine supplemental intake uridine supplementation Addition of medium-chain fatty acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of medium-chain fatty acid medium-chain fatty acid supplemental intake supplementation of medium-chain fatty acid medium-chain fatty acid supplementation Addition of essential fatty acid to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of essential fatty acid essential fatty acid supplemental intake supplementation of essential fatty acid essential fatty acid supplementation Addition of cholesterol to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z cholesterol supplemental intake dietary supplementation of cholesterol supplementation of cholesterol cholesterol supplementation Addition of elemental zinc to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of elemental zinc dietary supplementation of zin elemental zinc supplemental intake supplementation of elemental zinc supplementation of zinc zinc supplemental intake Addition of zinc to a the diet for complete nutrition support. zinc supplementation Addition of hydroxocobalamin to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of hydroxocobalamin hydroxocobalamin supplemental intake supplementation of hydroxocobalamin hydroxocobalamin supplementation Addition of cyanocob(III)alamin to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z cyanocob(III)alamin supplemental intake dietary supplementation of cyanocob(III)alamin supplementation of cyanocob(III)alamin cyanocobalamin supplementation Addition of methylcobalamin to a diet for complete nutrition support. http://orcid.org/0000-0001-7941-2961 2019-11-13T04:45:00Z dietary supplementation of methylcobalamin methylcobalamin supplemental intake supplementation of methylcobalamin methylcobalamin supplementation The surgical transfer of some or all of a(n) bone marrow from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2019-07-11T09:00:01Z NCIT:C15194 bone marrow grafting transplantation of bone marrow bone marrow transplantation The surgical transfer of some or all of a(n) bone tissue from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z transplantation of bone tissue bone grafting The surgical transfer of a whole heart from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z NCIT:C15246 heart transplantation transplantation of whole heart cardiac transplantation The surgical transfer of some or all of a(n) umbilical cord blood from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z UCBT cord blood transplantation transplantation of umbilical cord blood umbilical cord blood transplantation The surgical transfer of a whole cornea from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z NCIT:C50514 keratoplasty transplantation of whole cornea corneal transplantation The surgical transfer of some or all of a(n) dura mater from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z dura mater transplantation transplantation of dura mater dura mater graft The surgical transfer of some or all of a(n) intestine from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z transplantation of intestine intestinal transplantation The surgical transfer of some or all of a(n) small intestine from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z small bowel transplantation transplantation of small intestine small intestine transplantation The surgical transfer of a whole lung from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z NCIT:C15274 transplantation of whole lung whole lung transplantation surgical procedure whole lung transplantation The transfer of an organ, or organ subpart, from one body to another. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z NCIT:C122934 organ graft transplantation of organ organ transplantation The surgical transfer of a whole ovary from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z transplantation of whole ovary whole ovary transplantation ovarian transplantation The surgical transfer of some or all of a(n) zone of skin from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z NCIT:C15325 skin transplantation transplantation of zone of skin skin grafting The surgical transfer of a whole thymus from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-01-20T10:00:01Z thymus transplantation transplantation of whole thymus whole thymic transplantation whole thymus transplantation thymic transplantation The surgical transfer of a whole kidney from a donor to a patient. http://orcid.org/0000-0001-7941-2961 2020-04-07T10:00:01Z NCIT:C15265 transplantation of whole kidney whole kidney transplantation A medical requirement or recommendation of avoiding the consumption of alcoholic beverage. http://orcid.org/0000-0001-7941-2961 2019-11-18T11:00:00Z alcoholic beverage consumption avoidance alcoholic beverage restricted diet intake alcoholic beverage restriction avoid alcoholic beverage intake avoiding dietary alcoholic beverage intake alcohol intake avoidance A medical requirement or recommendation of avoiding the consumption of broad bean. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid broad bean intake avoiding dietary broad bean intake broad bean consumption avoidance broad bean restricted diet intake broad bean restriction fava bean avoidance fava bean consumption avoidance windsor bean intake avoidance fava bean intake avoidance A medical requirement or recommendation of avoiding the consumption of mammalian meat food product. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid mammalian meat food product intake avoiding dietary mammalian meat food product intake mammalian meat food product consumption avoidance mammalian meat food product restricted diet intake mammalian meat food product restriction dietary mammalian meat food product intake avoidance A medical requirement or recommendation of avoiding the consumption of nut food product. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid nut food product intake avoiding dietary nut food product intake nut food product consumption avoidance nut food product restricted diet intake nut food product restriction dietary nut food product intake avoidance A medical requirement or recommendation of avoiding the consumption of saffron food product. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid saffron food product intake avoiding dietary saffron food product intake saffron food product consumption avoidance saffron food product restricted diet intake saffron food product restriction dietary saffron food product intake avoidance A medical requirement or recommendation of avoiding the consumption of animal seafood product. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z animal seafood product consumption avoidance animal seafood product restricted diet intake animal seafood product restriction avoid animal seafood product intake avoiding dietary animal seafood product intake dietary animal seafood product intake avoidance A medical requirement or recommendation of avoiding the consumption of mussel food product. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid mussel food product intake avoiding dietary mussel food product intake mussel food product consumption avoidance mussel food product restricted diet intake mussel food product restriction dietary mussel food product intake avoidance A medical requirement or recommendation of avoiding the consumption of clove food product. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid clove food product intake avoiding dietary clove food product intake clove food product consumption avoidance clove food product restricted diet intake clove food product restriction dietary clove food product intake avoidance A medical requirement or recommendation of avoiding the consumption of dark chocolate. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid dark chocolate intake avoiding dietary dark chocolate intake dark chocolate consumption avoidance dark chocolate restricted diet intake dark chocolate restriction dietary dark chocolate intake avoidance A medical requirement or recommendation of avoiding the consumption of pumpkin seed (shell off). http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid pumpkin seed (shell off) intake avoiding dietary pumpkin seed (shell off) intake pumpkin seed (shell off) consumption avoidance pumpkin seed (shell off) restricted diet intake pumpkin seed (shell off) restriction pumpkin seed intake avoidance A medical requirement or recommendation of avoiding the consumption of sesame seed. http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid sesame seed intake avoiding dietary sesame seed intake sesame seed consumption avoidance sesame seed restricted diet intake sesame seed restriction dietary sesame seed intake avoidance A medical requirement or recommendation of avoiding the consumption of sunflower seed (whole kernel, raw). http://orcid.org/0000-0001-7941-2961 2020-01-13T11:00:00Z avoid sunflower seed (whole kernel, raw) intake avoiding dietary sunflower seed (whole kernel, raw) intake sunflower seed (whole kernel, raw) consumption avoidance sunflower seed (whole kernel, raw) restricted diet intake sunflower seed (whole kernel, raw) restriction sunflower seed intake avoidance A medical requirement or recommendation of avoiding the consumption of liver (raw). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid liver (raw) intake avoiding dietary liver (raw) intake liver (raw) consumption avoidance liver (raw) restricted diet intake liver (raw) restriction liver intake avoidance A medical requirement or recommendation of avoiding the consumption of egg or egg component. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid egg or egg component intake avoiding dietary egg or egg component intake egg or egg component consumption avoidance egg or egg component restricted diet intake egg or egg component restriction egg intake avoidance A medical requirement or recommendation of avoiding the consumption of kidney (raw). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid kidney (raw) intake avoiding dietary kidney (raw) intake kidney (raw) consumption avoidance kidney (raw) restricted diet intake kidney (raw) restriction kidney intake avoidance A medical requirement or recommendation of avoiding the consumption of peas (rehydrated, canned). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid peas (rehydrated, canned) intake avoiding dietary peas (rehydrated, canned) intake peas (rehydrated, canned) consumption avoidance peas (rehydrated, canned) restricted diet intake peas (rehydrated, canned) restriction pea intake avoidance A medical requirement or recommendation of avoiding the consumption of bean food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid bean food product intake avoiding dietary bean food product intake bean food product consumption avoidance bean food product restricted diet intake bean food product restriction bean intake avoidance A medical requirement or recommendation of avoiding the consumption of peanut. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid peanut intake avoiding dietary peanut intake peanut consumption avoidance peanut restricted diet intake peanut restriction peanut intake avoidance A medical requirement or recommendation of avoiding the consumption of soybean refined food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid soybean refined food product intake avoiding dietary soybean refined food product intake soya intake avoiance soybean refined food product consumption avoidance soybean refined food product restricted diet intake soybean refined food product restriction soy intake avoidance A medical requirement or recommendation of avoiding the consumption of 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) consumption avoidance 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) restricted diet intake 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) restriction avoid 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) intake avoid brassicas intake avoiding dietary 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) intake brassicas vegetable intake avoidance brassicas intake avoidance A medical requirement or recommendation of avoiding the consumption of brussels sprout food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid brussels sprout food product intake avoiding dietary brussels sprout food product intake brussels sprout food product consumption avoidance brussels sprout food product restricted diet intake brussels sprout food product restriction brussels sprout intake avoidance A medical requirement or recommendation of avoiding the consumption of broccoli food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid broccoli food product intake avoiding dietary broccoli food product intake broccoli food product consumption avoidance broccoli food product restricted diet intake broccoli food product restriction broccoli intake avoidance A medical requirement or recommendation of avoiding the consumption of cabbage head food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid cabbage head food product intake avoiding dietary cabbage head food product intake cabbage head food product consumption avoidance cabbage head food product restricted diet intake cabbage head food product restriction cabbage intake avoidance A medical requirement or recommendation of avoiding the consumption of cauliflower food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid cauliflower food product intake avoiding dietary cauliflower food product intake cauliflower food product consumption avoidance cauliflower food product restricted diet intake cauliflower food product restriction cauliflower intake avoidance A medical requirement or recommendation of avoiding the consumption of rapeseed food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid rapeseed food product intake avoiding dietary rapeseed food product intake rapeseed food product consumption avoidance rapeseed food product restricted diet intake rapeseed food product restriction rapeseed intake avoidance A medical requirement or recommendation of avoiding the consumption of rapeseed oil. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid rapeseed oil intake avoiding dietary rapeseed oil intake rapeseed oil consumption avoidance rapeseed oil restricted diet intake rapeseed oil restriction dietary rapeseed oil intake avoidance A medical requirement or recommendation of avoiding the consumption of rapeseed meal. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid rapeseed meal intake avoiding dietary rapeseed meal intake rapeseed meal consumption avoidance rapeseed meal restricted diet intake rapeseed meal restriction rapeseed flour intake avoidance A medical requirement or recommendation of avoiding the consumption of cephalopod. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid cephalopod intake avoiding dietary cephalopod intake cephalopod consumption avoidance cephalopod restricted diet intake cephalopod restriction dietary cephalopod intake avoidance A medical requirement or recommendation of avoiding the consumption of crustacean. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid crustacean intake avoiding dietary crustacean intake crustacean consumption avoidance crustacean restricted diet intake crustacean restriction dietary crustacean intake avoidance A medical requirement or recommendation of avoiding the consumption of barley malt beer beverage. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid barley malt beer beverage intake avoiding dietary barley malt beer beverage intake barley malt beer beverage consumption avoidance barley malt beer beverage restricted diet intake barley malt beer beverage restriction dietary barley malt beer beverage intake avoidance A medical requirement or recommendation of avoiding the consumption of corn syrup (high fructose). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid corn syrup (high fructose) intake avoiding dietary corn syrup (high fructose) intake corn syrup (high fructose) consumption avoidance corn syrup (high fructose) restricted diet intake corn syrup (high fructose) restriction dietary corn syrup (high fructose) intake avoidance A medical requirement or recommendation of avoiding the consumption of sorbitol syrup. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid sorbitol syrup intake avoiding dietary sorbitol syrup intake dietary sorbitol intake avoidance sorbitol intake avoidance sorbitol syrup consumption avoidance sorbitol syrup restricted diet intake sorbitol syrup restriction dietary sorbitol syrup intake avoidance A medical requirement or recommendation of avoiding the consumption of human milk based food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid human milk based food product intake avoiding dietary human milk based food product intake human milk based food product consumption avoidance human milk based food product restricted diet intake human milk based food product restriction human milk intake avoidance A medical requirement or recommendation of avoiding the consumption of cow milk based food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid cow milk based food product intake avoiding dietary cow milk based food product intake bovine milk intake avoidance cow milk based food product consumption avoidance cow milk based food product restricted diet intake cow milk based food product restriction cow milk intake avoidance A medical requirement or recommendation of avoiding the consumption of fruit (raw). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid fruit (raw) intake avoiding dietary fruit (raw) intake fruit (raw) consumption avoidance fruit (raw) restricted diet intake fruit (raw) restriction fruit intake avoidance A medical requirement or recommendation of avoiding the consumption of hen egg (shell off, raw). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid hen egg (shell off, raw) intake avoiding dietary hen egg (shell off, raw) intake hen egg (shell off, raw) consumption avoidance hen egg (shell off, raw) restricted diet intake hen egg (shell off, raw) restriction raw egg intake avoidance A medical requirement or recommendation of avoiding the consumption of fruit juice food product. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid fruit juice food product intake avoiding dietary fruit juice food product intake fruit juice food product consumption avoidance fruit juice food product restricted diet intake fruit juice food product restriction fruit juice intake avoidance A medical requirement or recommendation of avoiding the consumption of sugar cane juice (pure). http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid sugar cane juice (pure) intake avoiding dietary sugar cane juice (pure) intake sugar cane juice (pure) consumption avoidance sugar cane juice (pure) restricted diet intake sugar cane juice (pure) restriction cane juice intake avoidance A medical requirement or recommendation of avoiding the consumption of organ meat. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid organ meat intake avoiding dietary organ meat intake organ meat consumption avoidance organ meat restricted diet intake organ meat restriction dietary organ meat intake avoidance A medical requirement or recommendation of avoiding the consumption of isoleucine. http://orcid.org/0000-0001-7941-2961 2020-05-12T09:00:01Z avoid isoleucine intake avoiding dietary isoleucine intake isoleucine consumption avoidance isoleucine restricted diet intake isoleucine restriction dietary isoleucine intake avoidance A medical requirement or recommendation of avoiding the consumption of arginine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z arginine consumption avoidance arginine restricted diet intake arginine restriction avoid arginine intake avoiding dietary arginine intake dietary arginine intake avoidance A medical requirement or recommendation of avoiding the consumption of lysine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid lysine intake avoiding dietary lysine intake lysine consumption avoidance lysine restricted diet intake lysine restriction dietary lysine intake avoidance A medical requirement or recommendation of avoiding the consumption of methionine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid methionine intake avoiding dietary methionine intake methionine consumption avoidance methionine restricted diet intake methionine restriction dietary methionine intake avoidance A medical requirement or recommendation of avoiding the consumption of glycine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid glycine intake avoiding dietary glycine intake glycine consumption avoidance glycine restricted diet intake glycine restriction dietary glycine intake avoidance A medical requirement or recommendation of avoiding the consumption of phenylalanine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid phenylalanine intake avoiding dietary phenylalanine intake phenylalanine consumption avoidance phenylalanine restricted diet intake phenylalanine restriction dietary phenylalanine intake avoidance A medical requirement or recommendation of avoiding the consumption of tyrosine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid tyrosine intake avoiding dietary tyrosine intake tyrosine consumption avoidance tyrosine restricted diet intake tyrosine restriction dietary tyrosine intake avoidance A medical requirement or recommendation of avoiding the consumption of sodium atom. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid sodium atom intake avoiding dietary sodium atom intake sodium atom consumption avoidance sodium atom restricted diet intake sodium atom restriction sodium restriction dietary sodium intake avoidance A medical requirement or recommendation of avoiding the consumption of galactose. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid galactose intake avoiding dietary galactose intake galactose consumption avoidance galactose restricted diet intake galactose restriction dietary galactose intake avoidance obsolete cholesterol intake avoidance true A medical requirement or recommendation of avoiding the consumption of cholesterol. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid cholesterol intake avoiding dietary cholesterol intake cholesterol consumption avoidance cholesterol restricted diet intake cholesterol restriction dietary cholesterol intake avoidance A medical requirement or recommendation of avoiding the consumption of iron atom. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid iron atom intake avoiding dietary iron atom intake dietary iron restriction dietary iron supplementation avoidance excessive iron consumption avoidance iron atom consumption avoidance iron atom restricted diet intake iron atom restriction dietary iron intake avoidance A medical requirement or recommendation of avoiding the consumption of ascorbic acid. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z ascorbic acid consumption avoidance ascorbic acid restricted diet intake ascorbic acid restriction avoid ascorbic acid intake avoiding dietary ascorbic acid intake dietary ascorbic acid intake avoidance A medical requirement or recommendation of avoiding the consumption of branched-chain amino acid. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z BCAA-free diet recommendation avoid branched chain amino acids ingestion avoid branched-chain amino acid intake avoiding dietary branched-chain amino acid intake branched chain amino acid intake avoidance branched chain amino acid restriction branched-chain amino acid consumption avoidance branched-chain amino acid restricted diet intake branched-chain amino acid restriction low BCAA diet intake low BCAA diet recommendation dietary branched-chain amino acid intake avoidance A medical requirement or recommendation of avoiding the consumption of trimethylamine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid trimethylamine intake avoiding dietary trimethylamine intake trimethylamine consumption avoidance trimethylamine restricted diet intake trimethylamine restriction dietary trimethylamine intake avoidance A medical requirement or recommendation of avoiding the consumption of choline. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid choline intake avoiding dietary choline intake choline consumption avoidance choline restricted diet intake choline restriction dietary choline intake avoidance A medical requirement or recommendation of avoiding the consumption of trimethylamine N-oxide. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid trimethylamine N-oxide intake avoiding dietary trimethylamine N-oxide intake trimethylamine N-oxide consumption avoidance trimethylamine N-oxide restricted diet intake trimethylamine N-oxide restriction dietary trimethylamine N-oxide intake avoidance A medical requirement or recommendation of avoiding the consumption of lecithin. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid lecithin intake avoiding dietary lecithin intake lecithin consumption avoidance lecithin restricted diet intake lecithin restriction dietary lecithin intake avoidance A medical requirement or recommendation of avoiding the consumption of sterol. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid sterol intake avoiding dietary sterol intake sterol consumption avoidance sterol restricted diet intake sterol restriction dietary sterol intake avoidance A medical requirement or recommendation of avoiding the consumption of purine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid purine intake avoiding dietary purine intake purine consumption avoidance purine restricted diet intake purine restriction dietary purine intake avoidance A medical requirement or recommendation of avoiding the consumption of fructose. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid fructose intake avoiding dietary fructose intake fructose consumption avoidance fructose restricted diet intake fructose restriction low fructose diet intake dietary fructose intake avoidance A medical requirement or recommendation of avoiding the consumption of lactose. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid lactose intake avoiding dietary lactose intake lactose consumption avoidance lactose restricted diet intake lactose restriction dietary lactose intake avoidance A medical requirement or recommendation of avoiding the consumption of leucine. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid leucine intake avoiding dietary leucine intake leucine consumption avoidance leucine restricted diet intake leucine restriction dietary leucine intake avoidance A medical requirement or recommendation of avoiding the consumption of oxalate. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid oxalate intake avoiding dietary oxalate intake oxalate consumption avoidance oxalate restricted diet intake oxalate restriction dietary oxalate intake avoidance A medical requirement or recommendation of avoiding the consumption of phosphate. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid phosphate intake avoiding dietary phosphate intake phosphate consumption avoidance phosphate restricted diet intake phosphate restriction dietary phosphate intake avoidance A medical requirement or recommendation of avoiding the consumption of saturated fatty acid. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid saturated fatty acid intake avoiding dietary saturated fatty acid intake saturated fatty acid consumption avoidance saturated fatty acid restricted diet intake saturated fatty acid restriction saturated fat intake avoidance A medical requirement or recommendation of avoiding the consumption of calcium atom. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid calcium atom intake avoiding dietary calcium atom intake calcium atom consumption avoidance calcium atom restricted diet intake calcium atom restriction dietary calcium avoidance A medical requirement or recommendation of avoiding the consumption of sucrose. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid sucrose intake avoiding dietary sucrose intake sucrose consumption avoidance sucrose restricted diet intake sucrose restriction dietary sucrose intake avoidance A medical requirement or recommendation of avoiding the consumption of triglyceride. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid triglyceride intake avoiding dietary triglyceride intake triglyceride consumption avoidance triglyceride restricted diet intake triglyceride restriction dietary triglyceride intake avoidance A medical requirement or recommendation of avoiding the consumption of riboflavin. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z B12 restriction avoid riboflavin intake avoiding dietary riboflavin intake riboflavin consumption avoidance riboflavin restricted diet intake riboflavin restriction vitamin B12 intake avoidance dietary riboflavin intake avoidance A medical requirement or recommendation of avoiding the consumption of phytanic acid. http://orcid.org/0000-0001-7941-2961 2020-05-12T11:00:00Z avoid phytanic acid intake avoiding dietary phytanic acid intake phytanic acid consumption avoidance phytanic acid restricted diet intake phytanic acid restriction dietary phytanic acid intake avoidance Use of agent or drug to regulate reproduction. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z treatment with reproductive control drug reproductive control agent therapy The use of an agent or drug to interupt pregnancy after implantation. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z treatment with abortifacient aborifacient agent therapy Use of drug or agent to suppress uterine contractions thereby suppressing premature labor and birth. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z treatment with tocolytic agent tocolytic agent therapy Use of a drug or agent to prevent or reduce probability of contraception. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z treatment with contraceptive drug contraceptive agent therapy Use of drug or agent with contraceptive activity in females. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z treatment with female contraceptive drug female contraceptive agent therapy Use of a compound or agent to block ovulation and prevent occurance of pregnancy. http://orcid.org/0000-0001-7941-2961 2023-11-109T11:00:00Z birth control therapy treatment with oral contraceptive The use of these drugs or agents have many other uses beyond pregnancy control. oral contraceptive agent therapy Collection biological material from within the tongue with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2023-11-30T20:39:14Z swab collection of tongue tongue swab collection A method of ultrasound imaging in which the ultrasound probe is pressed against the skin of the abdomen in order to create an image of the abdominal organs. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z NCIT:C71375 TUS abdomen diagnostic sonography abdomen medical ultrasound abdomen sonography abdomen ultrasound examination abdomen ultrasound imaging procedure abdomen ultrasound procedure abdominal sonography abdominal ultrasound diagnostic abdominal ultrasound diagnostic transabdominal ultrasound medical transabdominal ultrasound sonography of abdomen transabdominal sonography transabdominal ultrasound ultrasonography of abdomen abdominal ultrasonography The use of ultrasound to produce images of structures in the body of uterus. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z body of uterus diagnostic sonography body of uterus medical ultrasound body of uterus sonography body of uterus ultrasound examination body of uterus ultrasound imaging procedure body of uterus ultrasound procedure sonography of body of uterus ultrasonography of body of uterus uterine ultrasonography The use of ultrasound to produce images of structures in the breast. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z breast diagnostic sonography breast medical ultrasound breast sonography breast ultrasound examination breast ultrasound imaging procedure breast ultrasound procedure sonography of breast ultrasonography of breast breast ultrasonography The use of ultrasound to produce images of structures in the heart. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z cardiac echo procedure echo procedure echocardiogram procedure heart diagnostic sonography heart medical ultrasound heart sonography heart ultrasound examination heart ultrasound imaging procedure heart ultrasound procedure sonography of heart ultrasonography of heart echocardiography The use of ultrasound to produce images of structures in the liver. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z liver diagnostic sonography liver medical ultrasound liver sonography liver ultrasound examination liver ultrasound imaging procedure liver ultrasound procedure sonography of liver ultrasonography of liver liver ultrasonography The use of ultrasound to produce images of structures in the lung. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z lung diagnostic sonography lung medical ultrasound lung sonography lung ultrasound examination lung ultrasound imaging procedure lung ultrasound procedure sonography of lung ultrasonography of lung lung ultrasonography The use of ultrasound to produce images of structures in the lymph node. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z lymph node diagnostic sonography lymph node medical ultrasound lymph node sonography lymph node ultrasound examination lymph node ultrasound imaging procedure lymph node ultrasound procedure sonography of lymph node ultrasonography of lymph node lymph node ultrasonography The use of ultrasound to produce images of structures in the musculoskeletal system. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z musculoskeletal system diagnostic sonography musculoskeletal system medical ultrasound musculoskeletal system sonography musculoskeletal system ultrasound examination musculoskeletal system ultrasound imaging procedure musculoskeletal system ultrasound procedure sonography of musculoskeletal system ultrasonography of musculoskeletal system musculoskeletal ultrasonography The use of ultrasound to produce images of structures in the neck. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z neck diagnostic sonography neck medical ultrasound neck sonography neck ultrasound examination neck ultrasound imaging procedure neck ultrasound procedure sonography of neck ultrasonography of neck neck ultrasonography The use of ultrasound to produce images of structures in the pancreas. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z pancreas diagnostic sonography pancreas medical ultrasound pancreas sonography pancreas ultrasound examination pancreas ultrasound imaging procedure pancreas ultrasound procedure sonography of pancreas ultrasonography of pancreas pancreatic ultrasonography The use of ultrasound to produce images of structures in the rectum. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z rectum diagnostic sonography rectum medical ultrasound rectum sonography rectum ultrasound examination rectum ultrasound imaging procedure rectum ultrasound procedure sonography of rectum ultrasonography of rectum rectal ultrasonography The use of ultrasound to produce images of structures in the scrotum. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z scrotum diagnostic sonography scrotum medical ultrasound scrotum sonography scrotum ultrasound examination scrotum ultrasound imaging procedure scrotum ultrasound procedure sonography of scrotum ultrasonography of scrotum scrotal ultrasonography The use of ultrasound to produce images of structures in the spleen. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of spleen spleen diagnostic sonography spleen medical ultrasound spleen sonography spleen ultrasound examination spleen ultrasound imaging procedure spleen ultrasound procedure ultrasonography of spleen spleen ultrasonography The use of ultrasound to produce images of structures in the stomach. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of stomach stomach diagnostic sonography stomach medical ultrasound stomach sonography stomach ultrasound examination stomach ultrasound imaging procedure stomach ultrasound procedure ultrasonography of stomach stomach ultrasonography The use of ultrasound to produce images of structures in the thyroid gland. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of thyroid gland thyroid gland diagnostic sonography thyroid gland medical ultrasound thyroid gland sonography thyroid gland ultrasound examination thyroid gland ultrasound imaging procedure thyroid gland ultrasound procedure ultrasonography of thyroid gland thyroid ultrasonography The use of ultrasound to produce images of structures in the urinary bladder. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of urinary bladder ultrasonography of urinary bladder urinary bladder diagnostic sonography urinary bladder medical ultrasound urinary bladder sonography urinary bladder ultrasound examination urinary bladder ultrasound imaging procedure urinary bladder ultrasound procedure bladder ultrasonography The use of ultrasound to produce images of structures in the vagina. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z sonography of vagina ultrasonography of vagina vagina diagnostic sonography vagina medical ultrasound vagina sonography vagina ultrasound examination vagina ultrasound imaging procedure vagina ultrasound procedure vaginal ultrasonography The use of ultrasound to produce images of structures in the kidney. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z kidney diagnostic sonography kidney medical ultrasound kidney sonography kidney ultrasound examination kidney ultrasound imaging procedure kidney ultrasound procedure sonography of kidney ultrasonography of kidney renal ultrasonography The use of ultrasound to produce images of structures in the carotid artery segment. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z carotid artery segment diagnostic sonography carotid artery segment medical ultrasound carotid artery segment sonography carotid artery segment ultrasound examination carotid artery segment ultrasound imaging procedure carotid artery segment ultrasound procedure carotid ultrasound imaging sonography of carotid artery segment ultrasonography of carotid artery segment carotid ultrasonography The use of ultrasound to produce images of structures in the pelvic region of trunk. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z pelvic region of trunk diagnostic sonography pelvic region of trunk medical ultrasound pelvic region of trunk sonography pelvic region of trunk ultrasound examination pelvic region of trunk ultrasound imaging procedure pelvic region of trunk ultrasound procedure pelvic sonography pelvis sonography sonography of pelvic region of trunk ultrasonography of pelvic region of trunk pelvis ultrasonography The use of ultrasound to produce images of structures in the prostate gland. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z prostate gland diagnostic sonography prostate gland medical ultrasound prostate gland sonography prostate gland ultrasound examination prostate gland ultrasound imaging procedure prostate gland ultrasound procedure sonography of prostate gland ultrasonography of prostate gland prostate ultrasonography obsolete testicular ultrasonography true The use of ultrasound to produce images of structures in the brain. http://orcid.org/0000-0001-7941-2961 2020-01-24T20:39:14Z brain diagnostic sonography brain medical ultrasound brain sonography brain ultrasound examination brain ultrasound imaging procedure brain ultrasound procedure sonography of brain ultrasonography of brain neurosonology Collection biological material from within the rectum with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2961 2020-03-27T20:39:14Z anal swab swab collection of rectum rectal swab collection Collection biological material from within the vagina with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2961 2020-03-27T20:39:14Z swab collection of vagina vaginal swab collection Collection biological material from within the buccal mucosa with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2961 2020-03-27T20:39:14Z oral swab swab collection of buccal mucosa buccal swab collection Collection biological material from within the nasal turbinal with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2974 2020-03-27T20:39:14Z swab collection of nasal turbinal nasal turbinal swab collection Collection biological material from within the nasopharynx with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2020-03-27T20:39:14Z swab collection of nasopharynx nasopharyngeal swab collection Collection biological material from within the zone of skin with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2020-03-27T20:39:14Z swab collection of zone of skin skin swab collection Collection biological material from within the oropharynx with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2020-03-27T20:39:14Z swab collection of oropharynx oropharyngeal swab collection Collection biological material from within the external naris with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2020-03-27T20:39:14Z anterior naris swab swab collection of external naris anterior nares swab collection Collection biological material from within the throat with a cotton swab for use in clinical tests. http://orcid.org/0000-0001-7941-2978 2020-03-27T20:39:14Z swab collection of throat throat swab collection The use of computed tomography to produce images of structures of the abdomen. http://orcid.org/0000-0001-7941-2961 2020-03-31T20:39:14Z CAT scan of abdomen CT of abdomen abdomen CAT scan abdomen CT examination abdomen computed tomography abdomen computerized axial tomography abdominal CT The use of computed tomography to produce images of structures of the head. http://orcid.org/0000-0001-7941-2961 2020-03-31T20:39:14Z CAT scan of head CT of head head CAT scan head CT examination head computed tomography head computerized axial tomography head CT The use of computed tomography to produce images of structures of the liver. http://orcid.org/0000-0001-7941-2965 2020-03-31T20:39:14Z CAT scan of liver CT of liver liver CAT scan liver CT examination liver computed tomography liver computerized axial tomography liver CT The use of computed tomography to produce images of structures of the lung. http://orcid.org/0000-0001-7941-2969 2020-03-31T20:39:14Z CAT scan of lung CT of lung lung CAT scan lung CT examination lung computed tomography lung computerized axial tomography lung CT The use of computed tomography to produce images of structures of the neck. http://orcid.org/0000-0001-7941-2979 2020-03-31T20:39:14Z CAT scan of neck CT of neck neck CAT scan neck CT examination neck computed tomography neck computerized axial tomography neck CT The use of computed tomography to produce images of structures of the brain. http://orcid.org/0000-0001-7941-3010 2020-03-31T20:39:14Z CAT scan of brain CT of brain brain CAT scan brain CT examination brain computed tomography brain computerized axial tomography brain CT The use of computed tomography to produce images of structures of the chest. http://orcid.org/0000-0001-7941-3010 2020-03-31T20:39:14Z CAT scan of chest CT of chest chest CAT scan chest CT examination chest computed tomography chest computerized axial tomography chest CT The use of computed tomography to produce images of structures of the skull. http://orcid.org/0000-0001-7941-3010 2020-03-31T20:39:14Z CAT scan of skull CT of skull skull CAT scan skull CT examination skull computed tomography skull computerized axial tomography skull CT The use of computed tomography to produce images of structures of the blood vasculature. http://orcid.org/0000-0001-7941-3010 2020-04-07T20:39:14Z CAT scan of blood vasculature CT of blood vasculature blood vasculature CAT scan blood vasculature CT examination blood vasculature computed tomography blood vasculature computerized axial tomography CT angiogram The use of computed tomography to produce images of structures of the pulmonary vascular system. http://orcid.org/0000-0001-7941-3010 2020-04-07T20:39:14Z CAT scan of pulmonary vascular system CT PE CT of pulmonary vascular system CT scan for pulmonary embolism pulmonary vascular system CAT scan pulmonary vascular system CT examination pulmonary vascular system computed tomography pulmonary vascular system computerized axial tomography CT pulmonary angiogram Avoid the administration or use of computed tomography procedure. http://orcid.org/0000-0001-7941-2961 2020-03-30T20:39:14Z avoid computed tomography procedure avoiding computed tomography procedure avoid CT scans Avoid the administration or use of ketogenic diet intake. http://orcid.org/0000-0001-7941-2961 2020-05-12T20:39:14Z avoid ketogenic diet intake avoiding ketogenic diet intake ketogenic diet intake avoidance Use of an imaging test that uses small amounts of radiation to produce pictures of abdomen. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z NCIT:C38102 abdomen X-ray procedure abdomen radiogram procedure abdominal X-ray procedure abdominal radiography radiograph of abdomen radiography of abdomen abdominal radiographic procedure Use of an imaging test that uses small amounts of radiation to produce pictures of head. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z head X-ray procedure head radiogram procedure radiograph of head radiography of head head radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of liver. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z liver X-ray procedure liver radiogram procedure radiograph of liver radiography of liver liver radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of lung. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z lung X-ray procedure lung radiogram procedure radiograph of lung radiography of lung lung radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of neck. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z neck X-ray procedure neck radiogram procedure radiograph of neck radiography of neck neck radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of chest. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z NCIT:C38103 chest X-ray procedure chest radiogram procedure radiograph of chest radiography of chest chest radiograph procedure The X-ray examination of the lower limbs of the body. http://orcid.org/0000-0001-7941-2961 2020-04-07T20:39:14Z NCIT:C20080 lower limb X-ray lower limb radiography lower limb segment X-ray procedure lower limb segment radiogram procedure radiograph of lower limb segment radiography of lower limb segment lower limb radiographic procedure obsolete angiography procedure true obsolete pulmonary angiography procedure true The radiographic examination of the tracheobronchial tree following the injection of a radiopaque material. http://orcid.org/0000-0001-7941-2961 2020-04-27T20:39:14Z NCIT:C38040 bronchographic image procedure bronchography radiograph of tracheobronchial tree radiography of tracheobronchial tree tracheobronchial tree X-ray procedure tracheobronchial tree radiogram procedure bronchography procedure The radiographic examination of the bile ducts after a contrast medium has been injected. http://orcid.org/0000-0001-7941-2961 2020-04-27T20:39:14Z NCIT:C61508 biliary tree X-ray procedure biliary tree radiogram procedure cholangiographic procedure cholangiography radiograph of biliary tree radiography of biliary tree cholangiography procedure A radiographic procedure to obtain an image of the urinary bladder by filling the bladder with contrast medium. http://orcid.org/0000-0001-7941-2961 2020-04-27T20:39:14Z NCIT:C38049 cystographic imaging procedure cystography radiograph of urinary bladder radiography of urinary bladder urinary bladder X-ray procedure urinary bladder radiogram procedure cystography procedure A type of radiography used specifically to examine breast tissue. The procedure utilizes a low-dose of x-rays or radiation to generate an image. A mammography exam or mammogram, is used as a screening tool to detect early breast cancer in women experiencing no symptoms and to detect and diagnose breast disease. http://orcid.org/0000-0001-7941-2961 2020-04-27T20:39:14Z NCIT:C16818 breast X-ray procedure breast radiogram procedure mammography radiograph of breast radiography of breast mammography procedure The radiographic examination of the spinal cord and nerve roots following the injection of a contrast medium into the spinal subarachnoid space. The X-rays taken may highlight conditions such as spinal tumors, spinal cord swelling and herniated discs. http://orcid.org/0000-0001-7941-2961 2020-04-27T20:39:14Z NCIT:C20175 myelography radiograph of spinal cord radiography of spinal cord spinal cord X-ray procedure spinal cord radiogram procedure myelography procedure A radiologic test that involves the examination of the entire body in a single procedure. 2020-04-27T20:39:14Z NCIT:C96640 total body X-ray whole body radiography total body radiography procedure A radiographic examination of the vagina using the intravaginal injection of contrast medium. http://orcid.org/0000-0001-7941-2961 2020-04-27T20:39:14Z NCIT:C38096 radiograph of vagina radiography of vagina vagina X-ray procedure vagina radiogram procedure vaginography vaginography procedure Any surgical procedure conducted on the cardiovascular system. http://orcid.org/0000-0001-7941-2961 2023-10-19T20:39:14Z cardiac surgery cardiovascular system surgical procedure heart surgery surgical procedure on cardiovascular system A surgery that fixes or mends heart. http://orcid.org/0000-0001-7941-2961 2022-07-25T20:39:14Z heart surgical repair heart repair Treatment to correct or improve vision. vision treatment Use of glasses to correct vision. glasses usage Any surgical procedure conducted on the nasolacrimal duct. dacryocystorhinostomy nasolacrimal duct surgical procedure tear duct surgery surgical procedure on nasolacrimal duct A surgical procedure to correct strabismus in the eye. strabismus surgery The ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. keto diet intake classic ketogenic diet intake low glycemic index treatment medium-chain triglyceride(s) (MCT) ketogenic diet intake modified Atkins diet intake ketogenic diet intake The ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. PMID:23419562 PMID:27759811 PMID:28701250 Texture-modified foods and thickened drinks used to reduce the risks of choking and aspiration for individuals with oropharyngeal incoordination or dysphagia. dysphagia diet intake thickness modification of food and fluid for ingestion pureed food intake texture modified food intake thickened liquid intake texture modified diet intake Texture-modified foods and thickened drinks used to reduce the risks of choking and aspiration for individuals with oropharyngeal incoordination or dysphagia. PMID:27913916 PMID:28343526 obsolete phenylalanine restricted diet intake true Supplementation of uncooked cornstarch intended to prevent hepatomegaly and hypoglycemia, typically for individuals with irregular hepatic glycogen storage. Supplementation can include both regular cornstarch and extended release cornstarch. 2019-09-05T20:57:49Z administration of uncooked cornstarch uncooked cornstarch therapy uncooked cornstarch supplementation Supplementation of uncooked cornstarch intended to prevent hepatomegaly and hypoglycemia, typically for individuals with irregular hepatic glycogen storage. Supplementation can include both regular cornstarch and extended release cornstarch. PMID:2403059 PMID:25266922 PMID:26303612 Use of an imaging test that uses small amounts of radiation to produce pictures of manus. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z hand radiograph procedure manus X-ray procedure manus radiogram procedure radiograph of manus radiograph of the hand radiography of manus hand radiography A procedure whre the radiographic film or sensor is placed inside the mouth and uses small amounts of radiation to produce pictures of teeth and other oral structures. 2023-02-20T17:13:55Z intraoral x-ray procedure radiograph inside the mouth intraoral radiography A technique to visualize the blood vessels in the back of the eye by injecting fluorescent dye and then imaging it. 2023-02-21T18:55:59Z fluorescein angiography A visualization of the fundus of the eye including the retina and optic nerve with a fundoscope, a device that projects light through the pupil of the eye and visualizes the fundus with magnification. 2023-02-24T19:06:03Z fundoscopic exam fundoscopy A quantitative measurement of a particular hormone present in a blood sample. 2023-04-11T12:00:00Z circulating hormone measurement Use of an imaging test that uses small amounts of radiation to produce pictures of pes. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z pes X-ray procedure pes radiogram procedure radiograph of foot radiograph of pes radiography of pes foot radiography Analysis of a cerebrospinal fluid sample. 2023-04-11T12:00:00Z cerebrospinal fluid analysis Use of an imaging test that uses small amounts of radiation to produce pictures of shoulder. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z radiograph of shoulder radiography of shoulder shoulder X-ray procedure shoulder radiogram procedure shoulder radiograph procedure A direct appraisal of a patient's condition by a dentist that is based on an oral exam, medical history, and the patient's account of symptoms. 2023-04-11T12:00:00Z examination by dentist A direct appraisal by a professional who is an expert in premature babies or newborns with high-risk or complex health conditions. The physician performs a physical exam and takes medical history. 2023-04-11T12:00:00Z examination by neonatologist Measurement of the functionality of an enzyme. 2023-04-11T12:00:00Z enzyme activity assessment A test that measures all areas of your eyesight including peripheral vision. 2023-04-11T12:00:00Z perimetry examination A medical examination performed using of magnetic resonance imaging to image the spinal cord. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z Nuclear magnetic resonance imaging of the spinal cord spinal cord MRI spinal cord magnetic resonance imaging MRI of the spinal cord A test to determine the smallest letters a patient can clearly see. 2023-04-11T12:00:00Z visual acuity assessment Microscopic examination of the hair (also called hair microscopy) is an inexpensive tool that may aid in the diagnosis of systemic disorders as the appearance, structure, and/or growth of hair are modified in various congenital and acquired diseases. (PMID:34843009) 2023-04-11T12:00:00Z hair microscopy Measurement of the functionality of an enzyme derived from leukocytes. 2023-04-11T12:00:00Z leukocyte enzyme activity assessment Measurement of the functionality of an enzyme derived from erythrocytes. 2023-04-11T12:00:00Z erythrocyte enzyme activity assessment Measurement of the functionality of an enzyme derived from a particular tissue 2023-04-11T12:00:00Z tissue enzyme activity assessment A test that measures the ability of the blood to bind iron. 2023-04-11T12:00:00Z iron-binding capacity assessment A quantitative measurement of metabolites present in a particular tissue. 2023-04-11T12:00:00Z tissue metabolite measurement A type of CT where the image resolution is enhanced to look at lung disease. 2023-04-11T12:00:00Z high-resolution pulmonary computed tomography A test that measures DNA damage/breakage in patient cells. DNA damage repair plays an important role in cancer initiation and progression, and in therapeutic resistance. 2023-04-11T12:00:00Z in vitro DNA repair study A quantitative measurement of immunoglobulins present in a blood sample. 2023-04-11T12:00:00Z circulating immunoglobulin measurement A test that measures the amount of oxygen, carbon dioxide, and pH in the blood of the umbilical cord. 2023-04-11T12:00:00Z blood gas assessment in umbilical cord blood This test is used to measure the amount of L-Selectin (CD62L) shed from the surface of neutrophils before and after stimulation of the TLR pathway. The test can help identify patients with defects in their toll-like receptor signalling pathway and can be used to diagnose IRAK-4, MyD88 and UNC93B deficiency. (NHS) 2023-04-11T12:00:00Z L-selectin shedding study A quantitative measurement of metabolites present in a cerebrospinal fluid sample. 2023-04-11T12:00:00Z cerebrospinal fluid metabolite measurement The time an indigestible, non-absorbable markers takes to be excreted. 2023-04-11T12:00:00Z gastrointestinal transit measurement A quantitative measurement of xenobiotics (a chemical foreign to the body) present in a stool sample. 2023-04-11T12:00:00Z stool xenobiotic measurement A quantitative measurement of xenobiotics (a chemical foreign to the body) present in gastric fluid. 2023-04-11T12:00:00Z gastric fluid xenobiotic measurement A quantitative measurement of xenobiotics (a chemical foreign to the body) present in a hair sample. 2023-04-11T12:00:00Z hair xenobiotic measurement A medical examination performed using of magnetic resonance imaging to image the bony pelvis. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z MRI of the pelvis Nuclear magnetic resonance imaging of the bony pelvis bony pelvis MRI bony pelvis magnetic resonance imaging pelvis MRI Use of an imaging test that uses small amounts of radiation to produce pictures of lymphatic part of lymphoid system. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z lymphatic part of lymphoid system X-ray procedure lymphatic part of lymphoid system radiogram procedure radiograph of lymphatic part of lymphoid system radiograph of lymphatic system radiography of lymphatic part of lymphoid system lymphography A laboratory test in which blood, taken from the patient, is inoculated into bottles containing culture media to determine whether infection-causing microorganisms (bacteria or fungi) are present in the patient's bloodstream. 2023-04-11T12:00:00Z blood culture procedure Inspection of stomach using an endoscope. http://orcid.org/0000-0001-7941-2961 2023-04-19T20:39:14Z endoscopy of stomach stomach endoscope gastroscopy An x-ray of blood vessels after a contrast dye is added intraveniously. 2023-02-21T18:18:48Z NCIT:C20080 CT angiography X-ray angiography X-ray of the blood vessels contrast angiography procedure Is an imaging procedure often using a specific contrast dye for evaluation of pelvic floor, anorectal muscle contractions and relaxation (sphincters), and certain structural abnormalities. 2023-02-23T16:22:32Z defecography A procedure where fluid is removed from the abdomen using a needle. 2023-04-11T12:00:00Z abdominal paracentesis A comprehensive set of tests designed to assess all aspects of a child's development, including cognition, language, motor, and social skills. 2023-04-11T12:00:00Z neurodevelopmental assessment Inspection of duodenum using an endoscope. http://orcid.org/0000-0001-7941-2961 2023-04-19T20:39:14Z duodenum endoscope endoscopy of duodenum duodenoscopy Use of an imaging test that uses small amounts of radiation to produce pictures of forelimb. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z forelimb X-ray procedure forelimb radiogram procedure radiograph of forelimb radiograph of upper limb radiography of forelimb upper limb radiography The use of computed tomography to produce images of structures of the heart. http://orcid.org/0000-0001-7941-3010 2023-04-19T20:39:14Z CAT scan of heart CT of heart heart CAT scan heart CT examination heart computed tomography heart computerized axial tomography cardiac CT A motility study to assess motor function of the upper esophageal sphincter, esophageal body and lower esophageal sphincter. 2023-04-11T12:00:00Z esophageal manometry A quantitative measurement of metabolites present in a stool sample. 2023-04-11T12:00:00Z stool metabolite measurement A radiographic examination of the upper gastrointestinal tract in which the esophagus, stomach, and duodenum are made visible by barium or a water-soluble contrast administered orally prior to the examination. 2023-02-22T20:53:16Z contrast examination of the upper gastrointestinal tract barrium swallow test of the upper GI upper GI radiography with contrast A combined endoscopic and fluoroscopic procedure in which an upper endoscope is led into a second part of the duodenum, making it possible for passage of other tools via the major duodenal papilla into the biliary and pancreatic ducts. Contrast material may be injected in these ducts, allowing for radiologic visualization and therapeutic interventions when indicated. 2023-02-20T17:37:27Z ERCP endoscopic retrograde cholangiopancreatography A combined endoscopic and fluoroscopic procedure in which an upper endoscope is led into a second part of the duodenum, making it possible for passage of other tools via the major duodenal papilla into the biliary and pancreatic ducts. Contrast material may be injected in these ducts, allowing for radiologic visualization and therapeutic interventions when indicated. PMID:29630212 Use of an imaging test that uses small amounts of radiation to produce pictures of vertebral column. http://orcid.org/0000-0001-7941-2961 2023-02-21T20:39:14Z radiograph of vertebral column radiography of vertebral column vertebral column X-ray procedure vertebral column radiogram procedure spine radiography A medical examination performed using of magnetic resonance imaging to image the muscle organ. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z MRI of muscle Nuclear magnetic resonance imaging of the muscle organ muscle organ MRI muscle organ magnetic resonance imaging MRI of the muscle organ Use of an imaging test that uses small amounts of radiation to produce pictures of hip. http://orcid.org/0000-0001-7941-2961 2023-04-19T20:39:14Z hip X-ray procedure hip radiogram procedure radiograph of hip radiography of hip . hip radiography The use of ultrasound to produce images of structures in the ovary. http://orcid.org/0000-0001-7941-2961 2023-03-02T20:39:14Z ovarian ultrasound ovary diagnostic sonography ovary medical ultrasound ovary sonography ovary ultrasound examination ovary ultrasound imaging procedure ovary ultrasound procedure sonography of ovary ultrasonography of ovary ovary ultrasonography Assessment of the degree or kind of protein glycosylation (covalent attachment of a carbohydrate moiety to a protein). 2023-04-11T12:00:00Z protein glycosylation assay A technique for counting, examining and sorting microscopic particles suspended in a stream of fluid. NCIT:C16585 2023-04-11T12:00:00Z flow cytometry procedure Reproductive endocrinology and infertility is a surgical subspecialty of obstetrics and gynecology that trains physicians in reproductive medicine addressing hormonal functioning as it pertains to reproduction as well as the issue of infertility. 2023-04-11T12:00:00Z reproductive endocrinologist assessment A quantitative measurement of a particular hormone present in a sample. 2023-04-11T12:00:00Z hormone measurement A test to determine the electrical conduction of the motor and sensory nerves of the human body. 2023-04-11T12:00:00Z nerve conduction study The time taken for neural impulses to travel through the central nervous system on their way to the target muscles. PMID: 24112910 2023-04-11T12:00:00Z central motor conduction time study The use of computed tomography to produce images of structures of the bony pelvis. http://orcid.org/0000-0001-7941-3010 2023-04-12T20:39:14Z CAT scan of bony pelvis CT of bony pelvis CT of pelvis bony pelvis CAT scan bony pelvis CT examination bony pelvis computed tomography bony pelvis computerized axial tomography pelvic CT A quantitative measurement of a particular hormone present in a sample of urine. 2023-04-11T12:00:00Z urine hormone measurement A technique that combines EEG and EMG to assess myoclonus; it use electromyography (EMG) electrodes for the arms or legs, and correlates averaged EEG responses with EMG bursts used as a trigger. PMID: 1464676 2023-04-11T12:00:00Z jerk-locked averaging The transmission electron microscope (TEM) is a diagnostic tool to screen human tissues at high magnification to visualize the ultrastructural level. 2023-04-11T12:00:00Z electron microscopic study A procedure where a dental professional who was not previously involved in a patient's treatment, reviews a patient's medical history, examines the patient, and makes recommendations as to care and treatment. 2023-04-11T12:00:00Z dentist evaluation Measurement of somatosensory evoked potentials (SEPs), which reflect the electrical activity of the brain that results from the stimulation of touch. SEP monitoring may be employed intraoperatively to identify, and ideally, avoid impending permanent damage to neurologic structures. PMID: 31335078 2023-04-11T12:00:00Z somatosensory evoked potential assessment In the perchlorate discharge test, first radioactive iodine is administered, sufficient time is allowed to pass so that the radioactive iodine is captured by the thyroid, and then, perchlorate is administered orally. The perchlorate displaces non-organified iodide from the thyroid. The perchlorate discharge test is considered positive (abnormal) if there is an abnormally rapid loss of radioactive iodine from the thyroid. 2023-04-11T12:00:00Z perchlorate discharge test An assay of the physiology of natural killer (NK) cells. 2023-04-11T12:00:00Z natural killer cell function test Dysmorphology refers to the study of human congenital malformations and syndromes. A dysmorphology evaluation includes an assessment of facial features and also features of the entire body especially with respect to manifestations of hereditary (Mendelian) disease). 2023-04-11T12:00:00Z dysmorphology assessment The determination of the amount of reactive oxygen species present in the sample. http://orcid.org/0000-0001-7941-2961 2022-04-12T13:40:00Z reactive oxygen species assessment reactive oxygen species test reactive oxygen species measurement A determination of the structure of leukocyte. http://orcid.org/0000-0001-7941-2961 2023-03-03T20:39:14Z leukocyte morphology assessment leukocyte morphology measurement A determination of the structure of megakaryocyte. http://orcid.org/0000-0001-7941-2961 2023-03-06T20:39:14Z megakaryocyte morphology assessment megakaryocyte morphology measurement Use of an imaging test that uses small amounts of radiation to produce pictures of ankle joint. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z ankle joint X-ray procedure ankle joint radiogram procedure radiograph of ankle joint radiography of ankle joint ankle radiography Quantification of sperm cell characteristics, including morphology, motility, and number. 2023-04-11T12:00:00Z sperm analysis A complement test is a blood test that measures the activity of one or more proteins that make up the complement system in blood circulation. 2023-04-11T12:00:00Z complement assay The test measures the T cell responses to antigens of common infections as well as to mitogens, allowing detection of deficiencies in this arm of the immune response. 2023-04-11T12:00:00Z functional T cell assessment A complete evaluation of the respiratory system including patient history, physical examinations, and tests of pulmonary function. The primary purpose of pulmonary function testing is to identify the severity of pulmonary impairment. 2023-04-11T12:00:00Z pulmonary function testing Examination by a doctor who specializes in the care of newborn babies. 2023-04-11T12:00:00Z neonatologist evaluation A test to determine if cells are undergoing programmed cell death. 2023-04-11T12:00:00Z apoptosis assay A contrast-enhanced radiographic study commonly used to assess structural characteristics of the entire esophagus. 2023-02-20T17:57:19Z X-ray of upper GI barium esophagogram procedure barium esophagography barium swallow study barium swallow radiograph procedure A contrast-enhanced radiographic study commonly used to assess structural characteristics of the entire esophagus. PMID:29630228 Computed tomography (CT) examination of the kidneys, ureters and bladder following administration of intravenous contrast material. 2023-04-11T12:00:00Z CT urogram Determination of serum uric acid following the administration of an oral bolus of fructose to assess the ability of an individual to digest fructose. 2023-04-11T12:01:00Z fructose tolerance test Use of an imaging test that uses small amounts of radiation to produce pictures of cervical region of vertebral column. http://orcid.org/0000-0001-7941-2961 2023-02-10T20:39:14Z cervical region of vertebral column X-ray procedure cervical region of vertebral column radiogram procedure radiograph of cervical region of vertebral column radiograph of cervical spine radiography of cervical region of vertebral column cervical spine radiography The use of ultrasound to produce images of structures in the artery. http://orcid.org/0000-0001-7941-2961 2023-03-02T20:39:14Z arterial ultrasound artery diagnostic sonography artery medical ultrasound artery sonography artery ultrasound examination artery ultrasound imaging procedure artery ultrasound procedure sonography of artery ultrasonography of artery arterial ultrasonograpy Removal and examination of tissue, cells, or fluids from the peripheral nerve for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2023-02-24T20:39:14Z ganglion of peripheral nervous system biopsy peripheral nerve biopsy biopsy of peripheral nerve A procedure that uses radio waves and a powerful magnet linked to a computer to create detailed pictures of the blood vessels and blood flow inside the body. A dye may be injected into a vein to make the blood vessels and blood flow easier to see. (NCI) 2023-02-21T19:27:13Z MR angiography MRA magnetic resonance angiography procedure Inspection of nasal vestibule using an endoscope. http://orcid.org/0000-0001-7941-2961 2023-04-12T20:39:14Z endoscopy of nasal vestibule nasal vestibule endoscope nasal endoscopy An imaging procedure in which a radioactive tracer is injected intravenously. The tracer is taken up by bile producing cells and subsequently travels with the bile into the gallbladder and through the bile ducts to the small intestine. THe hepatobiliary iminodiacetic acid (HIDA) scan can be used to visualize the liver, gallbladder and bile ducts. 2023-04-11T12:00:00Z hepatobiliary iminodiacetic acid scan Electromyography (EMG) is a diagnostic procedure that evaluates the muscle response to electrical impulses from the nerves that control them, called motor neurons. The test is used to help detect neuromuscular abnormalities. It is usually performed after a nerve conduction study. 2023-04-11T12:00:00Z electromyography procedure A kind of renal function test that assesses the proportion of electrolytes that are retained (or excreted) by the kidney (primarily the renal tubule). 2023-04-11T12:00:00Z fractional excretion assessment A measurement of the speed at which red blood cells in anticoagulated whole blood descend in a standardized tube in one hour. Increased erythrocyte sedimentation rate is a nonspecific sign of inflammation. 2023-04-11T12:00:00Z erythrocyte sedimentation rate measurement An assessment of how well platelets aggregate (clump together) in the process of blood clotting. 2023-04-11T12:00:00Z https://orcid.org/0000-0001-7941-2961 platelet aggregation assay Radiographic examination of veins following injection of contrast material. 2023-04-12T17:56:44Z vein radiograph venography procedure The hydrogen breath test is a noninvasive procedure to diagnose dietary intolerance (e.g., lactose or galactose intolerance) and related conditions by measuring the amount of hydrogen exhaled in the breath following ingestion of the relevant sugar. 2023-04-11T12:00:00Z breath hydrogen test An evaluation of the visual pathway of the nervous system by means of analysis of electrical waves measured by electrodes that are applied to the head. 2023-04-11T12:00:00Z visual evoked potential procedure Removal and examination of tissue, cells, or fluids from artery for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2023-02-24T20:39:14Z artery biopsy biopsy of artery The electroretinogram (ERG) is a diagnostic test that measures the electrical activity of the retina in response to a light stimulus. 2023-04-11T12:00:00Z electroretinogram procedure A test that applied electric or magnetic stimulation to the neck to measure the response of the phrenic nerve. 2023-04-11T12:00:00Z phrenic nerve stimulation test The water deprivation test, also known as the indirect water deprivation test should potentially be able to distinguish the various forms of DI. Deprivation of water intake should allow patients with primary polydipsia to concentrate their urine while those with central or nephrogenic DI continue to excrete dilute urine. Administration of desmopressin (Deamino-8-D-arginine vasopressin), the synthetic analog of AVP, after water deprivation should help with differentiating patients with central DI from those with nephrogenic DI as the former should be able to concentrate the urine once the deficient action of AVP is replaced with desmopressin, while the latter should not show a significant response due to end-organ resistance to the action of AVP or its analogs. PMID:30779536 2023-04-11T12:00:00Z indirect water deprivation test water deprivation test A vision test that determines the presence of myopia, hyperopia, or astigmatism. 2023-04-11T12:00:00Z refraction test A neurophysiological examination that monitors the corticospinal tract beginning with a stimulus at the motor cortex, which travels along the corticospinal tract of the spinal cord to the nerve root, and then the peripheral nerve before terminating in a muscle belly. PMID:35593855 2023-04-11T12:00:00Z motor evoked potential evaluation A determination of the amount of protein present in blood 2023-04-11T12:00:00Z salivary cortisol test A procedure that removes peritoneal fluid from the abdomen (peritoneal cavity) through a needle or catheter to obtain ascitic fluid for diagnostic or therapeutic purposes. 2023-04-11T12:00:00Z paracentesis Removal and examination of tissue, cells, or fluids from carotid artery segment for the purpose of detecting or characterizing disease. http://orcid.org/0000-0001-7941-2961 2023-04-12T20:39:14Z carotid artery biopsy carotid artery segment biopsy biopsy of carotid artery A quantitative measurement of the amount of an electrolyte present in sweat. 2023-04-11T12:00:00Z https://orcid.org/0000-0001-7941-2961 sweat electrolyte test An assay to assess the presence of immune complexes in the blood circulation. 2023-04-11T12:00:00Z immune complex assay A medical test that evaluates the ability to taste. The tests are either chemical or electrical in nature. Chemical testing uses the natural stimuli and chemical tastants (sweet, sour, salty, bitter, and umami) to assess taste, whereas electrical testing adopts electrical currents applied directly to the surface of the tongue. Other investigations are employed in the assessment of gustatory dysfunction, such as certain imaging techniques, though these are not as useful in quantifying taste disorders. PMID:33620811 2023-04-11T12:00:00Z gustatory function testing taste function test gustatory testing A type of electron microscopy in which a beam of electrons is transmitted through a thin section in order to visualize the internal structures of platelets. platelet transmission electron microscopy Measurement of peripheral blood lymphocyte response following stimulation to assess the degree of functionality of the cell-mediated immune response. A variety of tests exist to measure intracellular ATP levels, proliferation, and other functional responses. immune cell function assay A type of cerebral magnetic resonance (MR) imaging that measures random Brownian motion of water molecules within each voxel of imaged brain tissue. 2023-04-11T12:00:00Z diffusion weighted cerebral MRI A type of cardiac test in which the patient walks on a treadmill or rides a stationary bike, while cardiovascular parameters such as heart rhythm, blood pressure and breathing are measured. 2023-04-11T12:00:00Z cardiac exercise stress test A procedure in which a catheter (thin hollow tube) is threaded into the heart via a large blood vessel, generally with contrast dye being injected through the catheter to visualize the heart chambers and coronary arteries. 2023-04-11T12:00:00Z cardiac catheterization A form of Doppler ultrasound examination that examines blood vessels and blood flow. 2023-04-11T12:00:00Z duplex ultrasound with color flow imaging Investigation of heart sounds with a stethoscope. auscultation of the heart heart auscultation heart sounds auscultation cardiac auscultation An electrophysiologic test that measures the existing resting electrical potential between the cornea and Bruch's membrane. The most common use of the electrooculogram is to confirm disease. 2023-04-11T15:47:43Z EOG electrooculogram procedure An assessment of cell function. 2023-04-11T12:00:00Z cell function assay Test for viral infection based on cytopathic effect and/or antibody staining. 2023-04-11T12:00:00Z viral cell culture A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos stationary movement behavior_ontology body part movement Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences. 2011-04-14T01:03:39Z George Gkoutos affective behaviour mood behavior_ontology emotional behavior Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences. wikipedia:Emotions The act of moving any of the tissues and hard structures surrounding the mouth other than teeth, jaws or filter structures [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos mouth part movement other moved mouth parts behavior_ontology mouth movement Behavior directly related to the production of offspring [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos reproduction reproductive behaviour behavior_ontology GO:0019098 reproductive behavior "A behavior that occurs predominantly or only, in individuals that are part of a group." [Wikipedia:Social_behavior] 2011-04-14T01:03:39Z George Gkoutos social behaviour behavior_ontology GO:0035176 social behavior Emotional behavior related to fear or anxiety. 2011-04-14T01:03:39Z George Gkoutos fear/anxiety related behaviour behavior_ontology fear/anxiety related behavior Emotional behavior related to fear or anxiety. NBO:GVG Behaviour related to the activity which primary purpose is the sexual reproduction. 2011-04-14T01:03:39Z George Gkoutos behavior_ontology sexual actions sexual activity Behaviour related to the activity which primary purpose is the sexual reproduction. NBO:GVG Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos copulate behavior_ontology copulation The act of repeated grinding, tearing, and or crushing with teeth or jaws [NBO:SMAC] 2011-04-14T01:20:02Z George Gkoutos chew gnaw mastication behavior_ontology chewing Emotional behavior related to excitement or restlessness. 2011-03-31T12:22:11Z George Gkoutos behavior_ontology agitation behavior Emotional behavior related to excitement or restlessness. NBO:GVG Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing. 2011-04-04T10:00:45Z George Gkoutos NBO:0000454 behavior involving perception perception behavior behavior_ontology Example: moving head to watch passing object. sensation behavior Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing. NBO:GVG "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] 2011-04-05T09:53:10Z George Gkoutos NBO:0000000 behavior behaviour behavior_ontology GO:0007610 behavior process Behavior related to the awareness of body balance and movement. 2011-04-05T10:40:36Z George Gkoutos proprioception behavior_ontology vestibular behavior Behavior related to the awareness of body balance and movement. MBP:GVG Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints. 2011-04-05T11:01:08Z George Gkoutos behavior_ontology Sensations arising from the internal organs (the viscera), such as pain or the sense of fullness of the stomach or bladder, may therefore be included, although they are usually considered separately as visceral sensations. Pain arising from the viscera is often felt as though it comes from some part of the body surface or underlying tissue. somatic sensation related behavior Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints. OBP:GVG "Movement behavior of the body or its parts." 2011-04-05T02:08:47Z George Gkoutos behavior_ontology kinesthetic behavior "The coordination of combinations of body movements created with the kinematic (such as spatial direction) and kinetic (force) parameters that result in intended actions." [wikipedia:Motor_coordination] 2011-04-05T03:32:44Z George Gkoutos NBO:0000340 behavior_ontology motor coordination The coordination of large muscle groups and whole body movement. 2011-04-05T04:10:52Z George Gkoutos large muscle coordination whole body coordination behavior_ontology gross motor coordination The coordination of large muscle groups and whole body movement. NBO:GVG Behavior related to movements that occur independent of planning. 2011-04-06T02:35:38Z George Gkoutos behavior_ontology Movevents listed here are involuntary, but may be also generated by free will, like blinking of the eyelids and respiratory movements. involuntary movement behavior Behavior related to movements that occur independent of planning. NBO:GVG Behavior related to involuntary movement in response to a stimulus. 2011-04-06T02:36:55Z George Gkoutos NBO:0000004 reflex behaviour behavior_ontology reflexive behavior Behavior related to involuntary movement in response to a stimulus. NBO:GVG Behavior related to movements executed with intent. 2011-04-06T03:32:28Z George Gkoutos behavior_ontology voluntary movement behavior Behavior related to movements executed with intent. NBO:GVG "Behavior related to how the body reacts to a stressor ( a stimulus that causes stress), real or imagined." [wikipedia:Stress_(biological)] 2011-04-08T01:52:36Z George Gkoutos behavior_ontology It refers to the consequence of the failure of an organism to respond adequately to mental, emotional or physical demands, whether actual or imagined. stress related behavior "A social behavior characterised by conscious or unconscious constraint of a behavior that might be considered objectionable in a social setting." [wikipedia:Social_inhibition] 2011-04-14T03:33:25Z George Gkoutos behavior_ontology social inhibition Behaviour related to cognitive processes. 2011-04-14T03:51:13Z George Gkoutos behavior_ontology cognitive behavior Behaviour related to cognitive processes. NBO:JH 2012-03-17T09:51:17Z gkoutos behavior_ontology jaw movement 2012-03-16T05:23:06Z gkoutos behavior_ontology perception behavior by means "Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795] George Gkoutos GO:0050795 regulation of behavior Behavior related to the intake of substances. George Gkoutos ingest consumption behavior Behavior related to the intake of substances. NBOC:GVG Behavior related to the intake of addictive substances. George Gkoutos consumption of an addictive substance Behavior related to the intake of addictive substances. NBOC:GVG Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli. George Gkoutos regulation of consumption behavior Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli. NBOC:GVG Any process that modulates the frequency, rate or extent of consumption of an addictive substance, the specific actions or reactions of an organism in response to external or internal stimuli. George Gkoutos regulation of consumption of an addictive substance Any process that modulates the frequency, rate or extent of consumption of an addictive substance, the specific actions or reactions of an organism in response to external or internal stimuli. NBOC:GVG Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli. George Gkoutos regulation of sexual activity Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli. NBOC:GVG Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 smoking behavior Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted. 0000-0002-4277-2151 https://en.wikipedia.org/wiki/Smoking Any habitual use of the tobacco plant leaf and its products. 2020-01-27T20:46:57Z tobacco consumption 2020-01-27T21:03:19Z cannabis consumption GC_ID:1 PMID:30365038 PMID:32761142 ncbi_taxonomy all NCBITaxon:1 root all GC_ID:1 ncbi_taxonomy NCBITaxon:1003878 Cucurbiteae GC_ID:1 PMID:15371245 ncbi_taxonomy NCBITaxon:10066 Muridae GC_ID:1 Mus mice mouse ncbi_taxonomy NCBITaxon:10088 Mus <genus> Mus mice mouse NCBITaxon:85055 GC_ID:1 house mouse mouse ncbi_taxonomy NCBITaxon:10090 Mus musculus house mouse mouse GC_ID:1 ncbi_taxonomy Vira Viridae viruses NCBITaxon:10239 Viruses Vira Viridae viruses GC_ID:1 PMID:18375151 ncbi_taxonomy NCBITaxon:102804 Asteroideae GC_ID:1 ncbi_taxonomy NCBITaxon:102814 Heliantheae GC_ID:1 ncbi_taxonomy NCBITaxon:117570 Teleostomi NCBITaxon:40673 GC_ID:1 bony vertebrates ncbi_taxonomy NCBITaxon:117571 Euteleostomi bony vertebrates GC_ID:1 charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group NCBITaxon:131221 Streptophytina charophyte/embryophyte group Charophyta/Embryophyta group GC_ID:1 ncbi_taxonomy biota NCBITaxon:131567 cellular organisms biota GC_ID:1 PMID:22839753 PMID:25450099 ncbi_taxonomy Archosauria-Testudines Testudines + Archosauria group NCBITaxon:1329799 Archelosauria Archosauria-Testudines Testudines + Archosauria group GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 Dipnotetrapodomorpha GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria NCBITaxon:1437010 Boreoeutheria Boreotheria GC_ID:1 PMID:25249442 ncbi_taxonomy NCBITaxon:1437183 Mesangiospermae GC_ID:1 PMID:26350789 ncbi_taxonomy NCBITaxon:1437197 Petrosaviidae GC_ID:1 ncbi_taxonomy NCBITaxon:1437201 Pentapetalae GC_ID:1 ncbi_taxonomy NCBITaxon:1462606 Glycine subgen. Soja NCBITaxon:219388 GC_ID:1 ncbi_taxonomy Centothecoideae NCBITaxon:147369 Panicoideae Centothecoideae GC_ID:1 ncbi_taxonomy NCBITaxon:147370 PACMAD clade GC_ID:1 ncbi_taxonomy NCBITaxon:147429 Andropogoneae GC_ID:1 true yeasts ncbi_taxonomy NCBITaxon:147537 Saccharomycotina true yeasts GC_ID:1 PMID:11250829 ncbi_taxonomy NCBITaxon:163725 Dalbergieae GC_ID:1 ncbi_taxonomy NCBITaxon:163735 Phaseoleae GC_ID:1 ncbi_taxonomy Vicieae NCBITaxon:163743 Fabeae Vicieae GC_ID:1 ncbi_taxonomy NCBITaxon:1648029 Tripsacinae GC_ID:1 ncbi_taxonomy NCBITaxon:1648033 Andropogonodae GC_ID:1 mice and others ncbi_taxonomy Sciurognathi NCBITaxon:1963758 Myomorpha mice and others Sciurognathi GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:32628106 PMID:36748408 PMID:7520741 PMID:8123559 PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 eubacteria ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes NCBITaxon:2 Bacteria eubacteria Monera Procaryotae Prokaryota Prokaryotae bacteria prokaryote prokaryotes GC_ID:1 ncbi_taxonomy Homo/Pan/Gorilla group NCBITaxon:207598 Homininae Homo/Pan/Gorilla group GC_ID:11 PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11541975 PMID:11542064 PMID:11542149 PMID:11760965 PMID:12054223 PMID:2112744 PMID:25527841 PMID:270744 PMID:32628106 PMID:36748408 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes NCBITaxon:2157 Archaea Archaebacteria Mendosicutes Metabacteria Monera Procaryotae Prokaryota Prokaryotae archaea prokaryote prokaryotes GC_ID:1 PMID:21652332 ncbi_taxonomy canavanine-accumulating clade non-protein amino acid accumulating clade NCBITaxon:2231382 NPAAA clade canavanine-accumulating clade non-protein amino acid accumulating clade GC_ID:1 PMID:21652332 ncbi_taxonomy NCBITaxon:2231387 dalbergioids sensu lato GC_ID:1 PMID:11250829 ncbi_taxonomy NCBITaxon:2231390 Pterocarpus clade GC_ID:1 ncbi_taxonomy NCBITaxon:2231393 50 kb inversion clade GC_ID:1 ncbi_taxonomy NCBITaxon:2233838 Hologalegina GC_ID:1 PMID:21652332 ncbi_taxonomy inverted repeat lacking clade inverted repeat loss clade temperate herbaceous clade NCBITaxon:2233839 IRL clade inverted repeat lacking clade inverted repeat loss clade temperate herbaceous clade GC_ID:1 PMID:10719003 PMID:21652332 ncbi_taxonomy NCBITaxon:2233855 indigoferoid/millettioid clade NCBITaxon:55189 NCBITaxon:571644 GC_ID:1 PMID:19022233 lager yeast ncbi_taxonomy Saccharomyces carlsbergensis Saccharomyces monacensis Saccharomyces pasteurianus NCBITaxon:27292 Saccharomyces pastorianus lager yeast Saccharomyces carlsbergensis Saccharomyces monacensis Saccharomyces pasteurianus GC_ID:1 PMID:23020233 PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes NCBITaxon:2759 Eukaryota eucaryotes eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes GC_ID:1 ncbi_taxonomy NCBITaxon:27592 Bovinae GC_ID:1 PMID:11214318 PMID:11214319 PMID:12878460 ncbi_taxonomy NCBITaxon:314145 Laurasiatheria GC_ID:1 PMID:11214319 PMID:12082125 PMID:12878460 PMID:15522813 ncbi_taxonomy NCBITaxon:314146 Euarchontoglires GC_ID:1 PMID:11214319 PMID:12082125 PMID:15522813 Rodents and rabbits ncbi_taxonomy NCBITaxon:314147 Glires Rodents and rabbits GC_ID:1 ncbi_taxonomy Anthropoidea NCBITaxon:314293 Simiiformes Anthropoidea GC_ID:1 ape apes ncbi_taxonomy NCBITaxon:314295 Hominoidea ape apes GC_ID:1 higher plants land plants plants ncbi_taxonomy land plants NCBITaxon:3193 Embryophyta higher plants land plants plants land plants GC_ID:1 tetrapods ncbi_taxonomy NCBITaxon:32523 Tetrapoda tetrapods GC_ID:1 amniotes ncbi_taxonomy NCBITaxon:32524 Amniota amniotes GC_ID:1 Theria ncbi_taxonomy NCBITaxon:32525 Theria <mammals> Theria GC_ID:1 diapsids ncbi_taxonomy Diapsida NCBITaxon:32561 Sauria diapsids Diapsida GC_ID:1 PMID:16248873 PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta Chloroplastida green plants NCBITaxon:33090 Viridiplantae Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Chlorobionta Chloroplastida green plants GC_ID:1 ncbi_taxonomy Fungi/Metazoa group opisthokonts NCBITaxon:33154 Opisthokonta Fungi/Metazoa group opisthokonts GC_ID:1 metazoans multicellular animals ncbi_taxonomy Animalia animals NCBITaxon:33208 Metazoa metazoans multicellular animals Animalia animals GC_ID:1 ncbi_taxonomy NCBITaxon:33213 Bilateria GC_ID:1 deuterostomes ncbi_taxonomy NCBITaxon:33511 Deuterostomia deuterostomes GC_ID:1 PMID:15019624 PMID:15371245 ncbi_taxonomy NCBITaxon:337687 Muroidea GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae Magnoliophyta flowering plants NCBITaxon:3398 Magnoliopsida angiosperms flowering plants Angiospermae Magnoliophyta flowering plants GC_ID:1 ncbi_taxonomy NCBITaxon:35493 Streptophyta GC_ID:1 ncbi_taxonomy NCBITaxon:35500 Pecora GC_ID:1 cucumber family ncbi_taxonomy NCBITaxon:3650 Cucurbitaceae cucumber family GC_ID:1 marrows pumpkins squashes ncbi_taxonomy NCBITaxon:3660 Cucurbita marrows pumpkins squashes GC_ID:1 PMID:11782554 ncbi_taxonomy NCBITaxon:3663 Cucurbita pepo GC_ID:1 ncbi_taxonomy Capparales NCBITaxon:3699 Brassicales Capparales NCBITaxon:25773 GC_ID:1 Cruciferae mustard family ncbi_taxonomy NCBITaxon:3700 Brassicaceae Cruciferae mustard family GC_ID:1 ncbi_taxonomy NCBITaxon:3705 Brassica GC_ID:1 wild cabbage ncbi_taxonomy NCBITaxon:3712 Brassica oleracea wild cabbage GC_ID:1 Brassica oleracea Cauliflower Group cauliflower ncbi_taxonomy Brassica oleracea subsp. botrytis NCBITaxon:3715 Brassica oleracea var. botrytis Brassica oleracea Cauliflower Group cauliflower Brassica oleracea subsp. botrytis GC_ID:1 ncbi_taxonomy NCBITaxon:376913 Haplorrhini GC_ID:1 pea family ncbi_taxonomy Leguminosae NCBITaxon:3803 Fabaceae pea family Leguminosae NCBITaxon:186653 GC_ID:1 Indian corn Zea mays subsp. sacharata corn maize ncbi_taxonomy Zea mays subsp. amylacea Zea mays subsp. ceratina Zea mays subsp. everta Zea mays subsp. indurata Zea mays subsp. ramosa Zea mays subsp. saccharata Zea mays subsp. saccharata (Sturtev.) Zhuk., 1950 Zea mays subsp. tunicata Zea mays var. mays Zea mays var. saccharata Zea mays var. saccharata (Sturtev.) L.H.Bailey, 1902 Zea ramosa Zea saccharata NCBITaxon:381124 Zea mays subsp. mays Indian corn Zea mays subsp. sacharata corn maize Zea mays subsp. amylacea Zea mays subsp. ceratina Zea mays subsp. everta Zea mays subsp. indurata Zea mays subsp. ramosa Zea mays subsp. saccharata Zea mays subsp. saccharata (Sturtev.) Zhuk., 1950 Zea mays subsp. tunicata Zea mays var. mays Zea mays var. saccharata Zea mays var. saccharata (Sturtev.) L.H.Bailey, 1902 Zea ramosa Zea saccharata NCBITaxon:24958 GC_ID:1 ncbi_taxonomy Faboideae NCBITaxon:3814 Papilionoideae Faboideae GC_ID:1 ncbi_taxonomy NCBITaxon:3817 Arachis GC_ID:1 goober ground-nut peanut ncbi_taxonomy NCBITaxon:3818 Arachis hypogaea goober ground-nut peanut GC_ID:1 ncbi_taxonomy NCBITaxon:3846 Glycine GC_ID:1 soybean soybeans ncbi_taxonomy Phaseolus max NCBITaxon:3847 Glycine max soybean soybeans Phaseolus max NCBITaxon:4478 NCBITaxon:4727 GC_ID:1 PMID:26350789 ncbi_taxonomy NCBITaxon:38820 Poales GC_ID:1 ncbi_taxonomy NCBITaxon:3904 Vicia GC_ID:1 broad bean faba bean fava bean ncbi_taxonomy NCBITaxon:3906 Vicia faba broad bean faba bean fava bean NCBITaxon:109679 GC_ID:1 ncbi_taxonomy NCBITaxon:39107 Murinae GC_ID:1 mammals ncbi_taxonomy mammals NCBITaxon:40674 Mammalia mammals mammals NCBITaxon:4380 GC_ID:1 PMID:12144762 ncbi_taxonomy NCBITaxon:4209 Asterales GC_ID:1 PMID:18375151 Compositae daisy family ncbi_taxonomy NCBITaxon:4210 Asteraceae Compositae daisy family NCBITaxon:36497 GC_ID:1 sunflowers ncbi_taxonomy NCBITaxon:4231 Helianthus sunflowers GC_ID:1 common sunflower ncbi_taxonomy NCBITaxon:4232 Helianthus annuus common sunflower GC_ID:1 dinosaur dinosaurs ncbi_taxonomy NCBITaxon:436486 Dinosauria dinosaur dinosaurs GC_ID:1 ncbi_taxonomy NCBITaxon:436489 Saurischia GC_ID:1 ncbi_taxonomy NCBITaxon:436491 Theropoda GC_ID:1 ncbi_taxonomy NCBITaxon:436492 Coelurosauria GC_ID:1 PMID:25249442 monocots monocotyledons ncbi_taxonomy Monocotyledoneae monocots NCBITaxon:4447 Liliopsida monocots monocotyledons Monocotyledoneae monocots NCBITaxon:1661618 GC_ID:1 grass family ncbi_taxonomy Bambusaceae Gramineae NCBITaxon:4479 Poaceae grass family Bambusaceae Gramineae GC_ID:1 PMID:15689432 PMID:16151185 PMID:17010206 PMID:17051209 PMID:17572334 ncbi_taxonomy NCBITaxon:451864 Dikarya GC_ID:1 ncbi_taxonomy Euchlaena NCBITaxon:4575 Zea Euchlaena NCBITaxon:4578 GC_ID:1 maize ncbi_taxonomy Zea mays var. japonica NCBITaxon:4577 Zea mays maize Zea mays var. japonica GC_ID:1 PMID:26350789 ncbi_taxonomy Commelinidae Commeliniflorae NCBITaxon:4734 commelinids Commelinidae Commeliniflorae GC_ID:1 PMID:11062127 PMID:12684019 ncbi_taxonomy Mycota fungi NCBITaxon:4751 Fungi Mycota fungi GC_ID:1 PMID:17572334 ascomycetes sac fungi ncbi_taxonomy ascomycete fungi NCBITaxon:4890 Ascomycota ascomycetes sac fungi ascomycete fungi GC_ID:1 ncbi_taxonomy Hemiascomycetes NCBITaxon:4891 Saccharomycetes Hemiascomycetes GC_ID:1 ncbi_taxonomy Endomycetales budding yeasts NCBITaxon:4892 Saccharomycetales Endomycetales budding yeasts NCBITaxon:221665 NCBITaxon:44280 GC_ID:1 ncbi_taxonomy NCBITaxon:4893 Saccharomycetaceae NCBITaxon:36915 GC_ID:1 ncbi_taxonomy Pachytichospora NCBITaxon:4930 Saccharomyces Pachytichospora GC_ID:1 vascular plants ncbi_taxonomy vascular plants NCBITaxon:58023 Tracheophyta vascular plants vascular plants GC_ID:1 seed plants ncbi_taxonomy seed plants NCBITaxon:58024 Spermatophyta seed plants seed plants GC_ID:1 ncbi_taxonomy NCBITaxon:6072 Eumetazoa GC_ID:1 ncbi_taxonomy NCBITaxon:71239 Cucurbitales NCBITaxon:3399 GC_ID:1 PMID:25249442 PMID:26724406 ncbi_taxonomy Dicotyledoneae dicots dicotyledons eudicots NCBITaxon:71240 eudicotyledons Dicotyledoneae dicots dicotyledons eudicots GC_ID:1 PMID:12144762 Asteridae ncbi_taxonomy NCBITaxon:71274 asterids Asteridae GC_ID:1 ncbi_taxonomy Rosidae NCBITaxon:71275 rosids Rosidae GC_ID:1 ncbi_taxonomy NCBITaxon:716545 saccharomyceta GC_ID:1 ncbi_taxonomy NCBITaxon:72025 Fabales GC_ID:1 echinoderms ncbi_taxonomy echinoderms NCBITaxon:7586 Echinodermata echinoderms echinoderms GC_ID:1 chordates ncbi_taxonomy chordates NCBITaxon:7711 Chordata chordates chordates GC_ID:1 Vertebrata vertebrates ncbi_taxonomy vertebrates NCBITaxon:7742 Vertebrata <vertebrates> Vertebrata vertebrates vertebrates GC_ID:1 Gnathostomata jawed vertebrates ncbi_taxonomy NCBITaxon:7776 Gnathostomata <vertebrates> Gnathostomata jawed vertebrates GC_ID:1 euphyllophytes ncbi_taxonomy NCBITaxon:78536 Euphyllophyta euphyllophytes GC_ID:1 ncbi_taxonomy NCBITaxon:8287 Sarcopterygii GC_ID:1 sauropsids ncbi_taxonomy NCBITaxon:8457 Sauropsida sauropsids GC_ID:1 ncbi_taxonomy NCBITaxon:8492 Archosauria GC_ID:1 Mus ncbi_taxonomy NCBITaxon:862507 Mus <subgenus> Mus GC_ID:1 birds ncbi_taxonomy avian birds NCBITaxon:8782 Aves birds avian birds GC_ID:1 Craniata ncbi_taxonomy NCBITaxon:89593 Craniata <chordates> Craniata GC_ID:1 PMID:18375151 ncbi_taxonomy NCBITaxon:911341 Heliantheae alliance GC_ID:1 whales, hippos, ruminants, pigs, camels etc. ncbi_taxonomy Cetartiodactyla even-toed ungulates NCBITaxon:91561 Artiodactyla whales, hippos, ruminants, pigs, camels etc. Cetartiodactyla even-toed ungulates NCBITaxon:1437200 GC_ID:1 core eudicots core eudicotyledons ncbi_taxonomy NCBITaxon:91827 Gunneridae core eudicots core eudicotyledons NCBITaxon:41939 NCBITaxon:4293 GC_ID:1 ncbi_taxonomy eurosids I NCBITaxon:91835 fabids eurosids I GC_ID:1 ncbi_taxonomy NCBITaxon:91836 malvids NCBITaxon:41940 NCBITaxon:4379 GC_ID:1 PMID:12144762 ncbi_taxonomy euasterids II NCBITaxon:91882 campanulids euasterids II GC_ID:1 eutherian mammals placental mammals placentals ncbi_taxonomy Placentalia placentals NCBITaxon:9347 Eutheria eutherian mammals placental mammals placentals Placentalia placentals GC_ID:1 primate ncbi_taxonomy Primata primates NCBITaxon:9443 Primates primate Primata primates GC_ID:1 ncbi_taxonomy NCBITaxon:9526 Catarrhini GC_ID:1 great apes ncbi_taxonomy Pongidae NCBITaxon:9604 Hominidae great apes Pongidae GC_ID:1 humans ncbi_taxonomy NCBITaxon:9605 Homo humans GC_ID:1 human ncbi_taxonomy NCBITaxon:9606 Homo sapiens human GC_ID:1 ncbi_taxonomy NCBITaxon:981071 Brassiceae GC_ID:1 ncbi_taxonomy NCBITaxon:9845 Ruminantia GC_ID:1 ncbi_taxonomy NCBITaxon:9895 Bovidae GC_ID:1 oxen, cattle ncbi_taxonomy NCBITaxon:9903 Bos oxen, cattle NCBITaxon:272461 GC_ID:1 bovine cattle cow dairy cow domestic cattle domestic cow ox ncbi_taxonomy Bos bovis Bos primigenius taurus NCBITaxon:9913 Bos taurus bovine cattle cow dairy cow domestic cattle domestic cow ox Bos bovis Bos primigenius taurus GC_ID:1 rodent ncbi_taxonomy rodents NCBITaxon:9989 Rodentia rodent rodents planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process collecting specimen with swab A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 OBIB collecting specimen with swab biopsy Biopsy of a potentially cancerous mole. A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. Damion Dooley Nicole Vasilevsky https://en.wikipedia.org/wiki/Biopsy biopsy image guided biopsy Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. A biopsy which uses an imaging procedure to guide a needle biopsy. Damion Dooley image guided needle biopsy image-guided biopsy imaging guided biopsy https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 image guided biopsy computed tomography assisted biopsy A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. A needle biopsy guided by real-time computed tomography (CT) scan images. Damion Dooley CT Assisted Biopsy CT Guided Biopsy Computed Tomography Assisted Biopsy Computed Tomography-Guided Needle Biopsy http://purl.obolibrary.org/obo/NCIT_C137909 computed tomography assisted biopsy ultrasound-guided needle biopsy An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. A needle biopsy guided by ultrasound visualization. Damion Dooley https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy ultrasound-guided needle biopsy needle biopsy A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin. A biopsy that uses a hollow needle to extract cells. Damion Dooley https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 needle biopsy fine needle aspiration biopsy A fine needle aspiration biopsy is commonly performed in order to test for cancer. A biopsy that uses a thin needle to extract cells. Chris Stoeckert, Helena Ellis, Jie Zheng FNA FNAB https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ NCI BBRB fine needle aspiration biopsy core needle biopsy A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed. A biopsy that uses a hollow tube to collect a core of tissue. Chris Stoeckert, Helena Ellis, Jie Zheng CNB https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ NCI BBRB core needle biopsy surgical biopsy Surgical biopsy may be required to collect hard-to-reach tissue. A biopsy involving a surgical incision into an organism to access the biopsy material. Damion Dooley excisional biopsy open biopsy https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 surgical biopsy organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A quality of inhering in a bearer by virtue of the bearer's disposition to move freely. quality PATO:0000004 Should be defined using translocation. mobility A quality of inhering in a bearer by virtue of the bearer's disposition to move freely. PATOC:GVG A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0002015 composed of compositionality content structure, composition quality PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATOC:GVG A time quality inhering in a bearer by virtue of the bearer's expected maximum age. quality PATO:0000050 life span A time quality inhering in a bearer by virtue of the bearer's expected maximum age. PATOC:GVG A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATO:0000156 PATO:0000158 temporal incidence quality PATO:0000057 occurrence A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATO:0000132 PATO:0001565 distribution quality pattern PATO:0000060 spatial pattern A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATOC:GVG quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation (from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG The number of entities of this type that are part of the whole organism. PATO:0000053 PATO:0000071 PATO:0001169 PATO:0001226 presence or absence in organism quantitative quality count in organism number presence PATO:0000070 This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. amount The number of entities of this type that are part of the whole organism. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. quality PATO:0000119 height A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. PATOC:GVG A 1-D extent quality which is equal to the distance between two points. https://github.com/pato-ontology/pato/issues/337 quality PATO:0000122 Length often refers to the longer or longest dimension of an object, however, this is not always true. See https://github.com/pato-ontology/pato/issues/337 for full discussion. length A 1-D extent quality which is equal to the distance between two points. PATOC:GVG A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. quality PATO:0000125 For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. PATOC:GVG A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. quality PATO:0000136 closure A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. PATOC:CJM PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG conformation VT:1000738 A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics. quality PATO:0000150 texture A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa A quality in which events occur in sequence. quality PATO:0000165 time A quality in which events occur in sequence. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. PATO:0001722 behavioural quality quality PATO:0000186 behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. PATOC:GVG A behavioral quality inhering in a bearer by virtue of the bearer's having or lacking skillful and effective interaction of movement. quality PATO:0000188 coordination A behavioral quality inhering in a bearer by virtue of the bearer's having or lacking skillful and effective interaction of movement. PATOC:GVG A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. quality PATO:0000261 maturity A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. Merriam-Webster:Merriam-Webster A mobility quality of inhering in a bearer by virtue of the bearer's disposition to move freely. quality PATO:0000299 mobile A mobility quality of inhering in a bearer by virtue of the bearer's disposition to move freely. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. quality PATO:0000330 irregular spatial pattern A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. PATOC:GVG A branchiness quality inhering in a bearer by virtue of the bearer's having branches. ramified ramiform quality PATO:0000402 branched A branchiness quality inhering in a bearer by virtue of the bearer's having branches. WordNet:WordNet A concave quality inhering in a bearer by virtue of the bearer's resembling a groove or fissure. quality PATO:0000403 cleft A concave quality inhering in a bearer by virtue of the bearer's resembling a groove or fissure. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals). PATO:0001363 spiral quality helical helicoid helicoidal helix-shaped PATO:0000404 coiled A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals). WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature. quality plate-like PATO:0000407 flat A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature. web:http://www.merriam-webster.com/ A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. quality round rounded PATO:0000411 circular A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. thefreedictionary.com:thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. quality aberrant atypia atypical defective PATO:0000460 abnormal A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A quality denoting the lack of an entity. PATO:0001996 absence absent from organism quality PATO:0000462 We recommend using the new absent terms (physical absence, absent anatomical entity, or absent process) instead of this class. This is a legacy term and will ultimately be obsoleted. See https://github.com/pato-ontology/pato/issues/331. absent A quality denoting the lack of an entity. thefreedictionary.:thefreedictionary. A quality inhering in a bearer by virtue of the bearer's existence. quality present in organism PATO:0000467 present A quality inhering in a bearer by virtue of the bearer's existence. PATOC:GVG An amount which is relatively high. PATO:0000420 PATO:0000650 increased number present in greater numbers in organism supernumerary quality accessory increased PATO:0000470 increased amount An amount which is relatively high. PATOC:GVG A duration quality of a process which is relatively high. PATO:0000715 high time increased period increased time quality chronic prolonged period slow time PATO:0000498 increased duration A duration quality of a process which is relatively high. PATOC:GVG A duration quality of a process which is relatively low. PATO:0000716 decreased period decreased time low period shortened period quality fast time PATO:0000499 decreased duration A duration quality of a process which is relatively low. PATOC:GVG A quality of a process which starts later than the natural start time or the reference process. quality late PATO:0000502 delayed A quality of a process which starts later than the natural start time or the reference process. PATOC:LC A height which is relatively low. quality short PATO:0000569 decreased height A height which is relatively low. PATOC:GVG A height which is relatively high. quality tall PATO:0000570 increased height A height which is relatively high. PATOC:GVG A length quality which is relatively large. long quality PATO:0000573 increased length A length quality which is relatively large. PATOC:GVG A length quality which is relatively small. short quality shortened stubby PATO:0000574 decreased length A length quality which is relatively small. PATOC:GVG An increased size quality inhering in a bearer by virtue of the bearer's exhibiting enlargement of a cell or constituent group of cells (for example, organ). hypertrophy quality PATO:0000584 hypertrophic An increased size quality inhering in a bearer by virtue of the bearer's exhibiting enlargement of a cell or constituent group of cells (for example, organ). PATOC:MAH A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ). PATO:0000412 shrunken quality PATO:0000585 hypotrophic A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ). PATOC:MAH A size quality which is relatively high. PATO:0001202 quality big enlarged expanded great large PATO:0000586 increased size A size quality which is relatively high. PATOC:GVG A size quality which is relatively low. hypoplasia underdeveloped quality reduced small tiny PATO:0000587 decreased size A size quality which is relatively low. PATOC:GVG A volume which is relatively high. high volume quality large volume PATO:0000595 increased volume A volume which is relatively high. PATOC:GVG A volume which is relatively low. low volume quality small volume PATO:0000596 decreased volume A volume which is relatively low. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. quality blocked PATO:0000608 closed A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. answers.com:answers.com A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view. quality PATO:0000609 closure incomplete A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view. quality PATO:0000610 open A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view. answers.com:answers.com A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. focal localised quality PATO:0000627 localized A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. WordNet:WordNet A structural quality inhering in a bearer whose structure deteriorates or is lost over time due to an active pathological process. degeneration quality PATO:0000639 degenerate A structural quality inhering in a bearer whose structure deteriorates or is lost over time due to an active pathological process. PATOC:PortlandMeetingFeb2015 PATOC:mb A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells. dysplasia quality PATO:0000640 dysplastic A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells. PATOC:MAH A physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting a decreased number of cells, typically associated with a decrease in size. PATO:0000942 hypoplasia quality underdeveloped PATO:0000645 hypoplastic A physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting a decreased number of cells, typically associated with a decrease in size. PATOC:GVG Wikipedia:Hypoplasia A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation. malformation quality PATO:0000646 malformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation. PATOC:MAH A rate which is relatively low. slow rate quality PATO:0000911 decreased rate A rate which is relatively low. PATO:GVG A rate which is relatively high. fast rate high rate quality PATO:0000912 increased rate A rate which is relatively high. PATO:GVG A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. quality PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. PATOC:GVG A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. ellipse-shaped ellipsoid elliptical quality oval ovoid PATO:0000947 elliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. PATOC:GVG An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. quality PATO:0000957 opacity An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. PATOC:GVG A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. non-transparent quality clouding cloudy PATO:0000963 opaque A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. PATOC:GVG A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. clear hyaline quality PATO:0000964 transparent A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. PATOC:GVG A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. quality PATO:0000992 viscosity A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. PATOC:GVG A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. quality PATO:0000998 viscous A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. PATOC:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality density PATO:0001019 mass density A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. WordNet:WordNet A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. quality PATO:0001025 pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way. quality PATO:0001031 elasticity A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way. merriam-webster:merriam-webster A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. resistance quality PATO:0001046 resistance to A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. PATOC:GVG A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. quality PATO:0001164 dense A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. PATOC:GVG An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way. quality PATO:0001171 elastic An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way. merriam-webster:merriam-webster A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. resistant quality PATO:0001178 resistant to A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. PATOC:GVG A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed. quality PATO:0001190 juvenile A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed. thefreedictionary.com:thefreedictionary.com A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity. quality PATO:0001195 proximal to A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity. PATOC:nw A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG An EM radiation quality that is independent of the EM wavelength range. quality PATO:0001292 full-spectrum EM radiation quality An EM radiation quality that is independent of the EM wavelength range. PATOC:GVG A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation. quality PATO:0001294 radiation reflective quality A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation. PATOC:GVG A radiation reflective quality inhering in a bearer by virtue of the ratio of the energy of a wave reflected from its surface to the energy possessed by the wave striking the bearer's surface. quality PATO:0001297 reflectivity A radiation reflective quality inhering in a bearer by virtue of the ratio of the energy of a wave reflected from its surface to the energy possessed by the wave striking the bearer's surface. PATOC:GVG An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. quality PATO:0001300 optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. PATOC:GVG A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. quality PATO:0001374 ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. Wikipedia:http://en.wikipedia.org/wiki/Ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. quality PATO:0001375 haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. quality PATO:0001377 polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. quality PATO:0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Euploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. quality PATO:0001394 The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fraction of cells that are polyploidy. diploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. Wikipedia:http://en.wikipedia.org/wiki/Diploid A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATOC:GVG A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. quality PATO:0001397 cellular potency A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. PATOC:GVG A cellular potency that is the capacity to produce only one differentiated cell type. quality PATO:0001400 Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. unipotent A cellular potency that is the capacity to produce only one differentiated cell type. Wikipedia:http://en.wikipedia.org/wiki/Unipotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. quality PATO:0001401 Less potent than multipotent, often thought of as precursor or progenitor cell status. oligopotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. PATOC:MAH A cellular potency that is the capacity to form multiple differentiated cell types. quality PATO:0001402 multipotent A cellular potency that is the capacity to form multiple differentiated cell types. Wikipedia:http://en.wikipedia.org/wiki/Multipotent A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. quality PATO:0001405 anucleate A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. quality PATO:0001406 binucleate A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. Biology-online:Biology-online A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. quality PATO:0001408 ciliatedness A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. Wikipedia:http://en.wikipedia.org/wiki/Ciliated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. quality PATO:0001410 striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. Biology-online:Biology-online A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). calcareous calcification quality PATO:0001447 calcified A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). thefreedictionary.com:thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's being present in two copies. doubled quality PATO:0001473 duplicated A quality inhering in a bearer by virtue of the bearer's being present in two copies. Dictionary.com:Dictionary.com A position which is relatively high. quality high position PATO:0001475 increased position A position which is relatively high. PATOC:GVG A positional which is relatively low. quality low position PATO:0001476 decreased position A positional which is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. quality underdeveloped PATO:0001501 immature A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. Merriam-Webster:Merriam-Webster A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s). quality PATO:0001509 functionality A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s). PATOC:MAH A functionality quality held by the bearer when the latter is able to perform a regular function(s). quality PATO:0001510 functional A functionality quality held by the bearer when the latter is able to perform a regular function(s). PATOC:MAH A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. quality PATO:0001543 flexibility A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. merriam-webster:merriam-webster A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. bendy quality PATO:0001544 flexible A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. merriam-webster:merriam-webster A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. solidity quality PATO:0001546 quality of a solid A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. gaseous quality PATO:0001547 quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm PATOC:GVG A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. liquidity quality PATO:0001548 quality of a liquid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. url:http://www.chemistry-dictionary.com/definition/liquid.php The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. OBO_REL:has_part extra or missing physical or functional parts has or lacks parts of type mereological quality number of quality cardinality number PATO:0001555 has number of The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. PATOC:CJM A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. quality PATO:0001558 lacking processual parts A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. PATOC:GVG A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s). having supernumerary functions quality PATO:0001559 having extra function A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s). PATO:MAH A mass which is lower than normal or average. PATO:0000579 low mass small mass quality PATO:0001562 decreased mass A mass which is lower than normal or average. PATO:GVG A mass which is higher than normal or average. PATO:0000578 high mass large mass quality PATO:0001563 increased mass A mass which is higher than normal or average. PATO:GVG A quality of a process inhering in a bearer by virtue of the bearer's processual parts. quality PATO:0001564 extra or missing processual parts A quality of a process inhering in a bearer by virtue of the bearer's processual parts. PATOC:GVG A pressure which is relatively low. low pressure quality PATO:0001575 decreased pressure A pressure which is relatively low. PATO:GVG A pressure which is relatively high. high pressure quality PATO:0001576 increased pressure A pressure which is relatively high. PATO:GVG A physical quality that is the ability to contract or shrink. quality PATO:0001579 contractility A physical quality that is the ability to contract or shrink. WordNet:WordNet A contractility which is relatively high. high contractility quality PATO:0001580 increased contractility A contractility which is relatively high. PATO:GVG A contractility which is relatively low. low contractility quality PATO:0001581 decreased contractility A contractility which is relatively low. PATO:GVG A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. quality PATO:0001591 curvature A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. WordNet:WordNet A life span which is relatively high. high life span quality PATO:0001603 increased life span A life span which is relatively high. PATO:GVG A life span which is relatively low. low life span quality PATO:0001604 decreased life span A life span which is relatively low. PATO:GVG A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. quality disfigured distorted PATO:0001617 deformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. thefreedictionary.com:thefreedictionary.com A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting. atrophic quality PATO:0001623 atrophied A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting. Wiikipedia:Wasting Wikipedia:Atrophy A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s). PATO:0001556 PATO:0001568 PATO:0001641 PATO:0001642 dysfunction dysfunctional having decreased function lacks function of type low functionality partial functionality quality impaired PATO:0001624 decreased functionality A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s). PATO:MAH A functional quality held by the bearer when the latter exhibits increased ability to perform a regular function(s). high functionality quality PATO:0001625 increased functionality A functional quality held by the bearer when the latter exhibits increased ability to perform a regular function(s). PATO:MAH An 1-D extent quality which is equal to the length of the closed curve of a circle. quality PATO:0001648 circumference An 1-D extent quality which is equal to the length of the closed curve of a circle. WordNet:WordNet A resistance to a stimulus which is relatively high. high resistance to increased resistance quality PATO:0001650 increased resistance to A resistance to a stimulus which is relatively high. PATOC:GVG A resistance to a stimulus which is relatively low. decreased resistance low resistance to quality PATO:0001651 decreased resistance to A resistance to a stimulus which is relatively low. PATOC:GVG A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. quality PATO:0001690 This refers to the disposition of the bearer. contractile A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. PATOC:GVG A viscosity which relatively high. high viscosity quality PATO:0001693 increased viscosity A viscosity which relatively high. PATOC:GVG A viscosity which relatively low. low viscosity quality PATO:0001694 decreased viscosity A viscosity which relatively low. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size quality PATO:0001708 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size quality PATO:0001710 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. PATOC:GVG An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. quality PATO:0001711 perimeter An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. Wikipedia:http://en.wikipedia.org/wiki/Perimeter A perimeter which is relatively high. quality PATO:0001712 increased perimeter A perimeter which is relatively high. PATOC:GVG A perimeter which is relatively low. quality PATO:0001713 decreased perimeter A perimeter which is relatively low. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. liquid quality PATO:0001735 liquid configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. PATOC:GVG A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave. quality PATO:0001748 invaginated A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave. PATOC:GVG A flexibility which is relatively high. high flexibility quality PATO:0001776 increased flexibility A flexibility which is relatively high. PATOC:GVG A flexibility which is relatively low. low flexibility quality PATO:0001777 decreased flexibility A flexibility which is relatively low. PATOC:GVG A size quality inhering in a bearer by virtue of the bearer's being abnormally developed, usually due to malnutrition. dystrophied quality dystrophy PATO:0001780 dystrophic A size quality inhering in a bearer by virtue of the bearer's being abnormally developed, usually due to malnutrition. Wiikipedia:Wiikipedia A density which is higher relative to the normal or average. high density quality PATO:0001788 increased mass density A density which is higher relative to the normal or average. PATOC:GVG A density which is lower relative to the normal or average. low density quality PATO:0001790 decreased mass density A density which is lower relative to the normal or average. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops. quality PATO:0001794 coiling A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops. Online_Dictionary:Online_Dictionary A coiling which is relatively high. high coiling quality PATO:0001795 increased coiling A coiling which is relatively high. PATOC:GVG A coiling which is relatively low. low coiling quality PATO:0001796 decreased coiling A coiling which is relatively low. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. quality PATO:0001818 progressive A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. PATOC:GVG A shape quality in a bearer by virtue of the bearer's curving inward. quality PATO:0001857 concave A shape quality in a bearer by virtue of the bearer's curving inward. WordNet:WordNet A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. quality PATO:0001863 chronic A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. PATOC:cjm A quality inhering in a bearer by virtue of the bearer's being abnormal and having a destructive effect on living tissue. quality PATO:0001869 pathological A quality inhering in a bearer by virtue of the bearer's being abnormal and having a destructive effect on living tissue. PATOC:cjm A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATO:0001203 rod-like rod-shaped tubulate quality PATO:0001873 cylindrical A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATOC:MAH A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. disc-shaped disk-shaped quality PATO:0001874 discoid A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. PATOC:cjm A circumference which is relatively high. quality PATO:0001898 increased circumference A circumference which is relatively high. PATOC:GVG A circumference which is relatively low. quality PATO:0001899 decreased circumference A circumference which is relatively low. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. quality PATO:0001908 multinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance. sacular quality PATO:0001987 saccular A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance. PATOC:MAH An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. quality PATO:0001992 cellularity An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. PATOC:GVG A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. quality PATO:0001993 multicellular A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. PATOC:GVG A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM An amount which is relatively low. PATO:0000419 PATO:0000468 decreased number present in fewer numbers in organism quality decreased reduced subnumerary PATO:0001997 decreased amount An amount which is relatively low. PATOC:GVG The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. loss of quality PATO:0001999 lacks parts or has fewer parts of type The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. PATOC:CJM A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATO:0001557 OBO_REL:lacks_part lacks all physical parts of type quality PATO:0002000 Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2. lacks all parts of type A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATOC:CJM The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATO:0001569 decreased number of has decreased number of has fewer physical parts of type quality PATO:0002001 Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type. has fewer parts of type The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATOC:CJM The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATO:0001560 has extra parts of has increased number of having extra physical parts having supernumerary physical parts increased number of quality PATO:0002002 In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger. has extra parts of type The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATOC:CJM Surface shape that refers to the inward or outward curvature of the surface. quality PATO:0002005 concavity Surface shape that refers to the inward or outward curvature of the surface. PATOC:MAH A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. PATOC:CJM A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. quality PATO:0002009 branchiness A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. PATOC:MAH A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas. quality PATO:0002014 structure, cavities A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer exhibiting deterioration of its structure. 2009-02-03T11:13:19Z quality PATO:0002037 degeneration A structural quality inhering in a bearer by virtue of the bearer exhibiting deterioration of its structure. PATOC:GVG A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. quality PATO:0002039 biconcave A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. PATOC:GVG A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure. 2009-02-15T08:11:41Z dendriform dendroid dendroidal quality PATO:0002045 dendritic A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure. PATOC:cvs An occurrence which is relatively high. 2009-03-26T11:10:11Z increased incidence quality PATO:0002051 increased occurrence An occurrence which is relatively high. PATOC:GVG An occurrence which is relatively low. 2009-03-26T11:12:35Z decreased incidence quality PATO:0002052 decreased occurrence An occurrence which is relatively low. PATOC:GVG 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within. 2009-09-18T02:19:20Z quality PATO:0002078 hollow A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within. url:http://www.merriam-webster.com/dictionary/hollow Having extra or fewer parts. 2009-09-21T10:41:58Z quality PATO:0002083 altered number of Having extra or fewer parts. PATOC:GVG An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions. 2009-10-05T12:05:23Z quality PATO:0002094 basophilic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. 2009-10-06T04:37:14Z quality PATO:0002124 laminar A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's changed direction of position towards another entity. 2010-02-25T09:14:42Z quality PATO:0002175 spatial deviation A spatial quality inhering in a bearer by virtue of the bearer's changed direction of position towards another entity. PATO:GVG A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the side. 2010-02-25T09:16:04Z quality PATO:0002176 deviation towards the lateral side A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the side. PATOC:GVG A quality inhering in a bearer by virtue of its constitution. 2010-03-15T04:35:27Z quality PATO:0002198 quality of a substance A quality inhering in a bearer by virtue of its constitution. PATOC:GVG Shape quality inhering in a bearer by virtue of the bearer's being shaped like a wing. 2010-07-23T02:19:14Z wing-shaped quality PATO:0002236 aliform Shape quality inhering in a bearer by virtue of the bearer's being shaped like a wing. url:http://www.thefreedictionary.com/aliform A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane. 2010-08-16T03:59:34Z quality compressed PATO:0002254 Becoming flat but not necessarily completely flat. flattened A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane. PATOC:CVS Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels. 2010-09-01T10:27:48Z quality channeled creased PATO:0002255 grooved Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels. PATOC:JE A shape that inheres in a 3 dimensional entity. 2010-10-05T12:31:16Z quality PATO:0002266 3-D shape A shape that inheres in a 3 dimensional entity. PATOC:OREGON A mobility which is relative high. 2011-03-09T09:16:03Z quality PATO:0002282 increased mobility A mobility which is relative high. PATO:GVG A mobility which is relative low. 2011-03-09T09:16:47Z quality PATO:0002283 decreased mobility A mobility which is relative low. PATOC:GVG An elasticity which is relatively high. 2011-03-30T11:50:21Z quality PATO:0002287 increased elasticity An elasticity which is relatively high. PATOC:GVG An elasticity which is relatively low. 2011-03-30T11:50:39Z quality PATO:0002288 decreased elasticity An elasticity which is relatively low. PATOC:GVG 2011-04-18T05:11:33Z quality PATO:0002290 aplastic/hypoplastic A cylindrical shape that is hollow. 2011-06-08T06:33:50Z tube like tube-shaped tubulate quality PATO:0002299 tubular A cylindrical shape that is hollow. PATOC:GVG A quality that has a value that is increased compared to normal or average. 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. 2011-06-16T06:40:15Z quality PATO:0002301 decreased quality A quality that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is decreased compared to normal or average. 2011-06-16T06:50:59Z quality PATO:0002302 decreased process quality A quality of a process that has a value that is decreased compared to normal or average. PATOC:GVG A quality of an object that has a value that is decreased compared to normal or average. 2011-06-16T06:51:54Z quality PATO:0002303 decreased object quality A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is increased compared to normal or average. 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt 2011-10-12T12:45:16Z Lamé curve quality PATO:0002318 superelliptic A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt wiktionary:superellipse A temporal distribution pattern of process occurrences within a regulation/reference process. 2011-11-22T01:12:28Z quality PATO:0002323 temporal distribution quality A temporal distribution pattern of process occurrences within a regulation/reference process. PATOC:LC The temporal relation between the start of the process with respect to a reference process. 2011-11-23T11:47:34Z quality initiation PATO:0002325 onset quality The temporal relation between the start of the process with respect to a reference process. PATOC:LC An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions. 2012-12-17T03:01:19Z eosinophilic quality PATO:0002418 Eosin stains acidophilic structures, hence eosinophilic is the same as acidophilic. acidophilic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions. PATOC:GVG Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry. 2012-12-17T03:11:10Z quality PATO:0002422 Acinus is Latin for berry. acinar Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry. wikipedia:https://en.wikipedia.org/wiki/Acinus A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material. 2013-01-29T11:03:49Z quality PATO:0002444 mineralized A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material. PATOC:WC A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen. 2013-09-15T11:34:15Z quality PATO:0002462 collagenous A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen. PATOC:WD A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching. 2013-09-15T11:48:26Z quality PATO:0002468 distensible A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. 2013-09-15T12:29:15Z quality PATO:0002478 transversely striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. PATOC:DS A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. 2013-10-21T05:44:34Z quality PATO:0002505 nucleated A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. PATOC:GVG A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin. 2014-02-04T12:38:14Z quality PATO:0002507 keratinous A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin. PATOC:EJS A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other. 2014-12-12T08:43:17Z quality PATO:0010001 disconnected A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other. GOC:dos A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen. quality PATO:0015008 distensibility A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen. GOC:CJM A rate which is relatively normal. quality PATO:0045000 normal rate A quality of an object that has a value that is normal or average. 2017-12-21T14:11:01Z quality PATO:0045001 normal object quality A coiling which is normal or average. 2017-12-22T14:16:43Z quality PATO:0045009 normal coiling A contractility which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045011 normal contractility An elasticity which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045016 normal elasticity A flexibility which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045021 normal flexibility A life span which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045026 normal life span A mass which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045030 normal mass A density which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045031 normal mass density A mobility which is relatively normal or average. 2017-12-22T14:16:43Z quality PATO:0045032 normal mobility A position which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045040 normal position A pressure which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045044 normal pressure A resistance to a stimulus which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045047 normal resistance to A size quality which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045050 normal size A height which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045053 normal height A length quality which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045054 normal length A perimeter which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045057 normal perimeter A circumference which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045058 normal circumference A volume which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045060 normal volume A quality of a process that has a value that is normal or average. 2017-12-21T14:11:01Z quality PATO:0045073 normal process quality A viscosity which is relatively normal or average 2017-12-22T14:16:43Z quality PATO:0045081 normal viscosity A duration quality of a process which is relatively normal. quality PATO:0045084 normal duration An occurrence which is relatively normal. quality PATO:0045086 normal occurrence A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components. http://orcid.org/0000-0001-7258-9596 quality PATO:0070044 anatomical structure quality A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes. http://orcid.org/0000-0001-7258-9596 quality PATO:0070045 anatomical histological quality An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain. http://orcid.org/0000-0001-7258-9596 quality PATO:0070046 neutrophillic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain. GOC:add An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. http://orcid.org/0000-0001-7258-9596 quality PATO:0070047 polychromatophilic An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions. GOC:add A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. quality PATO:0070060 quality of interaction of a substance with electromagnetic radiation A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. https://orcid.org/0000-0002-5111-7263 A plant structure (PO:0005679) which is a whole organism. genet (broad) ramet (broad) FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 FNA:99508f62-7116-4e2b-90c0-19ff55ebd967 FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0 FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8 PO_GIT:538 PO_GIT:69 planta entera (Spanish, exact) 植物体全体 (Japanese, exact) bush (narrow) frutex (narrow) frutices (narrow) gametophyte (narrow) herb (narrow) liana (narrow) prothalli (narrow) prothallium (narrow) prothallus (narrow) seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) suffrutices (narrow) tree (narrow) vine (narrow) woody clump (narrow) plant_anatomy clonal colony (related) colony (related) PO:0000003 Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). whole plant A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003). PO_GIT:465 portion of ovule primordium tissue (exact) primordio de &#243vulo (Spanish, exact) 胚珠原基（可視的） (Japanese, exact) plant_anatomy PO:0000018 The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210). ovule primordium A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062). PO_GIT:465 pistil primordium (exact) portion of gynoecium primordium tissue (exact) primordio de gineceo (Spanish, exact) 雌蕊原基(可視的） (Japanese, exact) plant_anatomy PO:0000019 Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030). gynoecium primordium A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). PO_GIT:234 &#225pice del epiblasto (epiblastema) (Spanish, exact) シュート頂、茎頂 (Japanese, exact) plant_anatomy PO:0000037 shoot axis apex A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395). PO:0006329 PO:0006373 PO:0006374 PO:0025091 floral meristem (exact) mersitema floral (Spanish, exact) 花芽分裂組織 (Japanese, exact) Poaceae floret meristem (narrow) ear floret meristem (narrow) floret meristem (narrow) tassel floret meristem (narrow) plant_anatomy floral apical meristem (related) PO:0000229 In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). flower meristem A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. CL:0000034 PO_GIT:272 c&#233lula meristem&#225tica (Spanish, exact) stem cell (exact) 分裂組織細胞 (Japanese, exact) plant_anatomy PO:0004010 meristematic cell A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). PO_GIT:472 PO_GIT:583 meristema del epiblasto (epiblastema) (Spanish, exact) シュート分裂組織 (Japanese, exact) plant_anatomy PO:0006079 shoot system meristem A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). PO_GIT:125 portion of protoderm tissue (exact) protodermis (Spanish, exact) 前表皮、原表皮 (Japanese, exact) plant_anatomy dermatogen cell (related) PO:0006210 A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. protoderm A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs. PO_GIT:36 meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact) 生殖シュート頂端 分裂組織 (Japanese, exact) plant_anatomy PO:0008028 reproductive shoot apical meristem A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). PO:0020067 PO:0020068 PO:0020069 PO:0020070 PO:0020071 PO:0020072 PO:0020073 PO:0020074 PO:0020076 PO:0020077 PO:0020078 PO:0020079 PO:0020080 PO:0020082 PO:0020083 PO:0020087 PO:0020107 aggregate fruit (broad) compound fruit (broad) dehiscent fruit (broad) diaspore (broad) indehiscent fruit (broad) multiple fruit (broad) propagule (broad) FNA:67fa41ae-b735-4d89-b5db-7631b873ef7a FNA:c13b1312-1cc5-4ace-98e2-fde12aec09da PO_GIT:76 frucht (exact, German) fruto (exact, Spanish) 果実 (exact, Japanese) coenocarp (narrow) syncarp (narrow) plant_anatomy PO:0009001 A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. fruit https://en.wikipedia.org/wiki/Fruit_anatomy A cell which is a plant structure (PO:0009011). cell (broad) GO:0005623 PO_GIT:56 c&#233lula vegetal (Spanish, exact) 植物細胞 (Japanese, exact) plant_anatomy PO:0009002 Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. plant cell A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. FNA:02756ad4-a09c-48d7-8754-903254e557a9 FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 PO_GIT:135 sistema de epiblasto (epiblastema) (Spanish, exact) シュート系、苗条系 (Japanese, exact) tree crown (narrow) plant_anatomy Poaceae crown (related) shoot (related) thalli (related) thallus (related) PO:0009006 The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. shoot system A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. portion of tissue (broad) tissue (broad) PO_GIT:59 porci&#243n de un tejido vegetal (Spanish, exact) 植物組織の一部 (Japanese, exact) plant_anatomy plant tissue (related) PO:0009007 A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. portion of plant tissue A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. organ (broad) PATO:01503 PO_GIT:55 &#243rgano vegetal (Spanish, exact) 植物 器官 (Japanese, exact) plant_anatomy compound plant organ (related) simple plant organ (related) PO:0009008 Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). plant organ A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631). embryo (broad) PO_GIT:92 embri&#243n (Spanish, exact) 植物胚 (Japanese, exact) plant_anatomy germ (related) PO:0009009 A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010). plant embryo A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088). diaspore (broad) FNA:f5c50e73-61e3-48ec-b918-6f85b3f40738 PO_GIT:405 semilla (Spanish, exact) 種子 (Japanese, exact) pyrene (narrow) plant_anatomy PO:0009010 A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms). seed A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. PO_GIT:57 estructura vegetal (Spanish, exact) 植物 構造 (Japanese, exact) plant_anatomy PO:0009011 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. plant structure A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. PO:0007021 PO_GIT:185 TAIR:0000205 etapa de desarrollo de estructura vegetal (Spanish, exact) plant growth and development stage (exact) plant_structure_development_stage Arabidopsis growth (related) PO:0009012 Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. plant structure development stage A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. PO_GIT:472 meristem (exact) meristema (Spanish, exact) meristematic tissue (exact) 分裂組織 (Japanese, exact) plant_anatomy PO:0009013 portion of meristem tissue A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part. PO:0004541 PO_GIT:160 PO_GIT:259 flor (Spanish, exact) 花 (Japanese, exact) Asteraceae floret (narrow) basal flower (narrow) double flower (narrow) hermaphrodite flower (narrow) monoclinous flower (narrow) perfect flower (narrow) plant_anatomy floret (related) PO:0009046 The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form. flower A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046). PO:0006317 PO:0006357 PO:0006365 PO:0006384 PO:0006391 PO:0006394 PO:0006403 PO:0006404 PO:0006423 PO:0006424 PO:0006425 PO:0006426 PO:0025089 pistil (broad) PO_GIT:470 PO_GIT:71 PO_GIT:98 ginoecio (Spanish, exact) gynaecium (exact) gynoecia (exact, plural) 雌蕊群 (Japanese, exact) Poaceae gynoecium (narrow) Zea gynoecium (narrow) apocarpous gynoecium (narrow) gynoecium of ear floret (narrow) gynoecium of lower floret of pedicellate spikelet of ear (narrow) gynoecium of lower floret of pedicellate spikelet of tassel (narrow) gynoecium of lower floret of sessile spikelet of ear (narrow) gynoecium of lower floret of sessile spikelet of tassel (narrow) gynoecium of tassel floret (narrow) gynoecium of upper floret of pedicellate spikelet of ear (narrow) gynoecium of upper floret of pedicellate spikelet of tassel (narrow) gynoecium of upper floret of sessile spikelet of ear (narrow) gynoecium of upper floret of sessile spikelet of tassel (narrow) syncarpous gynoecium (narrow) plant_anatomy PO:0009062 If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). gynoecium A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006). PO:0006457 PO:0006491 PO_GIT:464 PO_GIT:70 &#243vulo vegetal (Spanish, exact) 胚珠 (Japanese, exact) Poaceae ovule (narrow) Zea ovule (narrow) plant_anatomy PO:0020003 A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352). plant ovule A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). promeristem (broad) PO_GIT:579 AM (exact) meristema apical (Spanish, exact) 頂端分裂組織 (Japanese, exact) plant_anatomy primary meristem (related) PO:0020144 apical meristem A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). promeristem (broad) PO_GIT:472 SAM (exact) meristema apical del epiblasto (epiblastema) (Spanish, exact) 茎頂分裂組織 (Japanese, exact) plant_anatomy primary shoot meristem (related) PO:0020148 shoot apical meristem An axial plant organ (PO:0009008). rwalls 2010-07-01T03:44:41Z eje de la planta (Spanish, exact) plant axes (exact, plural) 植物軸（軸柱） (Japanese, exact) plant_anatomy PO:0025004 Includes roots and shoots. plant axis A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). rwalls 2010-02-09T04:12:11Z PO_GIT:63 estructura vegetal colectiva de &#243rgano (Spanish, exact) 集合植物器官構造 (Japanese, exact) plant_anatomy PO:0025007 Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. collective plant organ structure A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005). Laurel_Cooper 2010-04-28T11:04:34Z PO:0008033 cycle (broad) verticil (broad) FNA:12607624-3d2a-4113-bd86-0e2557f2f473 FNA:d42df0a9-60f4-4c24-9c0b-ba815272f2fe GO:0048438 GO:0048457 GO:0048458 GO:0048459 PO_GIT:90 PO_GIT:99 estructura colectiva del filoma (Spanish, exact) 葉的器官が集まった構造 (Japanese, exact) floral whorl (narrow) whorl (narrow) plant_anatomy phyllome whorl (related) PO:0025023 collective phyllome structure A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). rwalls 2010-07-01T03:46:35Z caullome (exact) eje del epiblasto (epiblastema) (Spanish, exact) シュート軸 (Japanese, exact) plant_anatomy shoot (related) PO:0025029 Often bears leaves and branches. In vascular plants, has at least one node and one internode. shoot axis A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094). rwalls 2010-09-17T09:49:10Z sistema de brote reproductivo (Spanish, exact) 生殖シュート 系、苗条系 (Japanese, exact) plant_anatomy PO:0025082 reproductive shoot system A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009). rwalls 2010-11-05T01:36:24Z PO_GIT:245 PO_GIT:339 embryonic plant structure (exact) estructura vegetal embri&#243nica (Spanish, exact) 胚性植物構造 (Japanese, exact) plant_anatomy PO:0025099 Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle). embryo plant structure A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). rwalls 2010-11-15T09:10:22Z PO_GIT:186 portion of primordial tissue (exact) portion of primordium tissue (exact) primordia (exact, plural) primordio (Spanish, exact) 原基（可視的） (Japanese, exact) plant_anatomy PO:0025127 A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. primordium An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z PO_GIT:224 entidad anat&#243mica vegetal (Spanish, exact) 植物 解剖学（形態）的実体 (Japanese, exact) plant_anatomy PO:0025131 Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity A shoot apex that has as part a reproductive shoot apical meristem. rwalls 2010-12-20T08:47:03Z &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact) 生殖シュート頂、茎頂 (Japanese, exact) plant_anatomy PO:0025222 reproductive shoot apex A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009). rwalls 2010-12-20T12:27:10Z portion of embryo tissue (broad) PO_GIT:338 portion of embryonic plant tissue (exact) tejido embri&#243nico vegetal (Spanish, exact) 植物胚性組織 の一部 (Japanese, exact) plant_anatomy PO:0025233 This class is for tissues that only occur as part of an embryo. portion of embryo plant tissue A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497). rwalls 2011-10-19T11:12:49Z PO_GIT:391 etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact) 集合的植物構造の発生過程 (Japanese, exact) plant_structure_development_stage PO:0025338 Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). collective plant organ structure development stage A plant organ (PO:0009008) that is part of a flower (PO:0009046). rwalls 2012-01-19T11:44:36Z PO_GIT:423 &#243rgano floral (Spanish, exact) flower organ (exact) 花器官 (Japanese, exact) plant_anatomy PO:0025395 Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores. floral organ A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222). rwalls 2012-04-26T03:57:09Z PO_GIT:465 floral structure primordia (exact, plural) portion of floral structure primordium tissue (exact) primordio de organo floral (Spanish, exact) 花器官原基 (Japanese, exact) plant_anatomy PO:0025477 If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089). floral organ primordium A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. Laurel_Cooper 2012-06-11T14:57:00Z PO_GIT:480 estructura vegetal con m&#250ltiples tejidos (Spanish, exact) 複数の組織からなる植物構造 (Japanese, exact) plant_anatomy PO:0025496 Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. multi-tissue plant structure A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). Laurel_Cooper 2012-06-11T15:09:20Z PO_GIT:479 estructura vegetal colectiva (Spanish, exact) 集合的植物構造 (Japanese, exact) plant_anatomy PO:0025497 This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). collective plant structure A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death. Laurel_Cooper 2012-12-13T18:21:19Z PO_GIT:517 plant_structure_development_stage PO:0025527 The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003). shoot system development stage A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082). Laurel_Cooper 2012-12-13T19:01:14Z PO_GIT:517 plant_structure_development_stage PO:0025530 reproductive shoot system development stage A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). Laurel_Cooper 2014-05-13T16:51:47Z PO_GIT:586 plant_anatomy PO:0025606 A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). native plant cell A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085). indehiscent fruit (broad) PO_GIT:652 bacca (exact) baya (exact, Spanish) beere (exact, German) berry (exact) pyrine (narrow) plant_anatomy PO:0030108 Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera). berry fruit A berry fruit (PO:0030108) which develops from an inferior carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and fleshy endocarp (PO:0009086), and has as a part a hard receptacle (PO:0009064) which surrounds, and is indistinct from, the exocarp (PO:0009085). indehiscent fruit (broad) panzerbeere (broad, German) (broad) PO_GIT:652 kürbisfrucht (exact, German) pepo (exact) pepónide (exact, Spanish) plant_anatomy PO:0030111 A pepo fruit (PO:0030111) is specialized type of berry fruit (PO:0030108) which is encapsuled by persistent, accrescent receptacle (PO:0009064) tissue. The rind, or tough outer covering, of pepo fruits comprises receptical tissue and at least the exocarp (PO:0009085) layer of the pericarp (PO:0009084). Examples: pumpkin (Cucurbita pepo), cucumber (Cucumis sativus), and watermelon (Citrullus lanatus) and banana (Musa acuminata). pepo fruit An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein protein PR:000000001 The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. PRO:DAN PRO:WCB natural protein PRO:DAN native protein IEDB:BP A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. IUPHARobj:2764 PIRSF:PIRSF016630 B-lymphocyte surface antigen B4 CD19 T-cell surface antigen Leu-12 differentiation antigen CD19 protein PR:000001002 Category=gene. Requested by=CL. CD19 molecule A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction. PMID:15778510 CD19 PRO:DNx A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. PIRSF:PIRSF028749 CD34 hematopoietic progenitor cell antigen CD34 protein PR:000001003 Category=gene. Requested by=CL. CD34 molecule A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved. PMID:16720896 PMID:8983065 CD34 PRO:DNx A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. PIRSF:PIRSF001977 CD4 T-cell differentiation antigen L3T4 T-cell surface antigen T4/Leu-3 T-cell surface glycoprotein CD4 protein PR:000001004 Category=gene. Requested by=CL. CD4 molecule A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. PMID:15326605 CD4 PRO:DNx An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. PIRSF:PIRSF002497 integrin alpha with I domain protein PR:000001005 Category=family. integrin alpha with A domain An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage. PIRSF:PIRSF002497 A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. T200 IUPHARobj:1852 PIRSF:PIRSF002004 L-CA PTPRC leukocyte common antigen ly-5 lymphocyte antigen 5 protein CD45 PR:000001006 Category=gene. Requested by=CL. receptor-type tyrosine-protein phosphatase C A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule. PMID:1351092 PRO:CNA T200 PRO:DNx PTPRC PRO:DNx CD45 An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. IUPHARobj:2452 CD11 antigen-like family member B CD11b CR-3 alpha chain ITGAM cell surface glycoprotein MAC-1 subunit alpha leukocyte adhesion receptor MO1 neutrophil adherence receptor protein CD11B CR3A PR:000001012 Category=gene. Requested by=CL. integrin alpha-M An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1. UniProtKB:P11215 ITGAM PRO:DNx CD11B CR3A An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis. IUPHARobj:2454 CD11 antigen-like family member C CD11c ITGAX Leu M5 leukocyte adhesion glycoprotein p150,95 alpha chain leukocyte adhesion receptor p150,95 protein CD11C PR:000001013 Category=gene. Requested by=CL. integrin alpha-X An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis. UniProtKB:P20702 ITGAX PRO:DNx CD11C A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-3 or a 1:1 ortholog thereof. CD45RABC PTPRC/iso:CD45RABC protein B220 CD45R PR:000001014 Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exons 4(A), 5(B), and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RABC A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-3 or a 1:1 ortholog thereof. PMID:1351092 PRO:CNA PRO:DAN PTPRC/iso:CD45RABC PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45R that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8 or a 1:1 ortholog thereof. CD45RA PTPRC/iso:CD45RA protein PR:000001015 Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RA A receptor-type tyrosine-protein phosphatase C isoform CD45R that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8 or a 1:1 ortholog thereof. PMID:1351092 PRO:CNA PRO:DAN PTPRC/iso:CD45RA PRO:DNx A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. PIRSF:PIRSF001993 CD3 subunit with Ig-like domain protein PR:000001018 Category=family. CD3 subunit with immunoglobulin domain A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. PMID:16473826 PMID:1724736 A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. IUPHARobj:2742 CD3E CD3e T-cell surface antigen T3/Leu-4 epsilon chain protein T3E PR:000001020 Category=gene. Requested by=CL. CD3 epsilon A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof. PRO:CNA CD3E PRO:DNx T3E A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. PIRSF:PIRSF002507 protein PR:000001022 Category=family. neural cell adhesion molecule A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain. PRO:CNA A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. PIRSF:PIRSF501037 protein PR:000001023 Category=family. neural cell adhesion molecule NCAM A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration. PMID:17975827 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. IUPHARobj:2769 CD56 N-CAM-1 NCAM-1 NCAM1 protein NCAM PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof. PRO:CNA NCAM1 PRO:DNx NCAM A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. IUPHARobj:2600 PIRSF:PIRSF001984 CD2 LFA-2 LFA-3 receptor T-cell surface antigen CD2 T-cell surface antigen T11/Leu-5 T-cell surface glycoprotein CD2 erythrocyte receptor ly-37 lymphocyte antigen 37 rosette receptor protein SRBC PR:000001083 Category=gene. Requested by=CL. CD2 molecule A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof. PRO:CNA CD2 PRO:DNx SRBC A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. CD8A CD8a T-cell surface glycoprotein Lyt-2 T-lymphocyte differentiation antigen T8/Leu-2 protein Lyt-2 Lyt2 MAL PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain. PMID:11114424 PRO:CNA Wikipedia:CD8 CD8A PRO:DNx Lyt-2 Lyt2 MAL A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions. IUPHAR:GPCRListForward?class=A PIRSF:PIRSF800006 class 1 G-protein coupled receptor class A G-protein coupled receptor fam:rhodopsin protein PR:000001094 Category=family. Classification based on GRAFS system. [PMID:12761335] rhodopsin-like G-protein coupled receptor A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions. PMID:12761335 PRO:DAN PRO:WCB class 1 G-protein coupled receptor PMID:15914470 class A G-protein coupled receptor IUPHAR:GPCRListForward?class=A fam:rhodopsin PRO:DAN A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines. IUPHARfam:14 PIRSF:PIRSF038545 protein PR:000001128 Category=family. Note: Only those that have been unequivocally shown to activate a G-protein coupled signaling pathway appear on the official IUPHAR list. chemokine receptor A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines. PMID:12037138 PRO:WCB PRO:XQ A chemokine receptor that is a translation product of the human CCR1 or CCR3 genes, the mouse CCR1L1 gene, 1:1 orthologs thereof, or a semi-ortholog thereof. PIRSF:PIRSF501024 protein PR:000001197 Category=family. chemokine receptor CCR1/3/1L A chemokine receptor that is a translation product of the human CCR1 or CCR3 genes, the mouse CCR1L1 gene, 1:1 orthologs thereof, or a semi-ortholog thereof. PRO:DAN PRO:WCB A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. IUPHARobj:58 C-C CKR-1 CC-CKR-1 CCR-1 CCR1 CD191 HM145 LD78 receptor MIP-1alpha-R RANTES-R chemokine receptor CCR1 macrophage inflammatory protein 1-alpha receptor protein CMKBR1 CMKR1 SCYAR1 PR:000001254 Category=gene. Requested by=CL. C-C chemokine receptor type 1 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof. PRO:WCB CCR1 PRO:DNx CMKBR1 CMKR1 SCYAR1 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. IUPHARobj:60 C-C CKR-3 CC-CKR-3 CCR-3 CCR3 CD193 CKR3 MIP-1 alpha RL2 chemokine receptor CCR3 eosinophil eotaxin receptor macrophage inflammatory protein 1-alpha receptor-like 2 protein CMKBR3 Cmkbr1l2 PR:000001255 Category=gene. Requested by=CL. C-C chemokine receptor type 3 A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof. PMID:12037138 PRO:WCB CCR3 PRO:DNx CMKBR3 Cmkbr1l2 A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267). PIRSF:PIRSF005736 protein PR:000001281 Category=family. ADP-ribosyl cyclase A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267). PRO:WCB A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. IUPHARobj:2628 PIRSF:PIRSF001995 B-cell differentiation antigen Ly-44 B-cell surface antigen CD20 B-lymphocyte antigen CD20 B-lymphocyte surface antigen B1 Bp35 MS4A1 leukocyte surface antigen Leu-16 lymphocyte antigen 44 protein CD20 Ly-44 Ms4a2 PR:000001289 Category=gene. Requested by=CL. membrane-spanning 4-domains subfamily A member 1 A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof. PRO:WCB MS4A1 PRO:DNx CD20 Ly-44 Ms4a2 A protein that is a translation product of the human CD207 gene or a 1:1 ortholog thereof. CD207 langerin protein CLEC4K PR:000001293 Category=gene. Requested by=CL. C-type lectin domain family 4 member K A protein that is a translation product of the human CD207 gene or a 1:1 ortholog thereof. PRO:WCB CD207 PRO:DNx CLEC4K A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. CD44 CD44 antigen CDw44 ECMR-III GP90 lymphocyte homing/adhesion receptor HUTCH-I PGP-1 epican extracellular matrix receptor III heparan sulfate proteoglycan hermes antigen hyaluronate receptor ly-24 lymphocyte antigen 24 phagocytic glycoprotein 1 phagocytic glycoprotein I protein LHR MDU2 MDU3 MIC4 PGP-I PR:000001307 Category=gene. Requested by=CL. CD44 molecule A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof. PRO:WCB CD44 PRO:DNx LHR MDU2 MDU3 MIC4 A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof. PIRSF:PIRSF001973 B-lymphocyte activation marker BLAST-1 BCM1 surface antigen BLAST-1 CD48 CD48 antigen HM48-1 MRC OX-45 surface antigen SLAM family member 2 SLAMF2 TCT.1 leukocyte antigen MEM-102 sgp-60 signaling lymphocytic activation molecule 2 protein BCM1 BLAST1 Bcm-1 PR:000001308 Category=gene. Requested by=CL. CD48 molecule A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof. PRO:WCB CD48 PRO:DNx BCM1 BLAST1 Bcm-1 A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. PIRSF:PIRSF002504 protein PR:000001327 Category=family. cadherin A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues. PRO:WCB A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. CD66b CD67 antigen CEACAM8 carcinoembryonic antigen CGM6 non-specific cross-reacting antigen NCA-95 protein CGM6 PR:000001332 Category=gene. Requested by=CL. carcinoembryonic antigen-related cell adhesion molecule 8 A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof. PRO:CNA CEACAM8 PRO:DNx CGM6 A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. AIM BL-AC/P26 C-type lectin domain family 2 member C CD69 EA1 GP32/28 MLR-3 activation inducer molecule early T-cell activation antigen p60 early activation antigen CD69 leukocyte surface antigen Leu-23 protein CLEC2C PR:000001343 Category=gene. Requested by=CL. CD69 molecule A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets. PMID:10466080 PRO:CNA UniProtKB:Q07108 CD69 PRO:DNx CLEC2C A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. CD203c E-NPP 3 ENPP3 PD-Ibeta ectonucleotide pyrophosphatase/phosphodiesterase 3 phosphodiesterase I beta phosphodiesterase I/nucleotide pyrophosphatase 3 protein PDNP3 PR:000001344 Category=gene. Requested by=CL. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof. PRO:WCB ENPP3 PRO:DNx PDNP3 A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. IUPHARobj:2895 PIRSF:PIRSF038746 CD105 ENG cell surface MJ7/18 antigen protein END Edg PR:000001345 Category=gene. Requested by=CL. endoglin A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof. PRO:CNA ENG PRO:DNx END Edg A protein that is the stand alone version of the Gamma-glutamyltranspeptidase (Pfam:PF01019) domain. The functional protein catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate), and consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. PIRSF:PIRSF000457 protein PR:000001351 Category=family. gamma-glutamyltranspeptidase A protein that is the stand alone version of the Gamma-glutamyltranspeptidase (Pfam:PF01019) domain. The functional protein catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate), and consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. InterPro:IPR000101 PRO:CNA A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. PIRSF:PIRSF001980 protein PR:000001355 Category=family. immunoglobulin gamma Fc receptor II/III/IV A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III. PRO:WCB A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof. p55 IUPHARobj:1695 PIRSF:PIRSF001954 CD25 IL-2 receptor subunit alpha IL-2-RA IL-2R subunit alpha IL2-RA IL2RA TAC antigen protein Il2r PR:000001380 Category=gene. Requested by=CL. interleukin-2 receptor subunit alpha A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof. PRO:CNA p55 PRO:DNx IL2RA PRO:DNx Il2r A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. p75 IUPHARobj:1696 CD122 IL-2 receptor subunit beta IL-2R subunit beta IL-2RB IL2RB high affinity IL-2 receptor subunit beta p70-75 protein IL15RB PR:000001381 Category=gene. Requested by=CL. interleukin-2 receptor subunit beta A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof. PRO:CNA p75 PRO:DNx IL2RB PRO:DNx IL15RB A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif. PIRSF:PIRSF002419 protein PR:000001403 Category=family. tetraspanin A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif. PRO:WCB Wikipedia:Tetraspanin An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. IUPHARobj:2766 2'-phospho-ADP-ribosyl cyclase 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase 2'-phospho-cyclic-ADP-ribose transferase ADP-ribosyl cyclase 1 ADPRC 1 CD38 I-19 NIM-R5 antigen T10 cADPr hydrolase 1 cyclic ADP-ribose hydrolase 1 protein PR:000001408 Category=gene. Requested by=CL. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof. PRO:WCB CD38 PRO:DNx A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. 7B4 antigen CD144 CDH5 VE-cadherin vascular endothelial cadherin protein PR:000001444 Category=gene. Requested by=CL. cadherin-5 A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof. PRO:WCB CDH5 PRO:DNx An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. CD32 Fc gamma receptor IIB Fc-gamma RII Fc-gamma-RIIB FcRII Fcgr2 IgG Fc receptor II beta ly-17 lymphocyte antigen 17 protein Fcgr2b PR:000001479 Category=gene. Requested by=CL. low affinity immunoglobulin gamma Fc region receptor II An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof. PRO:CNA CD32 PRO:DNx Fcgr2 PRO:DNx Fcgr2b An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. CD16 Fc-gamma RIII FcRIII Fcgr3 IgG Fc receptor III protein PR:000001483 Category=gene. Requested by=CL. low affinity immunoglobulin gamma Fc region receptor III An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof. PRO:CNA Fcgr3 PRO:DNx A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. PANTHER:PTHR22730 PIRSF:PIRSF017831 protein PR:000001785 Category=family. prominin A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. InterPro:IPR008795 PMID:11467842 A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. CD133 PROM1 antigen AC133 antigen AC133 homolog prominin-like protein 1 protein MSTP061 PROML1 Prom PR:000001786 Category=gene. Requested by=CL. prominin-1 A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof. PRO:CNA PROM1 PRO:DNx MSTP061 PROML1 Prom A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof. 5'-NT ecto-5'-nucleotidase IUPHARobj:1232 CD73 IMP-specific 5'-nucleotidase NT5E thymidylate 5'-phosphatase protein NT5 NTE PR:000001800 Category=gene. Requested by=CL. 5'-nucleotidase A protein that is a translation product of the human NT5E gene or a 1:1 ortholog thereof. PRO:WCB NT5E PRO:DNx NT5 NTE A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof. PIRSF:PIRSF038782 CD59-like protein PR:000001809 Category=gene. Requested by=CL. Pro-orthology refers to, in this case, after-speciation gene duplication in the non-human species (aka 1:many orthology). This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues. CD59-like glycoprotein A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof. PRO:WCB CD59-like PRO:DNx A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines. PIRSF:PIRSF000615 protein PR:000001810 Category=family. CSF-1/PDGF receptor-type tyrosine-protein kinase A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines. PRO:WCB A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof. CD150 CDw150 IPO-3 SLAMF1 protein SLAM PR:000001833 Category=gene. Requested by=CL. SLAM family member 1 A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof. PRO:WCB SLAMF1 PRO:DNx SLAM A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. PIRSF:PIRSF038791 CD7 GP40 T-cell antigen CD7 T-cell leukemia antigen T-cell surface antigen Leu-9 TP41 protein PR:000001836 Category=gene. Requested by=CL. CD7 molecule A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof. PRO:WCB CD7 PRO:DNx A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. CD5 Lyt-1 ly-1 lymphocyte antigen 1 lymphocyte antigen T1/Leu-1 protein LEU1 PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof. PRO:WCB CD5 PRO:DNx LEU1 A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. PIRSF:PIRSF038777 CD90 CDw90 THY1 Thy-1 antigen protein Thy-1 PR:000001843 Category=gene. Requested by=CL. Thy-1 membrane glycoprotein A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof. PRO:WCB THY1 PRO:DNx Thy-1 A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725). PIRSF:PIRSF002512 protein PR:000001861 Category=family. integrin beta A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725). PRO:WCB A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. IUPHARobj:1705 CD123 IL-3 receptor subunit alpha IL-3R subunit alpha IL-3R-alpha IL-3RA IL3RA interleukin-3 receptor class II alpha chain protein IL3R Sut-1 PR:000001865 Category=gene. Requested by=CL. interleukin-3 receptor class 2 alpha chain A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof. PRO:WCB IL3RA PRO:DNx IL3R Sut-1 A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. IUPHARobj:1706 PIRSF:PIRSF018419 CD125 CDw125 IL-5 receptor subunit alpha IL-5R subunit alpha IL-5R-alpha IL-5RA IL5RA protein IL5R PR:000001867 Category=gene. Requested by=CL. interleukin-5 receptor subunit alpha A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof. PRO:WCB IL5RA PRO:DNx IL5R A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. IUPHARobj:1698 PIRSF:PIRSF001960 CD127 CDw127 IL-7 receptor subunit alpha IL-7R subunit alpha IL-7R-alpha IL-7RA IL7R protein PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof. PRO:WCB IL7R PRO:DNx A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. PIRSF:PIRSF038804 protein PR:000001874 Category=family. Requested by=CL. KLRB1-like protein A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat. PRO:WCB A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. PIRSF:PIRSF001994 B-cell differentiation antigen LP-3 GALGP SPN galactoglycoprotein leukocyte sialoglycoprotein ly-48 lymphocyte antigen 48 sialophorin protein CD43 PR:000001879 Category=gene. Requested by=CL. leukosialin A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof. PRO:WCB SPN PRO:DNx CD43 A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. PIRSF:PIRSF002017 CD14 monocyte differentiation antigen CD14 myeloid cell-specific leucine-rich glycoprotein protein PR:000001889 Category=gene. Requested by=CL. CD14 molecule A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof. PRO:WCB CD14 PRO:DNx A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. IUPHARobj:2601 CD33 gp67 myeloid cell surface antigen CD33 sialic acid-binding Ig-like lectin 3 siglec-3 protein SIGLEC3 PR:000001892 Category=gene. Requested by=CL. CD33 molecule A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof. PRO:WCB CD33 PRO:DNx SIGLEC3 A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof. CD244 NAIL NK cell activation-inducing ligand NK cell type I receptor protein 2B4 NKR2B4 SLAM family member 4 SLAMF4 non-MHC restricted killing associated signaling lymphocytic activation molecule 4 protein 2B4 Nmrk PR:000001896 Category=gene. Requested by=CL. natural killer cell receptor 2B4 A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof. PRO:WCB CD244 PRO:DNx 2B4 Nmrk A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. IUPHARobj:1611 PIRSF:PIRSF501074 CALLA CD10 MME NEP SFE atriopeptidase common acute lymphocytic leukemia antigen enkephalinase neutral endopeptidase neutral endopeptidase 24.11 skin fibroblast elastase protein EPN PR:000001898 Category=gene. Requested by=CL. neprilysin A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof. PRO:WCB MME PRO:DNx EPN A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. B-cell-specific transcription factor BSAP PAX5 protein Pax-5 PR:000001903 Category=gene. Requested by=CL. paired box protein PAX-5 A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof. PRO:WCB PAX5 PRO:DNx Pax-5 A protein that is a translation product of the human CD163 gene or a 1:1 ortholog thereof. CD163 hemoglobin scavenger receptor protein M130 PR:000001925 Category=gene. Requested by=CL. scavenger receptor cysteine-rich type 1 protein M130 A protein that is a translation product of the human CD163 gene or a 1:1 ortholog thereof. PRO:WCB CD163 PRO:DNx M130 A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. CD24 HSA M1/69-J11D heat stable antigen R13-Ag X62 heat stable antigen ly-52 lymphocyte antigen 52 nectadrin small cell lung carcinoma cluster 4 antigen protein CD24A PR:000001932 Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL. signal transducer CD24 A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof. PRO:WCB CD24 PRO:DNx CD24A A protein that is a translation product of the human SDC1 gene or a 1:1 ortholog thereof. PIRSF:PIRSF015854 CD138 SDC1 SYND1 protein SDC Synd-1 PR:000001935 Category=gene. Requested by=CL. syndecan-1 A protein that is a translation product of the human SDC1 gene or a 1:1 ortholog thereof. PRO:WCB SDC1 PRO:DNx SDC Synd-1 A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. 31 kDa-transforming protein SFFV proviral integration 1 protein SPI1 protein Sfpi-1 Sfpi1 PR:000001944 Category=gene. Requested by=CL. transcription factor PU.1 A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof. PRO:WCB SPI1 PRO:DNx Sfpi-1 Sfpi1 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. p90 CD71 T9 TFRC TfR TfR1 protein TR Trfr PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof. PRO:WCB p90 PRO:DNx TFRC PRO:DNx Trfr A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. TRAP PIRSF:PIRSF016527 CD154 CD40-L CD40LG T-cell antigen Gp39 TNF-related activation protein protein CD40L TNFSF5 PR:000001950 Category=gene. Requested by=CL. tumor necrosis factor ligand superfamily member 5 A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof. PRO:WCB TRAP PRO:DNx CD40LG PRO:DNx CD40L TNFSF5 A protein that is a translation product of the human CD27 gene or a 1:1 ortholog thereof. IUPHARobj:1876 PIRSF:PIRSF001966 CD27 CD27L receptor T-cell activation antigen CD27 tumor necrosis factor receptor superfamily member 7 protein T14 TNFRSF7 PR:000001963 Category=gene. Requested by=CL. CD27 molecule A protein that is a translation product of the human CD27 gene or a 1:1 ortholog thereof. PRO:WCB CD27 PRO:DNx TNFRSF7 A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. PIRSF:PIRSF002022 CD87 PLAUR U-PAR monocyte activation antigen Mo3 uPAR protein MO3 UPAR PR:000001969 Category=gene. Requested by=CL. urokinase plasminogen activator surface receptor A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof. PRO:WCB PLAUR PRO:DNx MO3 UPAR A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PIRSF:PIRSF038502 protein PR:000001971 Category=family. vascular endothelial growth factor receptor A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain. PRO:WCB A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof. IUPHARobj:1807 PIRSF:PIRSF500949 FL cytokine receptor FLK-2 FLT-3 FLT3 Fms-like tyrosine kinase 3 fetal liver kinase 2 stem cell tyrosine kinase 1 tyrosine-protein kinase FLT3 tyrosine-protein kinase receptor FLT3 tyrosine-protein kinase receptor flk-2 protein CD135 FLK2 STK-1 STK1 PR:000002001 Category=gene. Requested by=CL. receptor-type tyrosine-protein kinase FLT3 A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof. PRO:WCB FLT3 PRO:DNx CD135 FLK2 STK1 A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. IUPHARobj:1805 PIRSF:PIRSF500951 CD117 KIT proto-oncogene c-Kit tyrosine-protein kinase Kit protein SCFR Sl PR:000002065 Category=gene. Requested by=CL. mast/stem cell growth factor receptor A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof. PRO:WCB KIT PRO:DNx SCFR Sl A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. IUPHARobj:1813 CD309 FLK-1 KDR VEGFR-2 fetal liver kinase 1 kinase NYK kinase insert domain receptor protein-tyrosine kinase receptor flk-1 protein FLK1 VEGFR2 PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof. PRO:WCB KDR PRO:DNx FLK1 VEGFR2 A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). PIRSF:PIRSF002021 protein PR:000002976 Category=family. Ly-6-like protein A protein that is the translation product of any of the LY6 genes (LY6A-LY6I). PRO:CNA A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof. CD161 antigen-like family member C CD161c Klrb1c NK1.1 NKR-P1 40 NKR-P1.9 NKR-P1C ly-55c lymphocyte antigen 55c natural killer cell surface protein P1-40 protein Ly55c Nkrp1c PR:000002977 Category=gene. Requested by=CL. killer cell lectin-like receptor subfamily B member 1C A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof. PRO:CNA Klrb1c PRO:DNx Ly55c Nkrp1c An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. Ly-6G Ly-6G.1 Ly6g protein PR:000002978 Category=gene. Requested by=CL. lymphocyte antigen 6G An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof. PRO:CNA Ly6g PRO:DNx An Ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof. Ly-6A.2/Ly-6E.1 Ly6a T-cell-activating protein stem cell antigen 1 protein Ly6 SCA-1 TAP PR:000002979 Category=gene. Requested by=CL. lymphocyte antigen 6A-2/6E-1 An Ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof. PRO:CNA Ly6a PRO:DNx Ly6 An Ly-6-like protein that is a translation product of the mouse Ly6c2 gene or a 1:1 ortholog thereof. Ly-6C2 Ly6c2 protein Ly6c PR:000002980 Category=gene. Requested by=CL. lymphocyte antigen 6C2 An Ly-6-like protein that is a translation product of the mouse Ly6c2 gene or a 1:1 ortholog thereof. PRO:CNA Ly6c2 PRO:DNx Ly6c A protein that is a translation product of the Ly76 gene in mouse. mLy76 ter-119 ter119 protein PR:000002981 Category=organism-gene. Requested by=CL. lymphocyte antigen 76 (mouse) A protein that is a translation product of the Ly76 gene in mouse. PMID:10848813 PRO:DAN mLy76 PRO:DNx A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof. RAG-1 RAG1 RING finger protein 74 protein RNF74 PR:000003457 Category=gene. Requested by=CL. V(D)J recombination-activating protein 1 A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof. PRO:CNA RAG1 PRO:DNx RNF74 A protein that is a translation product of the human RAG2 gene or a 1:1 ortholog thereof. RAG-2 RAG2 protein PR:000003460 Category=gene. Requested by=CL. V(D)J recombination-activating protein 2 A protein that is a translation product of the human RAG2 gene or a 1:1 ortholog thereof. PRO:CNA RAG2 PRO:DNx A protein that is a translation product of the human AFP gene or a 1:1 ortholog thereof. AFP alpha-1-fetoprotein alpha-fetoglobulin protein HPAFP PR:000003809 Category=gene. alpha-fetoprotein A protein that is a translation product of the human AFP gene or a 1:1 ortholog thereof. PRO:DNx AFP PRO:DNx HPAFP A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof. ALB serum albumin protein Alb-1 Alb1 GIG20 GIG42 PRO0903 PRO1708 PRO2044 PRO2619 PRO2675 UNQ696/PRO1341 PR:000003918 Category=gene. albumin A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof. PRO:DNx ALB PRO:DNx Alb-1 Alb1 GIG20 GIG42 PRO0903 PRO1708 PRO2044 PRO2619 PRO2675 UNQ696/PRO1341 A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. p24 5H9 antigen CD9 CD9 antigen MRP-1 cell growth-inhibiting gene 2 protein leukocyte antigen MIC3 motility-related protein tetraspanin-29 tspan-29 protein GIG2 MIC3 TSPAN29 PR:000005178 Category=gene. Requested by=CL. CD9 molecule A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof. PRO:DNx p24 PRO:DNx CD9 PRO:DNx GIG2 MIC3 TSPAN29 A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. C/EBP alpha CEBPA protein CEBP PR:000005307 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein alpha A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof. PRO:DNx CEBPA PRO:DNx CEBP A protein that is a translation product of the human CGA gene or a 1:1 ortholog thereof. CG-alpha CGA FSH-alpha LSH-alpha TSH-alpha anterior pituitary glycoprotein hormones common subunit alpha choriogonadotropin alpha chain chorionic gonadotrophin subunit alpha follicle-stimulating hormone alpha chain follitropin alpha chain luteinizing hormone alpha chain lutropin alpha chain thyroid-stimulating hormone alpha chain thyrotropin alpha chain protein PR:000005388 Category=gene. glycoprotein hormones alpha chain A protein that is a translation product of the human CGA gene or a 1:1 ortholog thereof. PRO:DNx CGA PRO:DNx A protein that is a translation product of the mouse Cd200r3 gene or a 1:1 ortholog thereof. CD200 cell surface glycoprotein receptor-like 3 CD200 cell surface glycoprotein receptor-like b CD200 receptor-like 3 CD200RLb Cd200r3 cell surface glycoprotein OX2 receptor 3 protein PR:000006169 Category=gene. Requested by=CL. cell surface glycoprotein CD200 receptor 3 A protein that is a translation product of the mouse Cd200r3 gene or a 1:1 ortholog thereof. PRO:DNx Cd200r3 PRO:DNx A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. DNTT terminal addition enzyme terminal deoxynucleotidyltransferase terminal transferase protein TDT PR:000006611 Category=gene. Requested by=CL. DNA nucleotidylexotransferase A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof. PRO:DNx DNTT PRO:DNx TDT An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. IUPHARobj:2933 FCER1A Fc-epsilon RI-alpha IgE Fc receptor subunit alpha protein FCE1A FcERI PR:000007431 Category=gene. Requested by=CL. high affinity immunoglobulin epsilon receptor subunit alpha An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof. PRO:DNx FCER1A PRO:DNx FCE1A A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof. FGF-8 FGF8 androgen-induced growth factor protein AIGF HBGF-8 heparin-binding growth factor 8 PR:000007499 Category=gene. fibroblast growth factor 8 A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof. PRO:DNx FGF8 PRO:DNx AIGF A protein that is a translation product of the human FOXN1 gene or a 1:1 ortholog thereof. IUPHARobj:2958 FOXN1 HNF-3/forkhead homolog 11 winged-helix transcription factor nude protein Fkh19 HFH-11 Hfh11 RONU WHN hepatocyte nuclear factor 3 forkhead homolog 11 PR:000007636 Category=gene. forkhead box protein N1 A protein that is a translation product of the human FOXN1 gene or a 1:1 ortholog thereof. PRO:DNx FOXN1 PRO:DNx Fkh19 Hfh11 RONU WHN A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. Eryf1 GATA-1 GATA-binding factor 1 GATA1 NF-E1 DNA-binding protein protein ERYF1 GF-1 GF1 PR:000007857 Category=gene. Requested by=CL. erythroid transcription factor A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof. PRO:DNx GATA1 PRO:DNx ERYF1 GF1 A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. GATA-binding protein 2 GATA2 protein PR:000007858 Category=gene. Requested by=CL. endothelial transcription factor GATA-2 A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof. PRO:DNx GATA2 PRO:DNx A protein that is a translation product of the human GOT1 gene or a 1:1 ortholog thereof. AAT ASAT AST AspAT SGO-T SGOT aspartate aminotransferase aspartate transaminase serum glutamic oxaloacetic transaminase transaminase A GOT1 cAST cAspAT cCAT cysteine aminotransferase, cytoplasmic cysteine transaminase, cytoplasmic glutamate oxaloacetate transaminase 1 protein PR:000008153 Category=gene. Note: This form is predominantly found in red blood cells and heart in humans. aspartate aminotransferase, cytoplasmic A protein that is a translation product of the human GOT1 gene or a 1:1 ortholog thereof. PRO:DNx AAT Wikipedia:Aspartate_transaminase ASAT Wikipedia:Aspartate_transaminase AST Wikipedia:Aspartate_transaminase AspAT Wikipedia:Aspartate_transaminase SGO-T Wikipedia:Aspartate_transaminase SGOT Wikipedia:Aspartate_transaminase aspartate aminotransferase Wikipedia:Aspartate_transaminase aspartate transaminase Wikipedia:Aspartate_transaminase serum glutamic oxaloacetic transaminase Wikipedia:Aspartate_transaminase transaminase A PRO:DNx GOT1 PRO:DNx cAST Wikipedia:Aspartate_transaminase A protein that is a translation product of the human GOT2 gene or a 1:1 ortholog thereof. AAT ASAT AST AspAT SGO-T SGOT aspartate aminotransferase aspartate transaminase fatty acid-binding protein serum glutamic oxaloacetic transaminase transaminase A FABP-1 FABPpm GOT2 glutamate oxaloacetate transaminase 2 kynurenine aminotransferase 4 kynurenine aminotransferase IV kynurenine--oxoglutarate transaminase 4 kynurenine--oxoglutarate transaminase IV mAST mAspAT plasma membrane-associated fatty acid-binding protein protein Got-2 KYAT4 PR:000008154 Category=gene. Note: This form is predominantly found in the liver in humans. aspartate aminotransferase, mitochondrial A protein that is a translation product of the human GOT2 gene or a 1:1 ortholog thereof. PRO:DNx AAT Wikipedia:Aspartate_transaminase ASAT Wikipedia:Aspartate_transaminase AST Wikipedia:Aspartate_transaminase AspAT Wikipedia:Aspartate_transaminase SGO-T Wikipedia:Aspartate_transaminase SGOT Wikipedia:Aspartate_transaminase aspartate aminotransferase Wikipedia:Aspartate_transaminase aspartate transaminase Wikipedia:Aspartate_transaminase fatty acid-binding protein PRO:DNx serum glutamic oxaloacetic transaminase Wikipedia:Aspartate_transaminase transaminase A PRO:DNx GOT2 PRO:DNx mAST Wikipedia:Aspartate_transaminase Got-2 KYAT4 A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof. HP protein PR:000008725 Category=gene. haptoglobin A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof. PRO:DNx HP PRO:DNx An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. insulin INS protein PR:000009054 Category=gene. insulin gene translation product An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof. PRO:DNx insulin PRO:DAN INS PRO:DNx An integrin alpha lacking A domain that is a translation product of the human ITGA2B gene or a 1:1 ortholog thereof. IUPHARobj:2441 CD41 GPIIb GPalpha IIb ITGA2B platelet membrane glycoprotein IIb protein GP2B ITGAB PR:000009127 Category=gene. Requested by=CL. integrin alpha-IIb An integrin alpha lacking A domain that is a translation product of the human ITGA2B gene or a 1:1 ortholog thereof. PRO:DNx ITGA2B PRO:DNx GP2B ITGAB An integrin beta that is a translation product of the human ITGB7 gene or a 1:1 ortholog thereof. IUPHARobj:2461 Gut homing receptor beta subunit ITGB7 M290 IEL antigen integrin beta-P protein PR:000009143 Category=gene. Requested by=CL. integrin beta-7 An integrin beta that is a translation product of the human ITGB7 gene or a 1:1 ortholog thereof. PRO:DNx ITGB7 PRO:DNx A protein that is a translation product of the human LTF gene or a 1:1 ortholog thereof. LTF lactoferrin talalactoferrin protein GIG12 LF PR:000009978 Category=gene. Requested by=CL. lactotransferrin A protein that is a translation product of the human LTF gene or a 1:1 ortholog thereof. PRO:DNx LTF PRO:DNx GIG12 LF A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof. HHG-1 SHH Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains ShhNC protein Hhg1 PR:000014841 Category=gene. sonic hedgehog protein A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof. PRO:DNx SHH PRO:DNx Hhg1 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. T-cell leukemia/lymphoma protein 5 TAL-1 TAL1 bHLHa17 class A basic helix-loop-helix protein 17 stem cell protein protein BHLHA17 SCL TCL5 PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof. PRO:DNx TAL1 PRO:DNx BHLHA17 SCL TCL5 A protein that is a translation product of the human TMED1 gene or a 1:1 ortholog thereof. TMED1 interleukin-1 receptor-like 1 ligand p24 family protein gamma-1 p24gamma1 putative T1/ST2 receptor-binding protein protein IL1RL1L IL1RL1LG PR:000016401 Category=gene. Requested by=CL. transmembrane emp24 domain-containing protein 1 A protein that is a translation product of the human TMED1 gene or a 1:1 ortholog thereof. PRO:DNx TMED1 PRO:DNx IL1RL1L IL1RL1LG A glycoprotein hormone beta chain that is a translation product of the human TSHB gene or a 1:1 ortholog thereof. TSH-B TSH-beta TSHB thyroid-stimulating hormone subunit beta thyrotropin alfa thyrotropin beta chain protein PR:000016724 Category=gene. thyrotropin subunit beta A glycoprotein hormone beta chain that is a translation product of the human TSHB gene or a 1:1 ortholog thereof. PRO:DNx TSHB PRO:DNx 2 An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. peptide polypeptide protein PR:000018263 Category=polymer. amino acid chain An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. PRO:DAN PRO:JSG peptide PRO:DAN polypeptide PRO:DAN A protein that is produced as the result of proteolytic processing of a longer protein. ClvPrd peptide polypeptide protein PR:000018264 proteolytic cleavage product A protein that is produced as the result of proteolytic processing of a longer protein. PRO:DAN ClvPrd PRO:DAN peptide PRO:DAN polypeptide PRO:DAN A CD19 molecule that has had the signal peptide removed. CD19/SigPep- protein PR:000018300 Category=modification. CD19 molecule, signal peptide removed form A CD19 molecule that has had the signal peptide removed. PRO:DNx CD19/SigPep- PRO:DNx A CD34 molecule that has had the signal peptide removed. CD34/SigPep- protein PR:000018302 Category=modification. CD34 molecule, signal peptide removed form A CD34 molecule that has had the signal peptide removed. PRO:DNx CD34/SigPep- PRO:DNx A CD4 molecule that has had the signal peptide removed. CD4/SigPep- protein PR:000018304 Category=modification. CD4 molecule, signal peptide removed form A CD4 molecule that has had the signal peptide removed. PRO:DNx CD4/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C that has had the signal peptide removed. PTPRC/SigPep- protein PR:000018306 Category=modification. receptor-type tyrosine-protein phosphatase C, signal peptide removed form A receptor-type tyrosine-protein phosphatase C that has had the signal peptide removed. PRO:DNx PTPRC/SigPep- PRO:DNx An integrin alpha-M that has had the signal peptide removed. ITGAM/SigPep- protein PR:000018315 Category=modification. integrin alpha-M, signal peptide removed form An integrin alpha-M that has had the signal peptide removed. PRO:DNx ITGAM/SigPep- PRO:DNx An integrin alpha-X that has had the signal peptide removed. ITGAX/SigPep- protein PR:000018317 Category=modification. integrin alpha-X, signal peptide removed form An integrin alpha-X that has had the signal peptide removed. PRO:DNx ITGAX/SigPep- PRO:DNx A CD3 epsilon that has had the signal peptide removed. CD3E/SigPep- protein PR:000018321 Category=modification. CD3 epsilon, signal peptide removed form A CD3 epsilon that has had the signal peptide removed. PRO:DNx CD3E/SigPep- PRO:DNx A neural cell adhesion molecule 1 that has had the signal peptide removed. NCAM1/SigPep- protein PR:000018325 Category=modification. neural cell adhesion molecule 1, signal peptide removed form A neural cell adhesion molecule 1 that has had the signal peptide removed. PRO:DNx NCAM1/SigPep- PRO:DNx A CD2 molecule that has had the signal peptide removed. CD2/SigPep- protein PR:000018333 Category=modification. CD2 molecule, signal peptide removed form A CD2 molecule that has had the signal peptide removed. PRO:DNx CD2/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 alpha chain that has had the signal peptide removed. CD8A/SigPep- protein PR:000018335 Category=modification. T-cell surface glycoprotein CD8 alpha chain, signal peptide removed form A T-cell surface glycoprotein CD8 alpha chain that has had the signal peptide removed. PRO:DNx CD8A/SigPep- PRO:DNx A CD48 molecule that has had the signal peptide removed. CD48/SigPep- protein PR:000018380 Category=modification. CD48 molecule, signal peptide removed form A CD48 molecule that has had the signal peptide removed. PRO:DNx CD48/SigPep- PRO:DNx A CD48 molecule that has been processed by proteolytic cleavage. CD48/ClvPrd protein PR:000018381 Category=modification. CD48 molecule proteolytic cleavage product A CD48 molecule that has been processed by proteolytic cleavage. PRO:DNx CD48/ClvPrd PRO:DNx A carcinoembryonic antigen-related cell adhesion molecule 8 that has had the signal peptide removed. CEACAM8/SigPep- protein PR:000018405 Category=modification. carcinoembryonic antigen-related cell adhesion molecule 8, signal peptide removed form A carcinoembryonic antigen-related cell adhesion molecule 8 that has had the signal peptide removed. PRO:DNx CEACAM8/SigPep- PRO:DNx A carcinoembryonic antigen-related cell adhesion molecule 8 that has been processed by proteolytic cleavage. CEACAM8/ClvPrd protein PR:000018406 Category=modification. carcinoembryonic antigen-related cell adhesion molecule 8 proteolytic cleavage product A carcinoembryonic antigen-related cell adhesion molecule 8 that has been processed by proteolytic cleavage. PRO:DNx CEACAM8/ClvPrd PRO:DNx An endoglin that has had the signal peptide removed. ENG/SigPep- protein PR:000018420 Category=modification. endoglin, signal peptide removed form An endoglin that has had the signal peptide removed. PRO:DNx ENG/SigPep- PRO:DNx An interleukin-2 receptor subunit alpha that has had the signal peptide removed. IL2RA/SigPep- protein PR:000018444 Category=modification. interleukin-2 receptor subunit alpha, signal peptide removed form An interleukin-2 receptor subunit alpha that has had the signal peptide removed. PRO:DNx IL2RA/SigPep- PRO:DNx An interleukin-2 receptor subunit beta that has had the signal peptide removed. IL2RB/SigPep- protein PR:000018446 Category=modification. interleukin-2 receptor subunit beta, signal peptide removed form An interleukin-2 receptor subunit beta that has had the signal peptide removed. PRO:DNx IL2RB/SigPep- PRO:DNx A low affinity immunoglobulin gamma Fc region receptor II that has had the signal peptide removed. Fcgr2/SigPep- protein PR:000018508 Category=modification. low affinity immunoglobulin gamma Fc region receptor II, signal peptide removed form A low affinity immunoglobulin gamma Fc region receptor II that has had the signal peptide removed. PRO:DNx Fcgr2/SigPep- PRO:DNx A 5'-nucleotidase that has had the signal peptide removed. NT5E/SigPep- protein PR:000018523 Category=modification. 5'-nucleotidase, signal peptide removed form A 5'-nucleotidase that has had the signal peptide removed. PRO:DNx NT5E/SigPep- PRO:DNx A 5'-nucleotidase that has been processed by proteolytic cleavage. NT5E/ClvPrd protein PR:000018524 Category=modification. 5'-nucleotidase proteolytic cleavage product A 5'-nucleotidase that has been processed by proteolytic cleavage. PRO:DNx NT5E/ClvPrd PRO:DNx A CD7 molecule that has had the signal peptide removed. CD7/SigPep- protein PR:000018537 Category=modification. CD7 molecule, signal peptide removed form A CD7 molecule that has had the signal peptide removed. PRO:DNx CD7/SigPep- PRO:DNx A T-cell surface glycoprotein CD5 that has had the signal peptide removed. CD5/SigPep- protein PR:000018539 Category=modification. T-cell surface glycoprotein CD5, signal peptide removed form A T-cell surface glycoprotein CD5 that has had the signal peptide removed. PRO:DNx CD5/SigPep- PRO:DNx A Thy-1 membrane glycoprotein that has had the signal peptide removed. THY1/SigPep- protein PR:000018545 Category=modification. Thy-1 membrane glycoprotein, signal peptide removed form A Thy-1 membrane glycoprotein that has had the signal peptide removed. PRO:DNx THY1/SigPep- PRO:DNx A Thy-1 membrane glycoprotein that has been processed by proteolytic cleavage. THY1/ClvPrd protein PR:000018546 Category=modification. Thy-1 membrane glycoprotein proteolytic cleavage product A Thy-1 membrane glycoprotein that has been processed by proteolytic cleavage. PRO:DNx THY1/ClvPrd PRO:DNx An interleukin-5 receptor subunit alpha that has had the signal peptide removed. IL5RA/SigPep- protein PR:000018555 Category=modification. interleukin-5 receptor subunit alpha, signal peptide removed form An interleukin-5 receptor subunit alpha that has had the signal peptide removed. PRO:DNx IL5RA/SigPep- PRO:DNx An interleukin-7 receptor subunit alpha that has had the signal peptide removed. IL7R/SigPep- protein PR:000018559 Category=modification. interleukin-7 receptor subunit alpha, signal peptide removed form An interleukin-7 receptor subunit alpha that has had the signal peptide removed. PRO:DNx IL7R/SigPep- PRO:DNx A leukosialin that has had the signal peptide removed. SPN/SigPep- protein PR:000018567 Category=modification. leukosialin, signal peptide removed form A leukosialin that has had the signal peptide removed. PRO:DNx SPN/SigPep- PRO:DNx A CD14 molecule that has had the signal peptide removed. CD14/SigPep- protein PR:000018574 Category=modification. CD14 molecule, signal peptide removed form A CD14 molecule that has had the signal peptide removed. PRO:DNx CD14/SigPep- PRO:DNx A natural killer cell receptor 2B4 that has had the signal peptide removed. CD244/SigPep- protein PR:000018580 Category=modification. natural killer cell receptor 2B4, signal peptide removed form A natural killer cell receptor 2B4 that has had the signal peptide removed. PRO:DNx CD244/SigPep- PRO:DNx A scavenger receptor cysteine-rich type 1 protein M130 that has been processed by proteolytic cleavage. CD163/ClvPrd protein PR:000018594 Category=modification. scavenger receptor cysteine-rich type 1 protein M130 proteolytic cleavage product A scavenger receptor cysteine-rich type 1 protein M130 that has been processed by proteolytic cleavage. PRO:DNx CD163/ClvPrd PRO:DNx A signal transducer CD24 that has had the signal peptide removed. CD24/SigPep- protein PR:000018598 Category=modification. signal transducer CD24, signal peptide removed form A signal transducer CD24 that has had the signal peptide removed. PRO:DNx CD24/SigPep- PRO:DNx A transferrin receptor protein 1 that has been processed by proteolytic cleavage. TFRC/ClvPrd protein PR:000018603 Category=modification. transferrin receptor protein 1 proteolytic cleavage product A transferrin receptor protein 1 that has been processed by proteolytic cleavage. PRO:DNx TFRC/ClvPrd PRO:DNx A tumor necrosis factor ligand superfamily member 5 that has been processed by proteolytic cleavage. CD40LG/ClvPrd protein PR:000018606 Category=modification. tumor necrosis factor ligand superfamily member 5 proteolytic cleavage product A tumor necrosis factor ligand superfamily member 5 that has been processed by proteolytic cleavage. PRO:DNx CD40LG/ClvPrd PRO:DNx A CD27 molecule that has had the signal peptide removed. CD27/SigPep- protein PR:000018620 Category=modification. CD27 molecule, signal peptide removed form A CD27 molecule that has had the signal peptide removed. PRO:DNx CD27/SigPep- PRO:DNx A urokinase plasminogen activator surface receptor that has had the signal peptide removed. PLAUR/SigPep- protein PR:000018628 Category=modification. urokinase plasminogen activator surface receptor, signal peptide removed form A urokinase plasminogen activator surface receptor that has had the signal peptide removed. PRO:DNx PLAUR/SigPep- PRO:DNx A lymphocyte antigen 6A-2/6E-1 that has had the signal peptide removed. Ly6a/SigPep- protein PR:000018773 Category=modification. lymphocyte antigen 6A-2/6E-1, signal peptide removed form A lymphocyte antigen 6A-2/6E-1 that has had the signal peptide removed. PRO:DNx Ly6a/SigPep- PRO:DNx A lymphocyte antigen 6C2 that has had the signal peptide removed. Ly6c2/SigPep- protein PR:000018775 Category=modification. lymphocyte antigen 6C2, signal peptide removed form A lymphocyte antigen 6C2 that has had the signal peptide removed. PRO:DNx Ly6c2/SigPep- PRO:DNx An alpha-fetoprotein that has had the signal peptide removed. AFP/SigPep- protein PR:000018921 Category=modification. alpha-fetoprotein, signal peptide removed form An alpha-fetoprotein that has had the signal peptide removed. PRO:DNx AFP/SigPep- PRO:DNx An albumin that has had the signal peptide removed. ALB/SigPep- protein PR:000018949 Category=modification. albumin, signal peptide removed form An albumin that has had the signal peptide removed. PRO:DNx ALB/SigPep- PRO:DNx An albumin that has been processed by proteolytic cleavage. ALB/ClvPrd protein PR:000018950 Category=modification. albumin proteolytic cleavage product An albumin that has been processed by proteolytic cleavage. PRO:DNx ALB/ClvPrd PRO:DNx A glycoprotein hormones alpha chain that has had the signal peptide removed. CGA/SigPep- protein PR:000019321 Category=modification. glycoprotein hormones alpha chain, signal peptide removed form A glycoprotein hormones alpha chain that has had the signal peptide removed. PRO:DNx CGA/SigPep- PRO:DNx A high affinity immunoglobulin epsilon receptor subunit alpha that has had the signal peptide removed. FCER1A/SigPep- protein PR:000019856 Category=modification. high affinity immunoglobulin epsilon receptor subunit alpha, signal peptide removed form A high affinity immunoglobulin epsilon receptor subunit alpha that has had the signal peptide removed. PRO:DNx FCER1A/SigPep- PRO:DNx A haptoglobin that has had the signal peptide removed. HP/SigPep- protein PR:000020179 Category=modification. haptoglobin, signal peptide removed form A haptoglobin that has had the signal peptide removed. PRO:DNx HP/SigPep- PRO:DNx A haptoglobin that has been processed by proteolytic cleavage. HP/ClvPrd protein PR:000020180 Category=modification. haptoglobin proteolytic cleavage product A haptoglobin that has been processed by proteolytic cleavage. PRO:DNx HP/ClvPrd PRO:DNx An insulin gene translation product that has had the signal peptide removed. Proinsulin consists of the insulin B and A chains linked by the C-peptide. Example: UniProtKB:P01308, 25-110. INS/SigPep- insulin, signal peptide removed form protein PR:000020310 Category=modification. proinsulin An insulin gene translation product that has had the signal peptide removed. Proinsulin consists of the insulin B and A chains linked by the C-peptide. Example: UniProtKB:P01308, 25-110. PRO:DAN INS/SigPep- PRO:DNx insulin, signal peptide removed form PRO:DNx An integrin alpha-IIb that has had the signal peptide removed. ITGA2B/SigPep- protein PR:000020328 Category=modification. integrin alpha-IIb, signal peptide removed form An integrin alpha-IIb that has had the signal peptide removed. PRO:DNx ITGA2B/SigPep- PRO:DNx An integrin alpha-IIb that has been processed by proteolytic cleavage. ITGA2B/ClvPrd protein PR:000020329 Category=modification. integrin alpha-IIb proteolytic cleavage product An integrin alpha-IIb that has been processed by proteolytic cleavage. PRO:DNx ITGA2B/ClvPrd PRO:DNx An integrin beta-7 that has had the signal peptide removed. ITGB7/SigPep- protein PR:000020347 Category=modification. integrin beta-7, signal peptide removed form An integrin beta-7 that has had the signal peptide removed. PRO:DNx ITGB7/SigPep- PRO:DNx A lactotransferrin that has had the signal peptide removed. LTF/SigPep- protein PR:000020496 Category=modification. lactotransferrin, signal peptide removed form A lactotransferrin that has had the signal peptide removed. PRO:DNx LTF/SigPep- PRO:DNx A lactotransferrin that has been processed by proteolytic cleavage. LTF/ClvPrd protein PR:000020497 Category=modification. lactotransferrin proteolytic cleavage product A lactotransferrin that has been processed by proteolytic cleavage. PRO:DNx LTF/ClvPrd PRO:DNx A sonic hedgehog protein that has had the signal peptide removed. SHH/SigPep- protein PR:000021467 Category=modification. sonic hedgehog protein, signal peptide removed form A sonic hedgehog protein that has had the signal peptide removed. PRO:DNx SHH/SigPep- PRO:DNx A sonic hedgehog protein that has been processed by proteolytic cleavage. SHH/ClvPrd protein PR:000021468 Category=modification. sonic hedgehog protein proteolytic cleavage product A sonic hedgehog protein that has been processed by proteolytic cleavage. PRO:DNx SHH/ClvPrd PRO:DNx A thyrotropin subunit beta that has had the signal peptide removed. TSHB/SigPep- protein PR:000021741 Category=modification. thyrotropin subunit beta, signal peptide removed form A thyrotropin subunit beta that has had the signal peptide removed. PRO:DNx TSHB/SigPep- PRO:DNx A thyrotropin subunit beta that has been processed by proteolytic cleavage. TSHB/ClvPrd protein PR:000021742 Category=modification. thyrotropin subunit beta proteolytic cleavage product A thyrotropin subunit beta that has been processed by proteolytic cleavage. PRO:DNx TSHB/ClvPrd PRO:DNx A protein that is a translation product of the Escherichia coli K-12 phoA gene or a 1:1 ortholog thereof. APase phoA protein PR:000023540 Category=gene. alkaline phosphatase A protein that is a translation product of the Escherichia coli K-12 phoA gene or a 1:1 ortholog thereof. PRO:DNx phoA PRO:DNx An alkaline phosphatase that has had the signal peptide removed. phoA/SigPep- protein PR:000024649 Category=modification. alkaline phosphatase, signal peptide removed form An alkaline phosphatase that has had the signal peptide removed. PRO:DNx phoA/SigPep- PRO:DNx A CD2 molecule that has been processed by proteolytic cleavage. CD2/ClvPrd protein PR:000025455 Category=modification. CD2 molecule proteolytic cleavage product A CD2 molecule that has been processed by proteolytic cleavage. PRO:DNx CD2/ClvPrd PRO:DNx A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. protein PR:000025796 Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575]. integrin alpha A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif. PMID:19693543 An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains. PIRSF:PIRSF005666 fam:ITGAsansA protein PR:000025797 Category=family. integrin alpha lacking A domain An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains. PRO:DAN fam:ITGAsansA PRO:DAN A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that has had the signal peptide removed. PTPRC/iso:CD45RABC/SigPep- protein PR:000025805 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RABC, signal peptide removed form A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that has had the signal peptide removed. PRO:DAN PTPRC/iso:CD45RABC/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RA that has had the signal peptide removed. PTPRC/iso:CD45RA/SigPep- protein PR:000025806 Category=modification. receptor-type tyrosine-protein phosphatase C isoform CD45RA, signal peptide removed form A receptor-type tyrosine-protein phosphatase C isoform CD45RA that has had the signal peptide removed. PMID:1351092 PRO:CNA PTPRC/iso:CD45RA/SigPep- PRO:DNx A transmembrane emp24 domain-containing protein 1 that has had the signal peptide removed. TMED1/SigPep- protein PR:000026631 Category=modification. transmembrane emp24 domain-containing protein 1, signal peptide removed form A transmembrane emp24 domain-containing protein 1 that has had the signal peptide removed. PRO:DNx TMED1/SigPep- PRO:DNx A protein that is a translation product of the human CALCA gene or a 1:1 ortholog thereof. CALCA protein CALC PR:000027222 Category=gene. CALCA gene translation product A protein that is a translation product of the human CALCA gene or a 1:1 ortholog thereof. MGI:2151253 PRO:CNA CALCA PRO:DNx A CALCA gene translation product that is encoded in the genome of mouse. mCALCA protein PR:000027223 Category=organism-gene. CALCA gene translation product (mouse) A CALCA gene translation product that is encoded in the genome of mouse. MGI:2151253 PRO:HJD mCALCA PRO:DNx A CALCA gene translation product that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P01258-1 or a 1:1 ortholog thereof. CALCA/iso:1 protein PR:000027224 Category=sequence. calcitonin isoform 1 A CALCA gene translation product that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P01258-1 or a 1:1 ortholog thereof. PMID:8806650 PRO:CNA CALCA/iso:1 PRO:DNx An integrin alpha-M, signal peptide removed form in human. Example: UniProtKB:P11215-1, 17-1152. Reactome:R-HSA-202757 Reactome:R-HSA-6799647 Reactome:R-HSA-6800979 hITGAM/SigPep- PRO_0000016289 UniProtKB:P11215-1, 17-1152 protein PR:000027393 Category=organism-modification. integrin alpha-M, signal peptide removed form (human) An integrin alpha-M, signal peptide removed form in human. Example: UniProtKB:P11215-1, 17-1152. PRO:DNx Reactome:R-HSA-202757 PR:000027393 located_in GO:0005886 Reactome:R-HSA-6799647 PR:000027393 located_in GO:0035579 Reactome:R-HSA-6800979 PR:000027393 located_in GO:0070821 hITGAM/SigPep- PRO:DNx PRO_0000016289 PRO:DNx UniProtKB:P11215-1, 17-1152 PRO:DNx 1 1 A protein-containing complex that is a heterodimer of an alpha subunit (CGA) common to several glycoprotein hormones and a beta subunit (TSHB) unique to thyroid stimulating hormone. TSH thyrotropin protein PR:000028269 Category=complex. Requested by=GOC. thyroid stimulating hormone A protein-containing complex that is a heterodimer of an alpha subunit (CGA) common to several glycoprotein hormones and a beta subunit (TSHB) unique to thyroid stimulating hormone. PRO:MSY An integrin alpha-IIb, signal peptide removed form in human. Example: UniProtKB:P08514-1, 32-1039. Reactome:R-HSA-57578 hITGA2B/SigPep- PRO_0000016275 UniProtKB:P08514-1, 32-1039 protein PR:000028409 Category=organism-modification. integrin alpha-IIb, signal peptide removed form (human) An integrin alpha-IIb, signal peptide removed form in human. Example: UniProtKB:P08514-1, 32-1039. PRO:DNx Reactome:R-HSA-57578 PR:000028409 located_in GO:0005886 hITGA2B/SigPep- PRO:DNx PRO_0000016275 PRO:DNx UniProtKB:P08514-1, 32-1039 PRO:DNx A CD4 molecule, signal peptide removed form in human. UniProtKB:P01730, 26-458. Reactome:R-HSA-167542 Reactome:R-HSA-180575 Reactome:R-HSA-182147 Reactome:R-HSA-8869082 PRO_0000014621 UniProtKB:P01730, 26-458 hCD4/SigPep- protein PR:000028418 Category=organism-modification. CD4 molecule, signal peptide removed form (human) A CD4 molecule, signal peptide removed form in human. UniProtKB:P01730, 26-458. PRO:DNx Reactome:R-HSA-167542 PR:000028418 located_in GO:0005886 Reactome:R-HSA-180575 PR:000028418 located_in GO:0005789 Reactome:R-HSA-182147 PR:000028418 located_in GO:0005769 Reactome:R-HSA-8869082 PR:000028418 located_in GO:0030665 PRO_0000014621 PRO:DNx UniProtKB:P01730, 26-458 PRO:DNx hCD4/SigPep- PRO:DNx A proteolytic cleavage product that is derived from any of the casein milk proteins. CN (f) protein PR:000028527 Category=modification. casein derived peptide A proteolytic cleavage product that is derived from any of the casein milk proteins. PRO:DAN CN (f) PRO:DAN A protein that is encoded in the genome of Mus musculus. mouse protein protein PR:000029032 Mus musculus protein A protein that is encoded in the genome of Mus musculus. PRO:DAN mouse protein PRO:DAN A protein that is encoded in the genome of Homo sapiens. human protein protein PR:000029067 Homo sapiens protein A protein that is encoded in the genome of Homo sapiens. PRO:DAN human protein PRO:DAN A CALCA gene translation product that is encoded in the genome of human. CALC1 (human) CGRP-I (human) alpha-type CGRP (human) calcitonin gene-related peptide I (human) hCALCA protein PR:000030026 Category=organism-gene. CALCA gene translation product (human) A CALCA gene translation product that is encoded in the genome of human. PRO:DNx UniProtKB:P06881 CALC1 (human) UniProtKB:P06881 CGRP-I (human) UniProtKB:P06881 alpha-type CGRP (human) UniProtKB:P06881 calcitonin gene-related peptide I (human) UniProtKB:P06881 hCALCA PRO:DNx A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit. 7TM receptor seven-transmembrane receptor IUPHARfam:694 fam:GPCR protein PR:000030035 Category=family. Classification based on GRAFS system. [PMID:12761335] G-protein coupled receptor A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit. IUPHARfam:694 PRO:DAN Wikipedia:GPCR 7TM receptor IUPHARfam:694 seven-transmembrane receptor IUPHARfam:694 fam:GPCR PRO:DAN A protein that is encoded in the genome of some Eukaryota. Eukaryota protein protein PR:000036194 eukaryotic protein A protein that is encoded in the genome of some Eukaryota. PRO:DAN Eukaryota protein PRO:DAN A sonic hedgehog protein, signal peptide removed form in mouse. UniProtKB:Q62226, 25-437. PRO_0000013211 UniProtKB:Q62226, 25-437 mSHH/SigPep- protein PR:000037272 Category=organism-modification. sonic hedgehog protein, signal peptide removed form (mouse) A sonic hedgehog protein, signal peptide removed form in mouse. UniProtKB:Q62226, 25-437. PMID:18794898 PRO:CNA PRO_0000013211 PRO:DNx UniProtKB:Q62226, 25-437 PRO:DNx mSHH/SigPep- PRO:DNx A protein that has a core domain composition consisting of a signal peptide followed by a single copy of the Cys_knot (Pfam:PF00007) domain. The Cysteine knot is a protein structural motif containing three disulfide bridges. PANTHER:PTHR11515 protein PR:000044813 Category=family. glycoprotein hormone beta chain A protein that has a core domain composition consisting of a signal peptide followed by a single copy of the Cys_knot (Pfam:PF00007) domain. The Cysteine knot is a protein structural motif containing three disulfide bridges. PRO:CNA Pfam:PF00007 A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide. fam:INS protein PR:000045358 Category=family. insulin family protein A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide. PRO:DAN fam:INS PRO:DAN An albumin (human) that has had the signal peptide removed. UniProtKB:P02768, 19-609. Reactome:R-HSA-114609 UniProtKB:P02768, 19-609 hALB/SigPep- protein PR:000046307 Category=organism-modification. albumin, signal peptide removed form (human) An albumin (human) that has had the signal peptide removed. UniProtKB:P02768, 19-609. PRO:DNx Reactome:R-HSA-114609 Reactome:R-HSA-114609 PR:000046307 located_in GO:0005576 UniProtKB:P02768, 19-609 PRO:DNx hALB/SigPep- PRO:DNx A scavenger receptor cysteine-rich type 1 protein M130 (human) that has had the signal peptide removed. UniProtKB:Q86VB7, 42-1156. Reactome:R-HSA-2168868 Reactome:R-HSA-2230974 PRO_0000238938 UniProtKB:Q86VB7, 42-1156 hCD163/SigPep- protein PR:000046610 Category=organism-modification. scavenger receptor cysteine-rich type 1 protein M130, signal peptide removed form (human) A scavenger receptor cysteine-rich type 1 protein M130 (human) that has had the signal peptide removed. UniProtKB:Q86VB7, 42-1156. PRO:DNx Reactome:R-HSA-2168868 Reactome:R-HSA-2230974 Reactome:R-HSA-2168868 PR:000046610 located_in GO:0005886 Reactome:R-HSA-2230974 PR:000046610 located_in GO:0030666 PRO_0000238938 PRO:DNx UniProtKB:Q86VB7, 42-1156 PRO:DNx hCD163/SigPep- PRO:DNx A B-lymphocyte antigen CD19 (human) that has had the signal peptide removed. UniProtKB:P15391, 20-556. Reactome:R-HSA-197740 PRO_0000014648 UniProtKB:P15391, 20-556 hCD19/SigPep- protein PR:000046612 Category=organism-modification. B-lymphocyte antigen CD19, signal peptide removed form (human) A B-lymphocyte antigen CD19 (human) that has had the signal peptide removed. UniProtKB:P15391, 20-556. PRO:DNx Reactome:R-HSA-197740 Reactome:R-HSA-197740 PR:000046612 located_in GO:0005886 PRO_0000014648 PRO:DNx UniProtKB:P15391, 20-556 PRO:DNx hCD19/SigPep- PRO:DNx A T-cell surface antigen CD2 (human) that has had the signal peptide removed. UniProtKB:P06729, 25-351. Reactome:R-HSA-197795 PRO_0000014600 UniProtKB:P06729, 25-351 hCD2/SigPep- protein PR:000046618 Category=organism-modification. T-cell surface antigen CD2, signal peptide removed form (human) A T-cell surface antigen CD2 (human) that has had the signal peptide removed. UniProtKB:P06729, 25-351. PRO:DNx Reactome:R-HSA-197795 Reactome:R-HSA-197795 PR:000046618 located_in GO:0005886 PRO_0000014600 PRO:DNx UniProtKB:P06729, 25-351 PRO:DNx hCD2/SigPep- PRO:DNx A natural killer cell receptor 2B4 (human) that has had the signal peptide removed. UniProtKB:Q9BZW8, 22-370. Reactome:R-HSA-197846 PRO_0000014668 UniProtKB:Q9BZW8, 22-370 hCD244/SigPep- protein PR:000046624 Category=organism-modification. natural killer cell receptor 2B4, signal peptide removed form (human) A natural killer cell receptor 2B4 (human) that has had the signal peptide removed. UniProtKB:Q9BZW8, 22-370. PRO:DNx Reactome:R-HSA-197846 Reactome:R-HSA-197846 PR:000046624 located_in GO:0005886 PRO_0000014668 PRO:DNx UniProtKB:Q9BZW8, 22-370 PRO:DNx hCD244/SigPep- PRO:DNx A CD27 antigen (human) that has had the signal peptide removed. UniProtKB:P26842, 20-260. Reactome:R-HSA-5666994 PRO_0000034571 UniProtKB:P26842, 20-260 hCD27/SigPep- protein PR:000046625 Category=organism-modification. CD27 antigen, signal peptide removed form (human) A CD27 antigen (human) that has had the signal peptide removed. UniProtKB:P26842, 20-260. PRO:DNx Reactome:R-HSA-5666994 Reactome:R-HSA-5666994 PR:000046625 located_in GO:0005886 PRO_0000034571 PRO:DNx UniProtKB:P26842, 20-260 PRO:DNx hCD27/SigPep- PRO:DNx A myeloid cell surface antigen CD33 (human) that has had the signal peptide removed. UniProtKB:P20138, 18-364. Reactome:R-HSA-197719 Reactome:R-HSA-6799615 Reactome:R-HSA-6800959 PRO_0000014878 UniProtKB:P20138, 18-364 hCD33/SigPep- protein PR:000046634 Category=organism-modification. myeloid cell surface antigen CD33, signal peptide removed form (human) A myeloid cell surface antigen CD33 (human) that has had the signal peptide removed. UniProtKB:P20138, 18-364. PRO:DNx Reactome:R-HSA-197719 Reactome:R-HSA-197719 PR:000046634 located_in GO:0005886 Reactome:R-HSA-6799615 PR:000046634 located_in GO:0035579 Reactome:R-HSA-6800959 PR:000046634 located_in GO:0070821 PRO_0000014878 PRO:DNx UniProtKB:P20138, 18-364 PRO:DNx hCD33/SigPep- PRO:DNx A T-cell surface glycoprotein CD3 epsilon chain (human) that has had the signal peptide removed. UniProtKB:P07766, 23-207. Reactome:R-HSA-197906 PRO_0000014607 UniProtKB:P07766, 23-207 hCD3E/SigPep- protein PR:000046639 Category=organism-modification. T-cell surface glycoprotein CD3 epsilon chain, signal peptide removed form (human) A T-cell surface glycoprotein CD3 epsilon chain (human) that has had the signal peptide removed. UniProtKB:P07766, 23-207. PRO:DNx Reactome:R-HSA-197906 Reactome:R-HSA-197906 PR:000046639 located_in GO:0005886 PRO_0000014607 PRO:DNx UniProtKB:P07766, 23-207 PRO:DNx hCD3E/SigPep- PRO:DNx A CD44 antigen (human) that has had the signal peptide removed. UniProtKB:P16070, 21-742. Reactome:R-HSA-1031688 Reactome:R-HSA-6804776 PRO_0000026687 UniProtKB:P16070, 21-742 hCD44/SigPep- protein PR:000046641 Category=organism-modification. CD44 antigen, signal peptide removed form (human) A CD44 antigen (human) that has had the signal peptide removed. UniProtKB:P16070, 21-742. PRO:DNx Reactome:R-HSA-1031688 Reactome:R-HSA-1031688 PR:000046641 located_in GO:0005886 Reactome:R-HSA-6804776 PR:000046641 located_in GO:0030667 PRO_0000026687 PRO:DNx UniProtKB:P16070, 21-742 PRO:DNx hCD44/SigPep- PRO:DNx A T-cell surface glycoprotein CD8 alpha chain (human) that has had the signal peptide removed. UniProtKB:P01732, 22-235. Reactome:R-HSA-197601 PRO_0000014638 UniProtKB:P01732, 22-235 hCD8A/SigPep- protein PR:000046653 Category=organism-modification. T-cell surface glycoprotein CD8 alpha chain, signal peptide removed form (human) A T-cell surface glycoprotein CD8 alpha chain (human) that has had the signal peptide removed. UniProtKB:P01732, 22-235. PRO:DNx Reactome:R-HSA-197601 Reactome:R-HSA-197601 PR:000046653 located_in GO:0005886 PRO_0000014638 PRO:DNx UniProtKB:P01732, 22-235 PRO:DNx hCD8A/SigPep- PRO:DNx A high affinity immunoglobulin epsilon receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P12319, 26-257. Reactome:R-HSA-197802 PRO_0000015161 UniProtKB:P12319, 26-257 hFCER1A/SigPep- protein PR:000047381 Category=organism-modification. high affinity immunoglobulin epsilon receptor subunit alpha, signal peptide removed form (human) A high affinity immunoglobulin epsilon receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P12319, 26-257. PRO:DNx Reactome:R-HSA-197802 Reactome:R-HSA-197802 PR:000047381 located_in GO:0005886 PRO_0000015161 PRO:DNx UniProtKB:P12319, 26-257 PRO:DNx hFCER1A/SigPep- PRO:DNx A receptor-type tyrosine-protein kinase FLT3 (human) that has had the signal peptide removed. UniProtKB:P36888, 27-993. Reactome:R-HSA-6786756 PRO_0000016778 UniProtKB:P36888, 27-993 hFLT3/SigPep- protein PR:000047430 Category=organism-modification. receptor-type tyrosine-protein kinase FLT3, signal peptide removed form (human) A receptor-type tyrosine-protein kinase FLT3 (human) that has had the signal peptide removed. UniProtKB:P36888, 27-993. PRO:DNx Reactome:R-HSA-6786756 Reactome:R-HSA-6786756 PR:000047430 located_in GO:0005886 PRO_0000016778 PRO:DNx UniProtKB:P36888, 27-993 PRO:DNx hFLT3/SigPep- PRO:DNx An interleukin-2 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P01589, 22-272. Reactome:R-HSA-450046 PRO_0000011024 UniProtKB:P01589, 22-272 hIL2RA/SigPep- protein PR:000048015 Category=organism-modification. interleukin-2 receptor subunit alpha, signal peptide removed form (human) An interleukin-2 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P01589, 22-272. PRO:DNx Reactome:R-HSA-450046 Reactome:R-HSA-450046 PR:000048015 located_in GO:0005886 PRO_0000011024 PRO:DNx UniProtKB:P01589, 22-272 PRO:DNx hIL2RA/SigPep- PRO:DNx An interleukin-2 receptor subunit beta (human) that has had the signal peptide removed. UniProtKB:P14784, 27-551. Reactome:R-HSA-197876 Reactome:R-HSA-8983172 PRO_0000010878 UniProtKB:P14784, 27-551 hIL2RB/SigPep- protein PR:000048016 Category=organism-modification. interleukin-2 receptor subunit beta, signal peptide removed form (human) An interleukin-2 receptor subunit beta (human) that has had the signal peptide removed. UniProtKB:P14784, 27-551. PRO:DNx Reactome:R-HSA-197876 Reactome:R-HSA-197876 PR:000048016 located_in GO:0005886 Reactome:R-HSA-8983172 PR:000048016 located_in GO:0005768 PRO_0000010878 PRO:DNx UniProtKB:P14784, 27-551 PRO:DNx hIL2RB/SigPep- PRO:DNx An interleukin-3 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P26951, 19-378. Reactome:R-HSA-879938 PRO_0000010883 UniProtKB:P26951, 19-378 hIL3RA/SigPep- protein PR:000048024 Category=organism-modification. interleukin-3 receptor subunit alpha, signal peptide removed form (human) An interleukin-3 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P26951, 19-378. PRO:DNx Reactome:R-HSA-879938 Reactome:R-HSA-879938 PR:000048024 located_in GO:0005886 PRO_0000010883 PRO:DNx UniProtKB:P26951, 19-378 PRO:DNx hIL3RA/SigPep- PRO:DNx An interleukin-5 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:Q01344, 21-420. Reactome:R-HSA-450072 PRO_0000010893 UniProtKB:Q01344, 21-420 hIL5RA/SigPep- protein PR:000048027 Category=organism-modification. interleukin-5 receptor subunit alpha, signal peptide removed form (human) An interleukin-5 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:Q01344, 21-420. PRO:DNx Reactome:R-HSA-450072 Reactome:R-HSA-450072 PR:000048027 located_in GO:0005886 PRO_0000010893 PRO:DNx UniProtKB:Q01344, 21-420 PRO:DNx hIL5RA/SigPep- PRO:DNx An interleukin-7 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P16871, 21-459. Reactome:R-HSA-449945 Reactome:R-HSA-9028500 PRO_0000010909 UniProtKB:P16871, 21-459 hIL7R/SigPep- protein PR:000048032 Category=organism-modification. interleukin-7 receptor subunit alpha, signal peptide removed form (human) An interleukin-7 receptor subunit alpha (human) that has had the signal peptide removed. UniProtKB:P16871, 21-459. PRO:DNx Reactome:R-HSA-449945 Reactome:R-HSA-449945 PR:000048032 located_in GO:0005886 Reactome:R-HSA-9028500 PR:000048032 located_in GO:0030669 PRO_0000010909 PRO:DNx UniProtKB:P16871, 21-459 PRO:DNx hIL7R/SigPep- PRO:DNx A proinsulin in human. UniProtKB:P01308, 25-110. Reactome:R-HSA-264893 UniProtKB:P01308, 25-110 hINS/SigPep- insulin, signal peptide removed form (human) protein PR:000048036 Category=organism-modification. Requested by=MAxO. proinsulin (human) A proinsulin in human. UniProtKB:P01308, 25-110. PRO:DAN Reactome:R-HSA-264893 Reactome:R-HSA-264893 PR:000048036 located_in GO:0005788 UniProtKB:P01308, 25-110 PRO:DNx hINS/SigPep- PRO:DNx insulin, signal peptide removed form (human) PRO:DNx An integrin alpha-X (human) that has had the signal peptide removed. UniProtKB:P20702, 20-1163. Reactome:R-HSA-202764 Reactome:R-HSA-6801289 Reactome:R-HSA-6801305 Reactome:R-HSA-6801314 PRO_0000016294 UniProtKB:P20702, 20-1163 hITGAX/SigPep- protein PR:000048068 Category=organism-modification. integrin alpha-X, signal peptide removed form (human) An integrin alpha-X (human) that has had the signal peptide removed. UniProtKB:P20702, 20-1163. PRO:DNx Reactome:R-HSA-202764 Reactome:R-HSA-202764 PR:000048068 located_in GO:0005886 Reactome:R-HSA-6801289 PR:000048068 located_in GO:0030667 Reactome:R-HSA-6801305 PR:000048068 located_in GO:0101003 Reactome:R-HSA-6801314 PR:000048068 located_in GO:0070821 PRO_0000016294 PRO:DNx UniProtKB:P20702, 20-1163 PRO:DNx hITGAX/SigPep- PRO:DNx A vascular endothelial growth factor receptor 2 (human) that has had the signal peptide removed. UniProtKB:P35968, 20-1356. Reactome:R-HSA-195382 PRO_0000016771 UniProtKB:P35968, 20-1356 hKDR/SigPep- protein PR:000048096 Category=organism-modification. vascular endothelial growth factor receptor 2, signal peptide removed form (human) A vascular endothelial growth factor receptor 2 (human) that has had the signal peptide removed. UniProtKB:P35968, 20-1356. PRO:DNx Reactome:R-HSA-195382 Reactome:R-HSA-195382 PR:000048096 located_in GO:0005886 PRO_0000016771 PRO:DNx UniProtKB:P35968, 20-1356 PRO:DNx hKDR/SigPep- PRO:DNx A mast/stem cell growth factor receptor Kit (human) that has had the signal peptide removed. UniProtKB:P10721, 26-976. Reactome:R-HSA-197662 PRO_0000016754 UniProtKB:P10721, 26-976 hKIT/SigPep- protein PR:000048127 Category=organism-modification. mast/stem cell growth factor receptor Kit, signal peptide removed form (human) A mast/stem cell growth factor receptor Kit (human) that has had the signal peptide removed. UniProtKB:P10721, 26-976. PRO:DNx Reactome:R-HSA-197662 Reactome:R-HSA-197662 PR:000048127 located_in GO:0005886 PRO_0000016754 PRO:DNx UniProtKB:P10721, 26-976 PRO:DNx hKIT/SigPep- PRO:DNx A lactotransferrin (human) that has had the signal peptide removed. UniProtKB:P02788, 20-710. Reactome:R-HSA-1222567 Reactome:R-HSA-6799629 Reactome:R-HSA-6800962 Reactome:R-HSA-977171 PRO_0000035732 UniProtKB:P02788, 20-710 hLTF/SigPep- protein PR:000048272 Category=organism-modification. lactotransferrin, signal peptide removed form (human) A lactotransferrin (human) that has had the signal peptide removed. UniProtKB:P02788, 20-710. PRO:DNx Reactome:R-HSA-1222567 Reactome:R-HSA-977171 Reactome:R-HSA-1222567 PR:000048272 located_in GO:0097013 Reactome:R-HSA-6799629 PR:000048272 located_in GO:0035580 Reactome:R-HSA-6800962 PR:000048272 located_in GO:1904724 Reactome:R-HSA-977171 PR:000048272 located_in GO:0005576 PRO_0000035732 PRO:DNx UniProtKB:P02788, 20-710 PRO:DNx hLTF/SigPep- PRO:DNx A neural cell adhesion molecule 1 (human) that has had the signal peptide removed. UniProtKB:P13591, 20-858. Reactome:R-HSA-190987 PRO_0000015009 UniProtKB:P13591, 20-858 hNCAM1/SigPep- protein PR:000048517 Category=organism-modification. neural cell adhesion molecule 1, signal peptide removed form (human) A neural cell adhesion molecule 1 (human) that has had the signal peptide removed. UniProtKB:P13591, 20-858. PRO:DNx Reactome:R-HSA-190987 Reactome:R-HSA-190987 PR:000048517 located_in GO:0005886 PRO_0000015009 PRO:DNx UniProtKB:P13591, 20-858 PRO:DNx hNCAM1/SigPep- PRO:DNx A urokinase plasminogen activator surface receptor (human) that has had the signal peptide removed. UniProtKB:Q03405, 23-335. Reactome:R-HSA-162866 UniProtKB:Q03405, 23-335 hPLAUR/SigPep- protein PR:000048798 Category=organism-modification. urokinase plasminogen activator surface receptor, signal peptide removed form (human) A urokinase plasminogen activator surface receptor (human) that has had the signal peptide removed. UniProtKB:Q03405, 23-335. PRO:DNx Reactome:R-HSA-162866 Reactome:R-HSA-162866 PR:000048798 located_in GO:0005789 UniProtKB:Q03405, 23-335 PRO:DNx hPLAUR/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C (human) that has had the signal peptide removed. UniProtKB:P08575, 24-1304. Reactome:R-HSA-197931 Reactome:R-HSA-6806150 PRO_0000025470 UniProtKB:P08575, 24-1304 hPTPRC/SigPep- protein PR:000048962 Category=organism-modification. receptor-type tyrosine-protein phosphatase C, signal peptide removed form (human) A receptor-type tyrosine-protein phosphatase C (human) that has had the signal peptide removed. UniProtKB:P08575, 24-1304. PRO:DNx Reactome:R-HSA-197931 Reactome:R-HSA-197931 PR:000048962 located_in GO:0005886 Reactome:R-HSA-6806150 PR:000048962 located_in GO:0030667 PRO_0000025470 PRO:DNx UniProtKB:P08575, 24-1304 PRO:DNx hPTPRC/SigPep- PRO:DNx A syndecan-1 (human) that has had the signal peptide removed. UniProtKB:P18827, 23-310. Reactome:R-HSA-174758 Reactome:R-HSA-2054105 Reactome:R-HSA-2090025 PRO_0000033499 UniProtKB:P18827, 23-310 hSDC1/SigPep- protein PR:000049172 Category=organism-modification. syndecan-1, signal peptide removed form (human) A syndecan-1 (human) that has had the signal peptide removed. UniProtKB:P18827, 23-310. PRO:DNx Reactome:R-HSA-174758 Reactome:R-HSA-2054105 Reactome:R-HSA-2090025 Reactome:R-HSA-174758 PR:000049172 located_in GO:0005886 Reactome:R-HSA-2054105 PR:000049172 located_in GO:0005796 Reactome:R-HSA-2090025 PR:000049172 located_in GO:0043202 PRO_0000033499 PRO:DNx UniProtKB:P18827, 23-310 PRO:DNx hSDC1/SigPep- PRO:DNx A leukosialin (human) that has had the signal peptide removed. UniProtKB:P16150, 20-400. Reactome:R-HSA-204438 PRO_0000021588 UniProtKB:P16150, 20-400 hSPN/SigPep- protein PR:000049328 Category=organism-modification. leukosialin, signal peptide removed form (human) A leukosialin (human) that has had the signal peptide removed. UniProtKB:P16150, 20-400. PRO:DNx Reactome:R-HSA-204438 Reactome:R-HSA-204438 PR:000049328 located_in GO:0005886 PRO_0000021588 PRO:DNx UniProtKB:P16150, 20-400 PRO:DNx hSPN/SigPep- PRO:DNx A receptor-type tyrosine-protein phosphatase C that is a translation product of a transcript that minimally includes the region encoded by the variable exon 4(A). CD45R PTPRC/iso:CD45R protein PR:000050216 Category=seqgroup. Requested by=CL. receptor-type tyrosine-protein phosphatase C isoform CD45R A receptor-type tyrosine-protein phosphatase C that is a translation product of a transcript that minimally includes the region encoded by the variable exon 4(A). GOC:add PRO:ADD PRO:DAN PTPRC/iso:CD45R PRO:DNx A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. fam:ALAT protein PR:000050219 Category=family. alanine aminotransferase A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. PRO:DAN fam:ALAT PRO:DAN A calcitonin isoform 1 that has had the signal peptide removed. Example: UniProtKB:P01258-1, 26-141. CALCA/iso:1/SigPep- PCT calcitonin isoform 1, signal peptide removed form proCT protein PR:000050333 Category=modification. Requested by=MAxO. procalcitonin A calcitonin isoform 1 that has had the signal peptide removed. Example: UniProtKB:P01258-1, 26-141. PMID:10984072 PRO:DAN CALCA/iso:1/SigPep- PRO:DAN PCT PRO:DAN calcitonin isoform 1, signal peptide removed form PRO:DAN proCT PRO:DAN A procalcitonin in human. UniProtKB:P01258-1, 26-141. PCT (human) UniProtKB:P01258-1, 26-141 calcitonin isoform 1, signal peptide removed form (human) hCALCA/iso:1/SigPep- proCT (human) protein PR:000050338 Category=organism-modification. Requested by=MAxO. procalcitonin (human) A procalcitonin in human. UniProtKB:P01258-1, 26-141. PRO:DAN PCT (human) PRO:DAN UniProtKB:P01258-1, 26-141 PRO:DAN calcitonin isoform 1, signal peptide removed form (human) PRO:DAN hCALCA/iso:1/SigPep- PRO:DAN proCT (human) PRO:DAN A proinsulin that has had the propeptide (C-peptide) excised, leaving the A chain (example: UniProtKB:P01308, 90-110) and B chain (example: UniProtKB:P01308, 25-54) connected by crosslinks. insulin protein PR:000050339 Category=modification. Requested by=MAxO. Note: Though the final product resembles a complex, insulin is produced directly from a single chain without going through an intermediate where the A chain and B chain are free entities. insulin hormone A proinsulin that has had the propeptide (C-peptide) excised, leaving the A chain (example: UniProtKB:P01308, 90-110) and B chain (example: UniProtKB:P01308, 25-54) connected by crosslinks. PRO:DAN insulin PRO:DAN An insulin hormone in human. insulin (human) protein PR:000050340 Category=organism-modification. Requested by=MAxO. insulin hormone (human) An insulin hormone in human. PRO:DAN insulin (human) PRO:DAN An alanine aminotransferase that is encoded in the genome of human. fam:hALAT protein PR:000050341 Category=organism-family. Requested by=MAxO. alanine aminotransferase (human) An alanine aminotransferase that is encoded in the genome of human. PRO:DAN fam:hALAT PRO:DAN A protein that is a translation product of any of the following genes in human: GOT1/GOT2. SGOT (human) serum glutamic oxaloacetic transaminase (human) AST (human) fam:hGOT protein PR:000050353 Category=organism-family. Requested by=MAxO. aspartate aminotransferase (human) A protein that is a translation product of any of the following genes in human: GOT1/GOT2. PRO:DAN SGOT (human) Wikipedia:Aspartate_transaminase serum glutamic oxaloacetic transaminase (human) Wikipedia:Aspartate_transaminase AST (human) Wikipedia:Aspartate_transaminase fam:hGOT PRO:DAN A protein-containing complex that is the remnant of fibrin mesh degradation (fibrinolysis) by plasmin in human. hFDP/D-dimer protein PR:000050369 Category=organism-complex. Requested by=MAxO. D-dimer (human) A protein-containing complex that is the remnant of fibrin mesh degradation (fibrinolysis) by plasmin in human. PMID:19008457 PRO:DAN Wikipedia:D-dimer hFDP/D-dimer PRO:DAN A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein PR:000050567 Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). protein-containing material entity A material entity that minimally consists of a protein. PRO:DAN protein PRO:DAN protein aggregate PRO:DAN protein complex PRO:DAN protein-containing complex PRO:DAN An endothelial transcription factor GATA-2 that is encoded in the genome of mouse. UniProtKB:O09100 GATA-binding protein 2 (mouse) mGATA2 protein Gata2 PR:O09100 Category=organism-gene. endothelial transcription factor GATA-2 (mouse) An endothelial transcription factor GATA-2 that is encoded in the genome of mouse. OMA:O09100 PRO:DNx GATA-binding protein 2 (mouse) UniProtKB:O09100 mGATA2 PRO:DNx Gata2 UniProtKB:O09100 An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of human. Reactome:R-HSA-8939012 UniProtKB:O14638 CD203c (human) E-NPP 3 (human) NPP3 (human) PD-Ibeta (human) hENPP3 phosphodiesterase I beta (human) phosphodiesterase I/nucleotide pyrophosphatase 3 (human) protein ENPP3 PDNP3 PR:O14638 Category=organism-gene. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (human) An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of human. PRO:WCB UniProtKB:O14638 Reactome:R-HSA-8939012 PR:O14638 located_in GO:0005886 CD203c (human) UniProtKB:O14638 E-NPP 3 (human) UniProtKB:O14638 NPP3 (human) UniProtKB:O14638 PD-Ibeta (human) UniProtKB:O14638 hENPP3 PRO:DNx phosphodiesterase I beta (human) UniProtKB:O14638 phosphodiesterase I/nucleotide pyrophosphatase 3 (human) UniProtKB:O14638 ENPP3 UniProtKB:O14638 PDNP3 UniProtKB:O14638 A forkhead box protein N1 that is encoded in the genome of human. UniProtKB:O15353 hFOXN1 winged-helix transcription factor nude (human) protein FOXN1 RONU WHN PR:O15353 Category=organism-gene. forkhead box protein N1 (human) A forkhead box protein N1 that is encoded in the genome of human. PRO:DNx UniProtKB:O15353 hFOXN1 PRO:DNx winged-helix transcription factor nude (human) UniProtKB:O15353 FOXN1 UniProtKB:O15353 RONU UniProtKB:O15353 WHN UniProtKB:O15353 A prominin-1 that is encoded in the genome of human. UniProtKB:O43490 CD133 (human) antigen AC133 (human) hPROM1 prominin-like protein 1 (human) protein MSTP061 PROM1 PROML1 PR:O43490 Category=organism-gene. prominin-1 (human) A prominin-1 that is encoded in the genome of human. PRO:CNA UniProtKB:O43490 CD133 (human) UniProtKB:O43490 antigen AC133 (human) UniProtKB:O43490 hPROM1 PRO:DNx prominin-like protein 1 (human) UniProtKB:O43490 MSTP061 UniProtKB:O43490 PROM1 UniProtKB:O43490 PROML1 UniProtKB:O43490 A prominin-1 that is encoded in the genome of mouse. UniProtKB:O54990 CD133 (mouse) antigen AC133 homolog (mouse) mPROM1 prominin-like protein 1 (mouse) protein Prom Prom1 Proml1 PR:O54990 Category=organism-gene. prominin-1 (mouse) A prominin-1 that is encoded in the genome of mouse. OMA:O54990 PRO:DNx CD133 (mouse) UniProtKB:O54990 antigen AC133 homolog (mouse) UniProtKB:O54990 mPROM1 PRO:DNx prominin-like protein 1 (mouse) UniProtKB:O54990 Prom UniProtKB:O54990 Prom1 UniProtKB:O54990 Proml1 UniProtKB:O54990 An aspartate aminotransferase, mitochondrial that is encoded in the genome of human. transaminase A (human) UniProtKB:P00505 FABP-1 (human) FABPpm (human) fatty acid-binding protein (human) glutamate oxaloacetate transaminase 2 (human) hGOT2 kynurenine aminotransferase 4 (human) kynurenine aminotransferase IV (human) kynurenine--oxoglutarate transaminase 4 (human) kynurenine--oxoglutarate transaminase IV (human) mAspAT (human) plasma membrane-associated fatty acid-binding protein (human) protein GOT2 KYAT4 PR:P00505 Category=organism-gene. aspartate aminotransferase, mitochondrial (human) An aspartate aminotransferase, mitochondrial that is encoded in the genome of human. PRO:DNx UniProtKB:P00505 transaminase A (human) UniProtKB:P00505 FABP-1 (human) UniProtKB:P00505 FABPpm (human) UniProtKB:P00505 fatty acid-binding protein (human) UniProtKB:P00505 glutamate oxaloacetate transaminase 2 (human) UniProtKB:P00505 hGOT2 PRO:DNx kynurenine aminotransferase 4 (human) UniProtKB:P00505 kynurenine aminotransferase IV (human) UniProtKB:P00505 kynurenine--oxoglutarate transaminase 4 (human) UniProtKB:P00505 kynurenine--oxoglutarate transaminase IV (human) UniProtKB:P00505 mAspAT (human) UniProtKB:P00505 plasma membrane-associated fatty acid-binding protein (human) UniProtKB:P00505 GOT2 UniProtKB:P00505 KYAT4 UniProtKB:P00505 A haptoglobin that is encoded in the genome of human. UniProtKB:P00738 hHP zonulin (human) protein HP PR:P00738 Category=organism-gene. haptoglobin (human) A haptoglobin that is encoded in the genome of human. PRO:DNx UniProtKB:P00738 hHP PRO:DNx zonulin (human) UniProtKB:P00738 HP UniProtKB:P00738 A glycoprotein hormones alpha chain that is encoded in the genome of human. UniProtKB:P01215 CG-alpha (human) FSH-alpha (human) LSH-alpha (human) TSH-alpha (human) anterior pituitary glycoprotein hormones common subunit alpha (human) choriogonadotropin alpha chain (human) chorionic gonadotrophin subunit alpha (human) follicle-stimulating hormone alpha chain (human) follitropin alpha chain (human) hCGA luteinizing hormone alpha chain (human) lutropin alpha chain (human) thyroid-stimulating hormone alpha chain (human) thyrotropin alpha chain (human) protein CGA PR:P01215 Category=organism-gene. glycoprotein hormones alpha chain (human) A glycoprotein hormones alpha chain that is encoded in the genome of human. PRO:DNx UniProtKB:P01215 CG-alpha (human) UniProtKB:P01215 FSH-alpha (human) UniProtKB:P01215 LSH-alpha (human) UniProtKB:P01215 TSH-alpha (human) UniProtKB:P01215 anterior pituitary glycoprotein hormones common subunit alpha (human) UniProtKB:P01215 choriogonadotropin alpha chain (human) UniProtKB:P01215 chorionic gonadotrophin subunit alpha (human) UniProtKB:P01215 follicle-stimulating hormone alpha chain (human) UniProtKB:P01215 follitropin alpha chain (human) UniProtKB:P01215 hCGA PRO:DNx luteinizing hormone alpha chain (human) UniProtKB:P01215 lutropin alpha chain (human) UniProtKB:P01215 thyroid-stimulating hormone alpha chain (human) UniProtKB:P01215 thyrotropin alpha chain (human) UniProtKB:P01215 CGA UniProtKB:P01215 A glycoprotein hormones alpha chain that is encoded in the genome of mouse. UniProtKB:P01216 FSH-alpha (mouse) LSH-alpha (mouse) TSH-alpha (mouse) anterior pituitary glycoprotein hormones common subunit alpha (mouse) follicle-stimulating hormone alpha chain (mouse) follitropin alpha chain (mouse) luteinizing hormone alpha chain (mouse) lutropin alpha chain (mouse) mCGA thyroid-stimulating hormone alpha chain (mouse) thyrotropin alpha chain (mouse) protein Cga PR:P01216 Category=organism-gene. glycoprotein hormones alpha chain (mouse) A glycoprotein hormones alpha chain that is encoded in the genome of mouse. OMA:P01216 PRO:DNx FSH-alpha (mouse) UniProtKB:P01216 LSH-alpha (mouse) UniProtKB:P01216 TSH-alpha (mouse) UniProtKB:P01216 anterior pituitary glycoprotein hormones common subunit alpha (mouse) UniProtKB:P01216 follicle-stimulating hormone alpha chain (mouse) UniProtKB:P01216 follitropin alpha chain (mouse) UniProtKB:P01216 luteinizing hormone alpha chain (mouse) UniProtKB:P01216 lutropin alpha chain (mouse) UniProtKB:P01216 mCGA PRO:DNx thyroid-stimulating hormone alpha chain (mouse) UniProtKB:P01216 thyrotropin alpha chain (mouse) UniProtKB:P01216 Cga UniProtKB:P01216 A thyrotropin subunit beta that is encoded in the genome of human. UniProtKB:P01222 TSH-B (human) TSH-beta (human) hTSHB thyroid-stimulating hormone subunit beta (human) thyrotropin alfa (human) thyrotropin beta chain (human) protein TSHB PR:P01222 Category=organism-gene. thyrotropin subunit beta (human) A thyrotropin subunit beta that is encoded in the genome of human. PRO:DNx UniProtKB:P01222 TSH-B (human) UniProtKB:P01222 TSH-beta (human) UniProtKB:P01222 hTSHB PRO:DNx thyroid-stimulating hormone subunit beta (human) UniProtKB:P01222 thyrotropin alfa (human) UniProtKB:P01222 thyrotropin beta chain (human) UniProtKB:P01222 TSHB UniProtKB:P01222 A calcitonin (human), isoforms 1 and 2. UniProtKB:P01258 hCALCA/iso:[1/h2] protein PR:P01258 Category=organism-seqgroup. calcitonin isoforms 1/2 (human) A calcitonin (human), isoforms 1 and 2. PRO:DAN UniProtKB:P01258 hCALCA/iso:[1/h2] PRO:DAN A calcitonin isoform 1 that is encoded in the genome of human. UniProtKB:P01258-1 hCALCA/iso:1 protein PR:P01258-1 Category=organism-sequence. calcitonin isoform 1 (human) A calcitonin isoform 1 that is encoded in the genome of human. PRO:DAN hCALCA/iso:1 PRO:DNx A CALCA gene translation product (human) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P01258-2. UniProtKB:P01258-2 hCALCA/iso:h2 protein PR:P01258-2 Category=organism-sequence. calcitonin isoform h2 (human) A CALCA gene translation product (human) that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P01258-2. PRO:DNx UniProtKB:P01258 hCALCA/iso:h2 PRO:DNx An insulin gene translation product that is encoded in the genome of human. UniProtKB:P01308 hINS protein PR:P01308 Category=organism-gene. insulin gene translation product (human) An insulin gene translation product that is encoded in the genome of human. PRO:DAN UniProtKB:P01308 hINS PRO:DNx An interleukin-2 receptor subunit alpha that is encoded in the genome of human. p55 (human) UniProtKB:P01589 CD25 (human) IL-2 receptor subunit alpha (human) IL-2-RA (human) IL-2R subunit alpha (human) IL2-RA (human) TAC antigen (human) hIL2RA protein IL2RA PR:P01589 Category=organism-gene. interleukin-2 receptor subunit alpha (human) An interleukin-2 receptor subunit alpha that is encoded in the genome of human. PRO:CNA UniProtKB:P01589 p55 (human) UniProtKB:P01589 CD25 (human) UniProtKB:P01589 IL-2 receptor subunit alpha (human) UniProtKB:P01589 IL-2-RA (human) UniProtKB:P01589 IL-2R subunit alpha (human) UniProtKB:P01589 IL2-RA (human) UniProtKB:P01589 TAC antigen (human) UniProtKB:P01589 hIL2RA PRO:DNx IL2RA UniProtKB:P01589 An interleukin-2 receptor subunit alpha that is encoded in the genome of mouse. p55 (mouse) UniProtKB:P01590 CD25 (mouse) IL-2 receptor subunit alpha (mouse) IL-2-RA (mouse) IL-2R subunit alpha (mouse) IL2-RA (mouse) mIL2RA protein Il2r Il2ra PR:P01590 Category=organism-gene. interleukin-2 receptor subunit alpha (mouse) An interleukin-2 receptor subunit alpha that is encoded in the genome of mouse. OMA:P01590 PRO:DNx p55 (mouse) UniProtKB:P01590 CD25 (mouse) UniProtKB:P01590 IL-2 receptor subunit alpha (mouse) UniProtKB:P01590 IL-2-RA (mouse) UniProtKB:P01590 IL-2R subunit alpha (mouse) UniProtKB:P01590 IL2-RA (mouse) UniProtKB:P01590 mIL2RA PRO:DNx Il2r UniProtKB:P01590 Il2ra UniProtKB:P01590 A CD4 molecule that is encoded in the genome of human. UniProtKB:P01730 T-cell surface antigen T4/Leu-3 (human) hCD4 protein CD4 PR:P01730 Category=organism-gene. T-cell surface glycoprotein CD4 (human) A CD4 molecule that is encoded in the genome of human. PRO:DNx UniProtKB:P01730 T-cell surface antigen T4/Leu-3 (human) UniProtKB:P01730 hCD4 PRO:DNx CD4 UniProtKB:P01730 A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse. UniProtKB:P01731 CD8a (mouse) T-cell surface glycoprotein Lyt-2 (mouse) mCD8A protein Cd8a Lyt-2 Lyt2 PR:P01731 Category=organism-gene. T-cell surface glycoprotein CD8 alpha chain (mouse) A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse. OMA:P01731 PRO:DNx CD8a (mouse) UniProtKB:P01731 T-cell surface glycoprotein Lyt-2 (mouse) UniProtKB:P01731 mCD8A PRO:DNx Cd8a UniProtKB:P01731 Lyt-2 UniProtKB:P01731 Lyt2 UniProtKB:P01731 A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human. UniProtKB:P01732 CD8a (human) T-lymphocyte differentiation antigen T8/Leu-2 (human) hCD8A protein CD8A MAL PR:P01732 Category=organism-gene. T-cell surface glycoprotein CD8 alpha chain (human) A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human. PRO:CNA UniProtKB:P01732 CD8a (human) UniProtKB:P01732 T-lymphocyte differentiation antigen T8/Leu-2 (human) UniProtKB:P01732 hCD8A PRO:DNx CD8A UniProtKB:P01732 MAL UniProtKB:P01732 A Thy-1 membrane glycoprotein that is encoded in the genome of mouse. UniProtKB:P01831 CD90 (mouse) Thy-1 antigen (mouse) mTHY1 protein Thy-1 Thy1 PR:P01831 Category=organism-gene. Thy-1 membrane glycoprotein (mouse) A Thy-1 membrane glycoprotein that is encoded in the genome of mouse. OMA:P01831 PRO:DNx CD90 (mouse) UniProtKB:P01831 Thy-1 antigen (mouse) UniProtKB:P01831 mTHY1 PRO:DNx Thy-1 UniProtKB:P01831 Thy1 UniProtKB:P01831 An albumin that is encoded in the genome of human. UniProtKB:P02768 hALB serum albumin (human) protein ALB GIG20 GIG42 PRO0903 PRO1708 PRO2044 PRO2619 PRO2675 UNQ696/PRO1341 PR:P02768 Category=organism-gene. albumin (human) An albumin that is encoded in the genome of human. PRO:DNx UniProtKB:P02768 hALB PRO:DNx serum albumin (human) UniProtKB:P02768 ALB UniProtKB:P02768 GIG20 UniProtKB:P02768 GIG42 UniProtKB:P02768 PRO0903 UniProtKB:P02768 PRO1708 UniProtKB:P02768 PRO2044 UniProtKB:P02768 PRO2619 UniProtKB:P02768 PRO2675 UniProtKB:P02768 UNQ696/PRO1341 UniProtKB:P02768 An alpha-fetoprotein that is encoded in the genome of human. UniProtKB:P02771 alpha-1-fetoprotein (human) alpha-fetoglobulin (human) hAFP protein AFP HPAFP PR:P02771 Category=organism-gene. alpha-fetoprotein (human) An alpha-fetoprotein that is encoded in the genome of human. PRO:DNx UniProtKB:P02771 alpha-1-fetoprotein (human) UniProtKB:P02771 alpha-fetoglobulin (human) UniProtKB:P02771 hAFP PRO:DNx AFP UniProtKB:P02771 HPAFP UniProtKB:P02771 An alpha-fetoprotein that is encoded in the genome of mouse. UniProtKB:P02772 alpha-1-fetoprotein (mouse) alpha-fetoglobulin (mouse) mAFP protein Afp PR:P02772 Category=organism-gene. alpha-fetoprotein (mouse) An alpha-fetoprotein that is encoded in the genome of mouse. OMA:P02772 PRO:DNx alpha-1-fetoprotein (mouse) UniProtKB:P02772 alpha-fetoglobulin (mouse) UniProtKB:P02772 mAFP PRO:DNx Afp UniProtKB:P02772 A transferrin receptor protein 1 that is encoded in the genome of human. TR (human) p90 (human) Reactome:R-HSA-434196 Reactome:R-HSA-434330 Reactome:R-HSA-8869124 Reactome:R-HSA-8961829 Reactome:R-HSA-917983 UniProtKB:P02786 CD71 (human) T9 (human) TfR (human) TfR1 (human) Trfr (human) hTFRC protein TFRC PR:P02786 Category=organism-gene. transferrin receptor protein 1 (human) A transferrin receptor protein 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P02786 TR (human) UniProtKB:P02786 p90 (human) UniProtKB:P02786 Reactome:R-HSA-434196 PR:P02786 located_in GO:0030659 Reactome:R-HSA-434330 PR:P02786 located_in GO:0000139 Reactome:R-HSA-8869124 PR:P02786 located_in GO:0030665 Reactome:R-HSA-8961829 PR:P02786 located_in GO:0010008 Reactome:R-HSA-917983 PR:P02786 located_in GO:0005886 CD71 (human) UniProtKB:P02786 T9 (human) UniProtKB:P02786 TfR (human) UniProtKB:P02786 TfR1 (human) UniProtKB:P02786 Trfr (human) UniProtKB:P02786 hTFRC PRO:DNx TFRC UniProtKB:P02786 A lactotransferrin that is encoded in the genome of human. UniProtKB:P02788 growth-inhibiting protein 12 (human) hLTF lactoferrin (human) talalactoferrin (human) protein GIG12 LF LTF PR:P02788 Category=organism-gene. lactotransferrin (human) A lactotransferrin that is encoded in the genome of human. PRO:DNx UniProtKB:P02788 growth-inhibiting protein 12 (human) UniProtKB:P02788 hLTF PRO:DNx lactoferrin (human) UniProtKB:P02788 talalactoferrin (human) UniProtKB:P02788 GIG12 UniProtKB:P02788 LF UniProtKB:P02788 LTF UniProtKB:P02788 A DNA nucleotidylexotransferase that is encoded in the genome of human. terminal transferase (human) UniProtKB:P04053 hDNTT terminal addition enzyme (human) terminal deoxynucleotidyltransferase (human) protein DNTT TDT PR:P04053 Category=organism-gene. DNA nucleotidylexotransferase (human) A DNA nucleotidylexotransferase that is encoded in the genome of human. PRO:DNx UniProtKB:P04053 terminal transferase (human) UniProtKB:P04053 hDNTT PRO:DNx terminal addition enzyme (human) UniProtKB:P04053 terminal deoxynucleotidyltransferase (human) UniProtKB:P04053 DNTT UniProtKB:P04053 TDT UniProtKB:P04053 A Thy-1 membrane glycoprotein that is encoded in the genome of human. UniProtKB:P04216 CD90 (human) CDw90 (human) Thy-1 antigen (human) hTHY1 protein THY1 PR:P04216 Category=organism-gene. Thy-1 membrane glycoprotein (human) A Thy-1 membrane glycoprotein that is encoded in the genome of human. PRO:WCB UniProtKB:P04216 CD90 (human) UniProtKB:P04216 CDw90 (human) UniProtKB:P04216 Thy-1 antigen (human) UniProtKB:P04216 hTHY1 PRO:DNx THY1 UniProtKB:P04216 An aspartate aminotransferase, cytoplasmic that is encoded in the genome of mouse. UniProtKB:P05201 cAspAT (mouse) cCAT (mouse) cysteine aminotransferase, cytoplasmic (mouse) cysteine transaminase, cytoplasmic (mouse) glutamate oxaloacetate transaminase 1 (mouse) mGOT1 protein Got1 transaminase A (mouse) PR:P05201 Category=organism-gene. aspartate aminotransferase, cytoplasmic (mouse) An aspartate aminotransferase, cytoplasmic that is encoded in the genome of mouse. OMA:P05201 PRO:DNx cAspAT (mouse) UniProtKB:P05201 cCAT (mouse) UniProtKB:P05201 cysteine aminotransferase, cytoplasmic (mouse) UniProtKB:P05201 cysteine transaminase, cytoplasmic (mouse) UniProtKB:P05201 glutamate oxaloacetate transaminase 1 (mouse) UniProtKB:P05201 mGOT1 PRO:DNx Got1 UniProtKB:P05201 transaminase A (mouse) UniProtKB:P05201 An aspartate aminotransferase, mitochondrial that is encoded in the genome of mouse. UniProtKB:P05202 FABP-1 (mouse) FABPpm (mouse) fatty acid-binding protein (mouse) glutamate oxaloacetate transaminase 2 (mouse) kynurenine aminotransferase 4 (mouse) kynurenine aminotransferase IV (mouse) kynurenine--oxoglutarate transaminase 4 (mouse) kynurenine--oxoglutarate transaminase IV (mouse) mAspAT (mouse) mGOT2 plasma membrane-associated fatty acid-binding protein (mouse) protein Got-2 Got2 transaminase A (mouse) PR:P05202 Category=organism-gene. aspartate aminotransferase, mitochondrial (mouse) An aspartate aminotransferase, mitochondrial that is encoded in the genome of mouse. OMA:P05202 PRO:DNx FABP-1 (mouse) UniProtKB:P05202 FABPpm (mouse) UniProtKB:P05202 fatty acid-binding protein (mouse) UniProtKB:P05202 glutamate oxaloacetate transaminase 2 (mouse) UniProtKB:P05202 kynurenine aminotransferase 4 (mouse) UniProtKB:P05202 kynurenine aminotransferase IV (mouse) UniProtKB:P05202 kynurenine--oxoglutarate transaminase 4 (mouse) UniProtKB:P05202 kynurenine--oxoglutarate transaminase IV (mouse) UniProtKB:P05202 mAspAT (mouse) UniProtKB:P05202 mGOT2 PRO:DNx plasma membrane-associated fatty acid-binding protein (mouse) UniProtKB:P05202 Got-2 UniProtKB:P05202 Got2 UniProtKB:P05202 transaminase A (mouse) UniProtKB:P05202 A mast/stem cell growth factor receptor that is encoded in the genome of mouse. UniProtKB:P05532 CD117 (mouse) SCFR (mouse) mKIT proto-oncogene c-Kit (mouse) tyrosine-protein kinase Kit (mouse) protein Kit Sl PR:P05532 Category=organism-gene. mast/stem cell growth factor receptor Kit (mouse) A mast/stem cell growth factor receptor that is encoded in the genome of mouse. OMA:MOUSE17014 PRO:DNx CD117 (mouse) UniProtKB:P05532 SCFR (mouse) UniProtKB:P05532 mKIT PRO:DNx proto-oncogene c-Kit (mouse) UniProtKB:P05532 tyrosine-protein kinase Kit (mouse) UniProtKB:P05532 Kit UniProtKB:P05532 Sl UniProtKB:P05532 A lymphocyte antigen 6A-2/6E-1 that is encoded in the genome of mouse. TAP (mouse) UniProtKB:P05533 Ly-6A.2/Ly-6E.1 (mouse) SCA-1 (mouse) Stem cell antigen 1 (mouse) T-cell-activating protein (mouse) mLy6a protein Ly6 Ly6a PR:P05533 Category=organism-gene. lymphocyte antigen 6A-2/6E-1 (mouse) A lymphocyte antigen 6A-2/6E-1 that is encoded in the genome of mouse. PRO:CNA UniProtKB:P05533 TAP (mouse) UniProtKB:P05533 Ly-6A.2/Ly-6E.1 (mouse) UniProtKB:P05533 SCA-1 (mouse) UniProtKB:P05533 Stem cell antigen 1 (mouse) UniProtKB:P05533 T-cell-activating protein (mouse) UniProtKB:P05533 mLy6a PRO:DNx Ly6 UniProtKB:P05533 Ly6a UniProtKB:P05533 An integrin alpha-M that is encoded in the genome of mouse. UniProtKB:P05555 CD11 antigen-like family member B (mouse) CD11b (mouse) CR-3 alpha chain (mouse) cell surface glycoprotein MAC-1 subunit alpha (mouse) leukocyte adhesion receptor MO1 (mouse) mITGAM protein Itgam PR:P05555 Category=organism-gene. integrin alpha-M (mouse) An integrin alpha-M that is encoded in the genome of mouse. PRO:DNx UniProtKB:P05555 CD11 antigen-like family member B (mouse) UniProtKB:P05555 CD11b (mouse) UniProtKB:P05555 CR-3 alpha chain (mouse) UniProtKB:P05555 cell surface glycoprotein MAC-1 subunit alpha (mouse) UniProtKB:P05555 leukocyte adhesion receptor MO1 (mouse) UniProtKB:P05555 mITGAM PRO:DNx Itgam UniProtKB:P05555 A T-cell surface glycoprotein CD5 that is encoded in the genome of human. UniProtKB:P06127 hCD5 lymphocyte antigen T1/Leu-1 (human) protein CD5 LEU1 PR:P06127 Category=organism-gene. T-cell surface glycoprotein CD5 (human) A T-cell surface glycoprotein CD5 that is encoded in the genome of human. PRO:WCB UniProtKB:P06127 hCD5 PRO:DNx lymphocyte antigen T1/Leu-1 (human) UniProtKB:P06127 CD5 UniProtKB:P06127 LEU1 UniProtKB:P06127 A CD4 molecule that is encoded in the genome of mouse. UniProtKB:P06332 CD4 (mouse) T-cell differentiation antigen L3T4 (mouse) T-cell surface antigen T4/Leu-3 (mouse) mCD4 protein Cd4 PR:P06332 Category=organism-gene. T-cell surface glycoprotein CD4 (mouse) A CD4 molecule that is encoded in the genome of mouse. OMA:P06332 PRO:DNx CD4 (mouse) UniProtKB:P06332 T-cell differentiation antigen L3T4 (mouse) UniProtKB:P06332 T-cell surface antigen T4/Leu-3 (mouse) UniProtKB:P06332 mCD4 PRO:DNx Cd4 UniProtKB:P06332 A CD2 molecule that is encoded in the genome of human. UniProtKB:P06729 LFA-2 (human) LFA-3 receptor (human) T-cell surface antigen T11/Leu-5 (human) erythrocyte receptor (human) hCD2 rosette receptor (human) protein CD2 SRBC PR:P06729 Category=organism-gene. T-cell surface antigen CD2 (human) A CD2 molecule that is encoded in the genome of human. PRO:CNA UniProtKB:P06729 LFA-2 (human) UniProtKB:P06729 LFA-3 receptor (human) UniProtKB:P06729 T-cell surface antigen T11/Leu-5 (human) UniProtKB:P06729 erythrocyte receptor (human) UniProtKB:P06729 hCD2 PRO:DNx rosette receptor (human) UniProtKB:P06729 CD2 UniProtKB:P06729 SRBC UniProtKB:P06729 A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of mouse. UniProtKB:P06800 CD45 (mouse) L-CA (mouse) T200 (mouse) leukocyte common antigen (mouse) lymphocyte antigen 5 (mouse) mPTPRC protein Ly-5 Ptprc PR:P06800 Category=organism-gene. receptor-type tyrosine-protein phosphatase C (mouse) A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of mouse. OMA:P06800 PRO:DNx CD45 (mouse) UniProtKB:P06800 L-CA (mouse) UniProtKB:P06800 T200 (mouse) UniProtKB:P06800 leukocyte common antigen (mouse) UniProtKB:P06800 lymphocyte antigen 5 (mouse) UniProtKB:P06800 mPTPRC PRO:DNx Ly-5 UniProtKB:P06800 Ptprc UniProtKB:P06800 An albumin that is encoded in the genome of mouse. UniProtKB:P07724 mALB serum albumin (mouse) protein Alb Alb-1 Alb1 PR:P07724 Category=organism-gene. albumin (mouse) An albumin that is encoded in the genome of mouse. OMA:P07724 PRO:DNx mALB PRO:DNx serum albumin (mouse) UniProtKB:P07724 Alb UniProtKB:P07724 Alb-1 UniProtKB:P07724 Alb1 UniProtKB:P07724 A CD3 epsilon that is encoded in the genome of human. UniProtKB:P07766 CD3e (human) T-cell surface antigen T3/Leu-4 epsilon chain (human) hCD3E protein CD3E T3E PR:P07766 Category=organism-gene. T-cell surface glycoprotein CD3 epsilon chain (human) A CD3 epsilon that is encoded in the genome of human. PRO:CNA UniProtKB:P07766 CD3e (human) UniProtKB:P07766 T-cell surface antigen T3/Leu-4 epsilon chain (human) UniProtKB:P07766 hCD3E PRO:DNx CD3E UniProtKB:P07766 T3E UniProtKB:P07766 A lactotransferrin that is encoded in the genome of mouse. UniProtKB:P08071 lactoferrin (mouse) mLTF protein Ltf PR:P08071 Category=organism-gene. lactotransferrin (mouse) A lactotransferrin that is encoded in the genome of mouse. OMA:P08071 PRO:DNx lactoferrin (mouse) UniProtKB:P08071 mLTF PRO:DNx Ltf UniProtKB:P08071 A low affinity immunoglobulin gamma Fc region receptor II that is encoded in the genome of mouse. UniProtKB:P08101 CD32 (mouse) Fc gamma receptor IIB (mouse) Fc-gamma RII (mouse) Fc-gamma-RIIB (mouse) FcRII (mouse) IgG Fc receptor II beta (mouse) lymphocyte antigen 17 (mouse) mFcgr2 protein Fcgr2 Fcgr2b Ly-17 PR:P08101 Category=organism-gene. low affinity immunoglobulin gamma Fc region receptor II (mouse) A low affinity immunoglobulin gamma Fc region receptor II that is encoded in the genome of mouse. PRO:CNA UniProtKB:P08101 CD32 (mouse) UniProtKB:P08101 Fc gamma receptor IIB (mouse) UniProtKB:P08101 Fc-gamma RII (mouse) UniProtKB:P08101 Fc-gamma-RIIB (mouse) UniProtKB:P08101 FcRII (mouse) UniProtKB:P08101 IgG Fc receptor II beta (mouse) UniProtKB:P08101 lymphocyte antigen 17 (mouse) UniProtKB:P08101 mFcgr2 PRO:DNx Fcgr2 UniProtKB:P08101 Fcgr2b UniProtKB:P08101 Ly-17 UniProtKB:P08101 A neprilysin that is encoded in the genome of human. UniProtKB:P08473 CALLA (human) CD10 (human) NEP (human) SFE (human) atriopeptidase (human) common acute lymphocytic leukemia antigen (human) enkephalinase (human) hMME neutral endopeptidase (human) neutral endopeptidase 24.11 (human) skin fibroblast elastase (human) protein EPN MME PR:P08473 Category=organism-gene. neprilysin (human) A neprilysin that is encoded in the genome of human. PRO:WCB UniProtKB:P08473 CALLA (human) UniProtKB:P08473 CD10 (human) UniProtKB:P08473 NEP (human) UniProtKB:P08473 SFE (human) UniProtKB:P08473 atriopeptidase (human) UniProtKB:P08473 common acute lymphocytic leukemia antigen (human) UniProtKB:P08473 enkephalinase (human) UniProtKB:P08473 hMME PRO:DNx neutral endopeptidase (human) UniProtKB:P08473 neutral endopeptidase 24.11 (human) UniProtKB:P08473 skin fibroblast elastase (human) UniProtKB:P08473 EPN UniProtKB:P08473 MME UniProtKB:P08473 A low affinity immunoglobulin gamma Fc region receptor III that is encoded in the genome of mouse. UniProtKB:P08508 CD16 (mouse) Fc-gamma RIII (mouse) FcRIII (mouse) IgG Fc receptor III (mouse) mFcgr3 protein Fcgr3 PR:P08508 Category=organism-gene. low affinity immunoglobulin gamma Fc region receptor III (mouse) A low affinity immunoglobulin gamma Fc region receptor III that is encoded in the genome of mouse. PRO:CNA UniProtKB:P08508 CD16 (mouse) UniProtKB:P08508 Fc-gamma RIII (mouse) UniProtKB:P08508 FcRIII (mouse) UniProtKB:P08508 IgG Fc receptor III (mouse) UniProtKB:P08508 mFcgr3 PRO:DNx Fcgr3 UniProtKB:P08508 An integrin alpha-IIb that is encoded in the genome of human. UniProtKB:P08514 CD41 (human) GPIIb (human) GPalpha IIb (human) hITGA2B platelet membrane glycoprotein IIb (human) protein GP2B ITGA2B ITGAB PR:P08514 Category=organism-gene. integrin alpha-IIb (human) An integrin alpha-IIb that is encoded in the genome of human. PRO:DNx UniProtKB:P08514 CD41 (human) UniProtKB:P08514 GPIIb (human) UniProtKB:P08514 GPalpha IIb (human) UniProtKB:P08514 hITGA2B PRO:DNx platelet membrane glycoprotein IIb (human) UniProtKB:P08514 GP2B UniProtKB:P08514 ITGA2B UniProtKB:P08514 ITGAB UniProtKB:P08514 A CD14 molecule that is encoded in the genome of human. UniProtKB:P08571 hCD14 myeloid cell-specific leucine-rich glycoprotein (human) protein CD14 PR:P08571 Category=organism-gene. monocyte differentiation antigen CD14 (human) A CD14 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P08571 hCD14 PRO:DNx myeloid cell-specific leucine-rich glycoprotein (human) UniProtKB:P08571 CD14 UniProtKB:P08571 A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of human. UniProtKB:P08575 L-CA (human) T200 (human) hPTPRC leukocyte common antigen (human) protein CD45 PTPRC PR:P08575 Category=organism-gene. receptor-type tyrosine-protein phosphatase C (human) A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of human. PRO:CNA UniProtKB:P08575 L-CA (human) UniProtKB:P08575 T200 (human) UniProtKB:P08575 hPTPRC PRO:DNx leukocyte common antigen (human) UniProtKB:P08575 CD45 UniProtKB:P08575 PTPRC UniProtKB:P08575 A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that is encoded in the genome of human. UniProtKB:P08575-3 hPTPRC/iso:CD45RABC protein PR:P08575-3 Category=organism-sequence. receptor-type tyrosine-protein phosphatase C isoform CD45RABC (human) A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that is encoded in the genome of human. PRO:DAN hPTPRC/iso:CD45RABC PRO:DNx A receptor-type tyrosine-protein phosphatase C isoform CD45RA that is encoded in the genome of human. UniProtKB:P08575-8 CD45RA (human) hPTPRC/iso:CD45RA protein PR:P08575-8 Category=organism-sequence. Requested by=CL. receptor-type tyrosine-protein phosphatase C isoform CD45RA (human) A receptor-type tyrosine-protein phosphatase C isoform CD45RA that is encoded in the genome of human. GOC:add PRO:ADD PRO:DAN hPTPRC/iso:CD45RA PRO:DNx A CD2 molecule that is encoded in the genome of mouse. UniProtKB:P08920 CD2 (mouse) LFA-2 (mouse) LFA-3 receptor (mouse) T-cell surface antigen T11/Leu-5 (mouse) lymphocyte antigen 37 (mouse) mCD2 protein Cd2 Ly-37 PR:P08920 Category=organism-gene. T-cell surface antigen CD2 (mouse) A CD2 molecule that is encoded in the genome of mouse. OMA:P08920 PRO:DNx CD2 (mouse) UniProtKB:P08920 LFA-2 (mouse) UniProtKB:P08920 LFA-3 receptor (mouse) UniProtKB:P08920 T-cell surface antigen T11/Leu-5 (mouse) UniProtKB:P08920 lymphocyte antigen 37 (mouse) UniProtKB:P08920 mCD2 PRO:DNx Cd2 UniProtKB:P08920 Ly-37 UniProtKB:P08920 A CD48 molecule that is encoded in the genome of human. UniProtKB:P09326 B-lymphocyte activation marker BLAST-1 (human) BCM1 surface antigen (human) SLAM family member 2 (human) SLAMF2 (human) TCT.1 (human) hCD48 leukocyte antigen MEM-102 (human) signaling lymphocytic activation molecule 2 (human) protein BCM1 BLAST1 CD48 PR:P09326 Category=organism-gene. CD48 antigen (human) A CD48 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P09326 B-lymphocyte activation marker BLAST-1 (human) UniProtKB:P09326 BCM1 surface antigen (human) UniProtKB:P09326 SLAM family member 2 (human) UniProtKB:P09326 SLAMF2 (human) UniProtKB:P09326 TCT.1 (human) UniProtKB:P09326 hCD48 PRO:DNx leukocyte antigen MEM-102 (human) UniProtKB:P09326 signaling lymphocytic activation molecule 2 (human) UniProtKB:P09326 BCM1 UniProtKB:P09326 BLAST1 UniProtKB:P09326 CD48 UniProtKB:P09326 A CD7 molecule that is encoded in the genome of human. UniProtKB:P09564 GP40 (human) T-cell leukemia antigen (human) T-cell surface antigen Leu-9 (human) TP41 (human) hCD7 protein CD7 PR:P09564 Category=organism-gene. T-cell antigen CD7 (human) A CD7 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P09564 GP40 (human) UniProtKB:P09564 T-cell leukemia antigen (human) UniProtKB:P09564 T-cell surface antigen Leu-9 (human) UniProtKB:P09564 TP41 (human) UniProtKB:P09564 hCD7 PRO:DNx CD7 UniProtKB:P09564 A DNA nucleotidylexotransferase that is encoded in the genome of mouse. UniProtKB:P09838 TDT (mouse) mDNTT terminal addition enzyme (mouse) terminal deoxynucleotidyltransferase (mouse) protein Dntt Tdt terminal transferase (mouse) PR:P09838 Category=organism-gene. DNA nucleotidylexotransferase (mouse) A DNA nucleotidylexotransferase that is encoded in the genome of mouse. OMA:P09838 PRO:DNx TDT (mouse) UniProtKB:P09838 mDNTT PRO:DNx terminal addition enzyme (mouse) UniProtKB:P09838 terminal deoxynucleotidyltransferase (mouse) UniProtKB:P09838 Dntt UniProtKB:P09838 Tdt UniProtKB:P09838 terminal transferase (mouse) UniProtKB:P09838 A lymphocyte antigen 6C2 that is encoded in the genome of mouse. UniProtKB:P0CW03 Ly-6C2 (mouse) mLy6c2 protein Ly6c Ly6c2 PR:P0CW03 Category=organism-gene. lymphocyte antigen 6C2 (mouse) A lymphocyte antigen 6C2 that is encoded in the genome of mouse. PRO:CNA UniProtKB:P0CW03 Ly-6C2 (mouse) UniProtKB:P0CW03 mLy6c2 PRO:DNx Ly6c UniProtKB:P0CW03 Ly6c2 UniProtKB:P0CW03 A mast/stem cell growth factor receptor that is encoded in the genome of human. DTO:03100231 UniProtKB:P10721 CD117 (human) PBT (human) hKIT p145 c-kit (human) piebald trait protein (human) proto-oncogene c-Kit (human) tyrosine-protein kinase Kit (human) v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (human) protein KIT SCFR PR:P10721 Category=organism-gene. mast/stem cell growth factor receptor Kit (human) A mast/stem cell growth factor receptor that is encoded in the genome of human. PRO:WCB UniProtKB:P10721 CD117 (human) UniProtKB:P10721 PBT (human) UniProtKB:P10721 hKIT PRO:DNx p145 c-kit (human) UniProtKB:P10721 piebald trait protein (human) UniProtKB:P10721 proto-oncogene c-Kit (human) UniProtKB:P10721 tyrosine-protein kinase Kit (human) UniProtKB:P10721 v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (human) UniProtKB:P10721 KIT UniProtKB:P10721 SCFR UniProtKB:P10721 A CD14 molecule that is encoded in the genome of mouse. UniProtKB:P10810 CD14 (mouse) mCD14 myeloid cell-specific leucine-rich glycoprotein (mouse) protein Cd14 PR:P10810 Category=organism-gene. monocyte differentiation antigen CD14 (mouse) A CD14 molecule that is encoded in the genome of mouse. OMA:P10810 PRO:WCB CD14 (mouse) UniProtKB:P10810 mCD14 PRO:DNx myeloid cell-specific leucine-rich glycoprotein (mouse) UniProtKB:P10810 Cd14 UniProtKB:P10810 An integrin alpha-M that is encoded in the genome of human. UniProtKB:P11215 CD11 antigen-like family member B (human) CR-3 alpha chain (human) cell surface glycoprotein MAC-1 subunit alpha (human) hITGAM leukocyte adhesion receptor MO1 (human) neutrophil adherence receptor (human) protein CD11B CR3A ITGAM PR:P11215 Category=organism-gene. integrin alpha-M (human) An integrin alpha-M that is encoded in the genome of human. PRO:DNx UniProtKB:P11215 CD11 antigen-like family member B (human) UniProtKB:P11215 CR-3 alpha chain (human) UniProtKB:P11215 cell surface glycoprotein MAC-1 subunit alpha (human) UniProtKB:P11215 hITGAM PRO:DNx leukocyte adhesion receptor MO1 (human) UniProtKB:P11215 neutrophil adherence receptor (human) UniProtKB:P11215 CD11B UniProtKB:P11215 CR3A UniProtKB:P11215 ITGAM UniProtKB:P11215 A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human. UniProtKB:P11836 B-lymphocyte surface antigen B1 (human) Bp35 (human) hMS4A1 leukocyte surface antigen Leu-16 (human) membrane-spanning 4-domains subfamily A member 1 (human) protein CD20 MS4A1 PR:P11836 Category=organism-gene. B-lymphocyte antigen CD20 (human) A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P11836 B-lymphocyte surface antigen B1 (human) UniProtKB:P11836 Bp35 (human) UniProtKB:P11836 hMS4A1 PRO:DNx leukocyte surface antigen Leu-16 (human) UniProtKB:P11836 membrane-spanning 4-domains subfamily A member 1 (human) UniProtKB:P11836 CD20 UniProtKB:P11836 MS4A1 UniProtKB:P11836 A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of human. FcERI (human) UniProtKB:P12319 Fc-epsilon RI-alpha (human) IgE Fc receptor subunit alpha (human) hFCER1A protein FCE1A FCER1A PR:P12319 Category=organism-gene. high affinity immunoglobulin epsilon receptor subunit alpha (human) A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of human. PRO:DNx UniProtKB:P12319 FcERI (human) UniProtKB:P12319 Fc-epsilon RI-alpha (human) UniProtKB:P12319 IgE Fc receptor subunit alpha (human) UniProtKB:P12319 hFCER1A PRO:DNx FCE1A UniProtKB:P12319 FCER1A UniProtKB:P12319 A thyrotropin subunit beta that is encoded in the genome of mouse. UniProtKB:P12656 TSH-B (mouse) TSH-beta (mouse) mTSHB thyroid-stimulating hormone subunit beta (mouse) thyrotropin beta chain (mouse) protein Tshb PR:P12656 Category=organism-gene. thyrotropin subunit beta (mouse) A thyrotropin subunit beta that is encoded in the genome of mouse. OMA:P12656 PRO:DNx TSH-B (mouse) UniProtKB:P12656 TSH-beta (mouse) UniProtKB:P12656 mTSHB PRO:DNx thyroid-stimulating hormone subunit beta (mouse) UniProtKB:P12656 thyrotropin beta chain (mouse) UniProtKB:P12656 Tshb UniProtKB:P12656 A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse. UniProtKB:P13379 CD5 (mouse) Lyt-1 (mouse) lymphocyte antigen 1 (mouse) mCD5 protein Cd5 Ly-1 PR:P13379 Category=organism-gene. T-cell surface glycoprotein CD5 (mouse) A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse. OMA:P13379 PRO:DNx CD5 (mouse) UniProtKB:P13379 Lyt-1 (mouse) UniProtKB:P13379 lymphocyte antigen 1 (mouse) UniProtKB:P13379 mCD5 PRO:DNx Cd5 UniProtKB:P13379 Ly-1 UniProtKB:P13379 A neural cell adhesion molecule 1 that is encoded in the genome of human. UniProtKB:P13591 CD56 (human) N-CAM-1 (human) NCAM-1 (human) hNCAM1 protein NCAM NCAM1 PR:P13591 Category=organism-gene. neural cell adhesion molecule 1 (human) A neural cell adhesion molecule 1 that is encoded in the genome of human. PRO:CNA UniProtKB:P13591 CD56 (human) UniProtKB:P13591 N-CAM-1 (human) UniProtKB:P13591 NCAM-1 (human) UniProtKB:P13591 hNCAM1 PRO:DNx NCAM UniProtKB:P13591 NCAM1 UniProtKB:P13591 A neural cell adhesion molecule 1 that is encoded in the genome of mouse. UniProtKB:P13595 CD56 (mouse) N-CAM-1 (mouse) NCAM-1 (mouse) mNCAM1 protein Ncam Ncam1 PR:P13595 Category=organism-gene. neural cell adhesion molecule 1 (mouse) A neural cell adhesion molecule 1 that is encoded in the genome of mouse. OMA:P13595 PRO:DNx CD56 (mouse) UniProtKB:P13595 N-CAM-1 (mouse) UniProtKB:P13595 NCAM-1 (mouse) UniProtKB:P13595 mNCAM1 PRO:DNx Ncam UniProtKB:P13595 Ncam1 UniProtKB:P13595 An interleukin-2 receptor subunit beta that is encoded in the genome of human. p75 (human) UniProtKB:P14784 CD122 (human) IL-2 receptor subunit beta (human) IL-2R subunit beta (human) IL-2RB (human) hIL2RB high affinity IL-2 receptor subunit beta (human) interleukin-15 receptor subunit beta (human) p70-75 (human) protein IL15RB IL2RB PR:P14784 Category=organism-gene. interleukin-2 receptor subunit beta (human) An interleukin-2 receptor subunit beta that is encoded in the genome of human. PRO:CNA UniProtKB:P14784 p75 (human) UniProtKB:P14784 CD122 (human) UniProtKB:P14784 IL-2 receptor subunit beta (human) UniProtKB:P14784 IL-2R subunit beta (human) UniProtKB:P14784 IL-2RB (human) UniProtKB:P14784 hIL2RB PRO:DNx high affinity IL-2 receptor subunit beta (human) UniProtKB:P14784 interleukin-15 receptor subunit beta (human) UniProtKB:P14784 p70-75 (human) UniProtKB:P14784 IL15RB UniProtKB:P14784 IL2RB UniProtKB:P14784 A CD44 molecule that is encoded in the genome of mouse. UniProtKB:P15379 CD44 (mouse) ECMR-III (mouse) GP90 lymphocyte homing/adhesion receptor (mouse) HUTCH-I (mouse) PGP-1 (mouse) PGP-I (mouse) extracellular matrix receptor III (mouse) hermes antigen (mouse) hyaluronate receptor (mouse) lymphocyte antigen 24 (mouse) mCD44 phagocytic glycoprotein 1 (mouse) phagocytic glycoprotein I (mouse) protein Cd44 Ly-24 PR:P15379 Category=organism-gene. CD44 antigen (mouse) A CD44 molecule that is encoded in the genome of mouse. OMA:P15379 PRO:WCB CD44 (mouse) UniProtKB:P15379 ECMR-III (mouse) UniProtKB:P15379 GP90 lymphocyte homing/adhesion receptor (mouse) UniProtKB:P15379 HUTCH-I (mouse) UniProtKB:P15379 PGP-1 (mouse) UniProtKB:P15379 PGP-I (mouse) UniProtKB:P15379 extracellular matrix receptor III (mouse) UniProtKB:P15379 hermes antigen (mouse) UniProtKB:P15379 hyaluronate receptor (mouse) UniProtKB:P15379 lymphocyte antigen 24 (mouse) UniProtKB:P15379 mCD44 PRO:DNx phagocytic glycoprotein 1 (mouse) UniProtKB:P15379 phagocytic glycoprotein I (mouse) UniProtKB:P15379 Cd44 UniProtKB:P15379 Ly-24 UniProtKB:P15379 A CD19 molecule that is encoded in the genome of human. UniProtKB:P15391 B-lymphocyte surface antigen B4 (human) T-cell surface antigen Leu-12 (human) differentiation antigen CD19 (human) hCD19 protein CD19 PR:P15391 Category=organism-gene. B-lymphocyte antigen CD19 (human) B-lymphocyte surface antigen B4 (human) UniProtKB:P15391 T-cell surface antigen Leu-12 (human) UniProtKB:P15391 differentiation antigen CD19 (human) UniProtKB:P15391 hCD19 PRO:DNx CD19 UniProtKB:P15391 A leukosialin that is encoded in the genome of mouse. UniProtKB:P15702 B-cell differentiation antigen LP-3 (mouse) CD43 (mouse) Ly-48 (mouse) leukocyte sialoglycoprotein (mouse) lymphocyte antigen 48 (mouse) mSPN sialophorin (mouse) protein Spn PR:P15702 Category=organism-gene. leukosialin (mouse) A leukosialin that is encoded in the genome of mouse. OMA:P15702 PRO:DNx B-cell differentiation antigen LP-3 (mouse) UniProtKB:P15702 CD43 (mouse) UniProtKB:P15702 Ly-48 (mouse) UniProtKB:P15702 leukocyte sialoglycoprotein (mouse) UniProtKB:P15702 lymphocyte antigen 48 (mouse) UniProtKB:P15702 mSPN PRO:DNx sialophorin (mouse) UniProtKB:P15702 Spn UniProtKB:P15702 A V(D)J recombination-activating protein 1 that is encoded in the genome of human. Reactome:R-HSA-5692681 UniProtKB:P15918 RAG-1 (human) RING finger protein 74 (human) hRAG1 protein RAG1 RNF74 PR:P15918 Category=organism-gene. V(D)J recombination-activating protein 1 (human) A V(D)J recombination-activating protein 1 that is encoded in the genome of human. PRO:CNA UniProtKB:P15918 Reactome:R-HSA-5692681 PR:P15918 located_in GO:0005654 RAG-1 (human) UniProtKB:P15918 RING finger protein 74 (human) UniProtKB:P15918 hRAG1 PRO:DNx RAG1 UniProtKB:P15918 RNF74 UniProtKB:P15918 A V(D)J recombination-activating protein 1 that is encoded in the genome of mouse. UniProtKB:P15919 RAG-1 (mouse) mRAG1 protein Rag1 PR:P15919 Category=organism-gene. V(D)J recombination-activating protein 1 (mouse) A V(D)J recombination-activating protein 1 that is encoded in the genome of mouse. OMA:P15919 PRO:DNx RAG-1 (mouse) UniProtKB:P15919 mRAG1 PRO:DNx Rag1 UniProtKB:P15919 An erythroid transcription factor that is encoded in the genome of human. GF-1 (human) Reactome:R-HSA-996772 UniProtKB:P15976 GATA-1 (human) GATA-binding factor 1 (human) NF-E1 DNA-binding protein (human) hGATA1 protein ERYF1 GATA1 GF1 PR:P15976 Category=organism-gene. erythroid transcription factor (human) An erythroid transcription factor that is encoded in the genome of human. PRO:DNx UniProtKB:P15976 GF-1 (human) UniProtKB:P15976 Reactome:R-HSA-996772 PR:P15976 located_in GO:0005654 GATA-1 (human) UniProtKB:P15976 GATA-binding factor 1 (human) UniProtKB:P15976 NF-E1 DNA-binding protein (human) UniProtKB:P15976 hGATA1 PRO:DNx ERYF1 UniProtKB:P15976 GATA1 UniProtKB:P15976 GF1 UniProtKB:P15976 A CD44 molecule that is encoded in the genome of human. PGP-I (human) UniProtKB:P16070 CDw44 (human) ECMR-III (human) GP90 lymphocyte homing/adhesion receptor (human) HUTCH-I (human) PGP-1 (human) epican (human) extracellular matrix receptor III (human) hCD44 heparan sulfate proteoglycan (human) hermes antigen (human) hyaluronate receptor (human) phagocytic glycoprotein 1 (human) phagocytic glycoprotein I (human) protein CD44 LHR MDU2 MDU3 MIC4 PR:P16070 Category=organism-gene. CD44 antigen (human) A CD44 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P16070 PGP-I (human) UniProtKB:P16070 CDw44 (human) UniProtKB:P16070 ECMR-III (human) UniProtKB:P16070 GP90 lymphocyte homing/adhesion receptor (human) UniProtKB:P16070 HUTCH-I (human) UniProtKB:P16070 PGP-1 (human) UniProtKB:P16070 epican (human) UniProtKB:P16070 extracellular matrix receptor III (human) UniProtKB:P16070 hCD44 PRO:DNx heparan sulfate proteoglycan (human) UniProtKB:P16070 hermes antigen (human) UniProtKB:P16070 hyaluronate receptor (human) UniProtKB:P16070 phagocytic glycoprotein 1 (human) UniProtKB:P16070 phagocytic glycoprotein I (human) UniProtKB:P16070 CD44 UniProtKB:P16070 LHR UniProtKB:P16070 MDU2 UniProtKB:P16070 MDU3 UniProtKB:P16070 MIC4 UniProtKB:P16070 A leukosialin that is encoded in the genome of human. UniProtKB:P16150 GALGP (human) GPL115 (human) galactoglycoprotein (human) hSPN leukocyte sialoglycoprotein (human) sialophorin (human) protein CD43 SPN PR:P16150 Category=organism-gene. leukosialin (human) A leukosialin that is encoded in the genome of human. PRO:WCB UniProtKB:P16150 GALGP (human) UniProtKB:P16150 GPL115 (human) UniProtKB:P16150 galactoglycoprotein (human) UniProtKB:P16150 hSPN PRO:DNx leukocyte sialoglycoprotein (human) UniProtKB:P16150 sialophorin (human) UniProtKB:P16150 CD43 UniProtKB:P16150 SPN UniProtKB:P16150 An interleukin-2 receptor subunit beta that is encoded in the genome of mouse. UniProtKB:P16297 CD122 (mouse) IL-2 receptor subunit beta (mouse) IL-2R subunit beta (mouse) IL-2RB (mouse) high affinity IL-2 receptor subunit beta (mouse) mIL2RB p70-75 (mouse) protein Il2rb PR:P16297 Category=organism-gene. interleukin-2 receptor subunit beta (mouse) An interleukin-2 receptor subunit beta that is encoded in the genome of mouse. OMA:P16297 PRO:DNx CD122 (mouse) UniProtKB:P16297 IL-2 receptor subunit beta (mouse) UniProtKB:P16297 IL-2R subunit beta (mouse) UniProtKB:P16297 IL-2RB (mouse) UniProtKB:P16297 high affinity IL-2 receptor subunit beta (mouse) UniProtKB:P16297 mIL2RB PRO:DNx p70-75 (mouse) UniProtKB:P16297 Il2rb UniProtKB:P16297 An interleukin-7 receptor subunit alpha that is encoded in the genome of human. UniProtKB:P16871 CD127 (human) CDw127 (human) IL-7 receptor subunit alpha (human) IL-7R subunit alpha (human) IL-7R-alpha (human) IL-7RA (human) hIL7R protein IL7R PR:P16871 Category=organism-gene. interleukin-7 receptor subunit alpha (human) An interleukin-7 receptor subunit alpha that is encoded in the genome of human. PRO:WCB UniProtKB:P16871 CD127 (human) UniProtKB:P16871 CDw127 (human) UniProtKB:P16871 IL-7 receptor subunit alpha (human) UniProtKB:P16871 IL-7R subunit alpha (human) UniProtKB:P16871 IL-7R-alpha (human) UniProtKB:P16871 IL-7RA (human) UniProtKB:P16871 hIL7R PRO:DNx IL7R UniProtKB:P16871 An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P16872 CD127 (mouse) IL-7 receptor subunit alpha (mouse) IL-7R subunit alpha (mouse) IL-7R-alpha (mouse) IL-7RA (mouse) mIL7R protein Il7r PR:P16872 Category=organism-gene. interleukin-7 receptor subunit alpha (mouse) An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse. OMA:P16872 PRO:DNx CD127 (mouse) UniProtKB:P16872 IL-7 receptor subunit alpha (mouse) UniProtKB:P16872 IL-7R subunit alpha (mouse) UniProtKB:P16872 IL-7R-alpha (mouse) UniProtKB:P16872 IL-7RA (mouse) UniProtKB:P16872 mIL7R PRO:DNx Il7r UniProtKB:P16872 An aspartate aminotransferase, cytoplasmic that is encoded in the genome of human. transaminase A (human) UniProtKB:P17174 cAspAT (human) cCAT (human) cysteine aminotransferase, cytoplasmic (human) cysteine transaminase, cytoplasmic (human) glutamate oxaloacetate transaminase 1 (human) hGOT1 protein GOT1 PR:P17174 Category=organism-gene. aspartate aminotransferase, cytoplasmic (human) An aspartate aminotransferase, cytoplasmic that is encoded in the genome of human. PRO:DNx UniProtKB:P17174 transaminase A (human) UniProtKB:P17174 cAspAT (human) UniProtKB:P17174 cCAT (human) UniProtKB:P17174 cysteine aminotransferase, cytoplasmic (human) UniProtKB:P17174 cysteine transaminase, cytoplasmic (human) UniProtKB:P17174 glutamate oxaloacetate transaminase 1 (human) UniProtKB:P17174 hGOT1 PRO:DNx GOT1 UniProtKB:P17174 A transcription factor PU.1 that is encoded in the genome of mouse. UniProtKB:P17433 31 kDa-transforming protein (mouse) SFFV proviral integration 1 protein (mouse) mSPI1 protein Sfpi-1 Sfpi1 Spi1 PR:P17433 Category=organism-gene. transcription factor PU.1 (mouse) A transcription factor PU.1 that is encoded in the genome of mouse. OMA:P17433 PRO:DNx 31 kDa-transforming protein (mouse) UniProtKB:P17433 SFFV proviral integration 1 protein (mouse) UniProtKB:P17433 mSPI1 PRO:DNx Sfpi-1 UniProtKB:P17433 Sfpi1 UniProtKB:P17433 Spi1 UniProtKB:P17433 A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human. Reactome:R-HSA-8956511 UniProtKB:P17542 Stem cell protein (human) T-cell leukemia/lymphoma protein 5 (human) TAL-1 (human) class A basic helix-loop-helix protein 17 (human) hTAL1 protein BHLHA17 SCL TAL1 TCL5 PR:P17542 Category=organism-gene. T-cell acute lymphocytic leukemia protein 1 (human) A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human. PRO:DNx UniProtKB:P17542 Reactome:R-HSA-8956511 PR:P17542 located_in GO:0005654 Stem cell protein (human) UniProtKB:P17542 T-cell leukemia/lymphoma protein 5 (human) UniProtKB:P17542 TAL-1 (human) UniProtKB:P17542 class A basic helix-loop-helix protein 17 (human) UniProtKB:P17542 hTAL1 PRO:DNx BHLHA17 UniProtKB:P17542 SCL UniProtKB:P17542 TAL1 UniProtKB:P17542 TCL5 UniProtKB:P17542 An erythroid transcription factor that is encoded in the genome of mouse. UniProtKB:P17679 Eryf1 (mouse) GATA-1 (mouse) GATA-binding factor 1 (mouse) GF-1 (mouse) NF-E1 DNA-binding protein (mouse) mGATA1 protein Gata1 Gf-1 PR:P17679 Category=organism-gene. erythroid transcription factor (mouse) An erythroid transcription factor that is encoded in the genome of mouse. OMA:P17679 PRO:DNx Eryf1 (mouse) UniProtKB:P17679 GATA-1 (mouse) UniProtKB:P17679 GATA-binding factor 1 (mouse) UniProtKB:P17679 GF-1 (mouse) UniProtKB:P17679 NF-E1 DNA-binding protein (mouse) UniProtKB:P17679 mGATA1 PRO:DNx Gata1 UniProtKB:P17679 Gf-1 UniProtKB:P17679 An endoglin that is encoded in the genome of human. UniProtKB:P17813 CD105 (human) hENG protein END ENG PR:P17813 Category=organism-gene. endoglin (human) An endoglin that is encoded in the genome of human. PRO:CNA UniProtKB:P17813 CD105 (human) UniProtKB:P17813 hENG PRO:DNx END UniProtKB:P17813 ENG UniProtKB:P17813 A transcription factor PU.1 that is encoded in the genome of human. Reactome:R-HSA-8865503 UniProtKB:P17947 31 kDa-transforming protein (human) hSPI1 protein SPI1 PR:P17947 Category=organism-gene. transcription factor PU.1 (human) A transcription factor PU.1 that is encoded in the genome of human. PRO:WCB UniProtKB:P17947 Reactome:R-HSA-8865503 PR:P17947 located_in GO:0005654 31 kDa-transforming protein (human) UniProtKB:P17947 hSPI1 PRO:DNx SPI1 UniProtKB:P17947 A CD48 molecule that is encoded in the genome of mouse. UniProtKB:P18181 BCM1 surface antigen (mouse) BLAST-1 (mouse) CD48 (mouse) HM48-1 (mouse) MRC OX-45 surface antigen (mouse) SLAM family member 2 (mouse) SLAMF2 (mouse) mCD48 sgp-60 (mouse) signaling lymphocytic activation molecule 2 (mouse) protein Bcm-1 Cd48 PR:P18181 Category=organism-gene. CD48 antigen (mouse) A CD48 molecule that is encoded in the genome of mouse. OMA:P18181 PRO:DNx BCM1 surface antigen (mouse) UniProtKB:P18181 BLAST-1 (mouse) UniProtKB:P18181 CD48 (mouse) UniProtKB:P18181 HM48-1 (mouse) UniProtKB:P18181 MRC OX-45 surface antigen (mouse) UniProtKB:P18181 SLAM family member 2 (mouse) UniProtKB:P18181 SLAMF2 (mouse) UniProtKB:P18181 mCD48 PRO:DNx sgp-60 (mouse) UniProtKB:P18181 signaling lymphocytic activation molecule 2 (mouse) UniProtKB:P18181 Bcm-1 UniProtKB:P18181 Cd48 UniProtKB:P18181 A syndecan-1 that is encoded in the genome of human. UniProtKB:P18827 CD138 (human) SYND1 (human) hSDC1 protein SDC SDC1 PR:P18827 Category=organism-gene. syndecan-1 (human) A syndecan-1 that is encoded in the genome of human. PRO:WCB UniProtKB:P18827 CD138 (human) UniProtKB:P18827 SYND1 (human) UniProtKB:P18827 hSDC1 PRO:DNx SDC UniProtKB:P18827 SDC1 UniProtKB:P18827 A syndecan-1 that is encoded in the genome of mouse. UniProtKB:P18828 CD138 (mouse) SYND1 (mouse) mSDC1 protein Sdc1 Synd-1 Synd1 PR:P18828 Category=organism-gene. syndecan-1 (mouse) A syndecan-1 that is encoded in the genome of mouse. OMA:P18828 PRO:DNx CD138 (mouse) UniProtKB:P18828 SYND1 (mouse) UniProtKB:P18828 mSDC1 PRO:DNx Sdc1 UniProtKB:P18828 Synd-1 UniProtKB:P18828 Synd1 UniProtKB:P18828 A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse. UniProtKB:P19437 B-cell differentiation antigen Ly-44 (mouse) CD20 (mouse) lymphocyte antigen 44 (mouse) mMS4A1 membrane-spanning 4-domains subfamily A member 1 (mouse) protein Cd20 Ly-44 Ms4a1 Ms4a2 PR:P19437 Category=organism-gene. B-lymphocyte antigen CD20 (mouse) A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse. OMA:P19437 PRO:DNx B-cell differentiation antigen Ly-44 (mouse) UniProtKB:P19437 CD20 (mouse) UniProtKB:P19437 lymphocyte antigen 44 (mouse) UniProtKB:P19437 mMS4A1 PRO:DNx membrane-spanning 4-domains subfamily A member 1 (mouse) UniProtKB:P19437 Cd20 UniProtKB:P19437 Ly-44 UniProtKB:P19437 Ms4a1 UniProtKB:P19437 Ms4a2 UniProtKB:P19437 A CD33 molecule that is encoded in the genome of human. UniProtKB:P20138 gp67 (human) hCD33 sialic acid-binding Ig-like lectin 3 (human) siglec-3 (human) protein CD33 SIGLEC3 PR:P20138 Category=organism-gene. myeloid cell surface antigen CD33 (human) A CD33 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P20138 gp67 (human) UniProtKB:P20138 hCD33 PRO:DNx sialic acid-binding Ig-like lectin 3 (human) UniProtKB:P20138 siglec-3 (human) UniProtKB:P20138 CD33 UniProtKB:P20138 SIGLEC3 UniProtKB:P20138 A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P20489 Fc-epsilon RI-alpha (mouse) IgE Fc receptor subunit alpha (mouse) mFCER1A protein FcERI (mouse) Fce1a Fcer1a PR:P20489 Category=organism-gene. high affinity immunoglobulin epsilon receptor subunit alpha (mouse) A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of mouse. OMA:P20489 PRO:DNx Fc-epsilon RI-alpha (mouse) UniProtKB:P20489 IgE Fc receptor subunit alpha (mouse) UniProtKB:P20489 mFCER1A PRO:DNx FcERI (mouse) UniProtKB:P20489 Fce1a UniProtKB:P20489 Fcer1a UniProtKB:P20489 An integrin alpha-X that is encoded in the genome of human. UniProtKB:P20702 CD11 antigen-like family member C (human) Leu M5 (human) hITGAX leukocyte adhesion glycoprotein p150,95 alpha chain (human) leukocyte adhesion receptor p150,95 (human) protein CD11C ITGAX PR:P20702 Category=organism-gene. integrin alpha-X (human) CD11 antigen-like family member C (human) UniProtKB:P20702 Leu M5 (human) UniProtKB:P20702 hITGAX PRO:DNx leukocyte adhesion glycoprotein p150,95 alpha chain (human) UniProtKB:P20702 leukocyte adhesion receptor p150,95 (human) UniProtKB:P20702 CD11C UniProtKB:P20702 ITGAX UniProtKB:P20702 An interleukin-5 receptor subunit alpha that is encoded in the genome of mouse. UniProtKB:P21183 CD125 (mouse) IL-5 receptor subunit alpha (mouse) IL-5R subunit alpha (mouse) IL-5R-alpha (mouse) IL-5RA (mouse) mIL5RA protein Il5r Il5ra PR:P21183 Category=organism-gene. interleukin-5 receptor subunit alpha (mouse) An interleukin-5 receptor subunit alpha that is encoded in the genome of mouse. OMA:P21183 PRO:DNx CD125 (mouse) UniProtKB:P21183 IL-5 receptor subunit alpha (mouse) UniProtKB:P21183 IL-5R subunit alpha (mouse) UniProtKB:P21183 IL-5R-alpha (mouse) UniProtKB:P21183 IL-5RA (mouse) UniProtKB:P21183 mIL5RA PRO:DNx Il5r UniProtKB:P21183 Il5ra UniProtKB:P21183 A 5'-nucleotidase that is encoded in the genome of human. 5'-NT (human) ecto-5'-nucleotidase (human) UniProtKB:P21589 CD73 (human) IMP-specific 5'-nucleotidase (human) hNT5E thymidylate 5'-phosphatase (human) protein 5'-deoxynucleotidase (human) NT5 NT5E NTE PR:P21589 Category=organism-gene. 5'-nucleotidase (human) A 5'-nucleotidase that is encoded in the genome of human. PRO:WCB UniProtKB:P21589 5'-NT (human) UniProtKB:P21589 ecto-5'-nucleotidase (human) UniProtKB:P21589 CD73 (human) UniProtKB:P21589 IMP-specific 5'-nucleotidase (human) UniProtKB:P21589 hNT5E PRO:DNx thymidylate 5'-phosphatase (human) UniProtKB:P21589 5'-deoxynucleotidase (human) UniProtKB:P21589 NT5 UniProtKB:P21589 NT5E UniProtKB:P21589 NTE UniProtKB:P21589 A V(D)J recombination-activating protein 2 that is encoded in the genome of mouse. UniProtKB:P21784 RAG-2 (mouse) mRAG2 protein Rag-2 Rag2 PR:P21784 Category=organism-gene. V(D)J recombination-activating protein 2 (mouse) A V(D)J recombination-activating protein 2 that is encoded in the genome of mouse. OMA:P21784 PRO:DNx RAG-2 (mouse) UniProtKB:P21784 mRAG2 PRO:DNx Rag-2 UniProtKB:P21784 Rag2 UniProtKB:P21784 A CD9 molecule that is encoded in the genome of human. p24 (human) UniProtKB:P21926 5H9 antigen (human) MRP-1 (human) cell growth-inhibiting gene 2 protein (human) hCD9 leukocyte antigen MIC3 (human) motility-related protein (human) tetraspanin-29 (human) tspan-29 (human) protein CD9 GIG2 MIC3 TSPAN29 PR:P21926 Category=organism-gene. CD9 antigen (human) A CD9 molecule that is encoded in the genome of human. PRO:DNx UniProtKB:P21926 p24 (human) UniProtKB:P21926 5H9 antigen (human) UniProtKB:P21926 MRP-1 (human) UniProtKB:P21926 cell growth-inhibiting gene 2 protein (human) UniProtKB:P21926 hCD9 PRO:DNx leukocyte antigen MIC3 (human) UniProtKB:P21926 motility-related protein (human) UniProtKB:P21926 tetraspanin-29 (human) UniProtKB:P21926 tspan-29 (human) UniProtKB:P21926 CD9 UniProtKB:P21926 GIG2 UniProtKB:P21926 MIC3 UniProtKB:P21926 TSPAN29 UniProtKB:P21926 A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse. UniProtKB:P22091 Stem cell protein (mouse) TAL-1 (mouse) mTAL1 protein Scl Tal-1 Tal1 PR:P22091 Category=organism-gene. T-cell acute lymphocytic leukemia protein 1 homolog (mouse) A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse. OMA:P22091 PRO:DNx Stem cell protein (mouse) UniProtKB:P22091 TAL-1 (mouse) UniProtKB:P22091 mTAL1 PRO:DNx Scl UniProtKB:P22091 Tal-1 UniProtKB:P22091 Tal1 UniProtKB:P22091 A CD3 epsilon that is encoded in the genome of mouse. UniProtKB:P22646 CD3e (mouse) T-cell surface antigen T3/Leu-4 epsilon chain (mouse) mCD3E protein Cd3e PR:P22646 Category=organism-gene. T-cell surface glycoprotein CD3 epsilon chain (mouse) A CD3 epsilon that is encoded in the genome of mouse. OMA:P22646 PRO:DNx CD3e (mouse) UniProtKB:P22646 T-cell surface antigen T3/Leu-4 epsilon chain (mouse) UniProtKB:P22646 mCD3E PRO:DNx Cd3e UniProtKB:P22646 An endothelial transcription factor GATA-2 that is encoded in the genome of human. Reactome:R-HSA-996735 UniProtKB:P23769 GATA-binding protein 2 (human) hGATA2 protein GATA2 PR:P23769 Category=organism-gene. endothelial transcription factor GATA-2 (human) An endothelial transcription factor GATA-2 that is encoded in the genome of human. PRO:DNx UniProtKB:P23769 Reactome:R-HSA-996735 PR:P23769 located_in GO:0005654 GATA-binding protein 2 (human) UniProtKB:P23769 hGATA2 PRO:DNx GATA2 UniProtKB:P23769 A signal transducer CD24 that is encoded in the genome of mouse. UniProtKB:P24807 CD24 (mouse) HSA (mouse) M1/69-J11D heat stable antigen (mouse) R13-Ag (mouse) X62 heat stable antigen (mouse) lymphocyte antigen 52 (mouse) mCD24 nectadrin (mouse) protein Cd24 Cd24a Ly-52 PR:P24807 Category=organism-gene. signal transducer CD24 (mouse) A signal transducer CD24 that is encoded in the genome of mouse. OMA:P24807 PRO:WCB CD24 (mouse) UniProtKB:P24807 HSA (mouse) UniProtKB:P24807 M1/69-J11D heat stable antigen (mouse) UniProtKB:P24807 R13-Ag (mouse) UniProtKB:P24807 X62 heat stable antigen (mouse) UniProtKB:P24807 lymphocyte antigen 52 (mouse) UniProtKB:P24807 mCD24 PRO:DNx nectadrin (mouse) UniProtKB:P24807 Cd24 UniProtKB:P24807 Cd24a UniProtKB:P24807 Ly-52 UniProtKB:P24807 A signal transducer CD24 that is encoded in the genome of human. UniProtKB:P25063 hCD24 small cell lung carcinoma cluster 4 antigen (human) protein CD24 CD24A PR:P25063 Category=organism-gene. signal transducer CD24 (human) A signal transducer CD24 that is encoded in the genome of human. PRO:WCB UniProtKB:P25063 hCD24 PRO:DNx small cell lung carcinoma cluster 4 antigen (human) UniProtKB:P25063 CD24 UniProtKB:P25063 CD24A UniProtKB:P25063 A CD19 molecule that is encoded in the genome of mouse. UniProtKB:P25918 CD19 (mouse) differentiation antigen CD19 (mouse) mCD19 protein Cd19 PR:P25918 Category=organism-gene. B-lymphocyte antigen CD19 (mouse) A CD19 molecule that is encoded in the genome of mouse. OMA:P25918 PRO:DNx CD19 (mouse) UniProtKB:P25918 differentiation antigen CD19 (mouse) UniProtKB:P25918 mCD19 PRO:DNx Cd19 UniProtKB:P25918 An integrin beta-7 that is encoded in the genome of human. UniProtKB:P26010 Gut homing receptor beta subunit (human) hITGB7 protein ITGB7 PR:P26010 Category=organism-gene. integrin beta-7 (human) An integrin beta-7 that is encoded in the genome of human. PRO:DNx UniProtKB:P26010 Gut homing receptor beta subunit (human) UniProtKB:P26010 hITGB7 PRO:DNx ITGB7 UniProtKB:P26010 An integrin beta-7 that is encoded in the genome of mouse. UniProtKB:P26011 M290 IEL antigen (mouse) integrin beta-P (mouse) mITGB7 protein Itgb7 PR:P26011 Category=organism-gene. integrin beta-7 (mouse) An integrin beta-7 that is encoded in the genome of mouse. OMA:P26011 PRO:DNx M290 IEL antigen (mouse) UniProtKB:P26011 integrin beta-P (mouse) UniProtKB:P26011 mITGB7 PRO:DNx Itgb7 UniProtKB:P26011 A CD27 molecule that is encoded in the genome of human. UniProtKB:P26842 CD27L receptor (human) T-cell activation antigen CD27 (human) T14 (human) hCD27 tumor necrosis factor receptor superfamily member 7 (human) protein CD27 TNFRSF7 PR:P26842 Category=organism-gene. CD27 antigen (human) A CD27 molecule that is encoded in the genome of human. PRO:WCB UniProtKB:P26842 CD27L receptor (human) UniProtKB:P26842 T-cell activation antigen CD27 (human) UniProtKB:P26842 T14 (human) UniProtKB:P26842 hCD27 PRO:DNx tumor necrosis factor receptor superfamily member 7 (human) UniProtKB:P26842 CD27 UniProtKB:P26842 TNFRSF7 UniProtKB:P26842 An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of human. UniProtKB:P26951 CD123 (human) IL-3 receptor subunit alpha (human) IL-3R subunit alpha (human) IL-3R-alpha (human) IL-3RA (human) hIL3RA protein IL3R IL3RA PR:P26951 Category=organism-gene. interleukin-3 receptor subunit alpha (human) An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of human. PRO:WCB UniProtKB:P26951 CD123 (human) UniProtKB:P26951 IL-3 receptor subunit alpha (human) UniProtKB:P26951 IL-3R subunit alpha (human) UniProtKB:P26951 IL-3R-alpha (human) UniProtKB:P26951 IL-3RA (human) UniProtKB:P26951 hIL3RA PRO:DNx IL3R UniProtKB:P26951 IL3RA UniProtKB:P26951 An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of mouse. UniProtKB:P26952 CD123 (mouse) IL-3 receptor subunit alpha (mouse) IL-3R subunit alpha (mouse) IL-3R-alpha (mouse) IL-3RA (mouse) interleukin-3 receptor class II alpha chain (mouse) mIL3RA protein Il3ra Sut-1 PR:P26952 Category=organism-gene. interleukin-3 receptor subunit alpha (mouse) An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of mouse. OMA:P26952 PRO:DNx CD123 (mouse) UniProtKB:P26952 IL-3 receptor subunit alpha (mouse) UniProtKB:P26952 IL-3R subunit alpha (mouse) UniProtKB:P26952 IL-3R-alpha (mouse) UniProtKB:P26952 IL-3RA (mouse) UniProtKB:P26952 interleukin-3 receptor class II alpha chain (mouse) UniProtKB:P26952 mIL3RA PRO:DNx Il3ra UniProtKB:P26952 Sut-1 UniProtKB:P26952 A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of mouse. UniProtKB:P27548 CD154 (mouse) CD40-L (mouse) T-cell antigen Gp39 (mouse) TNF-related activation protein (mouse) TRAP (mouse) mCD40LG tumor necrosis factor ligand superfamily member 5 (mouse) protein Cd40l Cd40lg Tnfsf5 PR:P27548 Category=organism-gene. CD40 ligand (mouse) A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of mouse. OMA:P27548 PRO:DNx CD154 (mouse) UniProtKB:P27548 CD40-L (mouse) UniProtKB:P27548 T-cell antigen Gp39 (mouse) UniProtKB:P27548 TNF-related activation protein (mouse) UniProtKB:P27548 TRAP (mouse) UniProtKB:P27548 mCD40LG PRO:DNx tumor necrosis factor ligand superfamily member 5 (mouse) UniProtKB:P27548 Cd40l UniProtKB:P27548 Cd40lg UniProtKB:P27548 Tnfsf5 UniProtKB:P27548 A killer cell lectin-like receptor subfamily B member 1C that is encoded in the genome of mouse. UniProtKB:P27814 CD161 antigen-like family member C (mouse) CD161c (mouse) Ly-55c (mouse) NK1.1 (mouse) NKR-P1 40 (mouse) NKR-P1.9 (mouse) NKR-P1C (mouse) lymphocyte antigen 55c (mouse) mKlrb1c natural killer cell surface protein P1-40 (mouse) protein Klrb1c Ly55c Nkrp1c PR:P27814 Category=organism-gene. killer cell lectin-like receptor subfamily B member 1C (mouse) A killer cell lectin-like receptor subfamily B member 1C that is encoded in the genome of mouse. PRO:CNA UniProtKB:P27814 CD161 antigen-like family member C (mouse) UniProtKB:P27814 CD161c (mouse) UniProtKB:P27814 Ly-55c (mouse) UniProtKB:P27814 NK1.1 (mouse) UniProtKB:P27814 NKR-P1 40 (mouse) UniProtKB:P27814 NKR-P1.9 (mouse) UniProtKB:P27814 NKR-P1C (mouse) UniProtKB:P27814 lymphocyte antigen 55c (mouse) UniProtKB:P27814 mKlrb1c PRO:DNx natural killer cell surface protein P1-40 (mouse) UniProtKB:P27814 Klrb1c UniProtKB:P27814 Ly55c UniProtKB:P27814 Nkrp1c UniProtKB:P27814 A CD34 molecule that is encoded in the genome of human. UniProtKB:P28906 hCD34 protein CD34 PR:P28906 Category=organism-gene. hematopoietic progenitor cell antigen CD34 (human) hCD34 PRO:DNx CD34 UniProtKB:P28906 An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of human. Reactome:R-HSA-8938080 UniProtKB:P28907 2'-phospho-ADP-ribosyl cyclase (human) 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (human) 2'-phospho-cyclic-ADP-ribose transferase (human) ADP-ribosyl cyclase 1 (human) ADPRC 1 (human) T10 (human) cADPr hydrolase 1 (human) cyclic ADP-ribose hydrolase 1 (human) hCD38 protein CD38 PR:P28907 Category=organism-gene. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (human) An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P28907 Reactome:R-HSA-8938080 PR:P28907 located_in GO:0005886 2'-phospho-ADP-ribosyl cyclase (human) UniProtKB:P28907 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (human) UniProtKB:P28907 2'-phospho-cyclic-ADP-ribose transferase (human) UniProtKB:P28907 ADPRC 1 (human) UniProtKB:P28907 T10 (human) UniProtKB:P28907 cADPr hydrolase 1 (human) UniProtKB:P28907 cyclic ADP-ribose hydrolase 1 (human) UniProtKB:P28907 hCD38 PRO:DNx CD38 UniProtKB:P28907 A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of human. Reactome:R-HSA-198113 UniProtKB:P29965 CD154 (human) CD40-L (human) T-cell antigen Gp39 (human) TNF-related activation protein (human) hCD40LG tumor necrosis factor ligand superfamily member 5 (human) protein CD40L CD40LG TNFSF5 TRAP PR:P29965 Category=organism-gene. CD40 ligand (human) A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of human. PRO:WCB UniProtKB:P29965 Reactome:R-HSA-198113 PR:P29965 located_in GO:0005886 CD154 (human) UniProtKB:P29965 CD40-L (human) UniProtKB:P29965 T-cell antigen Gp39 (human) UniProtKB:P29965 TNF-related activation protein (human) UniProtKB:P29965 hCD40LG PRO:DNx tumor necrosis factor ligand superfamily member 5 (human) UniProtKB:P29965 CD40L UniProtKB:P29965 CD40LG UniProtKB:P29965 TNFSF5 UniProtKB:P29965 TRAP UniProtKB:P29965 A carcinoembryonic antigen-related cell adhesion molecule 8 that is encoded in the genome of human. UniProtKB:P31997 CD66b (human) CD67 antigen (human) carcinoembryonic antigen CGM6 (human) hCEACAM8 non-specific cross-reacting antigen NCA-95 (human) protein CEACAM8 CGM6 PR:P31997 Category=organism-gene. carcinoembryonic antigen-related cell adhesion molecule 8 (human) A carcinoembryonic antigen-related cell adhesion molecule 8 that is encoded in the genome of human. PRO:CNA UniProtKB:P31997 CD66b (human) UniProtKB:P31997 CD67 antigen (human) UniProtKB:P31997 carcinoembryonic antigen CGM6 (human) UniProtKB:P31997 hCEACAM8 PRO:DNx non-specific cross-reacting antigen NCA-95 (human) UniProtKB:P31997 CEACAM8 UniProtKB:P31997 CGM6 UniProtKB:P31997 A C-C chemokine receptor type 1 that is encoded in the genome of human. DTO:02100053 Reactome:R-HSA-373107 UniProtKB:P32246 C-C CKR-1 (human) CC-CKR-1 (human) CCR-1 (human) CD191 (human) HM145 (human) LD78 receptor (human) MIP-1alpha-R (human) RANTES-R (human) hCCR1 macrophage inflammatory protein 1-alpha receptor (human) protein CCR1 CMKBR1 CMKR1 SCYAR1 PR:P32246 Category=organism-gene. C-C chemokine receptor type 1 (human) A C-C chemokine receptor type 1 that is encoded in the genome of human. PRO:WCB UniProtKB:P32246 Reactome:R-HSA-373107 PR:P32246 located_in GO:0005886 C-C CKR-1 (human) UniProtKB:P32246 CC-CKR-1 (human) UniProtKB:P32246 CCR-1 (human) UniProtKB:P32246 CD191 (human) UniProtKB:P32246 HM145 (human) UniProtKB:P32246 LD78 receptor (human) UniProtKB:P32246 MIP-1alpha-R (human) UniProtKB:P32246 RANTES-R (human) UniProtKB:P32246 hCCR1 PRO:DNx macrophage inflammatory protein 1-alpha receptor (human) UniProtKB:P32246 CCR1 UniProtKB:P32246 CMKBR1 UniProtKB:P32246 CMKR1 UniProtKB:P32246 SCYAR1 UniProtKB:P32246 A cadherin-5 that is encoded in the genome of human. UniProtKB:P33151 7B4 antigen (human) CD144 (human) VE-cadherin (human) hCDH5 vascular endothelial cadherin (human) protein CDH5 PR:P33151 Category=organism-gene. cadherin-5 (human) A cadherin-5 that is encoded in the genome of human. PRO:WCB UniProtKB:P33151 7B4 antigen (human) UniProtKB:P33151 CD144 (human) UniProtKB:P33151 VE-cadherin (human) UniProtKB:P33151 hCDH5 PRO:DNx vascular endothelial cadherin (human) UniProtKB:P33151 CDH5 UniProtKB:P33151 A urokinase plasminogen activator surface receptor that is encoded in the genome of mouse. UniProtKB:P35456 CD87 (mouse) U-PAR (mouse) mPLAUR uPAR (mouse) protein Plaur PR:P35456 Category=organism-gene. urokinase plasminogen activator surface receptor (mouse) A urokinase plasminogen activator surface receptor that is encoded in the genome of mouse. OMA:P35456 PRO:DNx CD87 (mouse) UniProtKB:P35456 U-PAR (mouse) UniProtKB:P35456 mPLAUR PRO:DNx uPAR (mouse) UniProtKB:P35456 Plaur UniProtKB:P35456 A lymphocyte antigen 6G that is encoded in the genome of mouse. UniProtKB:P35461 Ly-6G (mouse) Ly-6G.1 (mouse) mLy6g protein Ly6g PR:P35461 Category=organism-gene. lymphocyte antigen 6G (mouse) A lymphocyte antigen 6G that is encoded in the genome of mouse. PRO:CNA UniProtKB:P35461 Ly-6G (mouse) UniProtKB:P35461 Ly-6G.1 (mouse) UniProtKB:P35461 mLy6g PRO:DNx Ly6g UniProtKB:P35461 A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse. UniProtKB:P35918 CD309 (mouse) FLK-1 (mouse) VEGFR-2 (mouse) fetal liver kinase 1 (mouse) kinase NYK (mouse) mKDR protein-tyrosine kinase receptor flk-1 (mouse) protein Flk-1 Flk1 Kdr PR:P35918 Category=organism-gene. vascular endothelial growth factor receptor 2 (mouse) A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse. OMA:P35918 PRO:DNx CD309 (mouse) UniProtKB:P35918 FLK-1 (mouse) UniProtKB:P35918 VEGFR-2 (mouse) UniProtKB:P35918 fetal liver kinase 1 (mouse) UniProtKB:P35918 kinase NYK (mouse) UniProtKB:P35918 mKDR PRO:DNx protein-tyrosine kinase receptor flk-1 (mouse) UniProtKB:P35918 Flk-1 UniProtKB:P35918 Flk1 UniProtKB:P35918 Kdr UniProtKB:P35918 A vascular endothelial growth factor receptor 2 that is encoded in the genome of human. DTO:03100560 UniProtKB:P35968 CD309 (human) FLK-1 (human) VEGFR-2 (human) fetal liver kinase 1 (human) hKDR kinase insert domain receptor (human) protein-tyrosine kinase receptor flk-1 (human) protein FLK1 KDR VEGFR2 PR:P35968 Category=organism-gene. vascular endothelial growth factor receptor 2 (human) A vascular endothelial growth factor receptor 2 that is encoded in the genome of human. PRO:WCB UniProtKB:P35968 CD309 (human) UniProtKB:P35968 FLK-1 (human) UniProtKB:P35968 VEGFR-2 (human) UniProtKB:P35968 fetal liver kinase 1 (human) UniProtKB:P35968 hKDR PRO:DNx kinase insert domain receptor (human) UniProtKB:P35968 protein-tyrosine kinase receptor flk-1 (human) UniProtKB:P35968 FLK1 UniProtKB:P35968 KDR UniProtKB:P35968 VEGFR2 UniProtKB:P35968 A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of human. STK-1 (human) DTO:03100154 UniProtKB:P36888 FL cytokine receptor (human) FLK-2 (human) FLT-3 (human) Stem cell tyrosine kinase 1 (human) fetal liver kinase-2 (human) fms-like tyrosine kinase 3 (human) hFLT3 protein CD135 FLK2 FLT3 STK1 PR:P36888 Category=organism-gene. receptor-type tyrosine-protein kinase FLT3 (human) A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of human. PRO:WCB UniProtKB:P36888 STK-1 (human) UniProtKB:P36888 FL cytokine receptor (human) UniProtKB:P36888 FLK-2 (human) UniProtKB:P36888 FLT-3 (human) UniProtKB:P36888 Stem cell tyrosine kinase 1 (human) UniProtKB:P36888 fetal liver kinase-2 (human) UniProtKB:P36888 fms-like tyrosine kinase 3 (human) UniProtKB:P36888 hFLT3 PRO:DNx CD135 UniProtKB:P36888 FLK2 UniProtKB:P36888 FLT3 UniProtKB:P36888 STK1 UniProtKB:P36888 A CD69 molecule that is encoded in the genome of mouse. UniProtKB:P37217 CD69 (mouse) mCD69 protein Cd69 PR:P37217 Category=organism-gene. early activation antigen CD69 (mouse) A CD69 molecule that is encoded in the genome of mouse. OMA:P37217 PRO:DNx CD69 (mouse) UniProtKB:P37217 mCD69 PRO:DNx Cd69 UniProtKB:P37217 A fibroblast growth factor 8 that is encoded in the genome of mouse. UniProtKB:P37237 AIGF (mouse) FGF-8 (mouse) androgen-induced growth factor (mouse) mFGF8 protein Aigf Fgf8 HBGF-8 (mouse) heparin-binding growth factor 8 (mouse) PR:P37237 Category=organism-gene. fibroblast growth factor 8 (mouse) A fibroblast growth factor 8 that is encoded in the genome of mouse. OMA:P37237 PRO:DNx AIGF (mouse) UniProtKB:P37237 FGF-8 (mouse) UniProtKB:P37237 androgen-induced growth factor (mouse) UniProtKB:P37237 mFGF8 PRO:DNx Aigf UniProtKB:P37237 Fgf8 UniProtKB:P37237 HBGF-8 (mouse) UniProtKB:P37237 heparin-binding growth factor 8 (mouse) UniProtKB:P37237 A CD9 molecule that is encoded in the genome of mouse. UniProtKB:P40240 CD9 (mouse) mCD9 protein Cd9 PR:P40240 Category=organism-gene. CD9 antigen (mouse) A CD9 molecule that is encoded in the genome of mouse. OMA:P40240 PRO:DNx CD9 (mouse) UniProtKB:P40240 mCD9 PRO:DNx Cd9 UniProtKB:P40240 A CD27 molecule that is encoded in the genome of mouse. UniProtKB:P41272 CD27 (mouse) CD27L receptor (mouse) T-cell activation antigen CD27 (mouse) mCD27 tumor necrosis factor receptor superfamily member 7 (mouse) protein Cd27 Tnfrsf7 PR:P41272 Category=organism-gene. CD27 antigen (mouse) A CD27 molecule that is encoded in the genome of mouse. OMA:P41272 PRO:DNx CD27 (mouse) UniProtKB:P41272 CD27L receptor (mouse) UniProtKB:P41272 T-cell activation antigen CD27 (mouse) UniProtKB:P41272 mCD27 PRO:DNx tumor necrosis factor receptor superfamily member 7 (mouse) UniProtKB:P41272 Cd27 UniProtKB:P41272 Tnfrsf7 UniProtKB:P41272 A CCAAT/enhancer-binding protein alpha that is encoded in the genome of human. Reactome:R-HSA-381289 UniProtKB:P49715 C/EBP alpha (human) hCEBPA protein CEBP CEBPA PR:P49715 Category=organism-gene. CCAAT/enhancer-binding protein alpha (human) A CCAAT/enhancer-binding protein alpha that is encoded in the genome of human. PRO:DNx UniProtKB:P49715 Reactome:R-HSA-381289 PR:P49715 located_in GO:0005654 C/EBP alpha (human) UniProtKB:P49715 hCEBPA PRO:DNx CEBP UniProtKB:P49715 CEBPA UniProtKB:P49715 A CD7 molecule that is encoded in the genome of mouse. UniProtKB:P50283 CD7 (mouse) mCD7 protein Cd7 PR:P50283 Category=organism-gene. T-cell antigen CD7 (mouse) A CD7 molecule that is encoded in the genome of mouse. OMA:P50283 PRO:DNx CD7 (mouse) UniProtKB:P50283 mCD7 PRO:DNx Cd7 UniProtKB:P50283 A C-C chemokine receptor type 1 that is encoded in the genome of mouse. UniProtKB:P51675 C-C CKR-1 (mouse) CC-CKR-1 (mouse) CCR-1 (mouse) CCR1 (mouse) CD191 (mouse) MIP-1alpha-R (mouse) RANTES-R (mouse) mCCR1 macrophage inflammatory protein 1-alpha receptor (mouse) protein Ccr1 Cmkbr1 PR:P51675 Category=organism-gene. C-C chemokine receptor type 1 (mouse) A C-C chemokine receptor type 1 that is encoded in the genome of mouse. OMA:P51675 PRO:DNx C-C CKR-1 (mouse) UniProtKB:P51675 CC-CKR-1 (mouse) UniProtKB:P51675 CCR-1 (mouse) UniProtKB:P51675 CCR1 (mouse) UniProtKB:P51675 CD191 (mouse) UniProtKB:P51675 MIP-1alpha-R (mouse) UniProtKB:P51675 RANTES-R (mouse) UniProtKB:P51675 mCCR1 PRO:DNx macrophage inflammatory protein 1-alpha receptor (mouse) UniProtKB:P51675 Ccr1 UniProtKB:P51675 Cmkbr1 UniProtKB:P51675 A C-C chemokine receptor type 3 that is encoded in the genome of human. DTO:02100055 Reactome:R-HSA-373106 UniProtKB:P51677 C C CKR3 (human) C-C CKR-3 (human) CC-CKR-3 (human) CCR-3 (human) CD193 (human) CKR 3 (human) CKR3 (human) eosinophil eotaxin receptor (human) hCCR3 protein CCR3 CMKBR3 PR:P51677 Category=organism-gene. C-C chemokine receptor type 3 (human) A C-C chemokine receptor type 3 that is encoded in the genome of human. PRO:WCB UniProtKB:P51677 Reactome:R-HSA-373106 PR:P51677 located_in GO:0005886 C C CKR3 (human) UniProtKB:P51677 C-C CKR-3 (human) UniProtKB:P51677 CC-CKR-3 (human) UniProtKB:P51677 CCR-3 (human) UniProtKB:P51677 CD193 (human) UniProtKB:P51677 CKR 3 (human) UniProtKB:P51677 CKR3 (human) UniProtKB:P51677 eosinophil eotaxin receptor (human) UniProtKB:P51677 hCCR3 PRO:DNx CCR3 UniProtKB:P51677 CMKBR3 UniProtKB:P51677 A C-C chemokine receptor type 3 that is encoded in the genome of mouse. UniProtKB:P51678 C-C CKR-3 (mouse) CC-CKR-3 (mouse) CCR-3 (mouse) CCR3 (mouse) CD193 (mouse) CKR3 (mouse) MIP-1 alpha RL2 (mouse) mCCR3 macrophage inflammatory protein 1-alpha receptor-like 2 (mouse) protein Ccr3 Cmkbr1l2 Cmkbr3 PR:P51678 Category=organism-gene. probable C-C chemokine receptor type 3 (mouse) A C-C chemokine receptor type 3 that is encoded in the genome of mouse. OMA:P51678 PRO:DNx C-C CKR-3 (mouse) UniProtKB:P51678 CC-CKR-3 (mouse) UniProtKB:P51678 CCR-3 (mouse) UniProtKB:P51678 CCR3 (mouse) UniProtKB:P51678 CD193 (mouse) UniProtKB:P51678 CKR3 (mouse) UniProtKB:P51678 MIP-1 alpha RL2 (mouse) UniProtKB:P51678 mCCR3 PRO:DNx macrophage inflammatory protein 1-alpha receptor-like 2 (mouse) UniProtKB:P51678 Ccr3 UniProtKB:P51678 Cmkbr1l2 UniProtKB:P51678 Cmkbr3 UniProtKB:P51678 A CCAAT/enhancer-binding protein alpha that is encoded in the genome of mouse. UniProtKB:P53566 C/EBP alpha (mouse) mCEBPA protein Cebp Cebpa PR:P53566 Category=organism-gene. CCAAT/enhancer-binding protein alpha (mouse) A CCAAT/enhancer-binding protein alpha that is encoded in the genome of mouse. OMA:P53566 PRO:DNx C/EBP alpha (mouse) UniProtKB:P53566 mCEBPA PRO:DNx Cebp UniProtKB:P53566 Cebpa UniProtKB:P53566 A fibroblast growth factor 8 that is encoded in the genome of human. HBGF-8 (human) heparin-binding growth factor 8 (human) UniProtKB:P55075 FGF-8 (human) androgen-induced growth factor (human) hFGF8 protein AIGF FGF8 PR:P55075 Category=organism-gene. fibroblast growth factor 8 (human) A fibroblast growth factor 8 that is encoded in the genome of human. PRO:DNx UniProtKB:P55075 HBGF-8 (human) UniProtKB:P55075 heparin-binding growth factor 8 (human) UniProtKB:P55075 FGF-8 (human) UniProtKB:P55075 androgen-induced growth factor (human) UniProtKB:P55075 hFGF8 PRO:DNx AIGF UniProtKB:P55075 FGF8 UniProtKB:P55075 A cadherin-5 that is encoded in the genome of mouse. UniProtKB:P55284 CD144 (mouse) VE-cadherin (mouse) mCDH5 vascular endothelial cadherin (mouse) protein Cdh5 PR:P55284 Category=organism-gene. cadherin-5 (mouse) A cadherin-5 that is encoded in the genome of mouse. OMA:P55284 PRO:DNx CD144 (mouse) UniProtKB:P55284 VE-cadherin (mouse) UniProtKB:P55284 mCDH5 PRO:DNx vascular endothelial cadherin (mouse) UniProtKB:P55284 Cdh5 UniProtKB:P55284 A V(D)J recombination-activating protein 2 that is encoded in the genome of human. Reactome:R-HSA-5692675 UniProtKB:P55895 RAG-2 (human) hRAG2 protein RAG2 PR:P55895 Category=organism-gene. V(D)J recombination-activating protein 2 (human) A V(D)J recombination-activating protein 2 that is encoded in the genome of human. PRO:CNA UniProtKB:P55895 Reactome:R-HSA-5692675 PR:P55895 located_in GO:0005654 RAG-2 (human) UniProtKB:P55895 hRAG2 PRO:DNx RAG2 UniProtKB:P55895 An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of mouse. UniProtKB:P56528 2'-phospho-ADP-ribosyl cyclase (mouse) 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (mouse) 2'-phospho-cyclic-ADP-ribose transferase (mouse) ADP-ribosyl cyclase 1 (mouse) ADPRC 1 (mouse) CD38 (mouse) I-19 (mouse) NIM-R5 antigen (mouse) cADPr hydrolase 1 (mouse) cyclic ADP-ribose hydrolase 1 (mouse) mCD38 protein Cd38 PR:P56528 Category=organism-gene. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (mouse) An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of mouse. OMA:P56528 PRO:DNx 2'-phospho-ADP-ribosyl cyclase (mouse) UniProtKB:P56528 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (mouse) UniProtKB:P56528 2'-phospho-cyclic-ADP-ribose transferase (mouse) UniProtKB:P56528 ADP-ribosyl cyclase 1 (mouse) UniProtKB:P56528 ADPRC 1 (mouse) UniProtKB:P56528 CD38 (mouse) UniProtKB:P56528 I-19 (mouse) UniProtKB:P56528 NIM-R5 antigen (mouse) UniProtKB:P56528 cADPr hydrolase 1 (mouse) UniProtKB:P56528 cyclic ADP-ribose hydrolase 1 (mouse) UniProtKB:P56528 mCD38 PRO:DNx Cd38 UniProtKB:P56528 A calcitonin isoform 1 that is encoded in the genome of mouse. PR:P70160 UniProtKB:P70160-1 mCALCA/iso:1 protein PR:P70160-1 Category=organism-sequence. calcitonin isoform 1 (mouse) A calcitonin isoform 1 that is encoded in the genome of mouse. PMID:8806650 PRO:HJD mCALCA/iso:1 PRO:DNx A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of mouse. UniProtKB:Q00342 CD135 (mouse) FL cytokine receptor (mouse) FLK-2 (mouse) FLT-3 (mouse) fetal liver kinase 2 (mouse) fms-like tyrosine kinase 3 (mouse) mFLT3 tyrosine-protein kinase receptor flk-2 (mouse) protein Flk-2 Flt-3 Flt3 PR:Q00342 Category=organism-gene. receptor-type tyrosine-protein kinase FLT3 (mouse) A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of mouse. OMA:Q00342 PRO:DNx CD135 (mouse) UniProtKB:Q00342 FL cytokine receptor (mouse) UniProtKB:Q00342 FLK-2 (mouse) UniProtKB:Q00342 FLT-3 (mouse) UniProtKB:Q00342 fetal liver kinase 2 (mouse) UniProtKB:Q00342 fms-like tyrosine kinase 3 (mouse) UniProtKB:Q00342 mFLT3 PRO:DNx tyrosine-protein kinase receptor flk-2 (mouse) UniProtKB:Q00342 Flk-2 UniProtKB:Q00342 Flt-3 UniProtKB:Q00342 Flt3 UniProtKB:Q00342 An interleukin-5 receptor subunit alpha that is encoded in the genome of human. UniProtKB:Q01344 CD125 (human) CDw125 (human) IL-5 receptor subunit alpha (human) IL-5R subunit alpha (human) IL-5R-alpha (human) IL-5RA (human) hIL5RA protein IL5R IL5RA PR:Q01344 Category=organism-gene. interleukin-5 receptor subunit alpha (human) An interleukin-5 receptor subunit alpha that is encoded in the genome of human. PRO:WCB UniProtKB:Q01344 CD125 (human) UniProtKB:Q01344 CDw125 (human) UniProtKB:Q01344 IL-5 receptor subunit alpha (human) UniProtKB:Q01344 IL-5R subunit alpha (human) UniProtKB:Q01344 IL-5R-alpha (human) UniProtKB:Q01344 IL-5RA (human) UniProtKB:Q01344 hIL5RA PRO:DNx IL5R UniProtKB:Q01344 IL5RA UniProtKB:Q01344 A paired box protein PAX-5 that is encoded in the genome of human. Reactome:R-HSA-158583 UniProtKB:Q02548 B-cell-specific transcription factor (human) BSAP (human) hPAX5 protein PAX5 PR:Q02548 Category=organism-gene. paired box protein Pax-5 (human) A paired box protein PAX-5 that is encoded in the genome of human. PRO:WCB UniProtKB:Q02548 Reactome:R-HSA-158583 PR:Q02548 located_in GO:0005654 B-cell-specific transcription factor (human) UniProtKB:Q02548 BSAP (human) UniProtKB:Q02548 hPAX5 PRO:DNx PAX5 UniProtKB:Q02548 A paired box protein PAX-5 that is encoded in the genome of mouse. UniProtKB:Q02650 B-cell-specific transcription factor (mouse) BSAP (mouse) mPAX5 protein Pax-5 Pax5 PR:Q02650 Category=organism-gene. paired box protein Pax-5 (mouse) A paired box protein PAX-5 that is encoded in the genome of mouse. OMA:Q02650 PRO:DNx B-cell-specific transcription factor (mouse) UniProtKB:Q02650 BSAP (mouse) UniProtKB:Q02650 mPAX5 PRO:DNx Pax-5 UniProtKB:Q02650 Pax5 UniProtKB:Q02650 A urokinase plasminogen activator surface receptor that is encoded in the genome of human. UniProtKB:Q03405 CD87 (human) U-PAR (human) hPLAUR monocyte activation antigen Mo3 (human) protein MO3 PLAUR UPAR PR:Q03405 Category=organism-gene. urokinase plasminogen activator surface receptor (human) A urokinase plasminogen activator surface receptor that is encoded in the genome of human. PRO:WCB UniProtKB:Q03405 CD87 (human) UniProtKB:Q03405 U-PAR (human) UniProtKB:Q03405 hPLAUR PRO:DNx monocyte activation antigen Mo3 (human) UniProtKB:Q03405 MO3 UniProtKB:Q03405 PLAUR UniProtKB:Q03405 UPAR UniProtKB:Q03405 A CD69 molecule that is encoded in the genome of human. UniProtKB:Q07108 AIM (human) BL-AC/P26 (human) C-type lectin domain family 2 member C (human) EA1 (human) GP32/28 (human) MLR-3 (human) activation inducer molecule (human) early T-cell activation antigen p60 (human) hCD69 leukocyte surface antigen Leu-23 (human) protein CD69 CLEC2C PR:Q07108 Category=organism-gene. early activation antigen CD69 (human) A CD69 molecule that is encoded in the genome of human. PRO:CNA UniProtKB:Q07108 AIM (human) UniProtKB:Q07108 BL-AC/P26 (human) UniProtKB:Q07108 C-type lectin domain family 2 member C (human) UniProtKB:Q07108 EA1 (human) UniProtKB:Q07108 GP32/28 (human) UniProtKB:Q07108 MLR-3 (human) UniProtKB:Q07108 activation inducer molecule (human) UniProtKB:Q07108 early T-cell activation antigen p60 (human) UniProtKB:Q07108 hCD69 PRO:DNx leukocyte surface antigen Leu-23 (human) UniProtKB:Q07108 CD69 UniProtKB:Q07108 CLEC2C UniProtKB:Q07108 A natural killer cell receptor 2B4 that is encoded in the genome of mouse. UniProtKB:Q07763 CD244 (mouse) NK cell type I receptor protein 2B4 (mouse) NKR2B4 (mouse) SLAM family member 4 (mouse) SLAMF4 (mouse) mCD244 non-MHC restricted killing associated (mouse) signaling lymphocytic activation molecule 4 (mouse) protein 2b4 Cd244 Nmrk PR:Q07763 Category=organism-gene. natural killer cell receptor 2B4 (mouse) A natural killer cell receptor 2B4 that is encoded in the genome of mouse. OMA:Q07763 PRO:DNx CD244 (mouse) UniProtKB:Q07763 NK cell type I receptor protein 2B4 (mouse) UniProtKB:Q07763 NKR2B4 (mouse) UniProtKB:Q07763 SLAM family member 4 (mouse) UniProtKB:Q07763 SLAMF4 (mouse) UniProtKB:Q07763 mCD244 PRO:DNx non-MHC restricted killing associated (mouse) UniProtKB:Q07763 signaling lymphocytic activation molecule 4 (mouse) UniProtKB:Q07763 2b4 UniProtKB:Q07763 Cd244 UniProtKB:Q07763 Nmrk UniProtKB:Q07763 A SLAM family member 1 that is encoded in the genome of human. UniProtKB:Q13291 CD150 (human) CDw150 (human) IPO-3 (human) SLAM family member 1 (human) hSLAMF1 protein SLAM SLAMF1 PR:Q13291 Category=organism-gene. signaling lymphocytic activation molecule (human) A SLAM family member 1 that is encoded in the genome of human. PRO:WCB UniProtKB:Q13291 CD150 (human) UniProtKB:Q13291 CDw150 (human) UniProtKB:Q13291 IPO-3 (human) UniProtKB:Q13291 SLAM family member 1 (human) UniProtKB:Q13291 hSLAMF1 PRO:DNx SLAM UniProtKB:Q13291 SLAMF1 UniProtKB:Q13291 A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of human. UniProtKB:Q13445 Tp24 (human) hTMED1 interleukin-1 receptor-like 1 ligand (human) p24 family protein gamma-1 (human) p24gamma1 (human) putative T1/ST2 receptor-binding protein (human) protein IL1RL1L IL1RL1LG TMED1 PR:Q13445 Category=organism-gene. transmembrane emp24 domain-containing protein 1 (human) A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of human. PRO:DNx UniProtKB:Q13445 Tp24 (human) UniProtKB:Q13445 hTMED1 PRO:DNx interleukin-1 receptor-like 1 ligand (human) UniProtKB:Q13445 p24 family protein gamma-1 (human) UniProtKB:Q13445 p24gamma1 (human) UniProtKB:Q13445 putative T1/ST2 receptor-binding protein (human) UniProtKB:Q13445 IL1RL1L UniProtKB:Q13445 IL1RL1LG UniProtKB:Q13445 TMED1 UniProtKB:Q13445 A sonic hedgehog protein that is encoded in the genome of human. UniProtKB:Q15465 HHG-1 (human) Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (human) ShhNC (human) hSHH protein SHH PR:Q15465 Category=organism-gene. sonic hedgehog protein (human) A sonic hedgehog protein that is encoded in the genome of human. PRO:DNx UniProtKB:Q15465 HHG-1 (human) UniProtKB:Q15465 Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (human) UniProtKB:Q15465 ShhNC (human) UniProtKB:Q15465 hSHH PRO:DNx SHH UniProtKB:Q15465 A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of mouse. UniProtKB:Q2VLH6 CD163 (mouse) mCD163 protein Cd163 M130 PR:Q2VLH6 Category=organism-gene. scavenger receptor cysteine-rich type 1 protein M130 (mouse) A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of mouse. OMA:Q2VLH6 PRO:DNx CD163 (mouse) UniProtKB:Q2VLH6 mCD163 PRO:DNx Cd163 UniProtKB:Q2VLH6 M130 UniProtKB:Q2VLH6 A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of mouse. UniProtKB:Q3V009 interleukin-1 receptor-like 1 ligand (mouse) mTMED1 p24 family protein gamma-1 (mouse) p24gamma1 (mouse) putative T1/ST2 receptor-binding protein (mouse) protein Il1rl1l Tmed1 PR:Q3V009 Category=organism-gene. transmembrane emp24 domain-containing protein 1 (mouse) A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of mouse. OMA:Q3V009 PRO:DNx interleukin-1 receptor-like 1 ligand (mouse) UniProtKB:Q3V009 mTMED1 PRO:DNx p24 family protein gamma-1 (mouse) UniProtKB:Q3V009 p24gamma1 (mouse) UniProtKB:Q3V009 putative T1/ST2 receptor-binding protein (mouse) UniProtKB:Q3V009 Il1rl1l UniProtKB:Q3V009 Tmed1 UniProtKB:Q3V009 A cell surface glycoprotein CD200 receptor 3 that is encoded in the genome of mouse. UniProtKB:Q5UKY4 CD200 cell surface glycoprotein receptor-like 3 (mouse) CD200 cell surface glycoprotein receptor-like b (mouse) CD200 receptor-like 3 (mouse) cell surface glycoprotein OX2 receptor 3 (mouse) mCd200r3 protein Cd200r3 Cd200rlb PR:Q5UKY4 Category=organism-gene. cell surface glycoprotein CD200 receptor 3 (mouse) A cell surface glycoprotein CD200 receptor 3 that is encoded in the genome of mouse. PRO:DNx UniProtKB:Q5UKY4 CD200 cell surface glycoprotein receptor-like 3 (mouse) UniProtKB:Q5UKY4 CD200 cell surface glycoprotein receptor-like b (mouse) UniProtKB:Q5UKY4 CD200 receptor-like 3 (mouse) UniProtKB:Q5UKY4 cell surface glycoprotein OX2 receptor 3 (mouse) UniProtKB:Q5UKY4 mCd200r3 PRO:DNx Cd200r3 UniProtKB:Q5UKY4 Cd200rlb UniProtKB:Q5UKY4 A neprilysin that is encoded in the genome of mouse. UniProtKB:Q61391 CD10 (mouse) NEP (mouse) SFE (mouse) atriopeptidase (mouse) enkephalinase (mouse) mMME neutral endopeptidase (mouse) neutral endopeptidase 24.11 (mouse) skin fibroblast elastase (mouse) protein Mme PR:Q61391 Category=organism-gene. neprilysin (mouse) A neprilysin that is encoded in the genome of mouse. OMA:Q61391 PRO:DNx CD10 (mouse) UniProtKB:Q61391 NEP (mouse) UniProtKB:Q61391 SFE (mouse) UniProtKB:Q61391 atriopeptidase (mouse) UniProtKB:Q61391 enkephalinase (mouse) UniProtKB:Q61391 mMME PRO:DNx neutral endopeptidase (mouse) UniProtKB:Q61391 neutral endopeptidase 24.11 (mouse) UniProtKB:Q61391 skin fibroblast elastase (mouse) UniProtKB:Q61391 Mme UniProtKB:Q61391 A 5'-nucleotidase that is encoded in the genome of mouse. UniProtKB:Q61503 CD73 (mouse) IMP-specific 5'-nucleotidase (mouse) mNT5E thymidylate 5'-phosphatase (mouse) protein 5'-NT (mouse) 5'-deoxynucleotidase (mouse) Nt5 Nt5e Nte ecto-5'-nucleotidase (mouse) PR:Q61503 Category=organism-gene. 5'-nucleotidase (mouse) A 5'-nucleotidase that is encoded in the genome of mouse. OMA:Q61503 PRO:DNx CD73 (mouse) UniProtKB:Q61503 IMP-specific 5'-nucleotidase (mouse) UniProtKB:Q61503 mNT5E PRO:DNx thymidylate 5'-phosphatase (mouse) UniProtKB:Q61503 5'-NT (mouse) UniProtKB:Q61503 5'-deoxynucleotidase (mouse) UniProtKB:Q61503 Nt5 UniProtKB:Q61503 Nt5e UniProtKB:Q61503 Nte UniProtKB:Q61503 ecto-5'-nucleotidase (mouse) UniProtKB:Q61503 A forkhead box protein N1 that is encoded in the genome of mouse. UniProtKB:Q61575 HFH-11 (mouse) HNF-3/forkhead homolog 11 (mouse) hepatocyte nuclear factor 3 forkhead homolog 11 (mouse) mFOXN1 winged-helix transcription factor nude (mouse) protein Fkh19 Foxn1 Hfh11 Whn PR:Q61575 Category=organism-gene. forkhead box protein N1 (mouse) A forkhead box protein N1 that is encoded in the genome of mouse. OMA:Q61575 PRO:DNx HFH-11 (mouse) UniProtKB:Q61575 HNF-3/forkhead homolog 11 (mouse) UniProtKB:Q61575 hepatocyte nuclear factor 3 forkhead homolog 11 (mouse) UniProtKB:Q61575 mFOXN1 PRO:DNx winged-helix transcription factor nude (mouse) UniProtKB:Q61575 Fkh19 UniProtKB:Q61575 Foxn1 UniProtKB:Q61575 Hfh11 UniProtKB:Q61575 Whn UniProtKB:Q61575 A haptoglobin that is encoded in the genome of mouse. UniProtKB:Q61646 mHP protein Hp PR:Q61646 Category=organism-gene. haptoglobin (mouse) A haptoglobin that is encoded in the genome of mouse. OMA:Q61646 PRO:DNx mHP PRO:DNx Hp UniProtKB:Q61646 A sonic hedgehog protein that is encoded in the genome of mouse. UniProtKB:Q62226 HHG-1 (mouse) SHH (mouse) Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (mouse) ShhNC (mouse) mSHH protein Hhg1 Shh PR:Q62226 Category=organism-gene. sonic hedgehog protein (mouse) A sonic hedgehog protein that is encoded in the genome of mouse. OMA:Q62226 PRO:DNx HHG-1 (mouse) UniProtKB:Q62226 SHH (mouse) UniProtKB:Q62226 Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (mouse) UniProtKB:Q62226 ShhNC (mouse) UniProtKB:Q62226 mSHH PRO:DNx Hhg1 UniProtKB:Q62226 Shh UniProtKB:Q62226 A transferrin receptor protein 1 that is encoded in the genome of mouse. UniProtKB:Q62351 CD71 (mouse) TfR (mouse) TfR1 (mouse) mTFRC protein TR (mouse) Tfrc Trfr PR:Q62351 Category=organism-gene. transferrin receptor protein 1 (mouse) A transferrin receptor protein 1 that is encoded in the genome of mouse. OMA:Q62351 PRO:DNx CD71 (mouse) UniProtKB:Q62351 TfR (mouse) UniProtKB:Q62351 TfR1 (mouse) UniProtKB:Q62351 mTFRC PRO:DNx TR (mouse) UniProtKB:Q62351 Tfrc UniProtKB:Q62351 Trfr UniProtKB:Q62351 An endoglin that is encoded in the genome of mouse. UniProtKB:Q63961 CD105 (mouse) cell surface MJ7/18 antigen (mouse) mENG protein Edg Eng PR:Q63961 Category=organism-gene. endoglin (mouse) An endoglin that is encoded in the genome of mouse. OMA:Q63961 PRO:DNx CD105 (mouse) UniProtKB:Q63961 cell surface MJ7/18 antigen (mouse) UniProtKB:Q63961 mENG PRO:DNx Edg UniProtKB:Q63961 Eng UniProtKB:Q63961 A CD33 molecule that is encoded in the genome of mouse. UniProtKB:Q63994 CD33 (mouse) mCD33 sialic acid-binding Ig-like lectin 3 (mouse) siglec-3 (mouse) protein Cd33 Siglec3 PR:Q63994 Category=organism-gene. myeloid cell surface antigen CD33 (mouse) A CD33 molecule that is encoded in the genome of mouse. PRO:WCB CD33 (mouse) UniProtKB:Q63994 mCD33 PRO:DNx sialic acid-binding Ig-like lectin 3 (mouse) UniProtKB:Q63994 siglec-3 (mouse) UniProtKB:Q63994 Cd33 UniProtKB:Q63994 Siglec3 UniProtKB:Q63994 A CD34 molecule that is encoded in the genome of mouse. UniProtKB:Q64314 CD34 (mouse) mCD34 protein Cd34 PR:Q64314 Category=organism-gene. hematopoietic progenitor cell antigen CD34 (mouse) A CD34 molecule that is encoded in the genome of mouse. OMA:Q64314 PRO:DNx CD34 (mouse) UniProtKB:Q64314 mCD34 PRO:DNx Cd34 UniProtKB:Q64314 An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of mouse. UniProtKB:Q6DYE8 CD203c (mouse) E-NPP 3 (mouse) PD-Ibeta (mouse) mENPP3 phosphodiesterase I beta (mouse) phosphodiesterase I/nucleotide pyrophosphatase 3 (mouse) protein Enpp3 PR:Q6DYE8 Category=organism-gene. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (mouse) An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of mouse. OMA:Q6DYE8 PRO:DNx CD203c (mouse) UniProtKB:Q6DYE8 E-NPP 3 (mouse) UniProtKB:Q6DYE8 PD-Ibeta (mouse) UniProtKB:Q6DYE8 mENPP3 PRO:DNx phosphodiesterase I beta (mouse) UniProtKB:Q6DYE8 phosphodiesterase I/nucleotide pyrophosphatase 3 (mouse) UniProtKB:Q6DYE8 Enpp3 UniProtKB:Q6DYE8 A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of human. UniProtKB:Q86VB7 hCD163 hemoglobin scavenger receptor (human) protein CD163 M130 PR:Q86VB7 Category=organism-gene. scavenger receptor cysteine-rich type 1 protein M130 (human) A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of human. PRO:WCB UniProtKB:Q86VB7 hCD163 PRO:DNx hemoglobin scavenger receptor (human) UniProtKB:Q86VB7 CD163 UniProtKB:Q86VB7 M130 UniProtKB:Q86VB7 A C-type lectin domain family 4 member K that is encoded in the genome of mouse. UniProtKB:Q8VBX4 CD207 (mouse) langerin (mouse) mCD207 protein Cd207 Clec4k PR:Q8VBX4 Category=organism-gene. C-type lectin domain family 4 member K (mouse) A C-type lectin domain family 4 member K that is encoded in the genome of mouse. OMA:Q8VBX4 PRO:DNx CD207 (mouse) UniProtKB:Q8VBX4 langerin (mouse) UniProtKB:Q8VBX4 mCD207 PRO:DNx Cd207 UniProtKB:Q8VBX4 Clec4k UniProtKB:Q8VBX4 A natural killer cell receptor 2B4 that is encoded in the genome of human. UniProtKB:Q9BZW8 NAIL (human) NK cell activation-inducing ligand (human) NK cell type I receptor protein 2B4 (human) NKR2B4 (human) SLAM family member 4 (human) SLAMF4 (human) h2B4 (human) hCD244 signaling lymphocytic activation molecule 4 (human) protein 2B4 CD244 PR:Q9BZW8 Category=organism-gene. natural killer cell receptor 2B4 (human) A natural killer cell receptor 2B4 that is encoded in the genome of human. PRO:WCB UniProtKB:Q9BZW8 NAIL (human) UniProtKB:Q9BZW8 NK cell activation-inducing ligand (human) UniProtKB:Q9BZW8 NK cell type I receptor protein 2B4 (human) UniProtKB:Q9BZW8 NKR2B4 (human) UniProtKB:Q9BZW8 SLAM family member 4 (human) UniProtKB:Q9BZW8 SLAMF4 (human) UniProtKB:Q9BZW8 h2B4 (human) UniProtKB:Q9BZW8 hCD244 PRO:DNx signaling lymphocytic activation molecule 4 (human) UniProtKB:Q9BZW8 2B4 UniProtKB:Q9BZW8 CD244 UniProtKB:Q9BZW8 An integrin alpha-IIb that is encoded in the genome of mouse. UniProtKB:Q9QUM0 CD41 (mouse) GPIIb (mouse) GPalpha IIb (mouse) mITGA2B platelet membrane glycoprotein IIb (mouse) protein Itga2b PR:Q9QUM0 Category=organism-gene. integrin alpha-IIb (mouse) An integrin alpha-IIb that is encoded in the genome of mouse. OMA:Q9QUM0 PRO:DNx CD41 (mouse) UniProtKB:Q9QUM0 GPIIb (mouse) UniProtKB:Q9QUM0 GPalpha IIb (mouse) UniProtKB:Q9QUM0 mITGA2B PRO:DNx platelet membrane glycoprotein IIb (mouse) UniProtKB:Q9QUM0 Itga2b UniProtKB:Q9QUM0 A SLAM family member 1 that is encoded in the genome of mouse. UniProtKB:Q9QUM4 CD150 (mouse) SLAM family member 1 (mouse) mSLAMF1 protein Slam Slamf1 PR:Q9QUM4 Category=organism-gene. signaling lymphocytic activation molecule (mouse) A SLAM family member 1 that is encoded in the genome of mouse. OMA:Q9QUM4 PRO:DNx CD150 (mouse) UniProtKB:Q9QUM4 SLAM family member 1 (mouse) UniProtKB:Q9QUM4 mSLAMF1 PRO:DNx Slam UniProtKB:Q9QUM4 Slamf1 UniProtKB:Q9QUM4 An integrin alpha-X that is encoded in the genome of mouse. UniProtKB:Q9QXH4 CD11 antigen-like family member C (mouse) CD11c (mouse) leukocyte adhesion glycoprotein p150,95 alpha chain (mouse) leukocyte adhesion receptor p150,95 (mouse) mITGAX protein Itgax PR:Q9QXH4 Category=organism-gene. integrin alpha-X (mouse) An integrin alpha-X that is encoded in the genome of mouse. OMA:Q9QXH4 PRO:DNx CD11 antigen-like family member C (mouse) UniProtKB:Q9QXH4 CD11c (mouse) UniProtKB:Q9QXH4 leukocyte adhesion glycoprotein p150,95 alpha chain (mouse) UniProtKB:Q9QXH4 leukocyte adhesion receptor p150,95 (mouse) UniProtKB:Q9QXH4 mITGAX PRO:DNx Itgax UniProtKB:Q9QXH4 A C-type lectin domain family 4 member K that is encoded in the genome of human. Reactome:R-HSA-1216519 Reactome:R-HSA-1236762 Reactome:R-HSA-1236852 UniProtKB:Q9UJ71 hCD207 langerin (human) protein CD207 CLEC4K PR:Q9UJ71 Category=organism-gene. C-type lectin domain family 4 member K (human) A C-type lectin domain family 4 member K that is encoded in the genome of human. PRO:WCB UniProtKB:Q9UJ71 Reactome:R-HSA-1216519 PR:Q9UJ71 located_in GO:0005886 Reactome:R-HSA-1236762 PR:Q9UJ71 located_in GO:0030669 Reactome:R-HSA-1236852 PR:Q9UJ71 located_in GO:0031901 hCD207 PRO:DNx langerin (human) UniProtKB:Q9UJ71 CD207 UniProtKB:Q9UJ71 CLEC4K UniProtKB:Q9UJ71 A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 http://www.jbiomedsem.com/content/4/1/43 system A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. sequence sequence SO:0000001 region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. SO:ke A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. SO:0000358 http://en.wikipedia.org/wiki/Polypeptide protein sequence SO:0000104 This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute. polypeptide A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. SO:ma http://en.wikipedia.org/wiki/Polypeptide wiki Any extent of continuous biological sequence. INSDC_feature:misc_feature INSDC_note:other INSDC_note:sequence_feature located_sequence_feature sequence feature sequence located sequence feature SO:0000110 sequence_feature Any extent of continuous biological sequence. LAMHDI:mb SO:ke A transcript that in its initial state requires modification to be functional. http://en.wikipedia.org/wiki/Primary_transcript INSDC_feature:precursor_RNA INSDC_feature:prim_transcript precursor RNA primary transcript sequence SO:0000185 primary_transcript A transcript that in its initial state requires modification to be functional. SO:ma http://en.wikipedia.org/wiki/Primary_transcript wiki A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. http://en.wikipedia.org/wiki/Mature_transcript mature transcript sequence SO:0000233 A processed transcript cannot contain introns. mature_transcript A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. SO:ke http://en.wikipedia.org/wiki/Mature_transcript wiki Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. http://en.wikipedia.org/wiki/MRNA http://www.gencodegenes.org/gencode_biotypes.html INSDC_feature:mRNA messenger RNA protein_coding_transcript sequence SO:0000234 An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. mRNA Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. SO:ma http://en.wikipedia.org/wiki/MRNA wiki http://www.gencodegenes.org/gencode_biotypes.html GENCODE A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. INSDC_feature:CDS coding sequence coding_sequence sequence SO:0000316 CDS A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. SO:ma The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. BS:00159 http://en.wikipedia.org/wiki/Signal_peptide INSDC_feature:sig_peptide signal peptide signal peptide coding sequence sequence signal SO:0000418 Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. signal_peptide The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. http://www.insdc.org/files/feature_table.html http://en.wikipedia.org/wiki/Signal_peptide wiki signal uniprot:feature_type An RNA synthesized on a DNA or RNA template by an RNA polymerase. INSDC_feature:misc_RNA http://en.wikipedia.org/wiki/RNA sequence SO:0000673 Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020. transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. SO:ma http://en.wikipedia.org/wiki/RNA wiki A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. http://en.wikipedia.org/wiki/Gene INSDC_feature:gene sequence SO:0000704 This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. gene A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. SO:immuno_workshop http://en.wikipedia.org/wiki/Gene wiki A region of a gene. gene member region sequence SO:0000831 A manufactured term used to allow the parts of a gene to have an is_a path to the root. gene_member_region A region of a gene. SO:ke A region of a transcript. transcript region sequence SO:0000833 This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. transcript_region A region of a transcript. SO:ke A region of a mature transcript. mature transcript region sequence SO:0000834 A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. mature_transcript_region A region of a mature transcript. SO:ke A region of an mRNA. mRNA region sequence SO:0000836 This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. mRNA_region A region of an mRNA. SO:cb Biological sequence region that can be assigned to a specific subsequence of a polypeptide. BS:00124 BS:00331 region site sequence positional positional polypeptide feature region or site annotation SO:0000839 Added to allow the polypeptide regions to have is_a paths back to the root. polypeptide_region Biological sequence region that can be assigned to a specific subsequence of a polypeptide. SO:GAR SO:ke region uniprot:feature_type site uniprot:feature_type A region of a CDS. CDS region sequence SO:0000851 CDS_region A region of a CDS. SO:cb Part of a peptide chain which is cleaved off during the formation of the mature protein. BS:00077 http://en.wikipedia.org/wiki/Propeptide INSDC_feature:propeptide sequence propep SO:0001062 Range. propeptide Part of a peptide chain which is cleaved off during the formation of the mature protein. EBIBS:GAR http://en.wikipedia.org/wiki/Propeptide wiki propep uniprot:feature_type An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. BS:00129 immature peptide region sequence SO:0001063 Range. immature_peptide_region An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. EBIBS:GAR A region defined by its disposition to be involved in a biological process. INSDC_misc_feature INSDC_note:biological_region biological region sequence SO:0001411 biological_region A region defined by its disposition to be involved in a biological process. SO:cb A region of peptide sequence used to target the polypeptide molecule to a specific organelle. kareneilbeck 2010-03-11T02:15:05Z peptide localization signal sequence localization signal SO:0001527 peptide_localization_signal A region of peptide sequence used to target the polypeptide molecule to a specific organelle. SO:ke A CDS region corresponding to a propeptide of a polypeptide. david 2020-05-13T13:40:30Z INSDC_feature:propeptide propeptide region of CDS sequence SO:0002250 Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484) propeptide_region_of_CDS A CDS region corresponding to a signal peptide of a polypeptide. david 2020-05-13T13:40:30Z INSDC_feature:sig_peptide Signal peptide region of CDS sequence SO:0002251 Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484) signal_peptide_region_of_CDS Transcription units or transcribed coding sequences. david 2020-08-05T11:49:30Z unit of gene expression sequence SO:0002300 Added as per Mejia-Almonte et.al PMID:32665585 unit_of_gene_expression Transcription units or transcribed coding sequences. Bacterial_regulation_working_group:CMA PMID:32665585 A collection of related genes. gene group sequence SO:0005855 gene_group A collection of related genes. SO:ma The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. cleaved peptide region sequence SO:0100011 Range. cleaved_peptide_region The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. EBIBS:GAR An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. BFO:0000003 uberon UBERON:0000000 processual entity An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. span:ProcessualEntity Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] cervical cervix BTO:0001421 BTO:0002249 CALOHA:TS-0134 EFO:0000979 EMAPA:29927 EV:0100114 FMA:17740 GAID:376 MA:0000392 MAT:0000292 MESH:D002584 NCIT:C12311 SCTID:181453009 UMLS:C0007874 VHOG:0001359 Wikipedia:Cervix galen:CervixUteri canalis cervicis uteri caudal segment of uterus cervical canal of uterus cervix uteri neck of uterus uterine cervix uberon cervical canal cervix of uterus UBERON:0000002 uterine cervix https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb Lower, narrow portion of the uterus where it joins with the top end of the vagina. Wikipedia:Cervix http://orcid.org/0000-0002-6601-2165 The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001359 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/uterine+cervix The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] 2012-09-17 VHOG:0001359 VHOG DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004) http://bgee.unil.ch/ cervix EFO:0000979 UMLS:C0007874 ncithesaurus:Cervix canalis cervicis uteri FMA:17740 FMA:TA cervical canal of uterus FMA:17740 cervix uteri EMAPA:29927 neck of uterus FMA:17740 uterine cervix FMA:17740 cervical canal FMA:17740 cervix of uterus BTO:0001421 Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. One of paired external openings of the nasal chamber.[AAO] Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure AAO:0000311 EHDAA2:0001225 EHDAA:9083 EMAPA:17847 MA:0000282 SCTID:272650008 VHOG:0000663 galen:Naris uberon UBERON:0000003 naris ZFA Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. http://orcid.org/0000-0001-9114-8737 One of paired external openings of the nasal chamber.[AAO] 2012-06-20 AAO:0000311 AAO AAO:EJS Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] 2012-09-17 VHOG:0000663 VHOG DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004) http://bgee.unil.ch/ we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure FMA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] BTO:0000840 CALOHA:TS-2037 EHDAA2:0001274 EHDAA:1502 EMAPA:16542 EV:0100037 EV:0100370 FMA:46472 GAID:77 MA:0000281 MAT:0000139 MESH:D009666 MIAA:0000139 NCIT:C12756 SCTID:181195007 TAO:0000047 UMLS:C0028429 Wikipedia:Nose ZFA:0000047 galen:Nose nasal sac nose peripheral olfactory organ uberon nasus olfactory apparatus proboscis UBERON:0000004 nose http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg FMA ZFA-def ZFA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:cjm Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. ZFA:0000047 a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. Wikipedia:Nose the organ that is specialized for smell and is part of the respiratory system MP:0002233 UMLS:C0028429 ncithesaurus:Nose nasal sac ZFA:0000047 nose MA:0000281 peripheral olfactory organ ZFA:0000047 nasus Wikipedia:Nose olfactory apparatus UBERON:cjm FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ FBbt:00005157 chemosensory sensory organ FBbt:00005157 The clusters of hormone-producing cells that are scattered throughout the pancreas. Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) AAO:0010406 BTO:0000991 CALOHA:TS-0741 EFO:0000856 EMAPA:32927 EV:0100130 FMA:16016 GAID:324 MA:0000127 MAT:0000076 MESH:D007515 MIAA:0000076 NCIT:C12608 UMLS:C0022131 VHOG:0000646 Wikipedia:Islets_of_Langerhans XAO:0000159 pancreatic insula pancreatic islet uberon island of Langerhans island of pancreas islets of Langerhans UBERON:0000006 islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png PMID:16417468 PMID:16417468 PMID:16417468 The clusters of hormone-producing cells that are scattered throughout the pancreas. MA:0000127 MESH:A03.734.414 MP:0005215 Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] 2012-06-20 AAO:0010406 AAO AAO:BJB Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] 2012-09-17 VHOG:0000646 VHOG PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995) http://bgee.unil.ch/ A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) PMID:16417468 UMLS:C0022131 ncithesaurus:Islet_of_Langerhans island of Langerhans BTO:0000991 island of pancreas BTO:0000991 The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9] Hp AAO:0010536 BAMS:PIT BAMS:Pit BIRNLEX:1353 BM:Die-Hy-HY BTO:0001073 CALOHA:TS-0798 DHBA:10505 EFO:0000857 EHDAA2:0001471 EHDAA:2183 EHDAA:4477 EMAPA:35998 EV:0100132 FMA:13889 GAID:457 HBA:4634 MA:0000176 MAT:0000077 MESH:D010902 MIAA:0000077 NCIT:C12399 SCTID:181125003 TAO:0000118 UMLS:C0032005 VHOG:0000143 Wikipedia:Pituitary_gland XAO:0000017 ZFA:0000118 neuronames:399 glandula pituitaria pituitary pituitary body uberon hypophysis hypophysis cerebri UBERON:0000007 Terminology note: hypophysis and pituitary gland are often used informally as synonyms, but the hypophysis also includes the small infundibular or pituitary stalk[Neumann 2020] pituitary gland http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png BTO EFO VHOG ZFA ZFA PMID:19084529 https://orcid.org/0000-0003-3308-6245 The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. Wikipedia:Pituitary_gland ZFIN:curator An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] 2012-06-20 AAO:0010536 AAO AAO:BJB An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] 2012-08-14 TAO:0000118 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000143 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 http://bgee.unil.ch/ Hp BIRNLEX:1353 NIFSTD:NeuroNames_abbrevSource UMLS:C0032005 BIRNLEX:1353 ncithesaurus:Pituitary_Gland neuronames:399 BIRNLEX:1353 glandula pituitaria Wikipedia:Pituitary_gland pituitary BTO:0001073 pituitary body BTO:0001073 hypophysis ZFA:0000118 hypophysis cerebri MA:0000176 A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. submucosal BTO:0002107 FMA:85391 FMA:85392 NCIT:C13167 SCTID:68439008 UMLS:C0225344 Wikipedia:Submucosa organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. Wikipedia:Submucosa UMLS:C0225344 ncithesaurus:Submucosa organ submucosa FMA:85391 region of submucosa FMA:85392 submucosa of organ FMA:85391 submucosa of region of organ FMA:85392 submucous layer BTO:0002107 tela submucosa BTO:0002107 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] PNS AAO:0000429 BAMS:PNS BILA:0000081 BIRNLEX:1111 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 NCIT:C12465 SCTID:362292005 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 Wikipedia:Peripheral_nervous_system XAO:0000178 ZFA:0000142 neuronames:3232 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png cjm A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GO:0007422 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000142 TAO ZFIN:curator Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] 2012-06-20 AAO:0000429 AAO AAO:BJB The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) http://neurolex.org/wiki/Cumbo_terms (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] 2012-09-17 VHOG:0000399 VHOG DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) http://bgee.unil.ch/ PNS FBbt:00005098 UMLS:C0206417 BIRNLEX:1111 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 BIRNLEX:1111 pars peripherica FMA:9903 FMA:TA Wikipedia:Peripheral_nervous_system systema nervosum periphericum FMA:9903 FMA:TA Wikipedia:Peripheral_nervous_system The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] AAO:0010488 BIRNLEX:2517 BTO:0001833 CALOHA:TS-2094 EFO:0000894 EHDA:10096 EHDAA2:0001402 EHDAA:4655 EMAPA:17270 FMA:9907 GAID:708 MA:0000223 MAT:0000101 MESH:D010275 MIAA:0000101 NCIT:C12764 SCTID:362496006 TAO:0001575 UMLS:C0030510 UMLS:C1305770 VHOG:0000755 Wikipedia:Parasympathetic_nervous_system ZFA:0001575 PNS - parasympathetic parasympathetic part of autonomic division of nervous system pars parasympathica divisionis autonomici systematis nervosi uberon pars parasympathica divisionis autonomici systematis nervosi UBERON:0000011 parasympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm FMA MA WP ZFA-modified-from-isa The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. GO:0048486 Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] 2012-06-20 AAO:0010488 AAO AAO:BJB In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000755 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998) http://bgee.unil.ch/ UMLS:C0030510 BIRNLEX:2517 ncithesaurus:Parasympathetic_Nervous_System UMLS:C1305770 BIRNLEX:2517 pars parasympathica divisionis autonomici systematis nervosi FMA:9907 FMA:TA pars parasympathica divisionis autonomici systematis nervosi Wikipedia:Parasympathetic_nervous_system Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. EFO:0000892 FMA:9904 MA:0002850 MAT:0000099 MIAA:0000099 NLXANAT:100301 Wikipedia:Somatic_nervous_system PNS - somatic somatic nervous system, somatic division somatic part of peripheral nervous system somatic peripheral nervous system uberon UBERON:0000012 somatic nervous system cjm Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. NLXANAT:100301 somatic nervous system, somatic division NLXANAT:100301 somatic part of peripheral nervous system UBERON:cjm somatic peripheral nervous system NLXANAT:100301 The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) AAO:0010487 BIRNLEX:2516 BTO:0001832 CALOHA:TS-2050 EFO:0000893 EHDAA2:0001971 EHDAA:3769 EMAPA:16985 FMA:9906 GAID:710 MA:0000225 MESH:D013564 MIAA:0000100 NCIT:C12795 SCTID:362484004 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 Wikipedia:Sympathetic_nervous_system ZFA:0001576 pars sympathica divisionis autonomici systematis nervosi sympathetic nervous system sympathetic part of autonomic division of nervous system uberon pars sympathica divisionis autonomici systematis nervosi UBERON:0000013 sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png cjm FMA MA ZFA-modified-from-isa The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. GO:0048485 Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] 2012-06-20 AAO:0010487 AAO AAO:BJB The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000384 VHOG http://bgee.unil.ch/ The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] 2012-09-17 VHOG:0000384 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463 http://bgee.unil.ch/ UMLS:C0039044 BIRNLEX:2516 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 BIRNLEX:2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi Wikipedia:Sympathetic_nervous_system Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 SCTID:20795001 VHOG:0000860 Wikipedia:Skin portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Wikipedia:Skin http://orcid.org/0000-0002-6601-2165 (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] 2012-09-17 VHOG:0000860 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) http://bgee.unil.ch/ skin MA:0000151 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 anatomical boundary uberon UBERON:0000015 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. non-material anatomical boundary CARO A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CARO:0000010 anatomical boundary CARO:0000010 The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. create a separate class for distributed pancreas, eg cyclostomes? The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys BTO:0000650 CALOHA:TS-1302 EFO:0002542 EMAPA:35305 EV:0100129 FMA:16018 MA:0001582 MESH:D007515 NCIT:C32509 SCTID:361339003 TAO:0001260 VHOG:0000049 Wikipedia:Islets_of_Langerhans ZFA:0001260 endocrine pancreas pars endocrina pancreatis uberon endocrine part of pancreas islets of Langerhans part of pancreas UBERON:0000016 endocrine pancreas ZFA AAO FMA XAO GO GO GO The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. GO:GO http://orcid.org/0000-0002-6601-2165 The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] 2012-09-17 VHOG:0000049 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Pancreas The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] 2012-08-14 TAO:0001260 TAO ZFIN:curator In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000049 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) http://bgee.unil.ch/ endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys PMID:20959416 MESH:D007515 https://github.com/biopragmatics/biomappings endocrine part of pancreas BTO:0000650 The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 MA:0002415 MESH:D046790 NCIT:C32546 SCTID:248202004 TAO:0001249 UMLS:C0553695 VHOG:0000048 Wikipedia:Exocrine_component_of_pancreas XAO:0000137 ZFA:0001249 exocrine pancreas pars exocrina pancreatis uberon exocrine component of pancreas exocrine part of pancreas UBERON:0000017 exocrine pancreas The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. GOC:GO http://orcid.org/0000-0002-6601-2165 The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] 2012-08-14 TAO:0001249 TAO ZFIN:curator The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] 2012-09-17 VHOG:0000048 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Pancreas In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000048 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) http://bgee.unil.ch/ MESH:D046790 https://github.com/biopragmatics/biomappings UMLS:C0553695 ncithesaurus:Exocrine_Pancreas exocrine part of pancreas BTO:0000434 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. A cavitated compound organ that transduces light waves into neural signals.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA:54448 MA:0000261 NCIT:C12401 SCTID:181143004 TAO:0000107 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 regio orbitalis vertebrate eye uberon camera-type eye plus associated structures eyes orbital part of face orbital region UBERON:0000019 camera-type eye definitional An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. GO:0043010 https://orcid.org/0000-0002-6601-2165 A cavitated compound organ that transduces light waves into neural signals.[TAO] 2012-08-14 TAO:0000107 TAO TAO:wd The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000275 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA eye FMA:54448 UMLS:C0015392 BIRNLEX:1169 ncithesaurus:Eye UMLS:C1280202 BIRNLEX:1169 regio orbitalis FMA:54448 FMA:TA eyes TAO:0000107 orbital part of face FMA:54448 orbital region FMA:54448 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 SCTID:244485009 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png An organ that is capable of transducing sensory stimulus to the nervous system. https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 FBbt:00005155 UMLS:C0935626 ncithesaurus:Organ_of_the_Special_Sense organ of sense organ system OBOL:accepted organ of sensory organ system OBOL:accepted organ of sensory system OBOL:accepted sense organ system organ OBOL:automatic sensory organ system organ OBOL:automatic sensory system organ OBOL:accepted sensillum WBbt:0006929 Sinnesorgan BTO:0000202 Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here. CALOHA:TS-0051 FMA:71012 SCTID:276160000 skin appendage epidermal appendage uberon epidermal growth UBERON:0000021 cutaneous appendage Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. https://orcid.org/0000-0002-6601-2165 skin appendage FMA:71012 Appendage that is shaped in order to produce lift for flight through the air. alar This class is not monophyletic. See also: GO:0007629 BTO:0001463 EFO:0000885 GAID:1217 MAT:0000202 MESH:D014921 MIAA:0000202 Wikipedia:Wing aliform appendage uberon UBERON:0000023 wing Appendage that is shaped in order to produce lift for flight through the air. http://orcid.org/0000-0002-6601-2165 bgee bgee Wikipedia:Flying_fish bgee bgee bgee we do not consider flying frogs to have wings bgee bgee bgee bgee bgee aliform appendage http://orcid.org/0000-0002-6601-2165 Forelimb that is used to produce lift for flight through the air. uberon UBERON:0000024 Examples: bat wing, bird wing forelimb wing Forelimb that is used to produce lift for flight through the air. http://orcid.org/0000-0002-6601-2165 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. http://orcid.org/0000-0002-6601-2165 Major subdivision of an organism that protrudes from the body[DOS, CARO]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. appendicular this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EMAPA:37283 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 NCIT:C61460 UMLS:C0598782 VSAO:0000075 Wikipedia:Appendage XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. GO:0048736 EMAPA:37283 MA:th FBbt:00007000 UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] BTO:0000784 CALOHA:TS-0579 EFO:0000872 EMAPA:35523 EV:0100050 FMA:5034 GAID:947 MA:0000139 MAT:0000442 MESH:D008198 NCIT:C12745 NCIT:C33027 SCTID:181756000 TAO_RETIRED:0005318 UMLS:C0024204 VHOG:0001273 Wikipedia:Lymph_node ZFA_RETIRED:0005318 galen:Lymphnode uberon lymph gland nodus lymphaticus UBERON:0000029 lymph node https://github.com/obophenotype/uberon/issues/650 http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. BTO:0000784 Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] 2012-09-17 VHOG:0001273 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630 http://bgee.unil.ch/ UMLS:C0024204 ncithesaurus:Lymph_Node lymph gland VHOG:0001273 nodus lymphaticus Wikipedia:Lymph_node A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. BTO:0002330 FMA:62517 NCIT:C32918 SCTID:298225002 UMLS:C1179187 Wikipedia:Lamina_propria lamina propria mucosa lamina propria mucosae uberon tunica propria UBERON:0000030 lamina propria https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. Wikipedia:Lamina_propria UMLS:C1179187 ncithesaurus:Lamina_Propria tunica propria BTO:0002330 A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 MA:0001858 NCIT:C49305 UMLS:C1710457 lamina propria mucosa of trachea lamina propria mucosa of windpipe lamina propria mucosae of trachea lamina propria mucosae of windpipe lamina propria of windpipe trachea lamina propria trachea lamina propria mucosa trachea lamina propria mucosae tracheal lamina propria windpipe lamina propria windpipe lamina propria mucosa windpipe lamina propria mucosae uberon UBERON:0000031 lamina propria of trachea true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a respiratory airway. OBOL:automatic UMLS:C1710457 ncithesaurus:Trachea_Lamina_Propria lamina propria mucosa of trachea OBOL:automatic lamina propria mucosa of windpipe OBOL:automatic lamina propria mucosae of trachea OBOL:automatic lamina propria mucosae of windpipe OBOL:automatic lamina propria of windpipe OBOL:automatic trachea lamina propria mucosa OBOL:automatic trachea lamina propria mucosae OBOL:automatic windpipe lamina propria OBOL:automatic windpipe lamina propria mucosa OBOL:automatic windpipe lamina propria mucosae OBOL:automatic The head is the anterior-most division of the body [GO]. Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 BIRNLEX:1230 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 SCTID:302548004 SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 Wikipedia:Head XAO:0003024 ZFA:0001114 galen:Head head (volume) adult head uberon cephalic area UBERON:0000033 head The head is the anterior-most division of the body [GO]. GO:0060322 Wikipedia:Head Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] 2012-06-20 AAO:0010335 AAO AAO:BJB Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] 2012-08-14 TAO:0001114 TAO ZFIN:curator Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] 2012-09-17 VHOG:0001644 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 http://bgee.unil.ch/ UMLS:C0018670 BIRNLEX:1230 ncithesaurus:Head head (volume) FMA:7154 cephalic area SPD:0000016 Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 NCIT:C13169 SCTID:362878009 TAO:0005425 UMLS:C0036760 Wikipedia:Serous_membrane ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. Wikipedia:Serous_membrane https://github.com/obophenotype/uberon/issues/86 A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] 2012-08-14 TAO:0005425 TAO Wikipedia:Serous_membrane a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] Wikipedia:Serous_membrane in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa Wikipedia:Serous_membrane Dense regular connective tissue that connects muscle to bone[VSAO]. Dense regular connective tissue that connects muscle to bone.[VSAO] Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 NCIT:C13045 SCTID:256667004 UMLS:C0039508 VHOG:0001286 VSAO:0000073 Wikipedia:Tendon XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg VSAO OG AEO Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 Wikipedia:Tendon http://dx.plos.org/10.1371/journal.pone.0051070 Dense regular connective tissue that connects muscle to bone.[VSAO] 2012-08-14 VSAO:0000073 VSAO PSPUB:0000170 Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] 2012-09-17 VHOG:0001286 VHOG DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) http://bgee.unil.ch/ in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis FMA UMLS:C0039508 ncithesaurus:Tendon sinew Wikipedia:Tendon tendo Wikipedia:Tendon A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] ganglionic AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 NCIT:C12719 NLXANAT:100302 TAO:0000190 TGMA:0001016 UMLS:C0017067 VHOG:0000156 WBbt:0005189 Wikipedia:Ganglion XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion https://github.com/obophenotype/uberon/issues/2495#issuecomment-1187364719 EHDAA2 Bgee:AN A biological tissue mass, most commonly a mass of nerve cell bodies. Wikipedia:Ganglion https://github.com/obophenotype/uberon/issues/300 A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures PMID:21062451 Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] 2012-06-20 AAO:0010426 AAO AAO:EJS Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000190 TAO ZFIN:curator Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. NLXANAT:100302 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000156 VHOG DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) http://bgee.unil.ch/ UMLS:C0017067 ncithesaurus:Ganglion neural ganglion BTO:0000497 An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 Wikipedia:Eye#Simple_eyes uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. Wikipedia:Eye#Simple_eyes A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. https://orcid.org/0000-0002-6601-2165 Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 NCIT:C12416 SCTID:302511008 UMLS:C0041951 VHOG:0000605 Wikipedia:Ureter XAO:0000144 galen:Ureter uberon metanephric duct UBERON:0000056 ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg GO Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. GO:0090189 Wikipedia:Ureter Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] 2012-06-20 AAO:0010254 AAO AAO:BJB The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000605 VHOG http://bgee.unil.ch/ The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000605 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 http://bgee.unil.ch/ UMLS:C0041951 ncithesaurus:Ureter metanephric duct ISBN:0073040584 VHOG:0000605 The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. urethral In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 NCIT:C12417 SCTID:302513006 UMLS:C0041967 VHOG:0001264 Wikipedia:Urethra XAO:0000153 galen:Urethra uberon UBERON:0000057 urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra Wikipedia Wikipedia The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. MGI:anna MP:0000537 UMLS:C0041967 ncithesaurus:Urethra A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 TAO:0005171 UMLS:C0687028 Wikipedia:Duct_(anatomy) XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct A tubular structure that transports secreted or excreted substances. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 FBbt:00100314 UMLS:C0687028 ncithesaurus:Duct ducts XAO:0004000 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:D007420 MIAA:0000046 NCIT:C12379 SCTID:181254001 UMLS:C0021851 VHOG:0000054 Wikipedia:Large_intestine_(anatomy) XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN:0073040584 Wikipedia:Large_intestine_(anatomy) Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 http://bgee.unil.ch/ UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. in FMA, serosa is a wall UBERON:0009915 wall EMAPA:25036 FMA:82482 galen:Wall wall of organ uberon organ wall UBERON:0000060 anatomical wall Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 in FMA, serosa is a wall FMA wall of organ FMA:82482 organ wall FMA:82482 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 FBbt:00007001 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) uberon anatomical unit body organ element UBERON:0000062 organ PMID:28192867 Anatomical structure that performs a specific function or group of functions [WP]. Wikipedia:Organ_(anatomy) Wikipedia Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element http://orcid.org/0000-0002-6601-2165 A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. FMA:86140 3 Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 1 organ region with fixed fiat boundary FMA:86140 organ segment FMA:86140 segment of organ FMA:86140 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 SCTID:113343008 SCTID:91717005 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. http://orcid.org/0000-0002-6601-2165 cardinal organ part FMA:82472 regional part of organ BIRNLEX:16 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 SCTID:361110005 VHOG:0000393 uberon UBERON:0000065 respiratory tract NCBIBook:NBK10107 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts. https://orcid.org/0000-0002-6601-2165 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 WBls:0000041 XtroDO:0000084 fully formed animal stage juvenile-adult stage uberon UBERON:0000066 fully formed stage https://github.com/obophenotype/uberon/issues/566 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. https://orcid.org/0000-0002-6601-2165 A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 SCTID:296280003 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. http://orcid.org/0000-0002-6601-2165 End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage End of the life of an organism. XAO:0000437 ncit:Death is an outcome ncit An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole EMAPA:16737 FMA:45660 MA:0000434 uberon respiratory tract subdivision of respiratory tract UBERON:0000072 proximo-distal subdivision of respiratory tract An section of a respiratory tract. http://orcid.org/0000-0002-6601-2165 MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole MA respiratory tract MA:0000434 Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. 2009-06-18T09:00:04Z BIRNLEX:1157 NCIT:C13040 SCTID:25087005 UMLS:C1518256 part of nervous system uberon UBERON:0000073 regional part of nervous system Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. BIRNLEX:1157 UMLS:C1518256 ncithesaurus:Nervous_System_Part part of nervous system BIRNLEX:1157 A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? 2009-06-18T09:26:37Z glomerulus BTO:0000530 CALOHA:TS-0862 EFO:0003667 EMAPA:28329 EV:0100386 FMA:15624 MA:0001657 MESH:D007678 NCIT:C13250 SCTID:362217000 TAO:0001288 UMLS:C0022663 Wikipedia:Glomerulus ZFA:0001288 renal glomeruli uberon Malphigian glomerulus Malpighian glomerulus Malpighian tuft glomerular capillary tuft glomerular tuft glomerulus renis renal corpuscle UBERON:0000074 renal glomerulus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg FMA MA A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. MP:0005325 Wikipedia:Glomerulus ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? ZFA UMLS:C0022663 ncithesaurus:Glomerulus renal glomeruli TAO:0001288 Malphigian glomerulus BTO:0000530 Malpighian glomerulus http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus Malpighian tuft http://medical-dictionary.thefreedictionary.com/malpighian+glomerulus glomerular capillary tuft ZFA:0001288 glomerular tuft glomerulus renis Wikipedia:Glomerulus renal corpuscle Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system cjm Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis BTO:0006242 EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 NCIT:C34309 UMLS:C1515087 Wikipedia:External_ectoderm surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png EHDAA2 EHDAA2 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. MGI:anna MP:0012532 BTO:0006242 https://github.com/biopragmatics/biomappings UMLS:C1515087 ncithesaurus:Surface_Ectoderm surface ectoderm MP:0012532 An anatomical structure that develops from the endoderm and the mesoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000077 mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. https://orcid.org/0000-0002-6601-2165 An anatomical structure that develops from the ectoderm, mesoderm and endoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000078 mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. https://orcid.org/0000-0002-6601-2165 The organs associated with producing offspring in the gender that produces spermatozoa. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000082 CALOHA:TS-1310 EFO:0000970 EHDAA2:0001054 EHDAA:8136 EMAPA:17968 EV:0100101 FBbt:00004927 FMA:45664 GAID:386 HAO:0000505 MA:0000396 MESH:D005837 NCIT:C12722 SCTID:361340001 TGMA:0000634 UMLS:C0017422 UMLS:C1963704 VHOG:0000725 Wikipedia:Male_reproductive_system_(human) XAO:0000155 genitalia of male organism male genital system male genitalia male genitals male organism genitalia male organism reproductive system reproductive system of male organism uberon male genital organ male genital tract male reproductive tract systema genitale masculinum UBERON:0000079 male reproductive system https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb The organs associated with producing offspring in the gender that produces spermatozoa. MP:0001145 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000725 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 http://bgee.unil.ch/ FBbt:00004927 UMLS:C0017422 ncithesaurus:Male_Genitalia UMLS:C1963704 ncithesaurus:Male_Reproductive_System genitalia of male organism OBOL:automatic male genital system FMA:45664 male organism genitalia OBOL:automatic male organism reproductive system OBOL:automatic reproductive system of male organism OBOL:automatic male genital organ BTO:0000082 male reproductive tract MA:0000396 systema genitale masculinum BTO:0000082 The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] mesonephric In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] AAO:0010384 BTO:0001542 CALOHA:TS-0624 EFO:0000928 EHDAA2:0001130 EHDAA:1581 EHDAA:5903 EMAPA:16744 FMA:72171 GAID:1308 MESH:D001755 NCIT:C26467 SCTID:308799002 TAO:0000529 UMLS:C0025492 VHOG:0000038 Wikipedia:Mesonephros XAO:0000141 ZFA:0000529 Wolffian body mesonephric kidney mesonephroi uberon amphibian adult kidney corpus Wolffi middle kidney opisthonephros opisto nephros opistonephros UBERON:0000080 mesonephros http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. GO:0001823 Wikipedia:Mesonephros A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000038 VHOG http://bgee.unil.ch/ Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] 2012-06-20 AAO:0010384 AAO AAO:BJB As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000038 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 http://bgee.unil.ch/ UMLS:C0025492 ncithesaurus:Mesonephros Wolffian body BTO:0001542 GOC:yaf MESH:A16.254.500 Wikipedia:Mesonephros mesonephric kidney XAO:0000141 mesonephroi http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron amphibian adult kidney XAO:0000141 corpus Wolffi BTO:0001542 middle kidney BTO:0001542 opisthonephros VHOG:0000038 XAO:0000141 opistonephros http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]. TODO check developmental relationships A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] metanephric During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis BTO:0001543 EHDAA2:0001137 EHDAA:3089 EHDAA:5911 EMAPA:17373 EMAPA_RETIRED:17207 FMA:72172 NCIT:C34209 SCTID:308797000 UMLS:C0231049 VHOG:0000039 Wikipedia:Metanephros#Metanephros metanephron uberon definite kidney definitive kidney hind kidney metanephric kidney UBERON:0000081 metanephros definitional GO ISBN:9780878932504 In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]. GO:0001656 Wikipedia:Metanephros#Metanephros A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000039 VHOG http://bgee.unil.ch/ The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0000039 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 http://bgee.unil.ch/ UMLS:C0231049 ncithesaurus:Metanephros metanephron BTO:0001543 definite kidney BTO:0001543 definitive kidney BTO:0001543 hind kidney BTO:0001543 metanephric kidney VHOG:0000039 A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. TODO check Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] AAO:0010389 EHDAA2:0001134 EMAPA:16747 VHOG:0000500 Wikipedia:Mesonephric_tubules XAO:0000148 uberon renal tubules tubuli mesonephrici UBERON:0000083 mesonephric tubule A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. Wikipedia:Mesonephric_tubules Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] 2012-09-17 VHOG:0000500 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mesonephric+tubule As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000500 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 http://bgee.unil.ch/ renal tubules VHOG:0000500 tubuli mesonephrici Wikipedia:Mesonephric_tubules An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] BTO:0001646 EHDAA2:0002140 EHDAA:3091 EHDAA:5917 EMAPA:17209 NCIT:C34207 SCTID:361528000 UMLS:C1284058 VHOG:0000541 Wikipedia:Ureteric_bud uberon diverticulum diverticulum metanephricum gemma ureterica metanephric bud metanephric diverticulum ureteric ampulla ureteric diverticulum UBERON:0000084 ureteric bud EHDAA2 EHDAA2 ISBN:9780878932504 An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. MP:0010979 PMID:19828308 Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] 2012-09-17 VHOG:0000541 VHOG http://bgee.unil.ch/ Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. VHOG:0000541 The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000541 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 http://bgee.unil.ch/ UMLS:C1284058 ncithesaurus:Metanephric_Diverticulum diverticulum BTO:0001646 diverticulum metanephricum Wikipedia:Ureteric_bud gemma ureterica Wikipedia:Ureteric_bud metanephric bud BTO:0001646 metanephric diverticulum Wikipedia:Metanephros#Metanephros ureteric diverticulum VHOG:0000541 A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. EHDAA2 has embryo starting later BTO:0001508 EHDAA2:0000005 FMA:292334 GAID:1295 MESH:D009028 NCIT:C34212 SCTID:361474003 UMLS:C0026573 Wikipedia:Morula uberon morula (2-16 cells) UBERON:0000085 morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png EHDAA2 A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. MP:0012130 EHDAA2 has embryo starting later EHDAA2 UMLS:C0026573 ncithesaurus:Morula morula (2-16 cells) EHDAA2:0000005 A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] zona pellucida - vitelline membrane BTO:0003135 EHDAA2:0002220 EHDAA:31 EHDAA:62 EMAPA:16035 FMA:18674 GAID:410 MA:0001715 MESH:D015044 NCIT:C33896 TAO:0001111 UMLS:C0043519 VHOG:0000720 Wikipedia:Zona_pellucida ZFA:0001111 uberon oolemma pellucid zone striated membrane vitelline envelope vitelline membrane zona radiata zona striata UBERON:0000086 zona pellucida http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Wikipedia:Zona_pellucida Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] 2012-09-17 VHOG:0000720 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159 http://bgee.unil.ch/ zona pellucida - vitelline membrane VHOG:0000720 UMLS:C0043519 ncithesaurus:Zona_Pellucida oolemma BTO:0003135 pellucid zone BTO:0003135 striated membrane BTO:0003135 zona radiata BTO:0003135 zona striata BTO:0003135 A mass of cells that develop into the body of the embryo and some extraembryonic tissues. A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass] EFO:0000547 EHDAA2:0000830 EHDAA:40 EMAPA:16041 FMA:86557 NCIT:C13740 SCTID:361456007 UMLS:C1283994 VHOG:0000742 Wikipedia:Inner_cell_mass uberon ICM early embryoblast embryoblast embryoblastus; massa cellularis interna; pluriblastus senior pluriblast UBERON:0000087 inner cell mass https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg Wikipedia Wikipedia A mass of cells that develop into the body of the embryo and some extraembryonic tissues. ISBN:0-683-40008-8 MGI:pvb A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] 2012-09-17 VHOG:0000742 VHOG http://bgee.unil.ch/ A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] 2012-09-17 VHOG:0000742 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 http://bgee.unil.ch/ UMLS:C1283994 ncithesaurus:Inner_Cell_Mass ICM VHOG:0000742 early embryoblast FMA:86557 embryoblastus; massa cellularis interna; pluriblastus senior Wikipedia:Inner_cell_mass The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta. the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] trophoblastic The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta BTO:0001079 CALOHA:TS-1070 EV:0100120 FMA:83029 GAID:1152 MESH:D014327 NCIT:C93292 SCTID:362839005 UMLS:C0041178 Wikipedia:Trophoblast trophoblast layer uberon massa cellularis externa trophoblastus trophoderm UBERON:0000088 Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast] trophoblast https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg MP-def PMID:19829370 The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta. ISBN:0-683-40008-8 MP:0005031 the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] 2012-08-23 MP:0005031 trophoblast layer MP ISBN:0-683-40008-8 The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta PMID:19829370 UMLS:C0041178 ncithesaurus:Trophoblast trophoblast layer MP:0005031 massa cellularis externa Wikipedia:Trophoblast trophoblastus Wikipedia:Trophoblast trophoderm BTO:0001079 A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. embryonic disc embryonic shield germinal disc germinal disk FMA:293863 NCIT:C34112 UMLS:C1283997 Wikipedia:Bilaminar_disc bilaminary embryonic disc bilaminary germ disc uberon bilaminar disk UBERON:0000091 bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png Wikipedia A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. MP:0003886 embryonic disc MP:0003886 embryonic shield MP:0003886 germinal disc MP:0003886 germinal disk MP:0003886 UMLS:C1283997 ncithesaurus:Bilaminar_Embryonic_Disc bilaminary germ disc ISBN:9780878932504 bilaminar disk Wikipedia:Bilaminar_disc Stage succeeding embryo, including mature structure. In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage https://github.com/obophenotype/uberon/issues/344 Stage succeeding embryo, including mature structure. https://orcid.org/0000-0002-6601-2165 Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]. 2009-07-30T05:19:13Z membrane FMA:7145 membrane of organ uberon UBERON:0000094 membrane organ FMA-def Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]. FMA:7145 Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]. A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. 2009-07-30T07:57:38Z TAO:0002173 Wikipedia:Cardiac_neural_crest XAO:0004190 ZFA:0001648 uberon cardiac neural crest complex complexus cristae neuralis cardiacus UBERON:0000095 cardiac neural crest Wikipedia Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]. Wikipedia:Cardiac_neural_crest A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. DOI:10.1242/dev.091751 ZFA treats this as a subtype of NC. ZFA cardiac neural crest complex Wikipedia:Cardiac_neural_crest complexus cristae neuralis cardiacus Wikipedia:Cardiac_neural_crest A lung lobe is one of the rounded projections that compose the lung[GO]. EMAPA:36281 FMA:7311 MA:0003098 NCIT:C34021 SCTID:245524004 UMLS:C0225752 galen:LobeOfLung lung lobe pulminory lobe pulmonary lobe uberon UBERON:0000101 lobe of lung FMA A lung lobe is one of the rounded projections that compose the lung[GO]. GOC:GO UMLS:C0225752 ncithesaurus:Lung_Lobe pulmonary lobe FMA:7311 The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. FMA:73750 lung vascular network pulmonary vasculature vascular network of lung vasculature of lung uberon UBERON:0000102 lung vasculature The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. GOC:GO lung vascular network OBOL:automatic pulmonary vasculature FMA:73750 vascular network of lung OBOL:automatic vasculature of lung OBOL:automatic An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 ncithesaurus:Life entire life cycle entire lifespan life lifespan uberon UBERON:0000104 life cycle https://github.com/obophenotype/uberon/issues/532 An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism. https://orcid.org/0000-0002-6601-2165 A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MESH:D008018 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. https://orcid.org/0000-0002-6601-2165 A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 Wikipedia:Zygote XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] 2012-09-17 VHOG:0000745 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 http://bgee.unil.ch/ IDOMAL:0000302 https://github.com/biopragmatics/biomappings fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum Wikipedia:Zygote The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:D002970 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 Wikipedia:Cleavage_(embryo) XAO:1000004 ZFS:0000046 uberon UBERON:0000107 cleavage stage The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. GO:0040016 Wikipedia:Cleavage_(embryo) An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. consider adding a preceding stage 'morula stage' as part of cleavage BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 WBls:0000005 Wikipedia:Blastula XAO:1000003 ZFS:0000045 uberon UBERON:0000108 blastula stage http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. Wikipedia:Blastula A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 WBls:0000010 XAO:1000005 ZFS:0000047 uberon blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage UBERON:0000109 gastrula stage BILS A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GO:0007369 blastocystis trilaminaris stage https://orcid.org/0000-0002-6601-2165 trilaminar blastocyst stage https://orcid.org/0000-0002-6601-2165 trilaminar blastoderm stage https://orcid.org/0000-0002-6601-2165 trilaminar disk stage https://orcid.org/0000-0002-6601-2165 trilaminar germ stage https://orcid.org/0000-0002-6601-2165 trilaminar stage https://orcid.org/0000-0002-6601-2165 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 uberon UBERON:0000110 neurula stage https://github.com/obophenotype/developmental-stage-ontologies/issues/84 https://github.com/obophenotype/uberon/issues/343 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001841 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 Wikipedia:Organogenesis uberon segmentation stage UBERON:0000111 organogenesis stage https://github.com/obophenotype/developmental-stage-ontologies/issues/84 https://github.com/obophenotype/uberon/issues/533 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. Wikipedia:Organogenesis The stage of being a sexually immature adult animal[XAO:1000010]. In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother) BILS:0000112 BTO:0002168 EFO:0001300 EV:0300051 MmusDv:0000043 OGES:000009 XAO:1000010 XtroDO:0000083 ZFS:0000051 immature stage juvenile stage uberon subadult stage UBERON:0000112 sexually immature stage https://github.com/obophenotype/uberon/issues/427 The stage of being a sexually immature adult animal[XAO:1000010]. XAO:1000010 immature stage VHOG:FB juvenile stage XAO:1000010 subadult stage http://eol.org/schema/terms/subadult The stage of being a sexually mature adult animal. adult stage BILS:0000113 EV:0300064 EV:0300070 MIAA:0000403 MmusDv:0000110 OGES:000026 OGES:000027 XAO:1000093 ZFS:0000044 uberon UBERON:0000113 post-juvenile adult stage https://github.com/obophenotype/uberon/issues/345 https://github.com/obophenotype/uberon/issues/499 The stage of being a sexually mature adult animal. https://orcid.org/0000-0002-6601-2165 The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin. it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces EMAPA:35521 FMA:27533 MA:0001782 SCTID:201609008 connective tissue of lung pulmonary interstitium uberon lung interstitial tissue lung interstitium pulmonary connective tissue pulmonary interstitial tissue UBERON:0000114 lung connective tissue The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin. ISBN:0-683-40008-8 MGI:anna MP:0002276 PMID:14635660 connective tissue of lung OBOL:automatic pulmonary interstitium FMA:27533 lung interstitial tissue MA:0001782 pulmonary connective tissue EMAPA:35521 The epithelial layer of the lung. A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469] BTO:0001653 EMAPA:32860 MA:0001783 epithelial tissue of lung epithelium of lung lung epithelial tissue uberon pulmonary epithelium UBERON:0000115 lung epithelium The epithelial layer of the lung. MP:0006382 epithelial tissue of lung OBOL:automatic epithelium of lung OBOL:automatic lung epithelial tissue OBOL:automatic pulmonary epithelium BTO:0001653 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment uberon airway UBERON:0000117 respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. GO:0030323 http://orcid.org/0000-0002-6601-2165 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) GO EMAPA:37946 MA:th segment of tracheobronchial tree FMA:12224 respiratory conducting tube MP:0004391 segment of tracheobronchial tree FMA:12224 tracheobronchial tree segment FMA:12224 Structure derived from foregut that becomes a lung[GO]. clarify successors - include bronchi? BTO:0001643 EHDAA2:0004089 NCIT:C34260 NCIT:C34282 SCTID:361427007 UMLS:C1514420 UMLS:C1514897 Wikipedia:Respiratory_bud uberon gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum UBERON:0000118 lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png GO:0060441 EHDAA2 Structure derived from foregut that becomes a lung[GO]. GO:0060431 Wikipedia:Respiratory_bud UMLS:C1514420 ncithesaurus:Primary_Bronchial_Bud UMLS:C1514897 ncithesaurus:Respiratory_Diverticulum gemma pulmonalis Wikipedia:Lung_buds gemma respiratoria Wikipedia:Lung_buds lung bud primary lung bud GO:0060572 respiratory diverticulum Wikipedia:Lung_buds A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 FBbt:00005099 NLX:147821 funiculus nerve fiber bundle neural fiber bundle uberon UBERON:0000122 neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 FBbt:00005099 nerve fiber bundle FBbt:00005099 A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO). Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. nucleus AEO:0000136 FMA:83686 NCIT:C13197 NLX:28443 Wikipedia:Nucleus_(neuroanatomy) nervous system nucleus neuraxis nucleus neuronal nucleus nucleus of CNS uberon nucleus of neuraxis UBERON:0000125 neural nucleus we limit this structure by definition to chordate and vertebrate nervous systems A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO). NLX:28443 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. GO_REF:0000021 neuraxis nucleus FMA:83686 neuronal nucleus AEO:0000136 nucleus of CNS NLX:28443 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves. EMAPA:37066 FMA:54501 NLX:28532 SCTID:280160003 Wikipedia:Cranial_nerve_nucleus cranial neural nucleus nucleus of cranial nerve uberon nucleus nervi cranialis UBERON:0000126 cranial nerve nucleus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves. NLX:28532 EMAPA:37066 MA:th cranial neural nucleus FMA:54501 nucleus nervi cranialis Wikipedia:Cranial_nerve_nucleus The group of motor neurons residing in the pons that innervate the muscles of facial expression. FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. BAMS:7 BAMS:7N BAMS:VII BM:Pons-VII DHBA:12420 EHDAA2:0004638 EMAPA:35338 EV:0100267 FMA:54572 MA:0001014 MESH:D065828 NCIT:C12898 SCTID:280166009 UMLS:C0228740 VHOG:0001412 facial VII nucleus facial nerve nucleus nucleus of facial nerve uberon facial VII motor nucleus UBERON:0000127 facial nucleus definitional The group of motor neurons residing in the pons that innervate the muscles of facial expression. ISBN:0838580343 MP:0000909 FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. FMA UMLS:C0228740 ncithesaurus:Facial_Nerve_Nucleus facial VII nucleus MA:0001014 nucleus of facial nerve FMA:54572 facial VII motor nucleus MA:0001014 uberon UBERON:0000153 anterior region of body lexical uberon UBERON:0000154 posterior region of body A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. membrane FMA:30322 FMA:82500 MESH:D008566 NCIT:C12749 membranous organ component uberon UBERON:0000158 membranous layer A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. ncithesaurus:Membrane membranous organ component FMA:82500 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. requires alignment with EHDAA2 and complete developmental relationships BTO:0001978 CALOHA:TS-2160 EMAPA:18256 FMA:15703 MA:0000330 MESH:D001003 NCIT:C12375 SCTID:245438008 UMLS:C0227411 Wikipedia:Anal_canal galen:AnalCanal anal canal anal canal viewed anatomically anatomical anal canal uberon anal pad anus canalis analis cloaca cloacal chamber mesenteron pars analis recti UBERON:0000159 anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png Wikipathways:WP2062 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. Wikipedia:Anal_canal MESH:D001003 https://github.com/biopragmatics/biomappings UMLS:C0227411 ncithesaurus:Anal_Canal canalis analis BTO:0001978 Wikipedia:Anal_canal pars analis recti BTO:0001978 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:D007422 MIAA:0000043 NCIT:C12736 SCTID:256876008 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 Wikipedia:Intestine XAO:0000129 ZFA:0001338 galen:Intestine bowel uberon intestinal tract UBERON:0000160 intestine cjm Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. GOC:GO Wikipedia:Intestine Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] 2012-06-20 AAO:0000246 AAO AAO:EJS The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000056 VHOG http://bgee.unil.ch/ UMLS:C0021853 ncithesaurus:Intestine Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 SCTID:91837002 anatomical orifice hilum uberon UBERON:0000161 orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 in FMA, this is an anatomical conduit *space*, rather than anatomical conduit FMA anatomical ostium FMA:3724 anatomical orifice FMA:3724 Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] cloacal Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 NCIT:C34127 SCTID:362857006 SCTID:370631000 UMLS:C0008987 VHOG:0001186 Wikipedia:Cloaca XAO:0000244 ZFA:0005781 uberon cloacal chamber vent UBERON:0000162 cloaca ZFA AAO Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. ISBN:0073040584 Wikipedia:Cloaca most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] 2012-09-17 VHOG:0001186 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/cloaca Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] 2012-06-20 AAO:0000095 AAO AAO:BJB A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001186 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 http://bgee.unil.ch/ hindgut endoderm and proctodeal ectoderm. WP UMLS:C0008987 ncithesaurus:Cloaca cloacal chamber AAO:0000095 vent XAO:0000244 Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 Wikipedia:Cloaca_(embryology) uberon cloaca UBERON:0000163 embryonic cloaca EHDAA2 EHDAA2 Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. MP:0010115 Wikipedia:Cloaca_(embryology) cloaca The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females. The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal urogenital sinus EHDAA2:0004060 EHDAA:5029 EHDAA:5919 EMAPA:17379 NCIT:C34322 SCTID:50961009 UMLS:C0231057 VHOG:0000414 Wikipedia:Definitive_urogenital_sinus UGS fetal UGS sinus urogenitalis uberon UBERON:0000164 primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png MP-def The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females. ISBN:0-683-40008-8 MP:0010116 The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] 2012-09-17 VHOG:0000414 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/urogenital+sinus In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] 2012-09-17 VHOG:0000414 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300 http://bgee.unil.ch/ the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal MP urogenital sinus MP:0010116 UMLS:C0231057 ncithesaurus:Urogenital_Sinus UGS MP:0010116 fetal UGS PMID:18977204 sinus urogenitalis The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 SCTID:21082005 TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 Wikipedia:Mouth XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg regio oralis adult mouth uberon cavital oralis cavitas oris cavum oris mouth cavity oral region oral vestibule rima oris stoma stomatodaeum trophic apparatus vestibule of mouth vestibulum oris UBERON:0000165 mouth https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] 2012-06-20 AAO:0010355 AAO AAO:BJB Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] 2012-09-17 VHOG:0000812 VHOG DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) http://bgee.unil.ch/ in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips FMA FBbt:00003126 regio oralis BTO:0004698 FMA:49184 FMA:TA cavital oralis Wikipedia:Mouth cavitas oris BTO:0001090 cavum oris BTO:0001090 mouth cavity BTO:0001090 oral region EHDAA2:0001326 oral vestibule BTO:0001090 rima oris BTO:0001090 stomatodaeum VHOG:0000812 trophic apparatus http://orcid.org/0000-0002-6601-2165 vestibule of mouth BTO:0001090 vestibulum oris BTO:0001090 The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] FMA:59806 oral fissure oral orifice uberon mouth oral part of face UBERON:0000166 oral opening FMA The orifice that connects the mouth to the exterior of the body. https://github.com/obophenotype/uberon/wiki/The-digestive-tract (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] 2012-09-17 VHOG:0000280 VHOG DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007) http://bgee.unil.ch/ oral fissure FMA:59806 oral orifice FMA:59806 mouth Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present). Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] AAO:0000053 AAO:0000960 BSA:0000107 CALOHA:TS-1315 EFO:0001975 EHDAA2:0001324 EHDAA:6970 EMAPA:17411 EMAPA:18399 EV:0100057 FMA:20292 HAO:0000669 MESH:D009055 NCIT:C12421 SCTID:181220002 TAO:0001027 TGMA:0000102 UMLS:C0226896 VHOG:0000188 WBbt:0005255 XAO:0000126 ZFA:0001027 buccal cavity cavity of mouth uberon bucca UBERON:0000167 oral cavity Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present). ISBN:0073040584 https://github.com/obophenotype/uberon/wiki/The-digestive-tract https://orcid.org/0000-0002-6601-2165 Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000960 AAO AAO:EJS The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] 2012-09-17 VHOG:0000188 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/oral+cavity Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] 2012-09-17 VHOG:0000188 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32 http://bgee.unil.ch/ MESH:D009055 https://github.com/biopragmatics/biomappings UMLS:C0226896 ncithesaurus:Oral_Cavity buccal cavity FMA:20292 ISBN:0073040584 A section dividing a colon along a proximal-distal axis. FMA:222905 uberon segment of colon UBERON:0000168 proximal-distal subdivision of colon 4 cjm A section dividing a colon along a proximal-distal axis. http://orcid.org/0000-0002-6601-2165 segment of colon FMA:222905 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 lungs lungs pair pulmones set of lungs uberon UBERON:0000170 pair of lungs FMA-abduced The pair of anatomical structures comprised of a left lung and right lung. http://orcid.org/0000-0002-6601-2165 pulmones FMA:68877 FMA:TA Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SCTID:272626006 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon gas exchange organ UBERON:0000171 respiration organ Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. GO:0007585 apparatus respiratorius organ OBOL:automatic organ of apparatus respiratorius OBOL:automatic organ of respiratory system OBOL:automatic respiratory system organ OBOL:automatic Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. BTO:0000068 CALOHA:TS-0034 EMAPA:36771 ENVO:02000021 EV:0100123 FMA:305905 GAID:1155 MA:0002893 MESH:D000653 NCIT:C13188 UMLS:C0002638 VHOG:0001267 uberon acqua amnii liquor amnii UBERON:0000173 amniotic fluid Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. ENVO:02000021 MP:MP UMLS:C0002638 ncithesaurus:Amniotic_Fluid acqua amnii BTO:0000068 liquor amnii BTO:0000068 A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. GO:0007588 http://orcid.org/0000-0002-6601-2165 portion of excreted substance FMA:9674 waste substance AEO:0000184 excretion BTO:0000491 Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells. biospecimen in NCIT ENVO:02000038 Wikipedia:Pus galen:Pus ncithesaurus:Pus uberon purulent exudate UBERON:0000177 pus http://upload.wikimedia.org/wikipedia/commons/9/90/Swollen_eye_with_conjunctivitis.jpg Pus is a bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. Pus is produced from the dead and living cells which travel into the intercellular spaces around the affected cells. ENVO:02000038 Wikipedia:Pus biospecimen in NCIT NCIT A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 TAO:0000007 UMLS:C0005767 VHOG:0000224 Wikipedia:Blood XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood CL:tm https://github.com/obophenotype/uberon/issues/1330 Bgee:AN A fluid that is composed of blood plasma and erythrocytes. FMA:9670 Wikipedia:Blood http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000007 TAO ZFIN:curator Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] 2012-06-20 AAO:0000046 AAO AAO:LAP relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000046 AAO Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] 2012-09-17 VHOG:0000224 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) http://bgee.unil.ch/ UMLS:C0005767 ncithesaurus:Blood whole blood BTO:0000089 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. http://orcid.org/0000-0002-6601-2165 Dorsal part (roof region) of the telencephalon[GO]. In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus 2009-04-18T12:03:09Z UBERON:0007333 BTO:0003399 DMBA:15903 EFO:0003534 SCTID:369224000 TAO:0000505 TAO:0007007 Wikipedia:Avian_pallium Wikipedia:Pallium_(neuroanatomy) ZFA:0000505 neuronames:3240 area dorsalis telencephali dorsal part of telencephalon dorsal telencephalic area dorsal telencephalon uberon UBERON:0000203 pallium https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87 Dorsal part (roof region) of the telencephalon[GO]. GO:0021543 ISBN:0471888893 Wikipedia:Pallium_(neuroanatomy) https://github.com/obophenotype/uberon/issues/287 PMID:8932866 In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. Wikipedia:Avian_pallium NCBITaxon:8782 In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus WP area dorsalis telencephali ZFA:0000505 dorsal part of telencephalon ISBN:0471888893 dorsal telencephalic area ZFA:0000505 dorsal telencephalon ZFA:0000505 The bone forming the forehead and roof of the eye orbit. fused in humans, paired in other animals In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993). AAO:0000206 EMAPA:19016 FMA:52734 GAID:226 MA:0001466 MESH:D005624 NCIT:C32635 SCTID:181793006 UMLS:C0016732 VHOG:0001324 VSAO:0000208 Wikipedia:Frontal_bone frontal frontal bone os frontal uberon os frontale UBERON:0000209 tetrapod frontal bone http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png FMA cjm The bone forming the forehead and roof of the eye orbit. ISBN:0-683-40008-8 MP:0000107 PMID:7914451 Wikipedia:Frontal_bone UMLS:C0016732 ncithesaurus:Frontal_Bone frontal AAO:0000206 frontal bone FMA:52734 MA:0001466 os frontal Wikipedia:Frontal_bone os frontale Wikipedia:Frontal_bone Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. Portion of connective tissue that connects bone or cartilage.[TAO] Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG] this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament CALOHA:TS-2145 EFO:0001966 EMAPA:35493 FMA:21496 FMA:30319 MA:0000113 MESH:D008022 NCIT:C13046 SCTID:182358004 TAO:0001682 UMLS:C0023685 VHOG:0001272 Wikipedia:Ligament XAO:0004031 ZFA:0001675 galen:Ligament ligament organ uberon UBERON:0000211 ligament https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. GO_REF:0000034 VSAO:0000073 http://dx.plos.org/10.1371/journal.pone.0051070 Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. FMA:21496 Portion of connective tissue that connects bone or cartilage.[TAO] 2012-08-14 TAO:0001682 TAO TAO:wd Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG] 2012-09-17 VHOG:0001272 VHOG PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996) http://bgee.unil.ch/ UMLS:C0023685 ncithesaurus:Ligament ligament organ FMA:21496 A neural arch that is part of a vertebral bone 2. FMA:24053 vertebral foramen of cervical vertebra 2 uberon UBERON:0000218 vertebral arch of axis A neural arch that is part of a vertebral bone 2. OBOL:automatic FMA:24293 SCTID:281228008 Wikipedia:Atlas_(anatomy)#Vertebral_foramen vertebral foramen of cervical vertebra 1 uberon UBERON:0000219 vertebral foramen of atlas The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital. FMA:24939 MESH:D001269 NCIT:C32158 SCTID:361831006 UMLS:C0004169 Wikipedia:Atlanto-occipital_joint ncithesaurus:Atlanto-occipital_Joint-Atlanto articulatio atlanto-occipitalis atlanto occipital joint atlantooccipital joint craniovertebral joint occipito atlantal joint occipito-atlantal joint uberon articulatio atlantooccipitalis UBERON:0000220 atlanto-occipital joint http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png FMA-abduced-lr The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital. Wikipedia:Atlanto-occipital_joint MESH:D001269 https://github.com/biopragmatics/biomappings UMLS:C0004169 ncithesaurus:Atlanto-occipital_Joint articulatio atlanto-occipitalis FMA:24939 craniovertebral joint FMA:24939 articulatio atlantooccipitalis Wikipedia:Atlanto-occipital_joint A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath. TODO - add layer relations. 'tendon sheath' GAT in FMA. BTO:0000051 FMA:45087 FMA:76715 NCIT:C96299 SCTID:361885006 UMLS:C0224856 Wikipedia:Tendon_sheath synovial tendon sheath uberon vagina tendinis UBERON:0000304 tendon sheath A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath. Wikipedia:Tendon_sheath UMLS:C0224856 ncithesaurus:Tendon_Sheath synovial tendon sheath FMA:45087 vagina tendinis Wikipedia:Tendon_sheath The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG] Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] amniotic BTO:0000065 CALOHA:TS-0033 EHDAA2:0000116 EHDAA:136 EMAPA:16109 EV:0100122 FMA:80223 GAID:1298 MESH:D000650 NCIT:C12365 SCTID:181457005 UMLS:C0002630 VHOG:0000721 Wikipedia:Amnion amnios uberon UBERON:0000305 amnion http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb Hymans ISBN:0073040584 ISBN:0073040584-table5.4 ISBN:0073040584-table5.4 The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. MGI:csmith MP:0005029 A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG] 2012-09-17 VHOG:0000721 VHOG http://bgee.unil.ch/ Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000721 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 http://bgee.unil.ch/ UMLS:C0002630 ncithesaurus:Amnion amnios http://placentation.ucsd.edu/glossfs.html Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 MESH:D036703 OGEM:000006 Wikipedia:Blastula blastula embryo uberon blastosphere UBERON:0000307 blastula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. Wikipedia:Blastula blastula embryo BILA:0000059 blastosphere Wikipedia:Blastula The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. defined generically to encompass both vertebrates and invertebrates the BTO class refers to earthworms. BTO:0000139 EMAPA:32761 FMA:10427 SCTID:281483004 galen:BodyWall wall fo trunk trunk wall wall of trunk uberon UBERON:0000309 body wall The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. MP:0003385 the BTO class refers to earthworms. BTO wall fo trunk FMA:10427 trunk wall FMA:10427 wall of trunk FMA:10427 The upper ventral region of the torso of an organism. The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. BTO:0000149 CALOHA:TS-2083 EV:0100124 FMA:9601 GAID:33 MESH:D001940 NCIT:C12971 SCTID:181131000 UMLS:C0006141 Wikipedia:Breast galen:Breast mammary part of chest mammary region uberon mamma UBERON:0000310 breast http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg The upper ventral region of the torso of an organism. Wikipedia:Breast The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. WP,unvetted UMLS:C0006141 ncithesaurus:Breast mammary part of chest FMA:9601 mammary region FMA:9601 mamma Wikipedia:Breast Cartilage pertaining to the tibia. This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia BTO:0000207 FMA:33923 tibial cartilage uberon cartilage of tibia UBERON:0000313 portion of cartilage tissue in tibia Cartilage pertaining to the tibia. Dorlands_Medical_Dictionary:MerckSource cartilage of tibia FMA:33923 A mucosa that is part of a cecum [Automatically generated definition]. BTO:0000213 FMA:14998 caecum mucosa caecum mucosa of organ caecum mucous membrane caecum organ mucosa cecal mucosa cecum mucosa of organ cecum mucous membrane cecum organ mucosa intestinum crassum caecum mucosa intestinum crassum caecum mucosa of organ intestinum crassum caecum mucous membrane intestinum crassum caecum organ mucosa mucosa of caecum mucosa of cecum mucosa of intestinum crassum caecum mucosa of organ of caecum mucosa of organ of cecum mucosa of organ of intestinum crassum caecum mucous membrane of caecum mucous membrane of cecum mucous membrane of intestinum crassum caecum organ mucosa of caecum organ mucosa of cecum organ mucosa of intestinum crassum caecum uberon UBERON:0000314 cecum mucosa A mucosa that is part of a cecum [Automatically generated definition]. OBOL:automatic caecum mucosa OBOL:automatic caecum mucosa of organ OBOL:automatic caecum mucous membrane OBOL:automatic caecum organ mucosa OBOL:automatic cecal mucosa FMA:14998 cecum mucosa of organ OBOL:automatic cecum mucous membrane OBOL:automatic cecum organ mucosa OBOL:automatic intestinum crassum caecum mucosa OBOL:automatic intestinum crassum caecum mucosa of organ OBOL:automatic intestinum crassum caecum mucous membrane OBOL:automatic intestinum crassum caecum organ mucosa OBOL:automatic mucosa of caecum OBOL:automatic mucosa of cecum OBOL:automatic mucosa of intestinum crassum caecum OBOL:automatic mucosa of organ of caecum OBOL:automatic mucosa of organ of cecum OBOL:automatic mucosa of organ of intestinum crassum caecum OBOL:automatic mucous membrane of caecum OBOL:automatic mucous membrane of cecum OBOL:automatic mucous membrane of intestinum crassum caecum OBOL:automatic organ mucosa of caecum OBOL:automatic organ mucosa of cecum OBOL:automatic organ mucosa of intestinum crassum caecum OBOL:automatic The space between the arachnoid and pia mater. BTO:0000230 EMAPA:32666 FMA:83716 GAID:689 MESH:D013346 SCTID:362311001 Wikipedia:Subarachnoid_space subarachnoid space of CNS subarachnoid space of central nervous system subarachnoid space of neuraxis uberon cavitas subarachnoidea cavum subarachnoideale spatium leptomeningeum spatium subarachnoideum subarachnoid cavity UBERON:0000315 subarachnoid space http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png ISBN:0471888893 The space between the arachnoid and pia mater. GOC:add Wikipedia:Subarachnoid_space https://sourceforge.net/p/obo/mammalian-phenotype-requests/1168/ subarachnoid space of neuraxis FMA:322060 cavitas subarachnoidea BTO:0000230 cavum subarachnoideale Wikipedia:Subarachnoid_space spatium leptomeningeum BTO:0000230 spatium subarachnoideum BTO:0000230 Wikipedia:Subarachnoid_space subarachnoid cavity BTO:0000230 A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 FMA:83689 MESH:D002582 Wikipedia:Mucus#Reproductive_system cervix mucus uberon UBERON:0000316 cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 Wikipedia:Cervix#Cervical_mucus Wikipedia:Mucus#Reproductive_system cervix mucus OBOL:automatic Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. UBERON:0003347 UBERON:0004981 BTO:0000271 CALOHA:TS-0164 EFO:0003038 EMAPA:27375 FMA:14984 FMA:85388 MA:0003194 SCTID:362157008 colon mucosa colon mucous membrane colonic mucosa colonic mucous membrane large bowel mucosa mucosa of colon mucosa of large bowel uberon UBERON:0000317 colonic mucosa Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. http://orcid.org/0000-0002-6601-2165 colon mucosa FMA:14984 colon mucous membrane OBOL:automatic colonic mucous membrane FMA:14984 large bowel mucosa OBOL:automatic mucosa of colon FMA:14984 mucosa of large bowel OBOL:automatic A mucosa that is part of a duodenum [Automatically generated definition]. UBERON:0003348 BTO:0000367 CALOHA:TS-0213 EMAPA:27235 FMA:14942 MA:0003207 SCTID:362146003 doudenal mucosa duodenal mucous membrane mucosa of duodenum mucous membrane of duodenum uberon duodenum mucosa UBERON:0000320 duodenal mucosa A mucosa that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal mucosa FMA:14942 duodenal mucous membrane FMA:14942 mucosa of duodenum OBOL:automatic mucous membrane of duodenum OBOL:automatic duodenum mucosa BTO:0000367 An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus. Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. BTO:0000449 CALOHA:TS-0360 EFO:0001323 FBbt:00005333 FMA:63919 GAID:552 MESH:D005333 NCIT:C13235 SCTID:83418008 UMLS:C0015965 fetus uberon embryo late growth stage embryo late stage UBERON:0000323 late embryo An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. https://orcid.org/0000-0003-3308-6245 Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. FMA:63919 FBbt:00005333 UMLS:C0015965 ncithesaurus:Fetus fetus BTO:0000449 embryo late growth stage BTO:0000449 embryo late stage BTO:0000449 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 FMA:14919 uberon UBERON:0000325 gastric gland cjm ISBN:0073040584 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. MGI:anna Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach. BTO:0000504 CALOHA:TS-2235 FMA:62973 GAID:1166 MESH:D010189 uberon pancreatic fluid pancreatic secretion succus pancreaticus UBERON:0000326 pancreatic juice Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach. GO:0030157 succus pancreaticus BTO:0000504 The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). We model the digestive tract as consisting of two parts: the wall and the lumen. BTO:0000547 FMA:45653 digestive tract wall wall of digestive tract wall of gut uberon wall of alimentary tract UBERON:0000328 gut wall The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). http://orcid.org/0000-0002-6601-2165 wall of gut FMA:45653 A mucosa that is part of a ileum [Automatically generated definition]. BTO:0000619 CALOHA:TS-0470 EMAPA:35424 FMA:14956 MA:0003216 SCTID:85458007 ileal mucous membrane ileum mucosa ileum mucosa of organ ileum mucous membrane ileum organ mucosa mucosa of ileum mucosa of organ of ileum mucous membrane of ileum organ mucosa of ileum uberon UBERON:0000331 ileal mucosa A mucosa that is part of a ileum [Automatically generated definition]. OBOL:automatic ileal mucous membrane FMA:14956 ileum mucosa FMA:14956 OBOL:automatic ileum mucosa of organ OBOL:automatic ileum mucous membrane OBOL:automatic ileum organ mucosa OBOL:automatic mucosa of ileum OBOL:automatic mucosa of organ of ileum OBOL:automatic mucous membrane of ileum OBOL:automatic organ mucosa of ileum OBOL:automatic Bone marrow in which the fat cells predominate in the meshes of the reticular network. BTO:0000635 FMA:74596 SCTID:328639002 SCTID:5023006 medulla ossium flava yellow marrow uberon fat marrow UBERON:0000332 yellow bone marrow Bone marrow in which the fat cells predominate in the meshes of the reticular network. http://medical-dictionary.thefreedictionary.com/Yellow+Marrow medulla ossium flava BTO:0000635 yellow marrow BTO:0000635 fat marrow BTO:0000635 A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. Note that some sources treat 'intestinal gland' as synonymous with crypts BTO:0000640 FMA:15052 SCTID:266297002 bowel mucosa gland bowel mucosa of organ gland bowel mucous membrane gland bowel organ mucosa gland gland of bowel mucosa gland of bowel mucosa of organ gland of bowel mucous membrane gland of bowel organ mucosa gland of intestinal mucosa gland of intestine mucosa gland of intestine mucosa of organ gland of intestine mucous membrane gland of intestine organ mucosa gland of mucosa of bowel gland of mucosa of intestine gland of mucosa of organ of bowel gland of mucosa of organ of intestine gland of mucous membrane of bowel gland of mucous membrane of intestine gland of organ mucosa of bowel gland of organ mucosa of intestine glandula intestinalis intestinal mucosa gland intestine mucosa gland intestine mucosa of organ gland intestine mucous membrane gland intestine organ mucosa gland mucosa of bowel gland mucosa of intestine gland mucosa of organ of bowel gland mucosa of organ of intestine gland mucous membrane of bowel gland mucous membrane of intestine gland organ mucosa of bowel gland organ mucosa of intestine gland uberon glandulae intestinales UBERON:0000333 intestinal gland A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. https://orcid.org/0000-0002-6601-2165 bowel mucosa gland OBOL:automatic bowel mucosa of organ gland OBOL:automatic bowel mucous membrane gland OBOL:automatic bowel organ mucosa gland OBOL:automatic gland of bowel mucosa OBOL:automatic gland of bowel mucosa of organ OBOL:automatic gland of bowel mucous membrane OBOL:automatic gland of bowel organ mucosa OBOL:automatic gland of intestinal mucosa OBOL:automatic gland of intestine mucosa OBOL:automatic gland of intestine mucosa of organ OBOL:automatic gland of intestine mucous membrane OBOL:automatic gland of intestine organ mucosa OBOL:automatic gland of mucosa of bowel OBOL:automatic gland of mucosa of intestine OBOL:automatic gland of mucosa of organ of bowel OBOL:automatic gland of mucosa of organ of intestine OBOL:automatic gland of mucous membrane of bowel OBOL:automatic gland of mucous membrane of intestine OBOL:automatic gland of organ mucosa of bowel OBOL:automatic gland of organ mucosa of intestine OBOL:automatic glandula intestinalis FMA:15052 intestinal mucosa gland OBOL:automatic intestine mucosa gland OBOL:automatic intestine mucosa of organ gland OBOL:automatic intestine mucous membrane gland OBOL:automatic intestine organ mucosa gland OBOL:automatic mucosa of bowel gland OBOL:automatic mucosa of intestine gland OBOL:automatic mucosa of organ of bowel gland OBOL:automatic mucosa of organ of intestine gland OBOL:automatic mucous membrane of bowel gland OBOL:automatic mucous membrane of intestine gland OBOL:automatic organ mucosa of bowel gland OBOL:automatic organ mucosa of intestine gland OBOL:automatic In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. gular The hyoid bone and the clavicle are the only bones located in the throat of mammals. BTO:0000828 EMAPA:37973 FMA:228738 NCIT:C54272 UMLS:C0230069 Wikipedia:Throat uberon gula UBERON:0000341 throat https://upload.wikimedia.org/wikipedia/commons/1/16/Throat_Diagram.png In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. Wikipedia:Throat EMAPA:37973 MA:th UMLS:C0230069 ncithesaurus:Throat gula A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]. mucosal FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 SCTID:361693009 UMLS:C0026724 Wikipedia:Mucous_membrane galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa uberon region of mucosa tunica mucosa UBERON:0000344 mucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]. Wikipedia:Mucous_membrane FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately FMA UMLS:C0026724 ncithesaurus:Mucosa mucosa of organ FMA:85355 mucosa of organ part FMA:85358 mucosal region FMA:85358 mucous membrane FMA:85355 organ mucosa FMA:85355 region of mucosa FMA:85358 tunica mucosa BTO:0000886 Wikipedia:Mucous_membrane The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead. Sensory medial ramus of the trigeminal nerve.[AAO] The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG] AAO:0010648 BTO:0000926 EHDAA2:0002088 EHDAA:3744 EMAPA:17800 FMA:52621 GAID:837 MA:0001104 MESH:D009882 NCIT:C33215 SCTID:280210000 UMLS:C0029082 VHOG:0001349 Wikipedia:Ophthalmic_nerve cranial nerve V, branch V1 first branch of fifth cranial nerve first division of fifth cranial nerve first division of trigeminal nerve nervus ophthalmicus (V1) nervus ophthalmicus (Va) nervus ophthalmicus [v1] nervus ophthalmicus [va] ophthalmic division [V1] ophthalmic division [Va] ophthalmic division of fifth cranial nerve ophthalmic division of trigeminal nerve (V1) ophthalmic division of trigeminal nerve (Va) ophthalmic nerve [V1] ophthalmic nerve [Va] opthalmic nerve ramus opthalmicus profundus (ramus V1) rostral branch of trigeminal nerve trigeminal V nerve ophthalmic division uberon ciliary nerve ethmoidal nerve ophthalmic division profundal nerve profundus profundus nerve trigeminal nerve ophthalmic division UBERON:0000348 Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html] ophthalmic nerve may be a distinct nerve in teleosts multiple The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead. MP:0009798 Wikipedia:Ophthalmic_nerve Sensory medial ramus of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010648 AAO AAO:EJS The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG] 2012-09-17 VHOG:0001349 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177 http://bgee.unil.ch/ UMLS:C0029082 ncithesaurus:Ophthalmic_Nerve cranial nerve V, branch V1 http://orcid.org/0000-0002-6601-2165 first branch of fifth cranial nerve http://orcid.org/0000-0002-6601-2165 first division of fifth cranial nerve FMA:52621 first division of trigeminal nerve FMA:52621 nervus ophthalmicus (V1) FMA:52621 nervus ophthalmicus (Va) FMA:52621 nervus ophthalmicus [v1] FMA:52621 FMA:TA nervus ophthalmicus [va] FMA:52621 FMA:TA ophthalmic division [V1] FMA:52621 ophthalmic division [Va] FMA:52621 ophthalmic division of fifth cranial nerve FMA:52621 ophthalmic division of trigeminal nerve (V1) FMA:52621 ophthalmic division of trigeminal nerve (Va) FMA:52621 ophthalmic nerve [V1] FMA:52621 ophthalmic nerve [Va] FMA:52621 opthalmic nerve Wikipedia:Ophthalmic_nerve ramus opthalmicus profundus (ramus V1) AAO:0010648 rostral branch of trigeminal nerve http://orcid.org/0000-0002-6601-2165 trigeminal V nerve ophthalmic division MA:0001104 ciliary nerve http://palaeos.com/vertebrates/glossary/glossaryPo.html ethmoidal nerve Wikipedia:Ophthalmic_nerve ophthalmic division BTO:0000926 Wikipedia:Ophthalmic_nerve profundal nerve http://orcid.org/0000-0002-6601-2165 profundus http://palaeos.com/vertebrates/glossary/glossaryPo.html profundus nerve http://palaeos.com/vertebrates/glossary/glossaryPo.html trigeminal nerve ophthalmic division EMAPA:17800 A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity. BTO:0000928 CALOHA:TS-1307 FMA:242000 GAID:615 MESH:D008032 NCIT:C94541 SCTID:361342009 UMLS:C0023715 Wikipedia:Limbic_system neuronames:2055 uberon visceral brain UBERON:0000349 includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia] limbic system https://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. BIRNLEX:Limbic_system Wikipedia:Limbic_system UMLS:C0023715 ncithesaurus:Limbic_System visceral brain ISBN:0123813611 A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae. In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head As it is required for running, not all animals have a nuchal ligament BTO:0000952 EMAPA:19207 FMA:13427 SCTID:166962007 Wikipedia:Nuchal_ligament ligament of neck ligamentum nuchae paddywhack uberon paxwax UBERON:0000351 nuchal ligament BTO C7 in humans A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae. Wikipedia:Nuchal_ligament ligament of neck FMA:13427 ligamentum nuchae FMA:13427 paddywhack NCBITaxon:9895 Wikipedia:Paddywhack Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchymal Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated BTO:0000999 BTO:0001539 EHDAA:3015 EHDAA:3905 EHDAA:3999 EHDAA:4005 EHDAA:6899 EHDAA:6903 EHDAA:6994 EHDAA:8086 EHDAA:9182 EHDAA:9190 EHDAA:9196 EHDAA:9202 FMA:45732 NCIT:C74601 UMLS:C0933845 Wikipedia:Parenchyma uberon UBERON:0000353 parenchyma Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Wikipedia:Parenchyma Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin WP the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated FMA BTO:0000999 https://github.com/biopragmatics/biomappings BTO:0001539 https://github.com/biopragmatics/biomappings UMLS:C0933845 ncithesaurus:Parenchyma A mucosa that is part of a pharynx [Automatically generated definition]. UBERON:0003344 BTO:0001047 EMAPA:26957 FMA:55031 MA:0003143 SCTID:362121003 mucosa of organ of pharynx mucosa of pharynx mucous membrane of pharynx organ mucosa of pharynx pharynx mucosa pharynx mucosa of organ pharynx mucous membrane pharynx organ mucosa tunica mucosa pharyngea tunica mucosa pharyngis uberon mucous membrane of the pharynx UBERON:0000355 pharyngeal mucosa A mucosa that is part of a pharynx [Automatically generated definition]. OBOL:automatic mucosa of organ of pharynx OBOL:automatic mucosa of pharynx OBOL:automatic mucous membrane of pharynx FMA:55031 OBOL:automatic organ mucosa of pharynx OBOL:automatic pharynx mucosa OBOL:automatic pharynx mucosa of organ OBOL:automatic pharynx mucous membrane OBOL:automatic pharynx organ mucosa OBOL:automatic tunica mucosa pharyngea FMA:55031 FMA:TA mucous membrane of the pharynx BTO:0001047 The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm) BTO:0001099 CALOHA:TS-0076 EFO:0000295 EMAPA:36035 EV:0100394 FMA:83041 GAID:1153 MESH:D001755 NCIT:C13739 SCTID:308837009 UMLS:C1281743 Wikipedia:Blastocyst uberon blastocystis blastula UBERON:0000358 blastocyst https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. GO:0001824 Wikipedia:Blastocyst UMLS:C1281743 ncithesaurus:Blastocyst blastocystis Wikipedia:Blastocyst blastula FMA:83041 The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. BTO:0001160 FMA:74595 SCTID:328538003 SCTID:75330005 medulla ossium rubra parenchymal red marrow red marrow uberon parenchyma of none marrow marrow UBERON:0000361 red bone marrow The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. http://medical-dictionary.thefreedictionary.com/red+marrow medulla ossium rubra BTO:0001160 parenchymal red marrow http://orcid.org/0000-0002-6601-2165 red marrow BTO:0001160 parenchyma of none marrow marrow http://orcid.org/0000-0002-6601-2165 The inner portion of the kidney consisting of the renal pyramids. The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water BTO:0001167 CALOHA:TS-1157 EMAPA:19279 GAID:425 MA:0000373 MESH:D007679 NCIT:C12740 SCTID:30737000 UMLS:C0022664 Wikipedia:Renal_medulla galen:MedullaOfKidney kidney medulla medulla of kidney medulla renalis pyramides renales renal medullae renal medullae set renal pyramids renal pyramids set uberon medullary pyramids renal marrow UBERON:0000362 Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different. renal medulla https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg The inner portion of the kidney consisting of the renal pyramids. ISBN:0-683-40008-8 MGI:smb MP:0003014 UMLS:C0022664 ncithesaurus:Renal_Medulla kidney medulla OBOL:automatic medulla of kidney OBOL:automatic medulla renalis FMA:74268 FMA:TA pyramides renales FMA:74268 FMA:TA renal medullae FMA:86327 renal medullae set FMA:86327 renal pyramids FMA:74268 renal pyramids set FMA:74268 medullary pyramids FMA:74268 renal marrow BTO:0001167 Extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated). BTO:0001335 EHDAA:129 EHDAA:91 EMAPA:16068 FMA:83040 NCIT:C33918 SCTID:256965005 UMLS:C1135936 Wikipedia:Syncytiotrophoblast syncytial trophoblast syntrophoblast layer uberon syncitiotrophoblast syncitiotrophoblastus syntrophoblast UBERON:0000371 syncytiotrophoblast http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png FMA EMAPA Extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated). Wikipedia:Syncytiotrophoblast http://embryology.med.unsw.edu.au/Notes/placenta5.htm UMLS:C1135936 ncithesaurus:Syncytiotrophoblast syncytial trophoblast FMA:83040 syntrophoblast layer ISBN:0073040584 syncitiotrophoblastus Wikipedia:Syncytiotrophoblast The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini. AAO:0010688 AAO:0010703 BTO:0001375 EHDAA2:0002086 EMAPA:17798 FMA:52996 GAID:834 MA:0001101 MESH:D008340 NCIT:C32779 SCTID:280212008 UMLS:C0024695 VHOG:0001345 Wikipedia:Mandibular_nerve inferior maxillary nerve mandibular division [V3] mandibular division [Vc] mandibular division of fifth cranial nerve mandibular division of trigeminal nerve [Vc; V3] mandibular nerve [V3] mandibular nerve [Vc] nervus mandibularis [Vc; V3] nervus mandibularis [v3] nervus mandibularis [vc] ramus mandibularis (ramus V3) third division of fifth cranial nerve third division of trigeminal nerve trigeminal V nerve mandibular division uberon n. mandibularis nervus mandibularis trigeminal nerve mandibular division UBERON:0000375 mandibular nerve http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini. MP:0009800 Wikipedia:Mandibular_nerve UMLS:C0024695 ncithesaurus:Inferior_Maxillary_Nerve inferior maxillary nerve FMA:52996 mandibular division [V3] FMA:52996 mandibular division [Vc] FMA:52996 mandibular division of fifth cranial nerve FMA:52996 mandibular division of trigeminal nerve [Vc; V3] FMA:52996 mandibular nerve [V3] FMA:52996 mandibular nerve [Vc] FMA:52996 nervus mandibularis [Vc; V3] FMA:52996 nervus mandibularis [v3] FMA:52996 FMA:TA nervus mandibularis [vc] FMA:52996 FMA:TA ramus mandibularis (ramus V3) AAO:0010688 third division of fifth cranial nerve FMA:52996 third division of trigeminal nerve FMA:52996 trigeminal V nerve mandibular division MA:0001101 n. mandibularis Wikipedia:Mandibular_nerve nervus mandibularis BTO:0001375 trigeminal nerve mandibular division EMAPA:17798 The part of the hindlimb between pelvis and the knee, corresponding to the femur. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] Naming conventions for pod terms under discussion within phenoscape group. BTO:0001376 CALOHA:TS-2039 EFO:0001943 EHDAA2:0002130 EHDAA:5171 EHDAA:6200 EMAPA:17499 FMA:24967 GAID:50 MA:0000052 MESH:D013848 NCIT:C33763 SCTID:302544002 UMLS:C0039866 VHOG:0000349 Wikipedia:Thigh galen:Thigh hind limb stylopod hind limb stylopodium hind propodium hindlimb propodium hindlimb stylopod hindlimb stylopodium proximal segment of free lower limb stylopod of hind limb stylopod of hindlimb stylopod of lower limb thigh upper leg uberon femur UBERON:0000376 hindlimb stylopod http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png MA The part of the hindlimb between pelvis and the knee, corresponding to the femur. http://orcid.org/0000-0002-6601-2165 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000349 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ Naming conventions for pod terms under discussion within phenoscape group. https://github.com/obophenotype/uberon/issues/61 UMLS:C0039866 ncithesaurus:Thigh hind limb stylopod OBOL:automatic hind limb stylopodium VHOG:0000349 hind propodium AAO:0000887 hindlimb propodium AAO:0000887 hindlimb stylopod OBOL:automatic hindlimb stylopodium OBOL:automatic proximal segment of free lower limb FMA:24967 stylopod of hind limb OBOL:automatic stylopod of hindlimb OBOL:automatic upper leg MA:0000052 femur Wikipedia:Thigh The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. Medial ramus (sensory) of the trigeminal nerve.[AAO] relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] AAO:0010670 BTO:0001378 EHDAA2:0002087 EMAPA:17799 FMA:52724 GAID:836 MA:0001103 MESH:D008442 SCTID:280211001 VHOG:0001346 Wikipedia:Maxillary_nerve maxillary division [V2] maxillary division [Vb] maxillary division of fifth cranial nerve maxillary division of trigeminal nerve (Vb; V2) maxillary nerve [V2] maxillary nerve [Vb] nervus maxillaris (Vb; V2) nervus maxillaris [v2] nervus maxillaris [vb] ramus maxillaris (ramus V2) second division of fifth cranial nerve second division of trigeminal nerve trigeminal V nerve maxillary division uberon n. maxillaris nervus maxillaris trigeminal nerve maxillary division UBERON:0000377 maxillary nerve http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. MP:0009799 Wikipedia:Maxillary_nerve Medial ramus (sensory) of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010670 AAO AAO:EJS relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] 2012-06-20 AAO:0010670 AAO maxillary division [V2] FMA:52724 maxillary division [Vb] FMA:52724 maxillary division of fifth cranial nerve FMA:52724 maxillary division of trigeminal nerve (Vb; V2) FMA:52724 maxillary nerve [V2] FMA:52724 maxillary nerve [Vb] FMA:52724 nervus maxillaris (Vb; V2) FMA:52724 nervus maxillaris [v2] FMA:52724 FMA:TA nervus maxillaris [vb] FMA:52724 FMA:TA ramus maxillaris (ramus V2) AAO:0010670 second division of fifth cranial nerve FMA:52724 second division of trigeminal nerve FMA:52724 trigeminal V nerve maxillary division MA:0001103 n. maxillaris Wikipedia:Maxillary_nerve nervus maxillaris BTO:0001378 trigeminal nerve maxillary division EMAPA:17799 The muscular portion of the tongue. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] BTO:0001386 EHDAA2:0002065 EHDAA:9146 EMAPA:17883 FMA:46689 MA:0001596 NCIT:C49301 NCIT:C52707 SCTID:244781004 UMLS:C0448325 UMLS:C1710437 VHOG:0001390 Wikipedia:Muscles_of_tongue muscle of tongue muscle organ of tongue skeletal muscle tissue of tongue tongue skeletal muscle tongue skeletal muscle tissue uberon musculi linguae UBERON:0000378 tongue muscle http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png FEED:rd FEED:rd ISBN:1607950324 The muscular portion of the tongue. MP:0004136 Wikipedia:Muscles_of_tongue The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0001390 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) http://bgee.unil.ch/ UMLS:C0448325 ncithesaurus:Tongue_Muscle UMLS:C1710437 ncithesaurus:Tongue_Skeletal_Muscle_Tissue muscle of tongue FMA:46689 muscle organ of tongue OBOL:accepted skeletal muscle tissue of tongue OBOL:automatic tongue skeletal muscle OBOL:automatic tongue skeletal muscle tissue OBOL:automatic musculi linguae Wikipedia:Muscles_of_tongue A mucosa that is part of a respiratory airway. BTO:0001390 FMA:7471 SCTID:660006 mucosa of organ of trachea mucosa of organ of windpipe mucosa of trachea mucosa of windpipe mucous membrane of trachea mucous membrane of windpipe organ mucosa of trachea organ mucosa of windpipe trachea mucosa trachea mucosa of organ trachea mucous membrane trachea organ mucosa tracheal mucous membrane tunica mucosa (tracheae) tunica mucosa tracheae windpipe mucosa windpipe mucosa of organ windpipe mucous membrane windpipe organ mucosa uberon UBERON:0000379 tracheal mucosa A mucosa that is part of a respiratory airway. OBOL:automatic mucosa of organ of trachea OBOL:automatic mucosa of organ of windpipe OBOL:automatic mucosa of trachea OBOL:automatic mucosa of windpipe OBOL:automatic mucous membrane of trachea FMA:7471 OBOL:automatic mucous membrane of windpipe OBOL:automatic organ mucosa of trachea OBOL:automatic organ mucosa of windpipe OBOL:automatic trachea mucosa OBOL:automatic trachea mucosa of organ OBOL:automatic trachea mucous membrane OBOL:automatic trachea organ mucosa OBOL:automatic tracheal mucous membrane FMA:7471 tunica mucosa (tracheae) FMA:7471 tunica mucosa tracheae FMA:7471 FMA:TA windpipe mucosa OBOL:automatic windpipe mucosa of organ OBOL:automatic windpipe mucous membrane OBOL:automatic windpipe organ mucosa OBOL:automatic Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP]. In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region. BTO:0001458 EMAPA:37426 FMA:59155 MESH:D001050 NCIT:C32132 SCTID:399916008 UMLS:C0930083 Wikipedia:Apocrine_sweat_gland glandula sudorifera apocrina uberon UBERON:0000382 apocrine sweat gland https://github.com/obophenotype/uberon/issues/2111 FMA Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP]. PMID:18489347 Wikipedia:Apocrine_sweat_gland http://www.nal.usda.gov/awic/pubs/swine/swine.htm EMAPA:37426 MA:th UMLS:C0930083 ncithesaurus:Apocrine_Sweat_Gland glandula sudorifera apocrina Wikipedia:Apocrine_sweat_gland The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 Anatomical system that consists of the muscles of the body.[VSAO] we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 VSAO:0000033 XAO:0004042 muscle system muscle system of body muscular system musculature system set of all muscles set of muscles of body vertebrate muscular system uberon muskelsystem UBERON:0000383 musculature of body The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 Anatomical system that consists of the muscles of the body.[VSAO] 2012-08-14 VSAO:0000033 VSAO VSAO:curator we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA MA muscular system FMA:72954 musculature system BILA:0000088 set of all muscles FMA:72954 set of muscles of body FMA:72954 vertebrate muscular system BTO:0001369 muskelsystem BTO:0001485 Tissue that surrounds the lens nucleus. BTO:0001632 CALOHA:TS-0542 FMA:58970 MESH:D007904 SCTID:280626006 cortex of lens uberon UBERON:0000389 lens cortex Tissue that surrounds the lens nucleus. http://www.thefreedictionary.com/lens+cortex cortex of lens FMA:58970 The core of the crystalline lens, surrounded by the cortex. BTO:0001633 FMA:58971 MESH:D007907 SCTID:280628007 nucleus of lens uberon UBERON:0000390 lens nucleus The core of the crystalline lens, surrounded by the cortex. BTO:0001633 nucleus of lens FMA:58971 Pia mater or arachnoid mater. check relationship to secondary meninx in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular BTO:0001634 CALOHA:TS-0546 FMA:231515 NCIT:C32979 NLXANAT:090207 SCTID:362303006 UMLS:C0228126 Wikipedia:Leptomeninges neuronames:2347 leptomeninges uberon arachnoid mater and pia mater arachnoidea mater et pia mater pia-arachnoid pia-arachnoid of neuraxis UBERON:0000391 leptomeninx Pia mater or arachnoid mater. Wikipedia:Leptomeninges https://github.com/obophenotype/uberon/issues/300 in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular FMA UMLS:C0228126 ncithesaurus:Leptomeninges leptomeninges NLXANAT:090207 arachnoid mater and pia mater FMA:231515 arachnoidea mater et pia mater BTO:0001634 pia-arachnoid BTO:0001634 pia-arachnoid of neuraxis FMA:231515 An epithelium that is part of a colon [Automatically generated definition]. Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] BTO:0001709 CALOHA:TS-0163 EMAPA:18941 FMA:17302 MA:0003195 SCTID:42978003 TAO:0005128 ZFA:0005128 colon epithelial tissue colon epithelium epithelial tissue of colon epithelial tissue of large bowel epithelium of colon epithelium of large bowel large bowel epithelial tissue large bowel epithelium posterior intestine epithelium uberon UBERON:0000397 colonic epithelium An epithelium that is part of a colon [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] 2012-08-14 TAO:0005128 TAO ZFIN:curator colon epithelial tissue OBOL:automatic colon epithelium FMA:17302 OBOL:automatic epithelial tissue of colon OBOL:automatic epithelial tissue of large bowel OBOL:automatic epithelium of colon OBOL:automatic epithelium of large bowel OBOL:automatic large bowel epithelial tissue OBOL:automatic large bowel epithelium OBOL:automatic posterior intestine epithelium ZFA:0005128 Any portion of cartilage tissue that is part of the sternum. FMA:32567 cartilage of sternum uberon UBERON:0000398 Examples: cartilage of manubrium, cartilage of xiphoid process cartilage tissue of sternum Any portion of cartilage tissue that is part of the sternum. https://orcid.org/0000-0002-6601-2165 cartilage of sternum FMA:32567 A mucosa that is part of a jejunum [Automatically generated definition]. BTO:0001742 CALOHA:TS-0495 EMAPA:27109 FMA:14949 MA:0003214 SCTID:362151009 jejunal mucous membrane jejunum mucosa jejunum mucosa of organ jejunum mucous membrane jejunum organ mucosa mucosa of jejunum mucosa of organ of jejunum mucous membrane of jejunum organ mucosa of jejunum uberon UBERON:0000399 jejunal mucosa A mucosa that is part of a jejunum [Automatically generated definition]. OBOL:automatic jejunal mucous membrane FMA:14949 jejunum mucosa FMA:14949 jejunum mucosa of organ OBOL:automatic jejunum mucous membrane OBOL:automatic jejunum organ mucosa OBOL:automatic mucosa of jejunum FMA:14949 mucosa of organ of jejunum OBOL:automatic mucous membrane of jejunum OBOL:automatic organ mucosa of jejunum OBOL:automatic An epithelium that is part of a jejunum. BTO:0001743 CALOHA:TS-0494 EMAPA:18668 FMA:17232 MA:0003215 SCTID:57300004 epithelium of jejunum uberon UBERON:0000400 jejunal epithelium FMA An epithelium that is part of a jejunum. OBOL:automatic The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. BTO:0001761 CALOHA:TS-0660 FMA:59644 SCTID:278940000 Wikipedia:Nasal_vestibule vestibular part of nasal cavity uberon vestibulum nasale vestibulum nasi UBERON:0000402 nasal vestibule http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. Wikipedia:Nasal_vestibule vestibular part of nasal cavity FMA:59644 vestibulum nasale BTO:0001761 vestibulum nasi BTO:0001761 Wikipedia:Nasal_vestibule A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. BTO:0001837 EMAPA:37950 FMA:62889 Wikipedia:Serous_gland uberon UBERON:0000409 serous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are serous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. MP:0008052 EMAPA:37950 MA:th A mucosa that is part of a bronchus [Automatically generated definition]. BTO:0001846 FMA:62652 SCTID:30802009 bronchi mucosa bronchi mucosa of organ bronchi mucous membrane bronchi organ mucosa bronchial trunk mucosa bronchial trunk mucosa of organ bronchial trunk mucous membrane bronchial trunk organ mucosa bronchus mucosa bronchus mucosa of organ bronchus mucous membrane bronchus organ mucosa mucosa of bronchi mucosa of bronchial trunk mucosa of bronchus mucosa of organ of bronchi mucosa of organ of bronchial trunk mucosa of organ of bronchus mucous membrane of bronchi mucous membrane of bronchial trunk mucous membrane of bronchus organ mucosa of bronchi organ mucosa of bronchial trunk organ mucosa of bronchus tunica mucosa bronchi uberon UBERON:0000410 bronchial mucosa A mucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic bronchi mucosa OBOL:automatic bronchi mucosa of organ OBOL:automatic bronchi mucous membrane OBOL:automatic bronchi organ mucosa OBOL:automatic bronchial trunk mucosa OBOL:automatic bronchial trunk mucosa of organ OBOL:automatic bronchial trunk mucous membrane OBOL:automatic bronchial trunk organ mucosa OBOL:automatic bronchus mucosa OBOL:automatic bronchus mucosa of organ OBOL:automatic bronchus mucous membrane OBOL:automatic bronchus organ mucosa OBOL:automatic mucosa of bronchi OBOL:automatic mucosa of bronchial trunk OBOL:automatic mucosa of bronchus OBOL:automatic mucosa of organ of bronchi OBOL:automatic mucosa of organ of bronchial trunk OBOL:automatic mucosa of organ of bronchus OBOL:automatic mucous membrane of bronchi OBOL:automatic mucous membrane of bronchial trunk OBOL:automatic mucous membrane of bronchus FMA:62652 OBOL:automatic organ mucosa of bronchi OBOL:automatic organ mucosa of bronchial trunk OBOL:automatic organ mucosa of bronchus OBOL:automatic tunica mucosa bronchi FMA:62652 FMA:TA A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] AAO:0010601 BTO:0001979 EMAPA:37913 FMA:62888 Wikipedia:Mucous_gland glandula mucosa uberon muciparous gland mucous secreting gland mucus gland mucus-secreting gland UBERON:0000414 mucous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are mucus secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] NCBITaxon:8292 ISBN:0073040584 EMAPA:37913 MA:th glandula mucosa Wikipedia:Mucous_gland muciparous gland BTO:0001979 An anatomical wall that is part of an artery [Automatically generated definition]. BTO:0002009 FMA:14155 galen:ArterialWall arterial wall wall of artery uberon UBERON:0000415 artery wall An anatomical wall that is part of an artery [Automatically generated definition]. OBOL:automatic arterial wall FMA:14155 wall of artery FMA:14155 The prostate epithelium. TODO - check 2 FMA IDs UBERON:0002452 BTO:0002397 CALOHA:TS-2065 EMAPA:35711 FMA:66812 FMA:79643 MA:0001737 NCIT:C13103 UMLS:C1179826 epithelial tissue of prostate epithelial tissue of prostate gland epithelium of prostate epithelium of prostate gland epithelium of prostatic gland prostate epithelial tissue prostate gland epithelial tissue prostate gland epithelium prostatic epithelium prostatic gland epithelium uberon UBERON:0000428 prostate epithelium The prostate epithelium. MP:0001168 UMLS:C1179826 ncithesaurus:Prostatic_Epithelium epithelial tissue of prostate OBOL:automatic epithelial tissue of prostate gland OBOL:automatic epithelium of prostate OBOL:automatic epithelium of prostate gland OBOL:automatic epithelium of prostatic gland FMA:79643 prostate epithelial tissue OBOL:automatic prostate gland epithelial tissue OBOL:automatic prostatic epithelium FMA:66812 The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges. BTO:0002500 FMA:83979 Wikipedia:Arachnoid_trabeculae uberon arachnoid trabeculae trabecula arachnoideum UBERON:0000439 arachnoid trabecula The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges. Wikipedia:Arachnoid_trabeculae arachnoid trabeculae trabecula arachnoideum A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]. trabecular BTO:0002501 FMA:85273 Wikipedia:Trabecula trabeculae uberon UBERON:0000440 trabecula A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]. GO:0060343 Wikipedia:Trabecula trabeculae A vein that drains the left pampiniform plexus and empties into the left renal vein. BTO:0002679 EMAPA:37383 FMA:14341 MA:0002220 NCIT:C52697 SCTID:53500001 right spermatic vein vena testicularis (adrenalis) dextra uberon vena testicularis dextra vena testicularis sinistra UBERON:0000442 right testicular vein A vein that drains the left pampiniform plexus and empties into the left renal vein. Dorlands_Medical_Dictionary:MerckSource EMAPA:37383 MA:th right spermatic vein MA:0002220 vena testicularis (adrenalis) dextra FMA:14341 vena testicularis dextra BTO:0002679 vena testicularis sinistra BTO:0002680 A vein that drains the right pampiniform plexus and empties into the inferior vena cava. BTO:0002680 EMAPA:37167 FMA:14345 MA:0002219 NCIT:C52696 SCTID:90988008 left spermatic vein uberon vena testicularis dextra vena testicularis sinistra UBERON:0000443 left testicular vein A vein that drains the right pampiniform plexus and empties into the inferior vena cava. Dorlands_Medical_Dictionary:MerckSource EMAPA:37167 MA:th left spermatic vein MA:0002219 vena testicularis dextra BTO:0002679 vena testicularis sinistra BTO:0002680 A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 secretion of exocrine gland A portion of organism substance that is produced by exocrine glands. http://orcid.org/0000-0002-6601-2165 BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions BTO secretion FMA:9675 UMLS:C1516992 ncithesaurus:Exocrine_Gland_Fluid_or_Secretion bodily secretion MESH:D012634 exocrine gland fluid/secretion MA:0002504 external secretion BTO:0002977 Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 FMA:70527 cavernous branch of cavernous part of internal carotid artery ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) uberon UBERON:0000457 cavernous artery Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 cavernous branch of cavernous part of internal carotid artery FMA:70527 ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) FMA:70527 FMA:TA The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 FMA:86485 NCIT:C12309 SCTID:264460007 UMLS:C0227837 uberon UBERON:0000458 endocervix The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 UMLS:C0227837 ncithesaurus:Endocervix An anatomical wall that is part of a uterus [Automatically generated definition]. BTO:0003083 FMA:17560 SCTID:245485002 anatomical wall of uterus uterus anatomical wall uterus wall wall of uterus uberon UBERON:0000459 uterine wall An anatomical wall that is part of a uterus [Automatically generated definition]. OBOL:automatic anatomical wall of uterus OBOL:automatic uterus anatomical wall OBOL:automatic uterus wall OBOL:automatic wall of uterus OBOL:automatic Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance this relationship may be too strong and may be weakened in future Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 FBbt:00007019 body fluid or substance MA:0002450 body substance FMA:9669 organism substance CARO:0000004 portion of body substance FMA:9669 portion of organism substance ZFA:0001487 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 FBbt:00007017 UMLS:C0524461 ncithesaurus:Lumen_Space anatomical spaces ZFA:0001643 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 FBbt:00007016 Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity uberon UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 FBbt:00007015 immaterial physical anatomical entity FMA:67112 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BIRNLEX:14 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 Wikipedia:Organ_system XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. CARO:0000011 system GO:0048731 FBbt:00004856 IDOMAL:0002460 https://github.com/biopragmatics/biomappings UMLS:C0460002 ncithesaurus:Organ_System body system BIRNLEX:14 connected anatomical system CARO:0000011 anatomical systems ZFA:0001439 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 SCTID:243928005 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 Wikipedia:Multi-cellular_organism XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. CARO:0000012 Wikipedia:Multi-cellular_organism http://orcid.org/0000-0001-9114-8737 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 FBbt:00000001 multi-cellular organism CARO:0000012 Koerper BTO:0001489 body AEO:0000103 BIRNLEX:18 FMA:256135 NCIT:C13041 whole body BTO:0001489 whole organism FBbt:00000001 Multi-tissue structure that is part of a compound organ. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010017 AEO:0000019 BILA:0000019 CARO:0000019 EHDAA2:0003019 HAO:0000019 TAO:0001489 TGMA:0001835 XAO:0003039 ZFA:0001489 uberon compound organ components UBERON:0000471 compound organ component Multi-tissue structure that is part of a compound organ. CARO:0000019 http://orcid.org/0000-0001-9114-8737 compound organ components ZFA:0001489 A gonad of a male animal. A gonad produces and releases sperm. Male reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] testicular The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally UBERON:0002117 AAO:0000606 BILA:0000124 BSA:0000085 BTO:0001363 CALOHA:TS-1030 EFO:0000984 EHDAA2:0002007 EHDAA:8146 EMAPA:17972 EV:0100102 FBbt:00004928 FMA:7210 GAID:396 HAO:0001007 MA:0000411 MAT:0000132 MESH:D013737 MIAA:0000132 NCIT:C12412 SCTID:181431007 TAO:0000598 UMLS:C0039597 VHOG:0000252 WBbt:0006794 Wikipedia:Testis XAO:0000157 ZFA:0000598 galen:Testis gonad of male genitalia gonad of male reproductive system male gonad testicle uberon orchis testes testiculus UBERON:0000473 testis http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png A gonad of a male animal. A gonad produces and releases sperm. http://orcid.org/0000-0002-6601-2165 Male reproductive organ.[TAO] 2012-08-14 TAO:0000598 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000252 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally ISBN:0123971756 NCBITaxon:40674 FBbt:00004928 UMLS:C0039597 ncithesaurus:Testis gonad of male genitalia OBOL:automatic gonad of male reproductive system OBOL:automatic male gonad OBOL:automatic testicle FMA:7210 orchis BTO:0001363 testes testiculus BTO:0001363 The organs and associated structures associated with bearing offspring in a female animal. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000083 CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 NCIT:C12402 SCTID:361386004 TGMA:0000635 UMLS:C0700038 VHOG:0000726 Wikipedia:Female_genitalia WikipediaCategory:Female_reproductive_system XAO:0000156 female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism uberon female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum UBERON:0000474 female reproductive system http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg The organs and associated structures associated with bearing offspring in a female animal. MP:0001119 Wikipedia:Female_genitalia http://orcid.org/0000-0002-6601-2165 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000726 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 http://bgee.unil.ch/ FBbt:00004864 UMLS:C0700038 ncithesaurus:Female_Reproductive_System female organism genitalia OBOL:automatic female organism reproductive system OBOL:automatic genitalia of female organism OBOL:automatic reproductive system of female organism OBOL:automatic female genitals XAO:0000156 female reproductive tract MA:0000381 gynaecological tissue BTO:0000083 systema genitale femininum BTO:0000083 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 Wikipedia:Body_part XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision CARO Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS http://orcid.org/0000-0001-9114-8737 FBbt:00007009 UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure CARO Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 FBbt:00007013 acellular anatomical structures ZFA:0000382 Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 anatomical cluster Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 FBbt:00007277 A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. AAO:0010020 AEO:0000042 BILA:0000042 CALOHA:TS-2119 CARO:0000042 EHDAA2:0003042 EHDAA:46 FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 SCTID:314908006 TAO:0000020 TGMA:0001843 UMLS:C1282438 VHOG:0000292 XAO:0004005 ZFA:0000020 extra-embryonic structure uberon extraembryonic structures extraembryonic tissue UBERON:0000478 see also conceptus extraembryonic component in EHDAA2. extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. CARO:DOS http://orcid.org/0000-0001-9114-8737 https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279 FBbt:00005835 UMLS:C1282438 ncithesaurus:Extraembryonic_Structure extraembryonic structures ZFA:0000020 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue CARO Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 FBbt:00007003 UMLS:C0040300 ncithesaurus:Tissue portion of tissue CARO:0000043 simple tissue AEO:0000043 Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. AAO:0010048 AEO:0000055 BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 VHOG:0001762 XAO:0003037 ZFA:0001488 uberon multi-tissue structures UBERON:0000481 multi-tissue structure CARO Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. CARO:0000055 http://orcid.org/0000-0001-9114-8737 FBbt:00007010 multi-tissue structures ZFA:0001488 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] epithelial AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 SCTID:31610004 TAO:0001486 UMLS:C0014609 VHOG:0000387 Wikipedia:Epithelium XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg http://palaeos.com/metazoa/porifera/homoscleromorpha.html Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] 2012-09-17 VHOG:0000387 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 http://bgee.unil.ch/ FBbt:00007005 UMLS:C0014609 ncithesaurus:Epithelium portion of epithelium FMA:9639 Unilaminar epithelium that consists of a single layer of cuboidal cells. needs to be synchronized with CL - there is no distinct cuboidal cell in CL AAO:0010064 AEO:0000067 BILA:0000067 CARO:0000067 EHDAA2:0003067 FMA:45566 HAO:0000067 NCIT:C33553 TAO:0001497 UMLS:C0836134 Wikipedia:Simple_cuboidal_epithelium XAO:0004009 ZFA:0001497 epithelium simplex cuboideum uberon simple cuboidal epithelia UBERON:0000484 simple cuboidal epithelium http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png Unilaminar epithelium that consists of a single layer of cuboidal cells. Wikipedia:Simple_cuboidal_epithelium http://orcid.org/0000-0001-9114-8737 UMLS:C0836134 ncithesaurus:Simple_Cuboidal_Epithelium simple cuboidal epithelia ZFA:0001497 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]. columnar epithelium columnar epithlium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 SCTID:32210007 TAO:0001496 UMLS:C0836135 Wikipedia:Simple_columnar_epithelium XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium uberon simple columnar epithelia UBERON:0000485 simple columnar epithelium http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]. FMA:FMA Wikipedia:Simple_columnar_epithelium http://orcid.org/0000-0001-9114-8737 columnar epithelium EHDAA2:0003068 columnar epithlium AEO:0000068 FBbt:00007027 UMLS:C0836135 ncithesaurus:Simple_Columnar_Epithelium simple columnar epithelia ZFA:0001496 Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]. Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 FMA:45562 HAO:0000069 NCIT:C33622 SCTID:309044005 TAO:0001494 UMLS:C0682575 Wikipedia:Stratified_epithelium XAO:0004006 ZFA:0001494 stratified epithelium uberon laminated epithelium UBERON:0000486 multilaminar epithelium Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]. FMA:FMA Wikipedia:Stratified_epithelium http://orcid.org/0000-0001-9114-8737 Epithelium that consists of more than one layer of epithelial cells.[CARO] 2012-06-20 CARO:0000069 CARO FMA:45562 http://orcid.org/0000-0001-9114-8737 UMLS:C0682575 ncithesaurus:Stratified_Epithelium laminated epithelium BTO:0002074 Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 NCIT:C13178 TAO:0001498 UMLS:C0836133 Wikipedia:Simple_squamous_epithelium XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. FMA:45565 Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] 2012-06-20 CARO:0000070 CARO FMA:45565 http://orcid.org/0000-0001-9114-8737 UMLS:C0836133 ncithesaurus:Simple_Squamous_Epithelium simple squamous epithelia ZFA:0001498 Epithelium that consists of epithelial cells not arranged in one ore more layers. AAO:0010057 AEO:0000071 BILA:0000071 CARO:0000071 EHDAA2:0003071 FMA:61741 HAO:0000071 TAO:0001493 XAO:0004004 ZFA:0001493 heterogenous epithelium uberon atypical epithelia UBERON:0000488 atypical epithelium Epithelium that consists of epithelial cells not arranged in one ore more layers. http://orcid.org/0000-0001-9114-8737 atypical epithelia ZFA:0001493 Compound organ that contains one or more macroscopic anatomical spaces. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ uberon cavitated compound organs UBERON:0000489 cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. http://orcid.org/0000-0001-9114-8737 cavitated organ FMA:55671 cavitated compound organs ZFA:0001490 Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 FMA:45561 HAO:0000073 NCIT:C33554 SCTID:309043004 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium uberon unilaminar epithelia UBERON:0000490 unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. FMA:45561 http://orcid.org/0000-0001-9114-8737 Epithelium that consists of a single layer of epithelial cells.[CARO] 2012-06-20 CARO:0000073 CARO FMA:45561 http://orcid.org/0000-0001-9114-8737 UMLS:C0682574 ncithesaurus:Simple_Epithelium simple epithelium FMA:45561 unilaminar epithelia ZFA:0001495 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. mucoid mucous CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 NCIT:C13259 UMLS:C0026727 Wikipedia:Mucus galen:Mucus uberon UBERON:0000912 mucus Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. Wikipedia:Mucus UMLS:C0026727 ncithesaurus:Mucus Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. ENVO:02000042 FMA:9673 NCIT:C120839 Wikipedia:Interstitial_fluid intercellular fluid tissue fluid uberon UBERON:0000913 interstitial fluid Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. Wikipedia:Interstitial_fluid intercellular fluid ENVO:02000042 tissue fluid ENVO:02000042 Subdivision of trunk that lies between the head and the abdomen. note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest EMAPA:35862 FMA:259209 MA:0000022 SCTID:302551006 Wikipedia:Thorax thorax uberon anterior subdivision of trunk upper body upper trunk UBERON:0000915 thoracic segment of trunk FMA Subdivision of trunk that lies between the head and the abdomen. http://orcid.org/0000-0002-6601-2165 thorax MA:0000022 upper trunk FMA:259209 The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:D000005 MIAA:0000298 SCTID:302553009 Wikipedia:Abdomen galen:Abdomen abdominopelvic region abdominopelvis uberon adult abdomen belly celiac region UBERON:0000916 abdomen MA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. http://orcid.org/0000-0002-6601-2165 abdominopelvic region FMA:9577 abdominopelvis FMA:9577 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 SCTID:57991002 UMLS:C0013935 VHOG:0001766 Wikipedia:Embryo XAO:0000113 ZFA:0000103 http://neurolex.org/wiki/Category:Embryonic_organism embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo https://github.com/obophenotype/uberon/issues/503 https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BTO:0000379 FB:FBrf0039741 FB:FBrf0041814 GO:0009790 Wikipedia:Embryo Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA FBbt:00000052 IDOMAL:0000646 https://github.com/biopragmatics/biomappings UMLS:C0013935 ncithesaurus:Embryo embryonic organism BILA:0000056 developing organism BILA:0000056 A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 NCIT:C12950 NCIT:C54105 TAO:0001122 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 Wikipedia:Germ_layer XAO:0003011 ZFA:0001122 germinal layer primary germ layer uberon embryonic germ layer embryonic germ layers UBERON:0000923 Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0001223 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ embryonic tissue FMA:69069 FBbt:00000110 UMLS:C0920502 ncithesaurus:Embryonic_Tissue UMLS:C1708239 ncithesaurus:Germinal_Layer germinal layer ncithesaurus:Germinal_Layer primary germ layer GO:0001704 ZFA:0001122 Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] ectodermal AAO:0000137 BILA:0000036 BTO:0000315 CALOHA:TS-0216 EFO:0000414 EHDAA2:0000428 EMAPA:16069 EV:0100003 FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 MAT:0000173 MESH:D004475 MIAA:0000173 NCIT:C12703 SCTID:362851007 TAO:0000016 UMLS:C0013574 VHOG:0000153 Wikipedia:Ectoderm XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png Bgee:AN Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] 2012-06-20 AAO:0000137 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000153 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ FBbt:00000111 UMLS:C0013574 ncithesaurus:Ectoderm embryonic ectoderm VHOG:0000153 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal AAO:0000139 BILA:0000038 BTO:0000800 CALOHA:TS-0273 EFO:0002545 EHDAA2:0000436 EMAPA:16062 EV:0100005 FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 MESH:D004707 MIAA:0000175 NCIT:C12706 SCTID:362855003 TAO:0000017 UMLS:C0014144 VHOG:0000154 Wikipedia:Endoderm XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png Bgee:AN Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000154 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ FBbt:00000125 UMLS:C0014144 ncithesaurus:Endoderm entoderm DOI:10.5962/bhl.title.1013 The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] mesodermal sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:D008648 MIAA:0000174 NCIT:C12750 SCTID:362854004 TAO:0000041 UMLS:C0025485 VHOG:0000152 Wikipedia:Mesoderm XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png sometimes not considered primary Bgee:AN The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm Primary germ layer that is the middle of the embryonic germ layers.[AAO] 2012-06-20 AAO:0000304 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000152 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates https://github.com/obophenotype/uberon/wiki/The-neural-crest FBbt:00000126 UMLS:C0025485 ncithesaurus:Mesoderm embryonic mesoderm VHOG:0000152 entire mesoderm SCTID:362854004 https://orcid.org/0000-0002-6601-2165 Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx stomodeal This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 TGMA:0000135 UMLS:C1514977 Wikipedia:Stomodeum XAO:0000269 ZFA:0001290 mouth primordium primitive oral cavity stomatodeum stomodaeum uberon mouth pit oral ectoderm oral pit UBERON:0000930 stomodeum http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. Wikipedia:Stomodeum http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] 2012-08-14 TAO:0001290 TAO ZFIN:curator the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx MP:0012522 NCBITaxon:40674 stomodeal-hypophyseal primordium XAO:0000269 FBbt:00000439 UMLS:C1514977 ncithesaurus:Stomodeum mouth primordium XAO:0000269 primitive oral cavity https://orcid.org/0000-0002-6601-2165 stomatodeum Wikipedia:Stomodeum mouth pit EMAPA:16263 oral ectoderm ZFA:0001290 ZFIN:ZDB-PUB-100726-23 oral pit EMAPA:16263 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 VHOG:0000139 Wikipedia:Proctodeum XAO:0001019 ZFA:0000066 embryonic proctodaeum proctodaeum amnioproctodeal invagination uberon anal pit anus porus UBERON:0000931 proctodeum https://github.com/obophenotype/uberon/issues/685 EHDAA2 EHDAA2 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. ZFA:0000066 https://github.com/obophenotype/uberon/issues/685 https://sourceforge.net/p/fbbtdv/tickets/52 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] 2012-08-14 TAO:0000066 TAO ZFIN:curator Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] 2012-06-20 AAO:0011087 AAO ZFA:0000066 FBbt:00000123 UMLS:C0231054 ncithesaurus:Proctodeum amnioproctodeal invagination FBbt:00000123 anal pit VHOG:0000139 anus porus XAO:0001019 A muscle that acts on the pharynx[WP, vetted]. A pharyngeal muscle is any muscle that forms part of the pharynx[GO]. BTO:0001048 EFO:0003504 EMAPA:18963 FMA:46619 GAID:154 MA:0001797 MESH:D010609 NCIT:C13075 SCTID:244798004 TAO:0000172 UMLS:C0031346 Wikipedia:Pharyngeal_muscles ZFA:0000172 branchial muscle muscle of pharynx muscle organ of pharynx pharyngeal muscle pharynx muscle pharynx muscle organ uberon branchial muscles musculi pharyngis musculus pharyngis tunica muscularis pharyngis UBERON:0000933 Innervation notes: They are innervated by the pharyngeal branch of the Vagus nerve (CN X) with the exception of the stylopharyngeus muscle which is innervated by the glossopharyngeal nerve (CN IX).[WP] chordate pharyngeal muscle http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png A muscle that acts on the pharynx[WP, vetted]. Wikipedia:Pharyngeal_muscles https://orcid.org/0000-0002-6601-2165 A pharyngeal muscle is any muscle that forms part of the pharynx[GO]. 2012-06-30 GO:0043282 does not quite work for some muscles such as stylopharyngeus GO GOC:go_curators UMLS:C0031346 ncithesaurus:Pharyngeal_Muscle branchial muscle ZFA:0000172 muscle organ of pharynx OBOL:automatic pharynx muscle organ OBOL:automatic branchial muscles TAO:0000172 musculi pharyngis Wikipedia:Pharyngeal_muscles musculus pharyngis BTO:0001048 tunica muscularis pharyngis Wikipedia:Pharyngeal_muscles An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:D013270 MIAA:0000051 NCIT:C12391 SCTID:181246003 TAO:0002121 UMLS:C0038351 VHOG:0000408 Wikipedia:Stomach XAO:0000128 galen:Stomach stomach chamber uberon anterior intestine gaster mesenteron ventriculus UBERON:0000945 stomach https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg cjm cjm absent in lampreys and hagfishes ISBN:0073040584 ISBN:0486692132 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. ISBN:0073040584 Wikipedia:Stomach https://orcid.org/0000-0002-6601-2165 Wikipedia Wikipedia ZFA Wikipedia Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] 2012-06-20 AAO:0000579 AAO AAO:EJS It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] 2012-09-17 VHOG:0000408 VHOG DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) http://bgee.unil.ch/ We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa WP:Stomach#In_other_animals UMLS:C0038351 ncithesaurus:Stomach gaster BTO:0001307 ventriculus Wikipedia:Stomach A membranous fold of the heart that prevents reflux of fluid. One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG] Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG] Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve BTO:0000564 EMAPA:17869 EV:0100024 FMA:7110 GAID:176 MA:0000086 MESH:D006351 NCIT:C12729 SCTID:181285005 TAO:0005065 UMLS:C0018826 VHOG:0000818 Wikipedia:Cardiac_valve XAO:0004126 ZFA:0005065 galen:HeartValve heart valve valve of heart uberon heart valve heart valves stomodaeal valve valvule UBERON:0000946 cardiac valve PMID:15797462 A membranous fold of the heart that prevents reflux of fluid. MESH:A07.541.510 MP:0000285 PMID:7926784 One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG] 2012-09-17 VHOG:0000818 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/heart+valve Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG] 2012-09-17 VHOG:0000818 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ UMLS:C0018826 ncithesaurus:Cardiac_Valve heart valve XAO:0004126 The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] aortic All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches AAO:0010213 BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 NCIT:C12669 SCTID:181298001 UMLS:C0003483 VHOG:0001523 Wikipedia:Aorta XAO:0003010 galen:Aorta trunk of aortic tree trunk of systemic arterial tree dorsal aorta uberon arteria maxima UBERON:0000947 aorta https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg MA EHDAA2 The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. ISBN:0-683-40008-8 MESH:A07.231.114.056 MP:0000272 Wikipedia:Aorta http://orcid.org/0000-0002-6601-2165 This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. WP The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] 2012-06-20 AAO:0010213 AAO AAO:BJB When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0001523 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0003483 ncithesaurus:Aorta dorsal aorta Wikipedia:Aorta#In_other_animals ZFA:0000014 arteria maxima Wikipedia:Aorta A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] cardiac AAO:0010210 BILA:0000020 BTO:0000562 CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 NCIT:C12727 SCTID:302509004 TAO:0000114 UMLS:C0018787 VHOG:0000276 Wikipedia:Heart XAO:0000064 ZFA:0000114 galen:Heart chambered heart vertebrate heart branchial heart uberon cardium UBERON:0000948 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb MA A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] 2012-08-14 TAO:0000114 TAO ZFIN:curator Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] 2012-06-20 AAO:0010210 AAO AAO:BJB relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0010210 AAO As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] 2012-09-17 VHOG:0000276 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ UMLS:C0018787 ncithesaurus:Heart chambered heart https://orcid.org/0000-0002-6601-2165 branchial heart cardium EMAPA:16105 Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 NCIT:C12705 SCTID:278876000 TAO:0001158 UMLS:C0014136 VHOG:0000098 Wikipedia:Endocrine_system XAO:0000158 ZFA:0001158 endocrine glandular system endocrine system systema endocrinum uberon UBERON:0000949 endocrine system Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. NLM:endocrine+system Wikipedia:Endocrine_system Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] 2012-06-20 AAO:0010279 AAO AAO:BJB Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] 2012-09-17 VHOG:0000098 VHOG DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) http://bgee.unil.ch/ FBbt:00005068 UMLS:C0014136 ncithesaurus:Endocrine_System endocrine glandular system EHDAA2:0002224 Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column. rotator muscle FMA:23081 SCTID:244872002 uberon UBERON:0000951 rotator muscle of the vertebral column Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column. http://medical-dictionary.thefreedictionary.com/rotator+muscle rotator muscle FMA:23081 The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BIRNLEX:796 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 PBA:3999 SCTID:258335003 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 Wikipedia:Brain XAO:0000010 ZFA:0000008 galen:Brain neuronames:21 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb GO FMA Bgee:AN The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. Wikipedia:Brain https://github.com/obophenotype/uberon/issues/300 Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] 2012-08-14 TAO:0000008 TAO ZFIN:curator Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] 2012-06-20 AAO:0010478 AAO AAO:BJB The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) http://neurolex.org/wiki/Cumbo_terms (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000157 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 http://bgee.unil.ch/ FBbt:00005095 UMLS:C0006104 BIRNLEX:796 ncithesaurus:Brain UMLS:C1269537 BIRNLEX:796 neuronames:21 BIRNLEX:796 encephalon BTO:0000142 suprasegmental levels of nervous system NeuroNames:21 suprasegmental structures NeuroNames:21 the brain NeuroNames:21 The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus). The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743] BAMS:C BAMS:CTX BAMS:Cerebral_cortex BAMS:Cx BIRNLEX:1494 BM:Tel-Cx BTO:0000233 CALOHA:TS-0091 DHBA:10159 EFO:0000328 EHDAA2:0000234 EHDAA:5464 EMAPA:17544 EV:0100166 FMA:61830 GAID:629 HBA:4008 MA:0000185 MAT:0000108 MBA:688 MESH:D002540 MIAA:0000108 NCIT:C12443 PBA:128011354 SCTID:362880003 UMLS:C0007776 VHOG:0000722 Wikipedia:Cerebral_cortex neuronames:39 cortex of cerebral hemisphere uberon brain cortex cortex cerebralis cortex cerebri cortical plate (CTXpl) cortical plate (areas) pallium of the brain UBERON:0000956 cerebral cortex http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg FMA GO ISBN:0471888893 FMA MA Wikipedia The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. BIRNLEX:1494 The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Wikipedia:Cerebral_cortex Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] 2012-09-17 VHOG:0000722 VHOG DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969) http://bgee.unil.ch/ UMLS:C0007776 BIRNLEX:1494 ncithesaurus:Cortex neuronames:39 BIRNLEX:1494 cortex of cerebral hemisphere BTO:0000233 FMA:61830 brain cortex BTO:0000233 cortex cerebralis NeuroNames:39 cortex cerebri Wikipedia:Cerebral_cortex cortical plate (CTXpl) NeuroNames:39 cortical plate (areas) NeuroNames:39 pallium of the brain BTO:0000233 Any thin layer or plate. TODO - merge with cell layer? laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon UBERON:0000957 lamina http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png Any thin layer or plate. Wikipedia:Lamina_of_the_vertebral_arch Middle part of an organ, surrounded by the cortex. this class is used in a very general sense medullary FMA:61108 galen:Medulla medulla uberon UBERON:0000958 medulla of organ Middle part of an organ, surrounded by the cortex. http://orcid.org/0000-0002-6601-2165 medulla FMA:61108 The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. BAMS:cern FMA:5859 NCIT:C32299 NLXANAT:20090207 SCTID:360497008 UMLS:C0228815 Wikipedia:Cervical_nerves neuronames:2351 cervical nerve cervical nerve tree cervical spinal nerve nervus cervicalis uberon UBERON:0000962 Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] nerve of cervical vertebra http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. Wikipedia:Cervical_nerves UMLS:C0228815 ncithesaurus:Cervical_Nerve cervical nerve FMA:5859 nervus cervicalis FMA:5859 FMA:TA The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. corneal Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 NCIT:C12342 SCTID:181162001 TAO:0000640 UMLS:C0010031 VHOG:0000164 Wikipedia:Cornea XAO:0000180 ZFA:0000640 cornea of camera-type eye uberon corneas tunica cornea UBERON:0000964 cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg MA MA FMA-isa definitional The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. ISBN:0-683-40008-8 MESH:A09.371.060.217 MP:0001312 UMLS:C0010031 ncithesaurus:Cornea cornea of camera-type eye GO:0061303 corneas ZFA:0000640 A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 EHDAA:9057 EMAPA:17838 EV:0100343 FMA:58241 MA:0000275 MAT:0000141 MESH:D007908 MIAA:0000141 NCIT:C12743 RETIRED_EHDAA2:0000975 SCTID:181169005 TAO:0000035 UMLS:C0023317 VHOG:0000169 Wikipedia:Lens_(anatomy) XAO:0000008 ZFA:0000035 camera-type eye lens eye lens lens lens crystallina uberon crystalline lens lenses ocular lens UBERON:0000965 The lens is avascular and nourished by diffusion from the aqueous and vitreous humors. lens of camera-type eye A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina. Wikipedia:Lens_(anatomy) http://orcid.org/0000-0002-6601-2165 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000169 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0023317 ncithesaurus:Crystalline_Lens camera-type eye lens GO:0002088 eye lens lens lens crystallina Wikipedia:Lens_(anatomy) crystalline lens BTO:0000723 PMID:36055924 lenses ZFA:0000035 ocular lens BTO:0000723 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] retinal AAO:0010352 BAMS:R BIRNLEX:1153 BTO:0001175 CALOHA:TS-0865 EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NCIT:C12343 NIFSTD_RETIRED:birnlex_1156 SCTID:181171005 TAO:0000152 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 Wikipedia:Retina XAO:0000009 ZFA:0000152 neuronames:1862 inner layer of eyeball retina of camera-type eye tunica interna of eyeball uberon Netzhaut retinas UBERON:0000966 Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png FMA FMA FMA EHDAA2 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. Wikipedia:Retina ZFIN:curator The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000152 TAO ZFIN:curator The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000229 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0035298 BIRNLEX:1153 ncithesaurus:Retina UMLS:C1278894 BIRNLEX:1153 retina of camera-type eye GO:0060041 Netzhaut BTO:0001175 retinas ZFA:0000152 An organ that detects light. This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) ocular optic Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 Wikipedia:Eye uberon light-detecting organ visual apparatus UBERON:0000970 eye PMID:21062451 PMID:21062451 An organ that detects light. https://orcid.org/0000-0002-6601-2165 FBbt:00005162 visual apparatus EV:0100336 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. cervical AEO:0000108 BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 NCIT:C13063 SCTID:302550007 UMLS:C0027530 Wikipedia:Neck galen:Neck uberon collum neck (volume) UBERON:0000974 neck https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. http://orcid.org/0000-0002-6601-2165 ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum Wikipedia:Neck neck (volume) FMA:7155 A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]. in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum Single element that constitutes the postzonal area of the pectoral girdle.[AAO] relationship loss: part_of postzonal element (AAO:0000938)[AAO] Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG] sternal It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life in birds, either ratite (no keel or carina) or carinate (keel and carina present) While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad]. AAO:0000765 BTO:0001302 CALOHA:TS-0972 EHDAA2:0001914 EHDAA:9561 EMAPA:18344 FMA:7485 GAID:246 MA:0001331 MESH:D013249 NCIT:C12793 SCTID:302522007 UMLS:C0038293 VHOG:0000856 Wikipedia:Sternum galen:Sternum vertebrate sternum uberon breastbone UBERON:0000975 sternum http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg ISBN:0073040584 FMA ISBN:0073040584 A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]. PHENOSCAPE:ad https://github.com/obophenotype/uberon/issues/67 Wikipedia Single element that constitutes the postzonal area of the pectoral girdle.[AAO] 2012-06-20 AAO:0000765 AAO AAO:LAP relationship loss: part_of postzonal element (AAO:0000938)[AAO] 2012-06-20 AAO:0000765 AAO Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG] 2012-09-17 VHOG:0000856 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294 http://bgee.unil.ch/ While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad]. WP UMLS:C0038293 ncithesaurus:Sternum breastbone BTO:0001302 Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]. Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] humeral AAO:0000679 CALOHA:TS-2202 EFO:0001398 EMAPA:19106 FMA:13303 GAID:183 MA:0001356 MESH:D006811 NCIT:C12731 SCTID:181923006 UMLS:C0020164 VHOG:0001158 Wikipedia:Humerus XAO:0003210 galen:Humerus humeri humerus bone uberon mesomere 1 of pectoral appendage proximal metapterygial mesomere of pectoral appendage proximal metapterygial mesomere of pectoral fin UBERON:0000976 humerus http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg definitional Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]. AAO:0000679 PHENOSCAPE:mah https://github.com/obophenotype/uberon/issues/106 Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO] 2012-06-20 AAO:0000679 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001158 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ UMLS:C0020164 ncithesaurus:Humerus humeri PHENOSCAPE:ad mesomere 1 of pectoral appendage ISBN:0226313409 proximal metapterygial mesomere of pectoral appendage ISBN:0226313409 proximal metapterygial mesomere of pectoral fin ISBN:0226313409 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] pleural In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86 BTO:0001791 CALOHA:TS-2081 EFO:0001980 EMAPA:16775 EV:0100044 FMA:9583 GAID:360 MA:0000433 MESH:D010994 NCIT:C12469 SCTID:181609007 UMLS:C0032225 VHOG:0000394 Wikipedia:Pleura wall of pleural sac uberon pleura pleural tissue UBERON:0000977 pleura http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png https://github.com/obophenotype/uberon/issues/86 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). ISBN:0-683-40008-8 MP:0010820 UBERON:cjm Wikipedia:Pulmonary_pleurae https://github.com/obophenotype/uberon/issues/1231 ISBN:978-0030223693 https://orcid.org/0000-0003-3308-6245 The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] 2012-09-17 VHOG:0000394 VHOG ISBN:0124020607 http://bgee.unil.ch/ UMLS:C0032225 ncithesaurus:Pleural_Tissue pleural tissue BTO:0001791 NCIT:C12469 The portion of the hindlimb that contains both the stylopod and zeugopod. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For BTO:0000721 CALOHA:TS-2206 EFO:0001411 EHDAA2:0000972 EHDAA:5151 EHDAA:6176 EHDAA:8289 EMAPA:17489 GAID:49 MA:0000047 MESH:D035002 VHOG:0000345 Wikipedia:Leg#Limb tetrapod leg uberon lower extremity UBERON:0000978 we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot leg The portion of the hindlimb that contains both the stylopod and zeugopod. Wikipedia:Leg#Limb Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000345 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For 3 lower extremity MESH:A01.378.610 The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]. One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO] AAO:0000890 BTO:0001252 CALOHA:TS-1048 EFO:0003054 EMAPA:19142 FMA:24476 GAID:204 MA:0001361 MESH:D013977 NCIT:C12800 SCTID:182061009 UMLS:C0040184 Wikipedia:Tibia galen:Tibia shankbone shinbone uberon UBERON:0000979 tibia http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]. PHENOSCAPE:mah One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO] 2012-06-20 AAO:0000890 AAO AAO:LAP UMLS:C0040184 ncithesaurus:Tibia shankbone Wikipedia:Tibia shinbone Wikipedia:Tibia Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO] Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] femoral AAO:0000887 AAO:0000889 BTO:0001284 CALOHA:TS-0322 EFO:0001396 EMAPA:19143 FMA:9611 GAID:199 MA:0001359 MESH:D005269 NCIT:C12717 SCTID:182046008 UMLS:C0015811 VHOG:0001159 VSAO:0000186 Wikipedia:Femur XAO:0003214 galen:Femur thigh bone uberon femoral bone mesomere 1 of pevlic appendage os femorale os femoris os longissimum proximal metapterygial mesomere of pelvic appendage proximal metapterygial mesomere of pelvic fin UBERON:0000981 femur http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png MA definitional Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. VSAO:0000186 Wikipedia:Femur Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO] 2012-08-14 VSAO:0000186 VSAO VSAO:NI Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO] 2012-06-20 AAO:0000889 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001159 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ UMLS:C0015811 ncithesaurus:Femur femoral bone BTO:0001284 mesomere 1 of pevlic appendage ISBN:0226313409 os femorale BTO:0001284 os femoris BTO:0001284 os longissimum Wikipedia:Femur proximal metapterygial mesomere of pelvic appendage ISBN:0226313409 proximal metapterygial mesomere of pelvic fin ISBN:0226313409 Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 RETIRED_EHDAA2:0003182 SCTID:302536002 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 Wikipedia:Joint XAO:0000171 ZFA:0001596 galen:Joint uberon articular joint joints UBERON:0000982 skeletal joint Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] 2012-08-14 VSAO:0000101 VSAO PSPUB:0000170 Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] 2012-08-14 TAO:0000367 TAO TAO:pem articulation VSAO:0000101 joint FMA:7490 VSAO:0000101 UMLS:C0022417 ncithesaurus:Joint articular joint BTO:0001686 joints ZFA:0001596 A metapodium region that is part of a pes. mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton CALOHA:TS-2221 FMA:24997 MA:0000049 SCTID:280711000 SCTID:370639003 hind metapodium metatarsal part of foot metatarsal region regio metatarsalis hindlimb cannon region hindlimb equine cannon region uberon metatarsus UBERON:0000983 metatarsus region PHENOSCAPE:ni A metapodium region that is part of a pes. OBOL:automatic hind metapodium AAO:0000221 MA:th http://en.wiktionary.org/wiki/metapodial metatarsal part of foot FMA:24997 metatarsal region FMA:24997 regio metatarsalis FMA:24997 FMA:TA hindlimb cannon region NCBITaxon:9788 http://orcid.org/0000-0002-6601-2165 hindlimb equine cannon region NCBITaxon:9788 http://orcid.org/0000-0002-6601-2165 metatarsus MA:0000049 Vein that drains the axilla. In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery EMAPA:18758 FMA:13329 GAID:527 MA:0002084 MESH:D001367 NCIT:C32171 SCTID:181389002 UMLS:C0004456 Wikipedia:Axillary_vein galen:AxillaryVein vena axillaris uberon subcostal vein UBERON:0000985 axillary vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png Vein that drains the axilla. http://orcid.org/0000-0002-6601-2165 In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery WP UMLS:C0004456 ncithesaurus:Axillary_Vein vena axillaris Wikipedia:Axillary_vein The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] BAMS:PONS BAMS:Pons BIRNLEX:733 BM:Pons BTO:0001101 CALOHA:TS-0813 DHBA:10661 EFO:0001394 EHDAA2:0004394 EMAPA:17563 EV:0100253 FMA:67943 GAID:578 HBA:9131 MA:0000204 MAT:0000115 MBA:771 MESH:D011149 MIAA:0000115 NCIT:C12511 SCTID:279103004 UMLS:C0032639 UMLS:C1280999 VHOG:0001176 Wikipedia:Pons neuronames:547 pons Varolii pons of Varolius uberon pons cerebri UBERON:0000988 pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png neuronames The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. VHOG:0001176 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] 2012-09-17 VHOG:0001176 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pons During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] 2012-09-17 VHOG:0001176 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474 http://bgee.unil.ch/ UMLS:C0032639 BIRNLEX:733 ncithesaurus:Pons_Varolii UMLS:C1280999 BIRNLEX:733 neuronames:547 BIRNLEX:733 pons Varolii ncithesaurus:Pons_Varolii pons cerebri NeuroNames:547 An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination. penile phallic Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca BTO:0000405 CALOHA:TS-0758 EFO:0000987 EHDAA2:0001433 EHDAA:9380 EMAPA:18682 EMAPA_RETIRED:18996 EV:0100107 FMA:9707 GAID:389 MA:0000408 MAT:0000186 MESH:D010413 MIAA:0000186 NCIT:C12409 SCTID:265793009 UMLS:C0030851 VHOG:0000727 Wikipedia:Penis galen:Penis uberon penes phallus UBERON:0000989 penis http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg Wikipedia Wikipedia EHDAA2 An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination. ISBN:0-683-40008-8 MP:0005187 Wikipedia:Penis http://orcid.org/0000-0002-6601-2165 Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca WP UMLS:C0030851 ncithesaurus:Penis penes Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2022-06-10T18:22:34Z AAO:0010258 BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 MESH:D005835 MIAA:0000305 NCIT:C12841 SCTID:278875001 TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 Wikipedia:Reproductive_system XAO:0000142 ZFA:0000632 genital system genitalia uberon Geschlechtsorgan animal reproductive system genital tract organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg Anatomical system that has as its parts the organs concerned with reproduction. Wikipedia:Reproductive_system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] 2012-06-20 AAO:0010258 AAO AAO:BJB Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2012-09-17 VHOG:0000182 VHOG PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) http://bgee.unil.ch/ FBbt:00004857 MESH:D005835 https://github.com/biopragmatics/biomappings UMLS:C1261210 ncithesaurus:Reproductive_System genitalia Geschlechtsorgan BTO:0000081 animal reproductive system BTO:0000081 organa genitalia BTO:0000081 reproductive tissue BTO:0000081 systemata genitalia Wikipedia:Reproductive_system Reproductive organ that produces and releases eggs (ovary) or sperm (testis). Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] gonadal FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 NCIT:C12725 SCTID:304623008 TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 Wikipedia:Gonad XAO:0003146 ZFA:0000413 gonada uberon gonads UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). ISBN:0140512888 Wikipedia:Gonad ZFA:0000413 ZFIN:curator Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] 2012-06-20 AAO:0000213 AAO AAO:BJB The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] 2012-08-14 TAO:0000413 TAO ZFIN:curator Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] 2012-09-17 VHOG:0000397 VHOG DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ FMA xref is a 'general anatomical term' FMA FBbt:00004858 UMLS:C0018067 ncithesaurus:Gonad gonads ZFA:0000413 The gonad of a female organism which contains germ cells. Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] Female reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] ovarian Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 FBbt:00004865 FMA:7209 GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 NCIT:C12404 SCTID:181464007 TAO:0000403 UMLS:C0029939 VHOG:0000251 Wikipedia:Ovary XAO:0000258 ZFA:0000403 animal ovary female gonad female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada uberon ovaries ovarium UBERON:0000992 ovary http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png The gonad of a female organism which contains germ cells. ISBN:0-683-40008-8 MP:0001126 Wikipedia:Ovary Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] 2012-06-20 AAO:0000371 AAO AAO:BJB Female reproductive organ.[TAO] 2012-08-14 TAO:0000403 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000251 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo WP FBbt:00004865 UMLS:C0029939 ncithesaurus:Ovary animal ovary EFO:0000973 female organism genitalia gonad OBOL:automatic female organism genitalia gonada OBOL:automatic female organism reproductive system gonad OBOL:automatic female organism reproductive system gonada OBOL:automatic female reproductive system gonad OBOL:automatic female reproductive system gonada OBOL:automatic genitalia of female organism gonad OBOL:automatic genitalia of female organism gonada OBOL:automatic gonad of female organism genitalia OBOL:automatic gonad of female organism reproductive system OBOL:automatic gonad of female reproductive system OBOL:automatic gonad of genitalia of female organism OBOL:automatic gonad of reproductive system of female organism OBOL:automatic gonada of female organism genitalia OBOL:automatic gonada of female organism reproductive system OBOL:automatic gonada of female reproductive system OBOL:automatic gonada of genitalia of female organism OBOL:automatic gonada of reproductive system of female organism OBOL:automatic ovum-producing ovary GO:0061039 reproductive system of female organism gonad OBOL:automatic reproductive system of female organism gonada OBOL:automatic ovaries ovarium Wikipedia:Ovary A tube or collection of tubes in an animal from the ovaries to the outside of the body. sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP] in birds divided into infundibulum, magnum, isthmus, uterus, and vagina AAO:0010533 BSA:0000083 BTO:0000980 EFO:0000974 EMAPA:18984 GAID:366 MAT:0000126 MESH:D010057 MIAA:0000126 NCIT:C77957 TAO:0000560 UMLS:C0029954 VHOG:0001136 Wikipedia:Oviduct XAO:0003052 ZFA:0000560 ovarian duct ovarian tube uterine tube uberon female reproductive tracts oviducts tuba uterina tuba uterinae tubular parts of female reproductive system UBERON:0000993 oviduct A tube or collection of tubes in an animal from the ovaries to the outside of the body. http://orcid.org/0000-0002-6601-2165 A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] 2012-09-17 VHOG:0001136 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/oviduct In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] 2012-09-17 VHOG:0001136 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688 http://bgee.unil.ch/ UMLS:C0029954 ncithesaurus:Oviduct ovarian duct http://orcid.org/0000-0002-6601-2165 ovarian tube http://orcid.org/0000-0002-6601-2165 female reproductive tracts http://orcid.org/0000-0002-6601-2165 oviducts ZFA:0000560 tuba uterina BTO:0000980 tuba uterinae BTO:0000980 tubular parts of female reproductive system http://orcid.org/0000-0002-6601-2165 The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] uterine Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] BTO:0001424 CALOHA:TS-1102 EFO:0000975 EMAPA:29915 EV:0100113 FMA:17558 GAID:172 MA:0000389 MAT:0000127 MESH:D014599 MIAA:0000127 NCIT:C12405 SCTID:181452004 UMLS:C0042149 VHOG:0001137 Wikipedia:Uterus galen:Uterus uberon UBERON:0000995 uterus http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png cjm The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. MGI:csmith MP:0001120 The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] 2012-09-17 VHOG:0001137 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/uterus An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] 2012-09-17 VHOG:0001137 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678 http://bgee.unil.ch/ UMLS:C0042149 ncithesaurus:Uterus A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] vaginal 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 BTO:0000243 CALOHA:TS-1103 EFO:0000976 EMAPA:18986 EV:0100117 FMA:19949 GAID:381 MA:0000394 MAT:0000128 MESH:D014621 MIAA:0000128 NCIT:C12407 SCTID:181441005 UMLS:C0042232 VHOG:0001138 Wikipedia:Vagina galen:Vagina uberon distal oviductal region distal portion of oviduct vaginae UBERON:0000996 vagina http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg cjm FMA Wikipedia A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Wikipedia:Vagina http://orcid.org/0000-0002-6601-2165 Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] 2012-11-29 FMA:19949 FMA The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001138 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/vagina The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] 2012-09-17 VHOG:0001138 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 http://bgee.unil.ch/ UMLS:C0042232 ncithesaurus:Vagina vaginae External genital organs of the female mammal[WP]. The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG] vulval BTO:0003101 CALOHA:TS-1168 EFO:0000978 EMAPA:36631 EV:0100118 FMA:20462 GAID:383 MA:0000395 MAT:0000169 MESH:D014844 MIAA:0000169 NCIT:C12408 SCTID:265796001 UMLS:C0042993 VHOG:0001458 Wikipedia:Vulva galen:Vulva female pudendum mammalian vulva puboperineal region pudendum femininum vulva uberon pudendum pudendum femininum pudendum muliebre UBERON:0000997 mammalian vulva http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg External genital organs of the female mammal[WP]. Wikipedia:Vulva The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001458 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/vulva UMLS:C0042993 ncithesaurus:Vulva female pudendum BTO:0003101 FMA:20462 doi:10.1002/ca.23705 puboperineal region FMA:20462 pudendum femininum FMA:20462 FMA:TA doi:10.1002/ca.23705 vulva MA:0000395 pudendum BTO:0003101 doi:10.1002/ca.23705 pudendum femininum Wikipedia:Vulva doi:10.1002/ca.23705 pudendum muliebre BTO:0003101 doi:10.1002/ca.23705 Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG] (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG] The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid. seminal gland AAO:0010788 BTO:0001234 CALOHA:TS-0919 EFO:0000986 EMAPA:19180 EV:0100106 FMA:19386 GAID:394 MA:0000410 MAT:0000171 MESH:D012669 MIAA:0000171 NCIT:C12787 SCTID:181434004 UMLS:C0036628 VHOG:0001379 Wikipedia:Seminal_vesicle uberon glandula seminalis glandula vesiculosa gonecyst vas efferens vesicula seminalis vesiculae seminales vesicular gland vesicular glands vesicular seminalis vesiculæ seminales UBERON:0000998 seminal vesicle http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. BTO:0001234 Wikipedia:Seminal_vesicle Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG] 2012-09-17 VHOG:0001379 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/prominence (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG] 2012-09-17 VHOG:0001379 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556 http://bgee.unil.ch/ UMLS:C0036628 ncithesaurus:Seminal_Vesicle glandula seminalis BTO:0001234 glandula vesiculosa BTO:0001234 vesicula seminalis BTO:0001234 Wikipedia:Seminal_vesicle vesiculae seminales Wikipedia:Seminal_vesicle vesicular gland Wikipedia:Seminal_vesicle vesicular glands Wikipedia:Seminal_vesicle vesicular seminalis Wikipedia:Seminal_vesicle vesiculæ seminales Wikipedia:Seminal_vesicle The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]. BTO:0001580 CALOHA:TS-0211 EFO:0000985 EMAPA:19088 FMA:19325 GAID:388 MA:0003247 MAT:0000170 MESH:D004543 MIAA:0000170 NCIT:C32493 SCTID:279665005 UMLS:C0013747 Wikipedia:Ejaculatory_duct ductus ejaculatorii ductus ejaculatorius uberon ductus ejaculatorii UBERON:0000999 ejaculatory duct https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]. Wikipedia:Ejaculatory_duct UMLS:C0013747 ncithesaurus:Ejaculatory_Duct ductus ejaculatorii BTO:0001580 ductus ejaculatorius BTO:0001580 ductus ejaculatorii Wikipedia:Ejaculatory_duct A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct. The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG] Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall. BTO:0001427 CALOHA:TS-1105 EFO:0000981 EMAPA:18681 EV:0100105 FMA:19234 GAID:404 MA:0000413 MESH:D014649 MIAA:0000129 NCIT:C12813 SCTID:245467009 UMLS:C0042360 VHOG:0001135 Wikipedia:Vas_deferens galen:VasDeferens deferent duct ductus deferens vas deferen uberon sperm duct vasa deferentia UBERON:0001000 vas deferens http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg FMA A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct. ISBN:0-683-40008-8 MGI:pvb MP:0002769 Wikipedia:Vas_deferens http://orcid.org/0000-0002-6601-2165 The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG] 2012-09-17 VHOG:0001135 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670 http://bgee.unil.ch/ Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall. WP UMLS:C0042360 ncithesaurus:Vas_Deferens ductus deferens Wikipedia:Vas_deferens The outer epithelial layer of the skin that is superficial to the dermis. A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] relationship loss: subclass external integument structures (AAO:0000961)[AAO] (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] epidermal Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 SCTID:361694003 TAO:0000105 UMLS:C0014520 VHOG:0000077 Wikipedia:Epidermis_(skin) XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin epidermis The outer epithelial layer of the skin that is superficial to the dermis. ISBN:0073040584 http://orcid.org/0000-0002-6601-2165 A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000105 TAO ZFIN:curator The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] 2012-06-20 AAO:0000143 AAO AAO:BJB relationship loss: subclass external integument structures (AAO:0000961)[AAO] 2012-06-20 AAO:0000143 AAO (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] 2012-09-17 VHOG:0000077 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72 http://bgee.unil.ch/ UMLS:C0014520 ncithesaurus:Epidermis Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 SCTID:278197002 TAO:0000272 UMLS:C0035237 VHOG:0000202 Wikipedia:Respiratory_system XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb Functional system which consists of structures involved in respiration. Wikipedia:Respiratory_system http://orcid.org/0000-0002-6601-2165 Wikipedia:Acoelomorpha The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] 2012-06-20 AAO:0000541 AAO AAO:BJB There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] 2012-09-17 VHOG:0000202 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23 http://bgee.unil.ch/ UMLS:C0035237 ncithesaurus:Respiratory_System Atmungssystem BTO:0000203 apparatus respiratorius BTO:0000203 systema respiratorium Wikipedia:Respiratory_system An airway through which respiratory air passes in organisms. This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends airway airways FMA:265130 SCTID:361380005 Wikipedia:Trachea uberon UBERON:0001005 respiratory airway An airway through which respiratory air passes in organisms. Wikipedia:Trachea airway http://orcid.org/0000-0002-6601-2165 airways http://orcid.org/0000-0002-6601-2165 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 SCTID:278859004 TADS:0000170 TAO:0000339 WBbt:0005748 Wikipedia:Digestive_system XAO:0000125 ZFA:0000339 galen:DigestiveSystem ncithesaurus:Digestive_System uberon alimentary system alimentary tract gastrointestinal system gut UBERON:0001007 digestive system Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. FB:gg NLM:alimentary+system Wikipedia:Digestive_system An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] 2012-06-20 AAO:0000129 AAO AAO:BJB many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class MA FBbt:00005055 The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans excretory system AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 SCTID:362204003 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 Wikipedia:Excretory_system XAO:0000143 ZFA:0000163 galen:UrinaryTract systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here renal system The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. DOI:10.1371/journal.pone.0099864 GO:0072001 Wikipedia Wikipedia:Acoelomorpha An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] 2012-06-20 AAO:0010257 AAO AAO:BJB Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] 2012-09-17 VHOG:0000723 VHOG ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 http://bgee.unil.ch/ In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels GO This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans DOI:10.1371/journal.pone.0099864 FBbt:00005056 UMLS:C1508753 ncithesaurus:Urinary_System systema urinaria FMA:7159 systema urinarium BTO:0003092 renal or urinary system EHDAA:5901 Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. the cardiovascular system and the lymphatic system are parts of the circulatory system Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon systema cardiovasculare UBERON:0001009 circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. Wikipedia:Circulatory_system Wikipedia:Acoelomorpha WBbt coelomocyte currently classified as circulating cell Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] 2012-06-20 AAO:0000959 AAO AAO:BJB We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] 2012-09-17 VHOG:0001248 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 http://bgee.unil.ch/ MESH:D002319 https://github.com/biopragmatics/biomappings systema cardiovasculare Wikipedia:Circulatory_system Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. Connective tissue in which fat is stored.[TAO] Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] adipose In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. in FMA this is dense irregular connective tissue AAO:0000001 AEO:000020 BTO:0001487 CALOHA:TS-0013 EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 NCIT:C12472 SCTID:55603005 TAO:0002134 UMLS:C0001527 VHOG:0001284 Wikipedia:Adipose_tissue XAO:0003049 ZFA:0005345 galen:FattyTissue fat fat tissue fatty tissue uberon adipose bodyfat fatty depot UBERON:0001013 adipose tissue FMA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. MESH:A10.165.114 MGI:cwg MP:0000003 Wikipedia:Adipose_tissue http://orcid.org/0000-0002-6601-2165 Connective tissue in which fat is stored.[TAO] 2012-08-14 TAO:0002134 TAO ZFIN:curator Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] 2012-06-20 AAO:0000001 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000001 AAO Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] 2012-09-17 VHOG:0001284 VHOG DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007) http://bgee.unil.ch/ in FMA this is dense irregular connective tissue FMA UMLS:C0001527 ncithesaurus:Adipose_Tissue fat MA:0000009 adipose BTO:0001487 bodyfat BTO:0001487 A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 NCIT:C13056 TAO:0000548 UMLS:C0026845 VSAO:0005038 WBbt:0005737 Wikipedia:Muscular_system ZFA:0000548 muscle group muscles set musculature musculi set of muscles set of skeletal muscles uberon muscle system muscles musculature system UBERON:0001015 musculature http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png A subdivision of the muscular system corresponding to a subdisivision of an organism. Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. FMA UMLS:C0026845 ncithesaurus:Muscle musculi FMA:32558 FMA:TA set of muscles FMA:32558 set of skeletal muscles MA:0000165 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] nervous neural AAO:0000324 BILA:0000079 BIRNLEX:844 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 NCIT:C12755 SCTID:278196006 TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 Wikipedia:Nervous_system XAO:0000177 ZFA:0000396 neuronames:3236 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png Bgee:AN The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. BIRNLEX:844 ISBN:0-14-051288-8 ISBN:3110148986 NLM:nervous+system WB:rynl Wikipedia:Nervous_system ZFIN:curator A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000396 TAO ZFIN:curator Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] 2012-06-20 AAO:0000324 AAO AAO:BJB Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] 2012-09-17 VHOG:0000402 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 http://bgee.unil.ch/ FBbt:00005093 UMLS:C0027763 ncithesaurus:Nervous_System neurological system GO:0050877 nerve net Wikipedia:Nerve_net systema nervosum Wikipedia:Nervous_system The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] The brain and spinal cord. Kimmel et al, 1995.[TAO] The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 BIRNLEX:1099 BTO:0000227 CALOHA:TS-0150 EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 NCIT:C12438 SCTID:278199004 TAO:0000012 UMLS:C0927232 VHOG:0000293 Wikipedia:Central_nervous_system XAO:0000215 ZFA:0000012 neuronames:854 CNS systema nervosum centrale cerebrospinal axis uberon neuraxis UBERON:0001017 central nervous system FBbt cjm Bgee:AN The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. GO:0021551 http://www.frontiersinzoology.com/content/7/1/29 https://sourceforge.net/p/geneontology/ontology-requests/11422/ Wikipedia:Acoelomorpha Part of the nervous system which includes the brain and spinal cord.[AAO] 2012-06-20 AAO:0000090 AAO AAO:BJB The brain and spinal cord. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000012 TAO ZFIN:curator The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). BIRNLEX:1099 (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] 2012-09-17 VHOG:0000293 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) http://bgee.unil.ch/ FBbt:00005094 UMLS:C0927232 BIRNLEX:1099 ncithesaurus:Central_Nervous_System CNS systema nervosum centrale FMA:55675 FMA:TA cerebrospinal axis FMA:55675 neuraxis FMA:55675 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. A portion of tissue which is a fasiculated group of axons.[TAO] nervous AAO:0011070 AEO:0000137 BAMS:n BIRNLEX:1615 BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 NCIT:C12466 NCIT:C12768 NLX:147826 SCTID:244457007 SCTID:256864008 TAO:0007009 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 Wikipedia:Nervous_system XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves peripheral nerve uberon neural subtree UBERON:0001021 nerve FBbt An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. FBbt:00005105 http://orcid.org/0000-0002-6601-2165 A portion of tissue which is a fasiculated group of axons.[TAO] 2012-08-14 TAO:0007009 TAO ZFIN:curator FBbt:00005105 UMLS:C0027740 ncithesaurus:Nerve UMLS:C0031119 ncithesaurus:Peripheral_Nerve nerves TAO:0007009 peripheral nerve http://orcid.org/0000-0002-6601-2165 neural subtree FMA:65132 A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 FBbt:00005136 FMA:5868 Wikipedia:Sensory_nerve nervus sensorius uberon afferent nerve UBERON:0001027 sensory nerve AEO A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. UBERON:cjm Wikipedia:Sensory_nerve FBbt:00005136 nervus sensorius Wikipedia:Sensory_nerve Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 NLXANAT:090816 TAO:0000282 VHOG:0001674 Wikipedia:Sensory_system XAO:0003194 ZFA:0000282 organa sensuum sense organ subsystem sense organs sense organs set sensory subsystem sensory systems uberon organa sensuum sensory organ system set of sense organs UBERON:0001032 sensory system http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] 2012-09-17 VHOG:0001674 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ FBbt:00007692 organa sensuum FMA:75259 FMA:TA sense organs FMA:75259 sense organs set FMA:75259 sensory systems TAO:0000282 organa sensuum Wikipedia:Sensory_system set of sense organs FMA:75259 The sensory system for the sense of taste. The sensory system for the sense of taste[NLXANAT:090803]. The sensory system used for the sense of taste.[AAO] gustatory in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 NLXANAT:090803 SCTID:423940004 TAO:0001101 Wikipedia:Gustatory_system XAO:0003197 ZFA:0001101 neuronames:2889 gustatory organ system taste system uberon UBERON:0001033 gustatory system The sensory system for the sense of taste. NLXANAT:090803 The sensory system for the sense of taste[NLXANAT:090803]. NLXANAT:090803 The sensory system used for the sense of taste.[AAO] 2012-06-20 AAO:0010577 AAO AAO:EJS in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes ZFA A filament, mostly protein, that grows from follicles found in the dermis[WP]. TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales) this class defines an individual hair BTO:0001501 CALOHA:TS-0430 EFO:0000958 EMAPA:18769 EV:0100157 FMA:53667 GAID:71 MA:0000155 MAT:0000160 MESH:D006197 MIAA:0000160 NCIT:C32705 SCTID:361702001 UMLS:C0018494 VHOG:0001191 Wikipedia:Hair hair uberon coat hair coat/ hair fur microchaeta quill setulae vibrissa whisker UBERON:0001037 strand of hair http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png FMA FMA FMA A filament, mostly protein, that grows from follicles found in the dermis[WP]. Wikipedia:Hair UMLS:C0018494 ncithesaurus:Hair quill vibrissa whisker A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. consider splitting class One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)] BTO:0001471 CALOHA:TS-1130 EFO:0003078 EHDAA2:0002212 EHDAA:164 EMAPA:16085 FMA:87180 GAID:1301 MESH:D015017 NCIT:C14128 SCTID:362845002 UMLS:C0043425 VHOG:0000830 Wikipedia:Yolk_sac uberon saccus vitellinus vesicula umbilicalis UBERON:0001040 yolk sac http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png https://github.com/obophenotype/uberon/issues/635 EHDAA2 ISBN:0073040584 ISBN:0073040584 A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. Wikipedia:Yolk_sac One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] 2012-09-17 VHOG:0000830 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/yolk+sac the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells MP:0001718 Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000830 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 http://bgee.unil.ch/ UMLS:C0043425 ncithesaurus:Yolk_Sac saccus vitellinus Wikipedia:Yolk_sac vesicula umbilicalis Wikipedia:Yolk_sac Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 SCTID:361409009 TGMA:0001014 UMLS:C0231051 VHOG:0000285 Wikipedia:Foregut XAO:0000232 uberon praeenteron proenteron UBERON:0001041 foregut http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png Anterior subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. MP:0000474 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000285 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ FBbt:00005379 UMLS:C0231051 ncithesaurus:Foregut praeenteron Wikipedia:Foregut proenteron Wikipedia:Foregut A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme pharynx AAO:0000967 BTO:0001049 CALOHA:TS-0785 EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA:0000432 MESH:D010614 NCIT:C12425 SCTID:181211006 TAO:0000056 UMLS:C0031354 VHOG:0000462 Wikipedia:Pharynx XAO:0003227 ZFA:0000056 galen:Pharynx uberon UBERON:0001042 Consider generalizing to deuterostome pharynx chordate pharynx EHDAA2 A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. http://www.feedexp.org A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. MESH:A03.867 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000967 AAO AAO:EJS Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000056 TAO ZFIN:curator Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000462 VHOG http://bgee.unil.ch/ relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] 2012-09-17 VHOG:0000462 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503 http://bgee.unil.ch/ MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA pharynx FMA:46688 UMLS:C0031354 ncithesaurus:Pharynx Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) AAO:0000145 ANISEED:1235301 BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:D004947 MIAA:0000048 NCIT:C12389 SCTID:181245004 TAO:0000204 UMLS:C0014876 VHOG:0000450 Wikipedia:Esophagus XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus uberon UBERON:0001043 esophagus http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Wikipedia:Esophagus http://www.rivm.nl/interspeciesinfo/inter/oesophagus/ Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] 2012-06-20 AAO:0000145 AAO AAO:EJS The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] 2012-09-17 VHOG:0000450 VHOG DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996) http://bgee.unil.ch/ esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) MA UMLS:C0014876 ncithesaurus:Esophagus Saliva-secreting exocrine glands of the oral cavity[GO]. currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands BTO:0001203 CALOHA:TS-0892 EFO:0000859 EHDAA2:0001775 EHDAA:7987 EMAPA:17751 EV:0100059 FBbt:00005382 FMA:9597 GAID:937 MA:0000346 MAT:0000079 MESH:D012469 MIAA:0000079 NCIT:C12426 SCTID:181236000 UMLS:C0036098 VHOG:0000376 Wikipedia:Salivary_gland galen:SalivaryGland salivary gland uberon glandulae salivariae UBERON:0001044 saliva-secreting gland http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg Saliva-secreting exocrine glands of the oral cavity[GO]. GO:0007431 Wikipedia:Salivary_gland currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. 3 A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000376 VHOG http://bgee.unil.ch/ In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] 2012-09-17 VHOG:0000376 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211 http://bgee.unil.ch/ FBbt:00005382 UMLS:C0036098 ncithesaurus:Salivary_Gland salivary gland MA:0000346 glandulae salivariae Wikipedia:Salivary_gland Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 SCTID:361410004 TGMA:0001036 UMLS:C0231052 VHOG:0000290 Wikipedia:Midgut XAO:0000103 uberon mesenteron UBERON:0001045 midgut http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. GO:0007494 Wikipedia:Midgut The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000290 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon WP in FMA this represents an embryonic region. FMA FBbt:00005383 UMLS:C0231052 ncithesaurus:Midgut mesenteron Wikipedia:Midgut The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class the caudal portion of the primitive digestive tube of the embryo The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 SCTID:362856002 TGMA:0001020 UMLS:C0231053 VHOG:0000459 Wikipedia:Hindgut XAO:0000104 uberon metenteron UBERON:0001046 hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png Wikipedia The caudalmost subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 the caudal portion of the primitive digestive tube of the embryo MP:0008786 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000459 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ in FMA this class has no children. In MA it has a single child hindgut epithelium FMA FBbt:00005384 UMLS:C0231053 ncithesaurus:Hindgut metenteron Wikipedia:Hindgut Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 UMLS:C0678727 Wikipedia:Primordium XAO:0003043 uberon bud future organ placode primordia rudiment UBERON:0001048 primordium EHDAA2 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. BTO:0001886 FB:DJS FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html FBbt:00005495 UMLS:C0678727 ncithesaurus:Primordium placode FBbt:00005495 primordia XAO:0003043 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16757 FMA:293882 MAT:0000069 MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 TAO:0001135 UMLS:C0231024 VHOG:0000307 Wikipedia:Neural_tube XAO:0003204 ZFA:0001135 neuronames:1365 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] 2012-06-20 AAO:0010617 AAO AAO:JOR The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000307 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/neural+tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000307 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium GO:0021915 MESH:D054259 https://github.com/biopragmatics/biomappings UMLS:C0231024 ncithesaurus:Neural_Tube tubus neuralis Wikipedia:Neural_tube Bottom part of the pharynx that connects to the esophagus. The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG] hypopharyngeal BTO:0001740 CALOHA:TS-2020 EFO:0001388 EHDAA2:0004574 EV:0100068 FMA:54880 GAID:338 MA:0001796 MESH:D007013 NCIT:C12246 SCTID:281490009 UMLS:C0020629 VHOG:0000445 Wikipedia:Hypopharynx laryngeal pharynx laryngopharynx uberon pars laryngea pharyngis UBERON:0001051 hypopharynx https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg Bottom part of the pharynx that connects to the esophagus. Wikipedia:Hypopharynx The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG] 2012-09-17 VHOG:0000445 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/hypopharynx UMLS:C0020629 ncithesaurus:Hypopharynx laryngeal pharynx FMA:54877 laryngopharynx FMA:54877 pars laryngea pharyngis BTO:0001740 Wikipedia:Hypopharynx The terminal portion of the intestinal tube, terminating with the anus. The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] rectal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:D012007 MIAA:0000050 NCIT:C12390 SCTID:181261002 UMLS:C0034896 VHOG:0001751 Wikipedia:Rectum XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb 4 cjm MA EHDAA2 ISBN:0073040584 The terminal portion of the intestinal tube, terminating with the anus. ISBN:0-683-40008-8 MP:0000492 http://orcid.org/0000-0002-6601-2165 The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001751 VHOG http://bgee.unil.ch/ UMLS:C0034896 ncithesaurus:Rectum intestinum rectum BTO:0001158 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BFO:0000004 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 http://orcid.org/0000-0001-9114-8737 FBbt:10000000 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. UBERON:0005627 pancreatic duct BTO:0002362 EHDAA2:0001396 EHDAA:6905 EMAPA:17510 FMA:16003 GAID:337 MA:0000126 MESH:D010183 NCIT:C12272 RETIRED_EHDAA2:0002177 SCTID:245385001 UMLS:C0030288 VHOG:0000256 Wikipedia:Pancreatic_duct chief pancreatic duct duct of Wirsung main pancreatic duct uberon canal of Wirsung ductus pancreatis ventralis hepaticopancreatic duct UBERON:0001064 EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue ventral pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png FMA EHDAA2 A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. Wikipedia:Pancreatic_duct These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] 2012-09-17 VHOG:0000256 VHOG DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005) http://bgee.unil.ch/ Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. WP pancreatic duct MESH:A03.734.667 UMLS:C0030288 ncithesaurus:Pancreatic_Duct chief pancreatic duct FMA:16003 duct of Wirsung Wikipedia:Pancreatic_duct main pancreatic duct MA:0000126 canal of Wirsung BTO:0002362 hepaticopancreatic duct BTO:0002362 A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core. strictly speaking the term intervertebral disk [applies to intervertebral cartilage] BTO:0003625 EFO:0001370 EMAPA:32739 FMA:10446 GAID:105 MA:0000110 MESH:D007403 NCIT:C49571 SCTID:244570000 UMLS:C0021815 Wikipedia:Intervertebral_disk discus intervertebralis intervertebral disc spinal disc uberon intervertebral fibrocartilage spinal disk UBERON:0001066 whose gel-like core is nucleus puloposus, by this definition only in mammals intervertebral disk http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core. ISBN:0073040584 Wikipedia:Intervertebral_disk UMLS:C0021815 ncithesaurus:Intervertebral_Disc discus intervertebralis FMA:10446 FMA:TA spinal disc Wikipedia:Spinal_disc intervertebral fibrocartilage BTO:0003625 spinal disk BTO:0003625 A zone of skin that is part of a back [Automatically generated definition]. EMAPA:36392 FMA:10462 FMA:22985 MA:0000498 SCTID:181492002 back skin back zone of skin skin, dorsal region zone of skin of back uberon UBERON:0001068 EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of back MA MA A zone of skin that is part of a back [Automatically generated definition]. OBOL:automatic back zone of skin OBOL:automatic skin, dorsal region https://orcid.org/0000-0002-6601-2165 zone of skin of back OBOL:automatic A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]. not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO AAO:0010218 AAO:0010416 BTO:0004696 EFO:0001953 EHDAA2:0000461 EMAPA:18611 FMA:10635 GAID:480 MA:0001929 MESH:D002342 NCIT:C32551 SCTID:362044002 UMLS:C0007275 VHOG:0000265 Wikipedia:External_carotid_artery XAO:0000345 external carotid uberon arteria carotis externa UBERON:0001070 external carotid artery https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif MA FMA EHDAA2 FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]. MGI:anna UMLS:C0007275 ncithesaurus:External_Carotid_Artery external carotid AAO:0010218 arteria carotis externa Wikipedia:External_carotid_artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 FMA:10665 MA:0002052 NCIT:C53005 SCTID:161746006 UMLS:C0226271 Wikipedia:Superficial_part_of_transverse_cervical_artery superficial branch of transverse cervical artery uberon UBERON:0001071 The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. Wikipedia:Superficial_part_of_transverse_cervical_artery EMAPA:37117 MA:th UMLS:C0226271 ncithesaurus:Superficial_Cervical_Artery superficial branch of transverse cervical artery Wikipedia:Superficial_part_of_transverse_cervical_artery A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] AAO:0011083 BTO:0002682 EHDAA2:0000611 EMAPA:18416 FMA:10951 GAID:548 MA:0000480 MESH:D014682 NCIT:C12815 SCTID:181369003 UMLS:C0042458 VHOG:0001194 Wikipedia:Inferior_vena_cava XAO:0000388 galen:InferiorVenaCava inferior caval vein inferior vena cava posterior vena cava uberon caudal vena cava postcava vena cava inferior UBERON:0001072 posterior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png lexical A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Wikipedia:Inferior_vena_cava http://orcid.org/0000-0002-6601-2165 Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. FMA:10951 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001194 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 http://bgee.unil.ch/ UMLS:C0042458 ncithesaurus:Inferior_Vena_Cava inferior caval vein http://orcid.org/0000-0002-6601-2165 inferior vena cava Wikipedia:Venae_cavae posterior vena cava Wikipedia:Venae_cavae caudal vena cava VHOG:0001194 vena cava inferior BTO:0002682 Wikipedia:Inferior_vena_cava A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice. EMAPA:37601 FMA:11338 MA:0000332 SCTID:264021000 ileocaecal junction uberon UBERON:0001073 ileocecal junction A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice. http://www.medilexicon.com/medicaldictionary.php?t=46539 EMAPA:37601 MA:th A potential space between the visceral and parietal layers of the pericardium. Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) BSA:0000091 EHDAA2:0001434 EMAPA:16131 EMAPA:16132 FMA:11350 MA:0000053 NCIT:C38662 SCTID:362027001 TAO:0002220 UMLS:C0225972 VHOG:0000556 Wikipedia:Pericardial_cavity ZFA:0001655 galen:PericardialSpace cavity of pericardial sac pericardial space uberon cavitas pericardiaca UBERON:0001074 pericardial cavity MA FMA Wikipedia A potential space between the visceral and parietal layers of the pericardium. Wikipedia:Pericardium Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] 2012-08-14 TAO:0002220 TAO ZFIN:curator In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000556 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) ZFA UMLS:C0225972 ncithesaurus:Pericardial_Cavity pericardial space Wikipedia:Pericardial_cavity cavitas pericardiaca Wikipedia:Pericardial_cavity Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO] Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO] The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]. The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO] VSAO definition states it surrounds notochord but not applicable to post-natal. AAO:0000697 EMAPA:36588 FMA:11945 MA:0001457 NCIT:C12852 SCTID:361745008 SCTID:362867001 TAO:0000126 UMLS:C0223084 Wikipedia:Body_of_vertebra ZFA:0000126 body of vertebra corpus vertebra corpus vertebrae (vertebrale) vertebral body arcocentrum autocentrum holocentrum uberon centra corpus vertebrae vertebral centra vertebral centrum UBERON:0001075 bony vertebral centrum http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. VSAO:0000183 VSAO:curator http://orcid.org/0000-0002-6601-2165 Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO] 2012-08-14 TAO:0000126 TAO ZFIN:curator Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO] 2012-06-20 AAO:0000697 AAO AAO:Duellman_and_Trueb_2008 The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]. Wikipedia:Body_of_vertebra The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO] 2012-09-06 VSAO:0000183 VSAO Curator VSAO definition states it surrounds notochord but not applicable to post-natal. VSAO UMLS:C0223084 ncithesaurus:Vertebral_Body body of vertebra FMA:11945 corpus vertebra corpus vertebrae (vertebrale) FMA:11945 vertebral body FMA:11945 arcocentrum PMID:11746457 autocentrum PMID:11746457 ZFA:0000126 holocentrum PMID:11746457 centra PHENOSCAPE:ad corpus vertebrae Wikipedia:Body_of_vertebra vertebral centra PHENOSCAPE:ad vertebral centrum MA:0001457 An extension of a neural arches dorsal to the neural canal[TAO,modified]. Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO] Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO] Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO] relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO] The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process] spinous process AAO:0000705 EMAPA:25107 FMA:11948 MA:0001455 NCIT:C116112 SCTID:264259004 TAO:0001336 Wikipedia:Spinous_process ZFA:0001336 processus spinosus processus spinosus vertebrae spinous process of vertebra vertebra spinous process uberon neural spine neural spines spine of verterba UBERON:0001076 neural spine http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png An extension of a neural arches dorsal to the neural canal[TAO,modified]. TAO:0001336 http://orcid.org/0000-0002-6601-2165 Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO] 2012-06-20 AAO:0000705 AAO AAO:Pugener_and_Maglia_2008 Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO] 2012-08-14 TAO:0001336 TAO ZFIN:curator Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO] 2012-06-20 AAO:0000739 AAO AAO:Pugener_2002 relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO] 2012-06-20 AAO:0000705 AAO spinous process of vertebra FMA:11948 vertebra spinous process MA:0001455 neural spines ZFA:0001336 spine of verterba FMA:11948 The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted]. Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae. AAO:0000698 FMA:11949 MA:0001456 SCTID:264238006 Wikipedia:Transverse_process XAO:0003102 processus transversus processus transversus vertebrae transverse process vertebra transverse process uberon diapophyses diapophysis UBERON:0001077 transverse process of vertebra http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted]. Wikipedia:Transverse_process Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae. AAO:0000698 Endocardium that is part of the cardiac ventricle. EMAPA:32747 FMA:12148 MA:0000079 SCTID:192172004 TAO:0002247 VHOG:0000607 ZFA:0001615 cardiac ventricle endocardium endocardium of cardiac ventricle endocardium of heart ventricle endocardium of lower chamber of heart endocardium of ventricle of heart heart ventricle endocardium lower chamber of heart endocardium ventricle endocardium ventricle of heart endocardium ventricular endocardium uberon ventricle endocardial tissue UBERON:0001081 endocardium of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Endocardium that is part of the cardiac ventricle. ZFIN:curator cardiac ventricle endocardium OBOL:automatic endocardium of cardiac ventricle OBOL:automatic endocardium of heart ventricle OBOL:automatic endocardium of lower chamber of heart OBOL:automatic endocardium of ventricle of heart OBOL:automatic heart ventricle endocardium OBOL:automatic lower chamber of heart endocardium OBOL:automatic ventricle of heart endocardium OBOL:automatic ventricle endocardial tissue VHOG:0000607 An epicardial layer that lines a cardiac ventricle. The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] FMA:12150 TAO:0005058 ZFA:0005058 cardiac ventricle epicardium ventricular epicardium uberon UBERON:0001082 epicardium of ventricle An epicardial layer that lines a cardiac ventricle. http://orcid.org/0000-0002-6601-2165 The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] 2012-08-14 TAO:0005058 TAO ZFIN:curator cardiac ventricle epicardium OBOL:automatic Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003088 EMAPA:32748 FMA:12151 MA:0000082 SCTID:192084000 TAO:0005061 VHOG:0000604 ZFA:0005061 ventricle myocardium ventricular myocardium uberon ventricle cardiac muscle UBERON:0001083 myocardium of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. ZFIN:curator Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] 2012-08-14 TAO:0005061 TAO ZFIN:curator As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000604 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ ventricle cardiac muscle VHOG:0000604 A zone of skin that is part of a head [Automatically generated definition]. FMA:12166 FMA:24756 MA:0000582 NCIT:C52757 SCTID:181484006 UMLS:C0205029 adult head zone of skin head skin head zone of skin zone of skin of adult head zone of skin of head uberon UBERON:0001084 EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of head A zone of skin that is part of a head [Automatically generated definition]. OBOL:automatic UMLS:C0205029 ncithesaurus:Head_Skin adult head zone of skin OBOL:automatic head zone of skin OBOL:automatic zone of skin of adult head OBOL:automatic zone of skin of head OBOL:automatic A zone of skin that is part of a trunk [Automatically generated definition]. EMAPA:37278 FMA:12167 FMA:23093 MA:0000517 NCIT:C12295 SCTID:181489001 UMLS:C0205031 torso zone of skin trunk skin trunk zone of skin zone of skin of torso zone of skin of trunk uberon UBERON:0001085 EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of trunk A zone of skin that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37278 MA:th UMLS:C0205031 ncithesaurus:Skin_of_the_Trunk torso zone of skin OBOL:automatic trunk zone of skin OBOL:automatic zone of skin of torso OBOL:automatic zone of skin of trunk OBOL:automatic Transudate contained in the pleural cavity. BTO:0003080 FMA:12273 MA:0002532 MAT:0000500 Wikipedia:Pleural_fluid ncithesaurus:Pleural_Fluid uberon UBERON:0001087 pleural fluid Transudate contained in the pleural cavity. FMA:12273 Excretion that is the output of a kidney. kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 UMLS:C0042036 Wikipedia:Urine galen:Urine uberon UBERON:0001088 urine Excretion that is the output of a kidney. Wikipedia:Urine https://github.com/geneontology/go-ontology/issues/11025 UMLS:C0042036 ncithesaurus:Urine Secretion produced by a sweat gland. BTO:0001254 ENVO:02000025 FMA:12275 GAID:1172 MA:0002539 MESH:D013542 NCIT:C13280 UMLS:C0038984 Wikipedia:Sweat uberon skin exudate UBERON:0001089 sweat Secretion produced by a sweat gland. FMA:12275 UMLS:C0038984 ncithesaurus:Sweat skin exudate BTO:0001254 Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] It provides nutrients and lubrication for articular cartilage The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 Wikipedia:Synovial_fluid ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid FMA Joint fluid is a transudate of plasma that is actively secreted by synovial cells. https://www.ncbi.nlm.nih.gov/books/NBK274/ Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] 2012-08-14 TAO:0005154 TAO ZFIN:curator UMLS:C0039097 ncithesaurus:Synovial_Fluid joint fluid https://www.ncbi.nlm.nih.gov/books/NBK274/ Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food. The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG] dental absent in living platypus, present in toothed Miocene platypus Obduron dicksoni AEO:0000220 BTO:0000397 CALOHA:TS-1055 EFO:0000839 EHDAA2:0004605 EMAPA:32906 EV:0100063 FMA:12516 GAID:1260 MA:0000348 MAT:0000041 MESH:D014070 MIAA:0000041 NCIT:C12506 SCTID:302214001 TAO:0001625 UMLS:C0040426 VHOG:0001733 Wikipedia:Tooth XAO:0000431 ZFA:0000694 dental element dentine containing tooth tooth vertebrate tooth uberon UBERON:0001091 EDITOR_NOTE we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures calcareous tooth http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg XAO-modified ZFA-modified cjm Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food. Wikipedia:Tooth_(animal) http://orcid.org/0000-0002-6601-2165 Wikipedia PMID:10210685 The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG] 2012-09-17 VHOG:0001733 VHOG PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009) http://bgee.unil.ch/ absent in living platypus, present in toothed Miocene platypus Obduron dicksoni PMID:10210685 UMLS:C0040426 ncithesaurus:Tooth dental element http://orcid.org/0000-0002-6601-2165 The first vertebral bone in the vertebral column. First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO] Vertebra that is posteriorly adjacent to the neurocranium.[TAO] 1 C1 AAO:0000709 EHDAA:10606 EMAPA:19431 FMA:12519 GAID:236 MA:0001421 MESH:D001270 NCIT:C32239 SCTID:181818007 TAO:0001167 UMLS:C0004170 Wikipedia:Atlas_(anatomy) ZFA:0001167 C1 vertebra atlas atlas (CI) atlas [C I] atlas vertebra cervical atlas cervical vertebra 1 first cervical vertebra vertebra 1 uberon UBERON:0001092 vertebral bone 1 The first vertebral bone in the vertebral column. http://orcid.org/0000-0002-6601-2165 First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO] 2012-06-20 AAO:0000709 AAO AAO:Duellman_and_Trueb_1994 Vertebra that is posteriorly adjacent to the neurocranium.[TAO] 2012-08-14 TAO:0001167 TAO TAO:wd UMLS:C0004170 ncithesaurus:C1_Vertebra atlas [C I] FMA:12519 FMA:TA cervical atlas MP:0011576 cervical vertebra 1 MA:0001421 vertebra 1 TAO:0001167 The second vertebral bone in the vertebral column. Vertebra that is posteriorly adjacent to vertebra 1.[TAO] not the same as ZFA term 'axis' 2 EHDAA:10608 EMAPA:19432 FMA:12520 GAID:237 MA:0001422 MESH:D001368 NCIT:C32240 SCTID:181819004 TAO:0001168 UMLS:C0004457 Wikipedia:Axis_(anatomy) ZFA:0001168 axis (CII) axis [C II] axis vertebra cervical axis vertebra 2 C2 vertebra cervical vertebra 2 second cervical vertebra uberon C2 axis UBERON:0001093 vertebral bone 2 FMA The second vertebral bone in the vertebral column. http://orcid.org/0000-0002-6601-2165 Vertebra that is posteriorly adjacent to vertebra 1.[TAO] 2012-08-14 TAO:0001168 TAO TAO:wd UMLS:C0004457 ncithesaurus:C2_Vertebra axis [C II] FMA:12520 FMA:TA cervical axis MP:0004608 vertebra 2 ZFA:0001168 cervical vertebra 2 MA:0001422 axis MA:0001422 A vertebra bone that is part of the sacral region of the vertebral column. Enlarged vertebra with transverse processes (diapophyses), and ocassionally ribs, that are modified and elaborated for support of the pelvic girdle.[AAO] AAO:0000552 EMAPA:18336 FMA:12526 MA:0000313 NCIT:C12853 SCTID:361773005 UMLS:C1261045 Wikipedia:Sacrum XAO:0003078 galen:SacralVertebra neuronames:1706 sacral segment segment of sacrum uberon UBERON:0001094 EDITOR_NOTE todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs) sacral vertebra A vertebra bone that is part of the sacral region of the vertebral column. http://orcid.org/0000-0002-6601-2165 Enlarged vertebra with transverse processes (diapophyses), and ocassionally ribs, that are modified and elaborated for support of the pelvic girdle.[AAO] 2012-06-20 AAO:0000552 AAO AAO:Duellman_and_Trueb_1994 UMLS:C1261045 ncithesaurus:Sacral_Vertebra Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] we deliberately merge the MA classes as we believe them equivalent UBERON:0006070 caudal vertebra EMAPA:18374 FMA:12527 MA:0000310 MA:0001420 NCIT:C32334 SCTID:361774004 TAO:0000326 UMLS:C0223616 Wikipedia:Caudal_vertebra XAO:0003079 ZFA:0000326 galen:CoccygealVertebra caudal vertebrae caudal vertebral bone caudal vertebral bone element coccygeal segment coccygeal vertebra fused tail vertebra uberon coccygea tail vertebra UBERON:0001095 Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae caudal vertebra Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). http://orcid.org/0000-0002-6601-2165 Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] 2012-08-14 TAO:0000326 TAO ZFIN:curator we deliberately merge the MA classes as we believe them equivalent MA caudal vertebra FMA:12527 UMLS:C0223616 ncithesaurus:Coccygeal_Vertebra caudal vertebrae coccygeal vertebra FMA:12527 fused tail vertebra https://orcid.org/0000-0002-6601-2165 coccygea MA:0001420 tail vertebra MA:0000310 An anatomical wall that is part of a esophagus [Automatically generated definition]. EMAPA:35326 FMA:12611 MA:0002691 anatomical wall of esophagus anatomical wall of gullet anatomical wall of oesophagus esophageal wall esophagus anatomical wall esophagus wall gullet anatomical wall gullet wall oesophagus anatomical wall oesophagus wall wall of gullet wall of oesophagus uberon UBERON:0001096 wall of esophagus An anatomical wall that is part of a esophagus [Automatically generated definition]. OBOL:automatic anatomical wall of esophagus OBOL:automatic anatomical wall of gullet OBOL:automatic anatomical wall of oesophagus OBOL:automatic esophagus anatomical wall OBOL:automatic gullet anatomical wall OBOL:automatic gullet wall OBOL:automatic oesophagus anatomical wall OBOL:automatic oesophagus wall OBOL:automatic wall of gullet OBOL:automatic wall of oesophagus OBOL:automatic A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] phrenic The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution) barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus breathing control originate from the cervical somites, likely C3-C5[PMID:23586979] BTO:0000341 CALOHA:TS-0198 EFO:0000937 EHDAA2:0003495 EMAPA:17701 EV:0100376 FMA:13295 GAID:158 MA:0001904 MAT:0000502 MESH:D003964 NCIT:C12702 SCTID:181614006 UMLS:C0011980 VHOG:0000713 Wikipedia:Thoracid_diaphragm diaphragm muscle diaphragm of thorax thoracic diaphragm uberon midriff phren UBERON:0001103 diaphragm PMID:23586979 definitional A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. MP:0002279 Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. GO:0060539 The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] 2012-09-17 VHOG:0000713 VHOG ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278 http://bgee.unil.ch/ UMLS:C0011980 ncithesaurus:Diaphragm diaphragm muscle BTO:0000341 midriff BTO:0000341 phren BTO:0000341 A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad]. Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO] relationship loss: part_of zonal element (AAO:0000936)[AAO] In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG] clavicular The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X]. In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. FMA and MA differ in whether they consider this part of the shoulder AAO:0000761 EMAPA:18721 FMA:13321 GAID:182 MA:0001329 MESH:D002968 MFMO:0000047 NCIT:C12695 SCTID:181910004 UMLS:C0008913 VHOG:0000849 VSAO:0005031 Wikipedia:Clavicle galen:Clavicle clavicle clavicula collar bone collarbone uberon UBERON:0001105 clavicle bone https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg FMA mah ISBN:978-0-12-319060-4 from secondary cartilage of fusion ISBN:978-0-12-319060-4 A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad]. PHENOSCAPE:ad https://github.com/obophenotype/uberon/issues/103 Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO] 2012-06-20 AAO:0000761 AAO AAO:LAP relationship loss: part_of zonal element (AAO:0000936)[AAO] 2012-06-20 AAO:0000761 AAO In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG] 2012-09-17 VHOG:0000849 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18 http://bgee.unil.ch/ In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. ISBN:978-0-12-319060-4 FMA and MA differ in whether they consider this part of the shoulder FMA UMLS:C0008913 ncithesaurus:Clavicle clavicle VSAO:0005031 clavicula VSAO:0005031 The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted]. In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192] EFO:0003067 EHDAA2:0000932 EHDAA:8307 EMAPA:18178 FMA:13357 MA:0002331 NCIT:C33150 SCTID:181747008 UMLS:C0224362 VHOG:0000930 Wikipedia:Latissimus_dorsi_muscle dorsal latissimus muscle latissimi dorsi latissimus dorsi musculus latissimus dorsi uberon musculus latissimus dorsi UBERON:0001112 Dorsal group[Kardong] latissimus dorsi muscle https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png EHDAA2 EHDAA2 spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula dbpedia floor of intertubercular groove of the humerus dbpedia dbpedia dbpedia The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted]. Wikipedia:Latissimus_dorsi_muscle UMLS:C0224362 ncithesaurus:Musculus_Latissimus_Dorsi latissimi dorsi musculus latissimus dorsi Wikipedia:Latissimus_dorsi_muscle Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts EMAPA:18306 FMA:13361 MA:0000360 NCIT:C49579 SCTID:245378000 UMLS:C0447541 Wikipedia:Liver#Lobes hepatic lobe liver lobe lobus hepatis uberon UBERON:0001113 lobe of liver FMA Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. Wikipedia:Liver#Lobes UMLS:C0447541 ncithesaurus:Liver_Lobe The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] EHDAA2:0001008 EHDAA:4001 EMAPA:18311 FMA:13362 MA:0000363 NCIT:C33481 SCTID:362182008 TAO:0005173 UMLS:C0227481 VHOG:0001424 Wikipedia:Right_lobe_of_liver ZFA:0005173 liver right lobe lobus hepaticus dexter right liver lobe uberon 2nd lobe gall bladder lobe lobus hepatis dexter right hepatic lobe second lobe UBERON:0001114 right lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. Wikipedia:Right_lobe_of_liver Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] 2012-08-14 TAO:0005173 TAO ZFIN:curator UMLS:C0227481 ncithesaurus:Right_Lobe_of_the_Liver lobus hepaticus dexter right liver lobe ZFA:0005173 2nd lobe TAO:0005173 gall bladder lobe ZFA:0005173 lobus hepatis dexter Wikipedia:Right_lobe_of_liver right hepatic lobe EMAPA:18311 second lobe TAO:0005173 The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. Portion of the liver which develops on the fish's left side.[TAO] EHDAA2:0001000 EHDAA:3995 EMAPA:18307 FMA:13363 MA:0000361 NCIT:C32965 SCTID:362183003 TAO:0005172 UMLS:C0227486 VHOG:0001423 Wikipedia:Left_lobe_of_liver ZFA:0005172 left liver lobe liver left lobe lobus hepaticus sinister uberon left hepatic lobe lobus hepatis sinister UBERON:0001115 left lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. Wikipedia:Left_lobe_of_liver Portion of the liver which develops on the fish's left side.[TAO] 2012-08-14 TAO:0005172 TAO ZFIN:curator UMLS:C0227486 ncithesaurus:Left_Lobe_of_the_Liver lobus hepaticus sinister left hepatic lobe EMAPA:18307 lobus hepatis sinister Wikipedia:Left_lobe_of_liver A lobe of tissue that is part of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] EHDAA2:0002032 EMAPA:18196 FMA:13367 MA:0000131 NCIT:C33784 SCTID:245537001 UMLS:C0447647 VHOG:0000732 Wikipedia:Lobes_of_thyroid_gland lobus (glandula thyroidea) lobus glandulae thyroideae thyroid gland lobe thyroid lobe uberon lobuli glandulae thyroideae UBERON:0001118 The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids lobe of thyroid gland http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png FMA-abduced-lr A lobe of tissue that is part of a thyroid gland. http://orcid.org/0000-0002-6601-2165 Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000732 VHOG http://bgee.unil.ch/ http://www.thyroidmanager.org/Chapter1/chapter01.htm UMLS:C0447647 ncithesaurus:Thyroid_Gland_Lobe lobus glandulae thyroideae FMA:13367 FMA:TA lobuli glandulae thyroideae Wikipedia:Lobes_of_thyroid_gland A lobe of thyroid gland that is in the right side of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001759 EMAPA:18198 FMA:13368 MA:0000729 NCIT:C33491 SCTID:170482008 UMLS:C0229581 VHOG:0000733 lobus dexter (glandula thyroidea) right thyroid lobe thyroid gland right lobe uberon UBERON:0001119 right lobe of thyroid gland A lobe of thyroid gland that is in the right side of a thyroid gland. OBOL:automatic Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000733 VHOG http://bgee.unil.ch/ http://www.thyroidmanager.org/Chapter1/chapter01.htm UMLS:C0229581 ncithesaurus:Right_Thyroid_Gland_Lobe A lobe of thyroid gland that is in the left side of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000965 EMAPA:18197 FMA:13369 MA:0000728 NCIT:C32973 SCTID:170784008 UMLS:C0229582 VHOG:0000734 left thyroid lobe lobus sinister (glandula thyroidea) thyroid gland left lobe uberon UBERON:0001120 left lobe of thyroid gland A lobe of thyroid gland that is in the left side of a thyroid gland. OBOL:automatic Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000734 VHOG http://bgee.unil.ch/ http://www.thyroidmanager.org/Chapter1/chapter01.htm UMLS:C0229582 ncithesaurus:Left_Thyroid_Gland_Lobe The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted]. EHDAA2:0001832 EHDAA:9463 EMAPA:18525 FMA:13397 MA:0002378 NCIT:C53014 SCTID:181748003 UMLS:C1710059 VHOG:0000679 Wikipedia:Serratus_anterior_muscle Boxer's muscle serratus anterior serratus anterior muscle serratus ventralis muscle uberon musculus serratus anterior serratus lateralis UBERON:0001125 serratus ventralis https://upload.wikimedia.org/wikipedia/commons/c/c6/Serratus_anterior.png long thoracic nerve dbpedia EHDAA2 fleshy slips from the outer surface of upper 8 or 9 ribs dbpedia costal aspect of medial margin of the scapula dbpedia dbpedia The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted]. Wikipedia:Serratus_anterior_muscle UMLS:C1710059 ncithesaurus:Serratus_Ventralis serratus anterior VHOG:0000679 musculus serratus anterior Wikipedia:Serratus_anterior_muscle serratus lateralis Wikipedia:Serratus_anterior_muscle Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton Anatomical cluster that consists of all the vertebra in the body.[VSAO] The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] spine AAO:0000699 AAO:0000734 BTO:0000818 EFO:0001369 EHDA:10119 EMAPA:35919 FMA:13478 GAID:106 MA:0002416 MESH:D013131 NCIT:C12998 NCIT:C33588 NIF_Subcellular:sao1145756102 SCTID:44300000 TAO:0001559 UMLS:C0037949 UMLS:C1519455 VHOG:0001142 VSAO:0000185 Wikipedia:Vertebral_column XAO:0003074 ZFA:0001559 galen:SpinalColumn backbone vertebral column skeleton uberon columna vertebralis dorsal spine spinal column vertebral region UBERON:0001130 vertebral column cjm Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. VSAO:0000185 https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/?func=detail&aid=3530322&group_id=76834&atid=2257941 Anatomical cluster that consists of all the vertebra in the body.[VSAO] 2012-08-14 VSAO:0000185 VSAO VSAO:curator The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0001142 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/vertebral+column Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] 2012-09-17 VHOG:0001142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53 http://bgee.unil.ch/ spine FMA:13478 UMLS:C0037949 ncithesaurus:Vertebral_Column UMLS:C1519455 ncithesaurus:Spinal_Cord_Column backbone FMA:13478 vertebral column skeleton AAO:0000699 columna vertebralis BTO:0000818 dorsal spine BTO:0000818 spinal column MESH:A02.835.232.834 A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] AAO:0000729 EMAPA:37803 FMA:13479 MA:0001454 SCTID:280734009 Wikipedia:Vertebral_foramen vertebra neural canal uberon foramen vertebrale UBERON:0001131 vertebral foramen http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Wikipedia:Vertebral_foramen http://orcid.org/0000-0002-6601-2165 Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] 2012-06-20 AAO:0000729 AAO AAO:LAP EMAPA:37803 MA:th foramen vertebrale Wikipedia:Vertebral_foramen The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG] Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO] The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG] Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP] In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. AAO:0010545 BTO:0000997 CALOHA:TS-0745 EFO:0000862 EMAPA:32812 EV:0100134 FMA:13890 GAID:452 MA:0000128 MAT:0000082 MESH:D010280 MIAA:0000082 NCIT:C12765 SCTID:181121007 UMLS:C0030518 VHOG:0001188 Wikipedia:Parathyroid_gland XAO:0000167 parathyroid uberon epithelial body parathyroid secreting cell UBERON:0001132 parathyroid gland PMID:16313389 Wikipedia The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. ISBN:0-683-40008-8 MP:0000678 Wikipedia:Parathyroid_gland Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG] 2012-09-17 VHOG:0001188 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/parathyroid+gland Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO] 2012-06-20 AAO:0010545 AAO AAO:BJB The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG] 2012-09-17 VHOG:0001188 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. PMID:16313389 UMLS:C0030518 ncithesaurus:Parathyroid_Gland epithelial body XAO:0000167 Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 TAO:0005280 Wikipedia:Cardiac_muscle ZFA:0005280 galen:CardiacMuscle galen:CardiacMuscleTissue ncithesaurus:Heart_Muscle cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis heart muscle muscle tissue heart muscle textus muscularis heart myocardium muscle tissue heart myocardium textus muscularis muscle of heart muscle tissue muscle of heart textus muscularis muscle tissue of cardiac muscle muscle tissue of heart muscle muscle tissue of heart myocardium muscle tissue of muscle of heart muscle tissue of myocardium myocardium muscle tissue myocardium textus muscularis textus muscularis of cardiac muscle textus muscularis of heart muscle textus muscularis of heart myocardium textus muscularis of muscle of heart textus muscularis of myocardium uberon cardiac musculature UBERON:0001133 cardiac muscle tissue Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. ZFA:0005280 cardiac muscle muscle tissue OBOL:automatic cardiac muscle textus muscularis OBOL:automatic heart muscle muscle tissue OBOL:automatic heart muscle textus muscularis OBOL:automatic heart myocardium muscle tissue OBOL:automatic heart myocardium textus muscularis OBOL:automatic muscle of heart muscle tissue OBOL:automatic muscle of heart textus muscularis OBOL:automatic muscle tissue of cardiac muscle OBOL:automatic muscle tissue of heart muscle OBOL:automatic muscle tissue of heart myocardium OBOL:automatic muscle tissue of muscle of heart OBOL:automatic muscle tissue of myocardium OBOL:automatic myocardium muscle tissue OBOL:automatic myocardium textus muscularis OBOL:automatic textus muscularis of cardiac muscle OBOL:automatic textus muscularis of heart muscle OBOL:automatic textus muscularis of heart myocardium OBOL:automatic textus muscularis of muscle of heart OBOL:automatic textus muscularis of myocardium OBOL:automatic cardiac musculature BILA:0000134 Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 MA:0002439 NCIT:C13050 SCTID:426215008 UMLS:C0242692 Wikipedia:Skeletal_striated_muscle uberon skeletal muscle system somatic muscle UBERON:0001134 skeletal muscle tissue https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg Muscle tissue that consists primarily of skeletal muscle fibers. https://github.com/obophenotype/uberon/issues/324 Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] 2012-08-14 TAO:0005277 TAO ZFIN:curator Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] FMA:14069 FMA This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] 2012-09-17 VHOG:0000319 VHOG PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) http://bgee.unil.ch/ UMLS:C0242692 ncithesaurus:Skeletal_Muscle_Tissue skeletal muscle system BTO:0001103 somatic muscle BTO:0001103 Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FMA:14070 GAID:167 MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 NCIT:C12437 TAO:0005274 UMLS:C1267092 VHOG:0001246 WBbt:0005781 Wikipedia:Smooth_muscle_tissue XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis nonstriatus visceral muscle visceral muscle tissue uberon textus muscularis levis; textus muscularis nonstriatus UBERON:0001135 smooth muscle tissue https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. GO:0006939 Wikipedia:Smooth_muscle_tissue A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] 2012-08-14 TAO:0005274 TAO ZFIN:curator Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] 2012-06-20 AAO:0010244 AAO AAO:CAM (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] 2012-09-17 VHOG:0001246 VHOG DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) http://bgee.unil.ch/ UMLS:C1267092 ncithesaurus:Smooth_Muscle_Tissue textus muscularis nonstriatus FMA:14070 FMA:TA visceral muscle visceral muscle tissue textus muscularis levis; textus muscularis nonstriatus Wikipedia:Smooth_muscle_tissue Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 CALOHA:TS-1183 EHDAA2_RETIRED:0003111 EHDAA:2331 EHDAA:2349 EHDAA:295 EHDAA:6073 EHDAA:640 EHDAA:646 EMAPA:32856 FMA:14074 MA:0000565 NCIT:C33105 SCTID:361918002 UMLS:C0086610 Wikipedia:Mesothelium uberon UBERON:0001136 mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg FMA Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). FMA:14074 Wikipedia:Mesothelium UMLS:C0086610 ncithesaurus:Mesothelium A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. dorsal In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 MESH:D001415 NCIT:C13062 SCTID:123961009 UMLS:C0004600 Wikipedia:Dorsum_(anatomy) galen:Back back back of body proper dorsal part of organism uberon UBERON:0001137 dorsum http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BSPO:0000063 UBERONREF:0000006 Wikipedia:Dorsum_(anatomy) UMLS:C0004600 ncithesaurus:Back back FMA:14181 back of body proper FMA:14181 In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002783 EHDAA2:0001951 EHDAA:5414 EMAPA:18643 FMA:14332 MA:0002179 NCIT:C33687 SCTID:278031001 UMLS:C0226742 VHOG:0000552 Wikipedia:Superior_mesenteric_vein uberon upper mesenteric vein vena mesenterica superior UBERON:0001138 superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png Wikipedia:Vitelline_vein In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. Wikipedia:Superior_mesenteric_vein UMLS:C0226742 ncithesaurus:Superior_Mesenteric_Vein upper mesenteric vein BTO:0002783 vena mesenterica superior Wikipedia:Superior_mesenteric_vein A vein that drains the pelvis and lower limbs into the inferior vena cava. In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries. EMAPA:17874 FMA:14333 MA:0002143 NCIT:C32359 SCTID:181398004 UMLS:C0226758 Wikipedia:Common_iliac_vein galen:CommonIliacVein common iliac venous tree uberon vena iliaca communis UBERON:0001139 common iliac vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif MA FMA-abduced-lr A vein that drains the pelvis and lower limbs into the inferior vena cava. MURDOCH:403 Wikipedia:Common_iliac_vein In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries. Wikipedia:Common_iliac_vein UMLS:C0226758 ncithesaurus:Common_Iliac_Vein vena iliaca communis Wikipedia:Common_iliac_vein Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney BTO:0002681 EHDAA2:0001602 EHDAA:8722 EMAPA:28376 FMA:14334 GAID:544 MA:0002210 MESH:D012082 NCIT:C33462 SCTID:116358006 UMLS:C0035092 Wikipedia:Renal_vein galen:RenalVein kidney vein renal venous tree vein of kidney uberon venae renales UBERON:0001140 renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. ISBN:0-683-40008-8 MGI:csmith MP:0011323 The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. Wikipedia:Renal_vein in EHDAA2, the renal vein is part of the kidney EHDAA2 UMLS:C0035092 ncithesaurus:Renal_Vein kidney vein OBOL:automatic vein of kidney OBOL:automatic venae renales Wikipedia:Renal_vein A renal vein that drains the right kidney. A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. EMAPA:37381 FMA:14335 MA:0002212 NCIT:C52695 SCTID:116357001 UMLS:C0508000 uberon UBERON:0001141 right renal vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb A renal vein that drains the right kidney. http://orcid.org/0000-0002-6601-2165 A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Right_Renal_Vein EMAPA:37381 MA:th UMLS:C0508000 ncithesaurus:Right_Renal_Vein A renal vein that drains the left kidney. A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. EMAPA:37166 FMA:14336 MA:0002211 NCIT:C52693 SCTID:116356005 UMLS:C0508001 uberon UBERON:0001142 left renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb A renal vein that drains the left kidney. http://orcid.org/0000-0002-6601-2165 A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Left_Renal_Vein EMAPA:37166 MA:th UMLS:C0508001 ncithesaurus:Left_Renal_Vein Vein that carries blood away from the liver[ZFA]. todo - add developmental relationships for other taxa AAO:0010216 EMAPA:19221 FMA:14337 GAID:534 MA:0003015 MESH:D006503 NCIT:C32736 SCTID:278191001 TAO:0000670 UMLS:C0019155 Wikipedia:Hepatic_vein XAO:0000387 ZFA:0000670 galen:HepaticVein liver vein vein of liver vena hepatica uberon hepatic veins venae hepaticae UBERON:0001143 hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png FMA-abduced-lr Vein that carries blood away from the liver[ZFA]. Wikipedia:Hepatic_vein ZFA:0000670 https://sourceforge.net/tracker/?func=detail&aid=3565355&group_id=76834&atid=1205376 UMLS:C0019155 ncithesaurus:Hepatic_Vein liver vein OBOL:automatic vein of liver OBOL:automatic vena hepatica hepatic veins venae hepaticae Wikipedia:Hepatic_vein A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis. TODO - check testicular vs spermatic vein (MA:0002218) In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel BTO:0002678 EMAPA:18647 FMA:14344 MA:0002218 MA:0002234 NCIT:C53050 SCTID:264496006 UMLS:C0226718 Wikipedia:Testicular_vein male gonadal vein spermatic vein testicle vein testicular venous tree vein of testicle uberon vena tesicularis vena testicularis dextra vena testicularis sinistra venae spermaticae UBERON:0001144 testicular vein http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis. Wikipedia:Testicular_vein http://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/?func=detail&aid=3220553&group_id=76834&atid=1205376 UMLS:C0226718 ncithesaurus:Spermatic_Vein male gonadal vein Wikipedia:Testicular_vein spermatic vein Wikipedia:Testicular_vein testicle vein OBOL:automatic testicular venous tree Wikipedia:Testicular_vein vein of testicle OBOL:automatic vena tesicularis BTO:0002678 vena testicularis dextra Wikipedia:Testicular_vein vena testicularis sinistra Wikipedia:Testicular_vein venae spermaticae Wikipedia:Testicular_vein A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. EMAPA:18644 FMA:14346 MA:0002186 NCIT:C53058 SCTID:278193003 UMLS:C0226720 Wikipedia:Ovarian_vein female reproductive system gonad vein female reproductive system gonada vein gonad of female reproductive system vein gonada of female reproductive system vein ovary vein vein of female reproductive system gonad vein of female reproductive system gonada vein of gonad of female reproductive system vein of gonada of female reproductive system vein of ovary uberon vena ovarica dextra vena ovarica sinistra UBERON:0001145 ovarian vein http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. Wikipedia:Ovarian_vein UMLS:C0226720 ncithesaurus:Ovarian_Vein female reproductive system gonad vein OBOL:automatic female reproductive system gonada vein OBOL:automatic gonad of female reproductive system vein OBOL:automatic gonada of female reproductive system vein OBOL:automatic ovary vein OBOL:automatic vein of female reproductive system gonad OBOL:automatic vein of female reproductive system gonada OBOL:automatic vein of gonad of female reproductive system OBOL:automatic vein of gonada of female reproductive system OBOL:automatic vein of ovary OBOL:automatic vena ovarica dextra Wikipedia:Ovarian_vein vena ovarica sinistra Wikipedia:Ovarian_vein A vein that drains the adrenal gland. EHDAA2:0001966 EHDAA:8731 FMA:14348 MA:0002081 MA:0002229 NCIT:C53129 SCTID:278194009 UMLS:C0226717 Wikipedia:Suprarenal_vein uberon adrenal vein UBERON:0001146 suprarenal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png A vein that drains the adrenal gland. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/mouse-anatomy-ontology/issues/110 UMLS:C0226717 ncithesaurus:Suprarenal_Vein adrenal vein MA:0002081 The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct. Duct that connects the gall bladder and the common bile duct.[TAO] The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EHDAA2:0000333 EHDAA:3045 EMAPA:16841 FMA:14539 GAID:290 MA:0000355 MESH:D003549 NCIT:C32421 SCTID:245398005 TAO:0005166 UMLS:C0010672 VHOG:0000213 Wikipedia:Cystic_duct ZFA:0005166 galen:CysticDuct uberon ductus cysticus UBERON:0001152 cystic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png FMA EHDAA2 The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct. ISBN:0-683-40008-8 MP:0009493 Duct that connects the gall bladder and the common bile duct.[TAO] 2012-08-14 TAO:0005166 TAO ZFIN:Curator The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000213 VHOG http://bgee.unil.ch/ UMLS:C0010672 ncithesaurus:Cystic_Duct ductus cysticus Wikipedia:Cystic_duct A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. caecal A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 MA:0000334 MESH:D002432 MIAA:0000288 NCIT:C12381 SCTID:181256004 UMLS:C0007531 VHOG:0001559 Wikipedia:Cecum galen:Cecum caecum cecum intestinum crassum caecum caeca ceca uberon blind intestine blindgut intestinum caecum intestinum crassum cecum UBERON:0001153 Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong] caecum http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb EHDAA2 Wikipedia Wikipedia A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. Wikipedia:Cecum Wikipedia A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. WP UMLS:C0007531 ncithesaurus:Cecum caecum VHOG:0001559 cecum FMA:14541 caeca NCBITaxon:8782 ceca NCBITaxon:8782 blind intestine BTO:0000166 blindgut BTO:0000166 intestinum caecum BTO:0000166 intestinum crassum cecum BTO:0000166 A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] appendiceal vermix BTO:0000084 CALOHA:TS-1267 EFO:0000849 EHDAA2:0000588 EMAPA:35140 EV:0100076 EV:0100080 FMA:14542 GAID:308 MA:0001540 MAT:0000287 MESH:D001065 MIAA:0000287 NCIT:C12380 SCTID:181255000 UMLS:C0003617 VHOG:0001306 Wikipedia:Vermiform_appendix galen:AppendixVermiformis appendix appendix vermiformis caecal appendix cecal appendix uberon apex of caecum apex of cecum appendix vermiformis UBERON:0001154 vermiform appendix http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb http://orcid.org/0000-0002-1572-1316 Wikipedia A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. Wikipedia:Vermiform_appendix https://orcid.org/0000-0002-6826-8770 Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. FMA:14542 A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] 2012-09-17 VHOG:0001306 VHOG DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009) http://bgee.unil.ch/ UMLS:C0003617 ncithesaurus:Vermiform_Appendix appendix vermiformis FMA:14542 FMA:TA apex of caecum EMAPA:35140 apex of cecum VHOG:0001306 appendix vermiformis Wikipedia:Vermiform_appendix A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. Some references do not consider the caecum to be part of the colon. TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] colonic In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] it extracts water and salt from solid wastes before they are eliminated from the body[WP] AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:D003106 NCIT:C12382 SCTID:302508007 TAO:0000706 UMLS:C0009368 VHOG:0000648 Wikipedia:Colon_(anatomy) XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon 3 cjm FMA A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. Wikipedia:Colon_(anatomy) ZFIN:curator http://orcid.org/0000-0002-2825-0621 http://orcid.org/0000-0002-6601-2165 Some references do not consider the caecum to be part of the colon. http://orcid.org/0000-0002-1572-1316 The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] 2012-06-20 AAO:0010400 AAO UBERON:0001155 The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0000706 TAO ZFIN:curator Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000648 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0009368 ncithesaurus:Colon Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified]. in MA, this is a subclass of colon BTO:0000270 CALOHA:TS-0057 EFO:0000843 EMAPA:35151 FMA:14545 MA:0001541 MAT:0000311 MESH:D044682 MIAA:0000311 NCIT:C12265 SCTID:362162009 UMLS:C0227375 Wikipedia:Ascending_colon galen:AscendingColon colon ascendens uberon spiral colon UBERON:0001156 ascending colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb FMA Wikipedia Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified]. FMA:14545 Wikipedia:Ascending_colon in MA, this is a subclass of colon MA MESH:D044682 https://github.com/biopragmatics/biomappings UMLS:C0227375 ncithesaurus:Ascending_Colon colon ascendens Wikipedia:Ascending_colon spiral colon Wikipedia:Spiral_colon The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 CALOHA:TS-2052 EFO:0000844 EMAPA:35880 FMA:14546 MA:0001543 MAT:0000312 MESH:D044684 MIAA:0000312 NCIT:C12385 SCTID:362163004 UMLS:C0227386 Wikipedia:Transverse_colon galen:TransverseColon colon transversum uberon UBERON:0001157 transverse colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb FMA Wikipedia The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 Wikipedia:Transverse_colon MESH:D044684 https://github.com/biopragmatics/biomappings UMLS:C0227386 ncithesaurus:Transverse_Colon colon transversum Wikipedia:Transverse_colon The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 CALOHA:TS-2010 EFO:0000845 EMAPA:35285 FMA:14547 MA:0001542 MAT:0000313 MESH:D044683 MIAA:0000313 NCIT:C12268 SCTID:362165006 UMLS:C0227389 Wikipedia:Descending_colon galen:DescendingColon colon descendens uberon UBERON:0001158 descending colon http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb FMA Wikipedia The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 MESH:D044683 https://github.com/biopragmatics/biomappings UMLS:C0227389 ncithesaurus:Descending_Colon colon descendens Wikipedia:Descending_colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:D012809 MIAA:0000314 NCIT:C12384 NCIT:C33550 SCTID:362166007 UMLS:C0227391 UMLS:C0682612 Wikipedia:Sigmoid_colon galen:SigmoidColon uberon colon sigmoideum pelvic colon sigmoid colon sigmoid flexure UBERON:0001159 sigmoid colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb FMA Wikipedia The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. Wikipedia:Sigmoid_colon UMLS:C0227391 ncithesaurus:Sigmoid_Colon UMLS:C0682612 ncithesaurus:Sigmoid_Flexure colon sigmoideum Wikipedia:Sigmoid_colon The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. we include this as zone of stomach even though it is not distinguished by gland type BTO:0000505 EMAPA:35810 FMA:14560 MA:0002559 NCIT:C12258 SCTID:362140009 UMLS:C0227230 Wikipedia:Body_of_stomach galen:GastricCorpus corpus gastricum (ventriculare) gastric body stomach body uberon corpus gastricum corpus ventriculare corpus ventriculi gastric corpus UBERON:0001161 body of stomach http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg FMA The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. GO:0014845 Wikipedia:Body_of_stomach UMLS:C0227230 ncithesaurus:Body_of_Stomach corpus gastricum BTO:0000505 Wikipedia:Body_of_stomach corpus ventriculare BTO:0000505 corpus ventriculi BTO:0000505 The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]. There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP] We follow Kardong in defining stomach regions by glands. UBERON:0004712 BTO:0000198 EMAPA:35811 FMA:14561 GAID:319 MA:0001609 MESH:D002299 NCIT:C12256 SCTID:362138004 UMLS:C0007144 Wikipedia:Cardia cardial part of stomach gastric cardia pars cardiaca (gaster) pars cardiaca gastricae stomach cardiac region uberon antrum cardiacum cardiac antrum cardiac orifice cardiac region cardial orifice UBERON:0001162 cardia of stomach https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg ISBN:0073040584 The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]. BTO:0000198 Wikipedia:Cardia UMLS:C0007144 ncithesaurus:Cardia pars cardiaca gastricae FMA:14561 FMA:TA stomach cardiac region MA:0001609 antrum cardiacum Wikipedia:Cardia cardiac orifice Wikipedia:Cardia cardiac region Wikipedia:Cardia cardial orifice Wikipedia:Cardia The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells. antrum BTO:0001732 EFO:0002555 EMAPA:17891 FMA:14579 GAID:332 MA:0001624 MESH:D011706 NCIT:C12259 SCTID:362142001 UMLS:C0034193 Wikipedia:Pyloric_antrum galen:PyloricAntrum antrum of stomach stomach pyloric antrum uberon antrum of Willis antrum pylori antrum pyloricum gastric antrum stomach antrum UBERON:0001165 pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg FMA Wikipedia The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells. ISBN:0-683-40008-8 MP:0010790 UMLS:C0034193 ncithesaurus:Antrum_Pylori antrum of Willis BTO:0001732 antrum pylori BTO:0001732 antrum pyloricum BTO:0001732 Wikipedia:Pyloric_antrum gastric antrum BTO:0001732 The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum. We follow Kardong in defining stomach regions by glands The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] pyloric BTO:0001146 EHDAA2:0001580 EHDAA:4860 EMAPA:17631 FMA:14581 GAID:333 MA:0002560 MESH:D011708 NCIT:C12260 SCTID:362143006 UMLS:C0034196 VHOG:0000420 Wikipedia:Pylorus galen:Pylorus pars pylorica pars pylorica gastricae pyloric part of stomach pyloric region stomach pyloric region uberon valvula pylori UBERON:0001166 pylorus http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum. MGI:csmith MP:0010785 The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000420 VHOG http://bgee.unil.ch/ Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000420 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0034196 ncithesaurus:Pylorus pars pylorica pars pylorica gastricae FMA:14581 FMA:TA stomach pyloric region EHDAA2:0001580 valvula pylori Wikipedia:Pylorus The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between. EMAPA:35826 FMA:14582 MA:0002692 SCTID:279995000 galen:WallOfStomach anatomical wall of stomach anatomical wall of ventriculus gastric wall stomach anatomical wall stomach wall ventriculus anatomical wall ventriculus wall wall of ventriculus uberon UBERON:0001167 wall of stomach The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between. MGI:csmith MP:0010783 anatomical wall of stomach OBOL:automatic anatomical wall of ventriculus OBOL:automatic stomach anatomical wall OBOL:automatic ventriculus anatomical wall OBOL:automatic ventriculus wall OBOL:automatic wall of ventriculus OBOL:automatic An anatomical wall that is part of a small intestine [Automatically generated definition]. EMAPA:35785 FMA:14615 MA:0002696 NCIT:C33573 UMLS:C1519375 anatomical wall of small bowel anatomical wall of small intestine small bowel anatomical wall small bowel wall small intestinal wall small intestine anatomical wall small intestine wall wall of small bowel uberon UBERON:0001168 wall of small intestine An anatomical wall that is part of a small intestine [Automatically generated definition]. OBOL:automatic UMLS:C1519375 ncithesaurus:Small_Intestinal_Wall_Tissue anatomical wall of small bowel OBOL:automatic anatomical wall of small intestine OBOL:automatic small bowel anatomical wall OBOL:automatic small bowel wall OBOL:automatic small intestine anatomical wall OBOL:automatic wall of small bowel OBOL:automatic An anatomical wall that is part of a large intestine [Automatically generated definition]. EMAPA:35470 FMA:14619 MA:0002695 anatomical wall of large intestine large intestinal wall large intestine anatomical wall large intestine wall uberon UBERON:0001169 wall of large intestine An anatomical wall that is part of a large intestine [Automatically generated definition]. OBOL:automatic anatomical wall of large intestine OBOL:automatic large intestine anatomical wall OBOL:automatic The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]. EMAPA:37745 FMA:14643 MA:0001555 SCTID:245456008 Wikipedia:Mesentery#Mesentery_.28proper.29 mesentery (proper) mesentery proper small intestinal mesentery small intestine mesentery uberon UBERON:0001170 mesentery of small intestine FMA The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]. Wikipedia:Mesentery#Mesentery_.28proper.29 EMAPA:37745 MA:th mesentery (proper) Wikipedia:Mesentery mesentery proper FMA:14643 small intestinal mesentery FMA:14643 small intestine mesentery OBOL:automatic The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. FMA:14653 MA:0002498 NCIT:C33341 UMLS:C0682620 uberon UBERON:0001171 portal lobule FMA MA MP The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. MP:0008992 UMLS:C0682620 ncithesaurus:Portal_Lobule The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. EMAPA:35497 FMA:14654 MA:0002496 NCIT:C32992 SCTID:272214009 UMLS:C0227519 liver acinus portal acinus uberon UBERON:0001172 hepatic acinus cjm The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. http://orcid.org/0000-0002-6601-2165 http://www.vivo.colostate.edu/hbooks/pathphys/digestion/liver/histo_acinus.html UMLS:C0227519 ncithesaurus:Liver_Acinus A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] AAO:0011020 EMAPA:35172 FMA:14665 MESH:D001659 SCTID:181267003 UMLS:C0005423 Wikipedia:Biliary_tract XAO:0000455 uberon biliary tract UBERON:0001173 The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] biliary tree A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. DOI:10.1002/ar.20664 Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] 2012-06-20 AAO:0011020 AAO UBERON:0001173 MESH:D001659 https://github.com/biopragmatics/biomappings UMLS:C0005423 ncithesaurus:Biliary_Tract biliary tract MA:0001273 The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct. Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] EHDAA2:0000303 EHDAA:3981 EMAPA:17201 FMA:14667 GAID:282 MA:0001631 MESH:D003135 NCIT:C12698 SCTID:362199009 TAO:0005165 UMLS:C0009437 VHOG:0000214 Wikipedia:Common_bile_duct ZFA:0005165 galen:CommonBileDuct ductus choledochus (biliaris) uberon ductus choledochus UBERON:0001174 common bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct. MGI:csmith MP:0009495 Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] 2012-08-14 TAO:0005165 TAO ZFIN:Curator The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000214 VHOG http://bgee.unil.ch/ UMLS:C0009437 ncithesaurus:Common_Bile_Duct ductus choledochus Wikipedia:Common_bile_duct Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EMAPA:19101 FMA:14668 GAID:286 MA:0002660 MESH:D006500 NCIT:C32356 SCTID:245403006 UMLS:C0019149 VHOG:0000220 Wikipedia:Common_hepatic_duct uberon ductus hepaticus communis hepatic duct UBERON:0001175 common hepatic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg FMA MA Wikipedia Wikipedia definitional Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. Wikipedia:Common_hepatic_duct ZFIN:curator The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000220 VHOG http://bgee.unil.ch/ UMLS:C0019149 ncithesaurus:Common_Hepatic_Duct ductus hepaticus communis Wikipedia:Common_hepatic_duct The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] EHDAA2:0001727 EHDAA:3992 EMAPA:32797 FMA:14669 MA:0001639 NCIT:C33476 SCTID:245401008 UMLS:C0227557 VHOG:0000217 uberon ductus hepaticus dexter UBERON:0001176 right hepatic duct The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. http://www.medterms.com/script/main/art.asp?articlekey=26034 The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] 2012-09-17 VHOG:0000217 VHOG http://bgee.unil.ch/ UMLS:C0227557 ncithesaurus:Right_Hepatic_Duct ductus hepaticus dexter The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] EHDAA2:0000941 EHDAA:3990 EMAPA:32795 FMA:14670 MA:0001638 NCIT:C32960 SCTID:245400009 UMLS:C0227560 VHOG:0000218 uberon ductus hepaticus sinister UBERON:0001177 left hepatic duct The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. http://www.medterms.com/script/main/art.asp?articlekey=26035 The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] 2012-09-17 VHOG:0000218 VHOG http://bgee.unil.ch/ UMLS:C0227560 ncithesaurus:Left_Hepatic_Duct ductus hepaticus sinister The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. EMAPA:16592 FMA:14703 SCTID:362702003 TAO:0005132 VHOG:0001528 Wikipedia:Visceral_peritoneum ZFA:0005132 visceral serous membrane of peritoneum uberon UBERON:0001178 visceral peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. Wikipedia:Peritoneum#Types http://orcid.org/0000-0002-6601-2165 visceral serous membrane of peritoneum UBERON:cjm Anatomical cavity bounded by visceral and parietal peritoneum. The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] BTO:0001782 EHDAA2:0001446 EMAPA:16138 FMA:14704 GAID:24 MA:0000054 MESH:D010529 NCIT:C12769 SCTID:181616008 UMLS:C1704247 VHOG:0000852 Wikipedia:Peritoneal_cavity uberon cavitas peritonealis saccus serosus peritonei UBERON:0001179 peritoneal cavity Wikipedia Anatomical cavity bounded by visceral and parietal peritoneum. Wikipedia:Peritoneal_cavity http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/86 The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] 2012-09-17 VHOG:0000852 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/peritoneal+cavity In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000852 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ UMLS:C1704247 ncithesaurus:Peritoneal_Cavity cavitas peritonealis BTO:0001782 Wikipedia:Peritoneal_cavity saccus serosus peritonei Wikipedia:Peritoneal_cavity Mesenteric artery that supplies the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra. Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon BTO:0002303 EHDAA2:0001949 EHDAA:3358 EHDAA:5313 EMAPA:18619 FMA:14749 GAID:502 MA:0002005 MESH:D017538 NCIT:C33685 SCTID:362048004 UMLS:C0162861 VHOG:0000754 Wikipedia:Superior_mesenteric_artery galen:SuperiorMesentericArtery superior mesenteric arterial tree uberon arteria mesenterica superior UBERON:0001182 superior mesenteric artery http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb Mesenteric artery that supplies the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra. MESH:A07.231.114.565.755 Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon BTO UMLS:C0162861 ncithesaurus:Superior_Mesenteric_Artery arteria mesenterica superior BTO:0002303 Wikipedia:Superior_mesenteric_artery Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]. IMA BTO:0002302 EHDAA2:0000817 EHDAA:4345 EMAPA:18618 FMA:14750 GAID:501 MA:0002004 MESH:D017537 NCIT:C32780 SCTID:181341006 UMLS:C0162860 VHOG:0001116 Wikipedia:Inferior_mesenteric_artery galen:InferiorMesentericArtery inferior mesenteric arterial tree uberon arteria mesenterica inferior UBERON:0001183 inferior mesenteric artery http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]. Wikipedia:Inferior_mesenteric_artery IMA UMLS:C0162860 ncithesaurus:Inferior_Mesenteric_Artery arteria mesenterica inferior BTO:0002302 Wikipedia:Inferior_mesenteric_artery One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability. Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] AAO:0010223 BTO:0001165 EFO:0002552 EHDAA2:0004100 EHDAA:5321 EHDAA:8594 EMAPA:28373 FMA:14751 GAID:507 MA:0002035 MESH:D012077 NCIT:C12778 RETIRED_EHDAA2:0001600 SCTID:181339005 TAO:0000420 UMLS:C0035065 Wikipedia:Renal_artery ZFA:0000420 galen:RenalArtery renal arterial tree uberon arteria renalis renal arteries UBERON:0001184 renal artery http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. ISBN:0073040584 Wikipedia:Renal_artery Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] 2012-06-20 AAO:0010223 AAO AAO:BJB The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] Wikipedia Wikipedia:Renal_artery UMLS:C0035065 ncithesaurus:Renal_Artery arteria renalis Wikipedia:Renal_artery renal arteries Renal artery that supplies the right kidney. EMAPA:37380 FMA:14752 MA:0002037 NCIT:C52740 SCTID:36800007 UMLS:C0226332 right renal arterial tree uberon UBERON:0001185 The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP] right renal artery http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb Renal artery that supplies the right kidney. https://orcid.org/0000-0002-6601-2165 EMAPA:37380 MA:th UMLS:C0226332 ncithesaurus:Right_Renal_Artery Renal artery that supplies the left kidney. EMAPA:37098 FMA:14753 MA:0002036 NCIT:C52741 SCTID:19215005 UMLS:C0226333 left renal arterial tree uberon UBERON:0001186 The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP] left renal artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb Renal artery that supplies the left kidney. https://orcid.org/0000-0002-6601-2165 EMAPA:37098 MA:th UMLS:C0226333 ncithesaurus:Left_Renal_Artery One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad. EMAPA:18621 FMA:14758 MA:0002063 SCTID:244281003 Wikipedia:Testicular_artery testicular arterial tree uberon arteria testicularis internal spermatic internal spermatic arteries internal spermatic artery internal spermatic vessels spermatic arteries spermatic artery spermatic vessels testicular arteries UBERON:0001187 testicular artery http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad. Wikipedia:Testicular_artery http://orcid.org/0000-0002-6601-2165 arteria testicularis Wikipedia:Testicular_artery internal spermatic Wikipedia:Testicular_artery internal spermatic arteries Wikipedia:Testicular_artery internal spermatic artery Wikipedia:Testicular_artery internal spermatic vessels Wikipedia:Testicular_artery spermatic arteries Wikipedia:Testicular_artery spermatic artery Wikipedia:Testicular_artery spermatic vessels Wikipedia:Testicular_artery testicular arteries Wikipedia:Testicular_artery A testicular artery that supplies a right testicle. EMAPA:37382 FMA:14759 MA:0002042 NCIT:C52738 UMLS:C0734076 right spermatic artery trunk of right testicular arterial tree uberon UBERON:0001188 right testicular artery A testicular artery that supplies a right testicle. OBOL:automatic EMAPA:37382 MA:th UMLS:C0734076 ncithesaurus:Right_Spermatic_Artery A testicular artery that supplies a left testicle. EMAPA:37099 FMA:14760 MA:0002041 NCIT:C52739 UMLS:C0734077 left spermatic artery trunk of left testicular arterial tree uberon UBERON:0001189 left testicular artery A testicular artery that supplies a left testicle. OBOL:automatic EMAPA:37099 MA:th UMLS:C0734077 ncithesaurus:Left_Spermatic_Artery An artery that supplies an ovary. In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. EMAPA:18620 FMA:14761 MA:0002012 NCIT:C33242 SCTID:244280002 UMLS:C0226411 Wikipedia:Ovarian_artery ovarian arterial tree uberon arteria ovarica UBERON:0001190 ovarian artery http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png An artery that supplies an ovary. OBOL:automatic In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. Wikipedia:Ovarian_artery UMLS:C0226411 ncithesaurus:Ovarian_Artery arteria ovarica Wikipedia:Ovarian_artery The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted]. EHDAA2:0000311 EHDAA:2553 EMAPA:17310 FMA:14764 MA:0001972 NCIT:C32357 SCTID:362050007 UMLS:C1261084 Wikipedia:Common_iliac_artery common iliac arterial tree uberon arteria iliaca communis UBERON:0001191 See notes for parent class common iliac artery http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG MA The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted]. Wikipedia:Common_iliac_artery UMLS:C1261084 ncithesaurus:Common_Iliac_Artery arteria iliaca communis Wikipedia:Common_iliac_artery An artery that supplies the liver. currently defined in a generic fashion. Artery that supplies blood to the liver.[TAO] BTO:0004307 EMAPA:17859 FMA:14769 GAID:496 MA:0001963 MESH:D006499 NCIT:C32729 SCTID:76015000 TAO:0005161 UMLS:C0019145 ZFA:0005161 galen:HepaticArtery arteria hepatica propria uberon arteria hepatica UBERON:0001193 hepatic artery http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png An artery that supplies the liver. Wikipedia:Hepatic_artery_proper https://orcid.org/0000-0002-6601-2165 Artery that supplies blood to the liver.[TAO] 2012-08-14 TAO:0005161 TAO ZFIN:curator UMLS:C0019145 ncithesaurus:Hepatic_Artery arteria hepatica propria arteria hepatica BTO:0004307 An artery that supplies the spleen. EMAPA:19216 FMA:14773 GAID:510 MA:0001991 MA:0003177 MESH:D013157 NCIT:C33597 SCTID:244266009 UMLS:C0037996 Wikipedia:Splenic_artery galen:SplenicArtery arteria splenica lienal artery uberon arteria lienalis UBERON:0001194 splenic artery https://github.com/obophenotype/uberon/issues/268 http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb An artery that supplies the spleen. http://orcid.org/0000-0002-6601-2165 UMLS:C0037996 ncithesaurus:Splenic_Artery arteria splenica Wikipedia:Splenic_artery lienal artery MA:0001991 arteria lienalis Wikipedia:Splenic_artery The middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers' breadth from the transverse colon, to which they distribute branches. [WP,unvetted]. EMAPA:37106 FMA:14810 MA:0002007 NCIT:C52981 SCTID:244276007 UMLS:C0226328 Wikipedia:Middle_colic_artery galen:MiddleColicArtery uberon arteria colica media UBERON:0001196 middle colic artery http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers' breadth from the transverse colon, to which they distribute branches. [WP,unvetted]. Wikipedia:Middle_colic_artery EMAPA:37106 MA:th UMLS:C0226328 ncithesaurus:Middle_Colic_Artery arteria colica media Wikipedia:Middle_colic_artery The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted]. EMAPA:37083 FMA:14815 MA:0001970 NCIT:C32760 SCTID:244279000 UMLS:C0226323 Wikipedia:Ileocolic_artery galen:IleocolicArtery uberon arteria ileocolica UBERON:0001197 ileocolic artery http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted]. Wikipedia:Ileocolic_artery EMAPA:37083 MA:th UMLS:C0226323 ncithesaurus:Ileo-colic_Artery arteria ileocolica Wikipedia:Ileocolic_artery The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:D005753 NCIT:C32656 SCTID:362131005 UMLS:C0017136 Wikipedia:Gastric_mucosa galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa uberon Magenschleimhaut tunica mucosa gastris UBERON:0001199 mucosa of stomach https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg The mucosal layer that lines the stomach. http://orcid.org/0000-0002-6601-2165 The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. Wikipedia:Gastric_mucosa UMLS:C0017136 ncithesaurus:Gastric_Mucosa mucosa of organ of stomach OBOL:automatic mucosa of organ of ventriculus OBOL:automatic mucosa of ventriculus OBOL:automatic mucous membrane of ventriculus OBOL:automatic organ mucosa of stomach OBOL:automatic organ mucosa of ventriculus OBOL:automatic stomach mucosa of organ OBOL:automatic stomach mucous membrane OBOL:automatic stomach organ mucosa OBOL:automatic tunica mucosa gastricae FMA:14907 FMA:TA ventriculus mucosa OBOL:automatic ventriculus mucosa of organ OBOL:automatic ventriculus mucous membrane OBOL:automatic ventriculus organ mucosa OBOL:automatic Magenschleimhaut BTO:0001308 tunica mucosa gastris BTO:0001308 Wikipedia:Gastric_mucosa The fibrous connective tissue layer beneath the stomach mucosa. BTO:0002110 EMAPA:35825 FMA:14908 MA:0002685 NCIT:C32663 SCTID:52459002 UMLS:C0227211 gastric submucosa stomach submucosa submucosa of ventriculus tela submucosa (gaster) tela submucosa gastricae ventriculus submucosa uberon submucous layer of stomach tela submucosa ventriculi UBERON:0001200 submucosa of stomach The fibrous connective tissue layer beneath the stomach mucosa. MGI:csmith MP:0010794 UMLS:C0227211 ncithesaurus:Gastric_Submucosa submucosa of ventriculus OBOL:automatic tela submucosa gastricae FMA:14908 FMA:TA ventriculus submucosa OBOL:automatic submucous layer of stomach BTO:0002110 tela submucosa ventriculi BTO:0002110 The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum. TODO - check serosa/peritoneum EMAPA:35822 FMA:14914 MA:0001626 NCIT:C32662 SCTID:1353004 UMLS:C1517453 anatomical wall of stomach serosa anatomical wall of stomach serous membrane anatomical wall of ventriculus serosa anatomical wall of ventriculus serous membrane gastric wall serosa gastric wall serous membrane serosa of anatomical wall of stomach serosa of anatomical wall of ventriculus serosa of gastric wall serosa of stomach anatomical wall serosa of stomach wall serosa of ventriculus anatomical wall serosa of ventriculus wall serosa of wall of stomach serosa of wall of ventriculus serous coat of stomach serous membrane of anatomical wall of stomach serous membrane of anatomical wall of ventriculus serous membrane of gastric wall serous membrane of stomach anatomical wall serous membrane of stomach wall serous membrane of ventriculus anatomical wall serous membrane of ventriculus wall serous membrane of wall of stomach serous membrane of wall of ventriculus stomach anatomical wall serosa stomach anatomical wall serous membrane stomach serosa stomach wall serosa stomach wall serous membrane tunica serosa (gaster) tunica serosa gastricae ventriculus anatomical wall serosa ventriculus anatomical wall serous membrane ventriculus wall serosa ventriculus wall serous membrane visceral peritoneum of stomach wall of stomach serosa wall of stomach serous membrane wall of ventriculus serosa wall of ventriculus serous membrane uberon gastric serosa UBERON:0001201 serosa of stomach The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum. MGI:csmith MP:0010793 UMLS:C1517453 ncithesaurus:Gastric_Serosal_Surface anatomical wall of stomach serosa OBOL:automatic anatomical wall of stomach serous membrane OBOL:automatic anatomical wall of ventriculus serosa OBOL:automatic anatomical wall of ventriculus serous membrane OBOL:automatic gastric wall serosa OBOL:automatic gastric wall serous membrane OBOL:automatic serosa of anatomical wall of stomach OBOL:automatic serosa of anatomical wall of ventriculus OBOL:automatic serosa of gastric wall OBOL:automatic serosa of stomach anatomical wall OBOL:automatic serosa of stomach wall OBOL:automatic serosa of ventriculus anatomical wall OBOL:automatic serosa of ventriculus wall OBOL:automatic serosa of wall of stomach OBOL:automatic serosa of wall of ventriculus OBOL:automatic serous membrane of anatomical wall of stomach OBOL:automatic serous membrane of anatomical wall of ventriculus OBOL:automatic serous membrane of gastric wall OBOL:automatic serous membrane of stomach anatomical wall OBOL:automatic serous membrane of stomach wall OBOL:automatic serous membrane of ventriculus anatomical wall OBOL:automatic serous membrane of ventriculus wall OBOL:automatic serous membrane of wall of stomach OBOL:automatic serous membrane of wall of ventriculus OBOL:automatic stomach anatomical wall serosa OBOL:automatic stomach anatomical wall serous membrane OBOL:automatic stomach wall serosa OBOL:automatic stomach wall serous membrane OBOL:automatic tunica serosa gastricae FMA:14914 FMA:TA ventriculus anatomical wall serosa OBOL:automatic ventriculus anatomical wall serous membrane OBOL:automatic ventriculus wall serosa OBOL:automatic ventriculus wall serous membrane OBOL:automatic wall of stomach serosa OBOL:automatic wall of stomach serous membrane OBOL:automatic wall of ventriculus serosa OBOL:automatic wall of ventriculus serous membrane OBOL:automatic A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] AAO:0011093 EMAPA:19251 FMA:14916 MA:0002952 NCIT:C33433 SCTID:268073008 UMLS:C0227238 VHOG:0001466 XAO:0000457 pyloric valve uberon UBERON:0001202 pyloric sphincter A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. https://orcid.org/0000-0002-6601-2165 (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] 2012-09-17 VHOG:0001466 VHOG DOI:10.1046/j.1525-142x.2000.00076.x http://bgee.unil.ch/ UMLS:C0227238 ncithesaurus:Pyloric_Sphincter pyloric valve Wikipedia:Pylorus A mucosa that is part of a small intestine [Automatically generated definition]. BTO:0001259 CALOHA:TS-0941 EMAPA:35780 FMA:14933 MA:0002686 NCIT:C33568 SCTID:362144000 UMLS:C0227261 mucosa of organ of small bowel mucosa of organ of small intestine mucosa of small bowel mucous membrane of small bowel mucous membrane of small intestine organ mucosa of small bowel organ mucosa of small intestine small bowel mucosa small bowel mucosa of organ small bowel mucous membrane small bowel organ mucosa small intestinal mucosa small intestine mucosa small intestine mucosa of organ small intestine mucous membrane small intestine organ mucosa tunica mucosa (intestinum tenue) tunica mucosa intestini tenuis uberon UBERON:0001204 mucosa of small intestine A mucosa that is part of a small intestine [Automatically generated definition]. OBOL:automatic UMLS:C0227261 ncithesaurus:Small_Intestinal_Mucosa mucosa of organ of small bowel OBOL:automatic mucosa of organ of small intestine OBOL:automatic mucosa of small bowel OBOL:automatic mucous membrane of small bowel OBOL:automatic organ mucosa of small bowel OBOL:automatic organ mucosa of small intestine OBOL:automatic small bowel mucosa OBOL:automatic small bowel mucosa of organ OBOL:automatic small bowel mucous membrane OBOL:automatic small bowel organ mucosa OBOL:automatic small intestine mucosa of organ OBOL:automatic small intestine organ mucosa OBOL:automatic tunica mucosa intestini tenuis FMA:14933 FMA:TA Submucosal tissue in the small intestines. BTO:0002112 EMAPA:37564 FMA:14934 MA:0001562 NCIT:C33572 SCTID:691000 UMLS:C0227268 Wikipedia:Small_intestinal_submucosa small bowel submucosa small intestinal submucosa small intestine submucosa submucosa of small bowel tela submucosa (intestinum tenue) tela submucosa intestini tenuis uberon UBERON:0001205 submucosa of small intestine Submucosal tissue in the small intestines. Wikipedia:Small_intestinal_submucosa EMAPA:37564 MA:th UMLS:C0227268 ncithesaurus:Small_Intestinal_Submucosa small bowel submucosa OBOL:automatic submucosa of small bowel OBOL:automatic tela submucosa intestini tenuis BTO:0002112 A serous membrane that is part of a small intestine [Automatically generated definition]. duodenum, 1st part serosa, 2nd - 4th adventitia EMAPA:37561 FMA:14938 MA:0001558 SCTID:8266009 serosa of small bowel serous coat of small intestine serous membrane of small bowel serous membrane of small intestine small bowel serosa small bowel serous membrane small intestinal serosa small intestine serosa small intestine serous membrane tunica serosa (intestinum tenue) tunica serosa intestini tenuis visceral peritoneum of small intestine uberon UBERON:0001206 serosa of small intestine A serous membrane that is part of a small intestine [Automatically generated definition]. OBOL:automatic EMAPA:37561 MA:th serosa of small bowel OBOL:automatic serous membrane of small bowel OBOL:automatic serous membrane of small intestine OBOL:automatic small bowel serosa OBOL:automatic small bowel serous membrane OBOL:automatic small intestine serous membrane OBOL:automatic tunica serosa intestini tenuis FMA:14938 FMA:TA A mucosa that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2106 EMAPA:35467 FMA:14969 MA:0002688 NCIT:C32926 UMLS:C0734203 large intestinal mucosa large intestine mucosa large intestine mucosa of organ large intestine mucous membrane large intestine organ mucosa mucosa of organ of large intestine mucous membrane of large intestine organ mucosa of large intestine tunica mucosa intestini crassi uberon UBERON:0001207 mucosa of large intestine A mucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic UMLS:C0734203 ncithesaurus:Large_Intestinal_Mucosa large intestine mucosa of organ OBOL:automatic large intestine mucous membrane OBOL:automatic large intestine organ mucosa OBOL:automatic mucosa of organ of large intestine OBOL:automatic organ mucosa of large intestine OBOL:automatic tunica mucosa intestini crassi FMA:14969 FMA:TA A submucosa that is part of a large intestine [Automatically generated definition]. BTO:0002111 EMAPA:37560 FMA:14970 MA:0002690 NCIT:C32930 UMLS:C0734204 large intestinal submucosa large intestine submucosa tela submucosa intestini crassi uberon submucous layer of large intestine UBERON:0001208 submucosa of large intestine A submucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37560 MA:th UMLS:C0734204 ncithesaurus:Large_Intestinal_Submucosa tela submucosa intestini crassi FMA:14970 FMA:TA submucous layer of large intestine BTO:0002111 A serous membrane that is part of a large intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37557 FMA:14975 MA:0001546 NCIT:C32929 UMLS:C1517727 large intestinal serosa large intestine serosa large intestine serous membrane serous coat of large intestine serous membrane of large intestine tunica serosa intestini crassi visceral peritoneum of large intestine uberon UBERON:0001209 serosa of large intestine A serous membrane that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37557 MA:th UMLS:C1517727 ncithesaurus:Large_Intestinal_Serosal_Surface large intestine serous membrane OBOL:automatic serous membrane of large intestine OBOL:automatic tunica serosa intestini crassi FMA:14975 FMA:TA A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. currently defined as equivalent to any submucosal gland in the duodenum. Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds BTO:0002376 EMAPA:36522 FMA:15060 GAID:314 MA:0001551 MESH:D002011 NCIT:C13010 SCTID:41298001 UMLS:C0006323 Wikipedia:Brunner's_glands Brunner's gland gland of Brunner submucosal gland of duodenum uberon glandula duodenales glandula duodenales Brunneri UBERON:0001212 duodenal gland compound tubular FMA, modified unclear for Aves ISBN:9780521617147 A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. Wikipedia:Brunner's_glands Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds ISBN:9780521617147 UMLS:C0006323 ncithesaurus:Brunner_s_Gland Brunner's gland FMA:15060 gland of Brunner FMA:15060 glandula duodenales BTO:0002376 glandula duodenales Brunneri BTO:0002376 The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold. in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] the BTO class refers to a generic villous UBERON:0007607 BTO:0003121 EMAPA:35784 FMA:15072 MA:0001563 NCIT:C33874 SCTID:23230007 TAO:0005125 UMLS:C1519988 Wikipedia:Intestinal_villus ZFA:0005125 enteric villi enteric villous enteric villus intestinal villi villi intestinales villus villus intestinalis (intestinum tenue) uberon intestinal villus layer small intestine villus villi intestinales UBERON:0001213 intestinal villus http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg FMA ZFA The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold. MGI:csmith MGI:rbabiuk MP:0008108 The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005125 TAO ZFIN:curator the BTO class refers to a generic villous BTO UMLS:C1519988 ncithesaurus:Villus enteric villi HP:0011473 enteric villous HP:0011473 enteric villus HP:0011473 intestinal villi ZFA:0005125 villi intestinales villus BTO:0003121 villus intestinalis (intestinum tenue) FMA:15072 small intestine villus MA:0001563 villi intestinales Wikipedia:Intestinal_villus A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 EHDAA2:0000819 EHDAA:8712 EMAPA:18642 FMA:15391 MA:0002178 NCIT:C32782 SCTID:281055007 UMLS:C0226754 VHOG:0001118 Wikipedia:Inferior_mesenteric_vein uberon lower mesenteric vein vena mesenterica inferior UBERON:0001215 inferior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA/obol A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. Wikipedia:Inferior_mesenteric_vein UMLS:C0226754 ncithesaurus:Inferior_Mesenteric_Vein lower mesenteric vein BTO:0002782 vena mesenterica inferior Wikipedia:Inferior_mesenteric_vein A tributary of the superior mesenteric vein that drains the jejunum. EMAPA:37160 FMA:15402 MA:0002153 Wikipedia:Jejunal_veins uberon venae jejunales UBERON:0001216 jejunal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA FMA/obol A tributary of the superior mesenteric vein that drains the jejunum. Wikipedia:Jejunal_veins http://orcid.org/0000-0002-6601-2165 EMAPA:37160 MA:th venae jejunales Wikipedia:Jejunal_veins The veins that drain blood from the ileum into the superior mesenteric vein. EMAPA:37149 FMA:15405 MA:0002140 NCIT:C53046 UMLS:C1301431 Wikipedia:Ileal_veins uberon UBERON:0001217 ileal vein FMA Wikipedia The veins that drain blood from the ileum into the superior mesenteric vein. ncithesaurus:Ileal_Vein EMAPA:37149 MA:th UMLS:C1301431 ncithesaurus:Ileal_Vein The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]. EMAPA:37174 FMA:15406 MA:0002181 SCTID:9018004 Wikipedia:Middle_colic_vein vena colica media (intermedia) uberon vena colica media UBERON:0001218 middle colic vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]. Wikipedia:Middle_colic_vein EMAPA:37174 MA:th vena colica media Wikipedia:Middle_colic_vein The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted]. EMAPA:37150 FMA:15408 MA:0002141 NCIT:C53047 SCTID:36208008 UMLS:C0226744 Wikipedia:Ileocolic_vein uberon vena ileocolica UBERON:0001219 ileocolic vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted]. Wikipedia:Ileocolic_vein EMAPA:37150 MA:th UMLS:C0226744 ncithesaurus:Ileocolic_Vein vena ileocolica Wikipedia:Ileocolic_vein An ureter that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37373 FMA:15571 MA:0001685 NCIT:C49327 SCTID:276251000 UMLS:C0227682 uberon UBERON:0001222 right ureter https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_R.glb An ureter that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37373 MA:th UMLS:C0227682 ncithesaurus:Right_Ureter An ureter that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37372 FMA:15572 MA:0001684 NCIT:C49324 SCTID:276340002 UMLS:C0227683 uberon UBERON:0001223 left ureter https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_L.glb An ureter that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37372 MA:th UMLS:C0227683 ncithesaurus:Left_Ureter A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. CALOHA:TS-2230 EMAPA:17948 FMA:15575 GAID:426 MA:0000374 MESH:D007682 NCIT:C12887 SCTID:362221007 UMLS:C0227666 Wikipedia:Renal_pelvis galen:RenalPelvis kidney pelvis pelvis of ureter uberon p. renallis pyelum UBERON:0001224 In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg MA FMA A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. MP:0004194 UMLS:C0227666 ncithesaurus:Renal_Pelvis p. renallis Wikipedia:Renal_pelvis pyelum MP:0004194 Outer cortical portion of the kidney, between the renal capsule and the renal medulla. In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP] BTO:0001166 CALOHA:TS-0503 EMAPA:17952 FMA:15581 GAID:424 MA:0000372 MESH:D007672 NCIT:C12739 SCTID:362211004 UMLS:C0022655 Wikipedia:Renal_cortex galen:CortexOfKidney cortex renalis kidney cortex renal cortex uberon UBERON:0001225 cortex of kidney https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg FMA Outer cortical portion of the kidney, between the renal capsule and the renal medulla. Wikipedia:Renal_cortex UMLS:C0022655 ncithesaurus:Renal_Cortex cortex renalis FMA:15581 FMA:TA The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron. A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] The part of the nephron that filters blood.[TAO] BTO:0000333 CALOHA:TS-1317 EMAPA:28236 EMAPA:35726 EV:0100385 FMA:15625 MA:0000376 NCIT:C33456 SCTID:361329009 TAO:0005281 UMLS:C0227635 VHOG:0001262 Wikipedia:Renal_corpuscle ZFA:0005281 Malphigian corpuscle Malpighian corpuscle corpusculum renale uberon corpusculum renis cortical renal corpuscle kidney corpuscle UBERON:0001229 Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg MA ZFA The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron. ISBN:0-683-40008-8 MP:0002827 A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] 2012-11-28 BTO:0000333 BTO BTO:curator A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] 2012-11-28 XAO:0000146 XAO XAO:curator The part of the nephron that filters blood.[TAO] 2012-08-14 TAO:0005281 TAO ZFIN:curator UMLS:C0227635 ncithesaurus:Renal_Corpuscle Malphigian corpuscle MA:0000376 Malpighian corpuscle ZFA:0005281 corpusculum renale corpusculum renis Wikipedia:Renal_corpuscle cortical renal corpuscle MA:0000376 kidney corpuscle Wikipedia:Renal_corpuscle A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus. Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]. One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP] AAO:0010526 BTO:0002297 EMAPA:27973 EMAPA:28257 FMA:15626 KUPO:0001001 MA:0001660 NCIT:C32225 SCTID:361331000 TAO:0005254 TAO:0005310 UMLS:C0524448 Wikipedia:Bowman%27s_capsule ZFA:0005254 ZFA:0005310 Bowman's capsule Bowmans capsule capsula glomerularis renal glomerular capsule uberon Bowman's capsule Malphigian capsule Malpighian capsule Mueller capsule Muellerian capsule capsula glomeruli pronephric glomerular capsule UBERON:0001230 glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg Wikipedia A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus. MGI:pvb MP:0002828 Wikipedia:Bowman%27s_capsule Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] 2012-06-20 AAO:0010526 AAO AAO:BJB UMLS:C0524448 ncithesaurus:Bowman_s_Capsule Bowman's capsule http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron Bowmans capsule KUPO:0001001 capsula glomerularis renal glomerular capsule TAO:0005254 Bowman's capsule TAO:0005254 Malphigian capsule BTO:0002297 Malpighian capsule UBERON:cjm Mueller capsule BTO:0002297 Muellerian capsule BTO:0002297 capsula glomeruli pronephric glomerular capsule TAO:0005310 An epithelial tube that is part of the nephron, the functional part of the kidney. note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA UBERON:0004210 renal tubule BTO:0000343 CALOHA:TS-1262 EFO:0003666 EMAPA:27782 EV:0100387 FMA:15627 GAID:433 MA:0000377 MESH:D007684 NCIT:C49274 SCTID:361332007 TAO:0001287 UMLS:C0022674 Wikipedia:Renal_tubule ZFA:0001287 kidney tubule tubulus renalis uberon uriniferous tubule UBERON:0001231 nephron tubule GO MA ZFA GO ZFA checkme An epithelial tube that is part of the nephron, the functional part of the kidney. GO:0072078 Wikipedia:Renal_tubule note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA MA UMLS:C0022674 ncithesaurus:Renal_Tubule kidney tubule GAID:433 uriniferous tubule MA:0000377 The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient. Renal duct that collects the output from renal tubules.[TAO] in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron BTO:0000761 CALOHA:TS-0860 EMAPA:28407 EV:0100391 FMA:15628 GAID:434 MA:0000371 MESH:D007685 SCTID:28202009 TAO:0005294 Wikipedia:Collecting_tubule ZFA:0005294 collecting duct kidney collecting duct renal collecting tubule tubulus renalis arcuatus tubulus renalis colligens uberon arcuate renal tubule collecting duct system collecting tubule junctional tube kidney collecting tubule ureteric tree UBERON:0001232 collecting duct of renal tubule checkme GO The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient. GO:0072044 Wikipedia:Collecting_tubule Renal duct that collects the output from renal tubules.[TAO] 2012-08-14 TAO:0005294 TAO ZFIN:curator in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron FMA collecting duct GO:0072044 renal collecting tubule FMA:15628 tubulus renalis arcuatus Wikipedia:Connecting_tubule arcuate renal tubule Wikipedia:Connecting_tubule collecting duct system BTO:0000761 junctional tube Wikipedia:Connecting_tubule ureteric tree EMAPA:28407 An adrenal gland that is in the right side of the abdomen. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, the right adrenal gland is triangular shaped EMAPA:37357 FMA:15629 MA:0000719 NCIT:C49325 SCTID:281625001 UMLS:C0229559 glandula suprarenalis dexter right suprarenal gland uberon UBERON:0001233 right adrenal gland An adrenal gland that is in the right side of the abdomen. OBOL:automatic In humans, the right adrenal gland is triangular shaped WP EMAPA:37357 MA:th UMLS:C0229559 ncithesaurus:Right_Adrenal_Gland glandula suprarenalis dexter An adrenal gland that is in the left side of the abdomen. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, the left adrenal gland is semilunar shaped EMAPA:37356 FMA:15630 MA:0000718 NCIT:C49322 SCTID:281626000 UMLS:C0229560 glandula suprarenalis sinister left suprarenal gland uberon UBERON:0001234 left adrenal gland An adrenal gland that is in the left side of the abdomen. OBOL:automatic In humans, the left adrenal gland is semilunar shaped WP EMAPA:37356 MA:th UMLS:C0229560 ncithesaurus:Left_Adrenal_Gland glandula suprarenalis sinister The thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone. All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO AAO:0011009 BTO:0000045 CALOHA:TS-0015 EFO:0000237 EMAPA:18427 EV:0100136 FMA:15632 GAID:447 MA:0000118 MAT:0000494 MESH:D000302 NCIT:C12396 SCTID:362584002 UMLS:C0001613 VHOG:0001481 Wikipedia:Adrenal_cortex XAO:0000165 adrenal gland cortex cortex (glandula suprarenalis) cortex of adrenal gland cortex of suprarenal gland suprarenal cortex uberon cortex glandulae suprarenalis suprarenal UBERON:0001235 adrenal cortex http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png The thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone. ISBN:0-683-40008-8 MGI:llw2 MP:0008288 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001481 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 http://bgee.unil.ch/ UMLS:C0001613 ncithesaurus:Adrenal_Cortex cortex glandulae suprarenalis BTO:0000045 Wikipedia:Adrenal_cortex The inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine. All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] AAO:0011010 BTO:0000049 CALOHA:TS-0018 EFO:0000852 EMAPA:18428 EV:0100137 FMA:15633 GAID:451 MA:0000119 MAT:0000495 MESH:D019439 NCIT:C12397 SCTID:362585001 UMLS:C0001629 VHOG:0001378 Wikipedia:Adrenal_medulla XAO:0000166 adrenal gland medulla medulla (glandula suprarenalis) medulla glandulae suprarenalis medulla of adrenal gland medulla of suprarenal gland suprarenal medulla uberon adrenal central medulla chromaffin cells medulla of glandula suprarenalis UBERON:0001236 adrenal medulla http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png FMA FMA Wikipedia The inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine. MESH:A06.407.071.265 MGI:llw2 MP:0008289 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001378 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 http://bgee.unil.ch/ UMLS:C0001629 ncithesaurus:Adrenal_Medulla medulla glandulae suprarenalis FMA:15633 FMA:TA medulla of adrenal gland OBOL:automatic medulla of glandula suprarenalis BTO:0000049 Lamina propria that is part_of the small intestine. EMAPA:35779 FMA:15651 MA:0001554 NCIT:C49297 SCTID:63588008 UMLS:C1711325 lamina propria mucosa of small bowel lamina propria mucosa of small intestine lamina propria mucosae of small bowel lamina propria mucosae of small intestine lamina propria of mucosa of small intestine lamina propria of small bowel small bowel lamina propria small bowel lamina propria mucosa small bowel lamina propria mucosae small intestine lamina propria small intestine lamina propria mucosa small intestine lamina propria mucosae uberon UBERON:0001238 lamina propria of small intestine Lamina propria that is part_of the small intestine. GOC:Obol UMLS:C1711325 ncithesaurus:Small_Intestinal_Lamina_Propria lamina propria mucosa of small bowel OBOL:automatic lamina propria mucosa of small intestine OBOL:automatic lamina propria mucosae of small bowel OBOL:automatic lamina propria of small bowel OBOL:automatic small bowel lamina propria OBOL:automatic small bowel lamina propria mucosa OBOL:automatic small bowel lamina propria mucosae OBOL:automatic small intestine lamina propria mucosa OBOL:automatic small intestine lamina propria mucosae OBOL:automatic Mucosal layer that lines the intestine. BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:D007413 NCIT:C49241 SCTID:362080002 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon UBERON:0001242 intestinal mucosa Mucosal layer that lines the intestine. UBERON:cjm UMLS:C0021839 ncithesaurus:Intestinal_Mucosa bowel mucosa OBOL:automatic bowel mucosa of organ OBOL:automatic bowel mucous membrane OBOL:automatic bowel organ mucosa OBOL:automatic intestine mucosa of organ OBOL:automatic intestine mucous membrane OBOL:automatic intestine organ mucosa OBOL:automatic mucosa of bowel OBOL:automatic mucosa of organ of bowel OBOL:automatic mucosa of organ of intestine OBOL:automatic mucous membrane of bowel OBOL:automatic mucous membrane of intestine OBOL:automatic organ mucosa of bowel OBOL:automatic organ mucosa of intestine OBOL:automatic A serous membrane that is part of a wall of intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37619 FMA:15701 MA:0001538 anatomical wall of bowel serosa anatomical wall of bowel serous membrane anatomical wall of intestine serosa anatomical wall of intestine serous membrane bowel anatomical wall serosa bowel anatomical wall serous membrane bowel wall serosa bowel wall serous membrane intestinal serosa intestinal wall serosa intestinal wall serous membrane intestine anatomical wall serosa intestine anatomical wall serous membrane intestine serosa intestine wall serosa intestine wall serous membrane serosa of anatomical wall of bowel serosa of anatomical wall of intestine serosa of bowel anatomical wall serosa of bowel wall serosa of intestinal wall serosa of intestine anatomical wall serosa of intestine wall serosa of wall of bowel serosa of wall of intestine serous membrane of anatomical wall of bowel serous membrane of anatomical wall of intestine serous membrane of bowel anatomical wall serous membrane of bowel wall serous membrane of intestinal wall serous membrane of intestine anatomical wall serous membrane of intestine wall serous membrane of wall of bowel serous membrane of wall of intestine visceral peritoneum of intestine wall of bowel serosa wall of bowel serous membrane wall of intestine serosa wall of intestine serous membrane uberon UBERON:0001243 serosa of intestine A serous membrane that is part of a wall of intestine [Automatically generated definition]. OBOL:automatic EMAPA:37619 MA:th anatomical wall of bowel serosa OBOL:automatic anatomical wall of bowel serous membrane OBOL:automatic anatomical wall of intestine serosa OBOL:automatic anatomical wall of intestine serous membrane OBOL:automatic bowel anatomical wall serosa OBOL:automatic bowel anatomical wall serous membrane OBOL:automatic bowel wall serosa OBOL:automatic bowel wall serous membrane OBOL:automatic intestinal wall serosa OBOL:automatic intestinal wall serous membrane OBOL:automatic intestine anatomical wall serosa OBOL:automatic intestine anatomical wall serous membrane OBOL:automatic intestine wall serosa OBOL:automatic intestine wall serous membrane OBOL:automatic serosa of anatomical wall of bowel OBOL:automatic serosa of anatomical wall of intestine OBOL:automatic serosa of bowel anatomical wall OBOL:automatic serosa of bowel wall OBOL:automatic serosa of intestinal wall OBOL:automatic serosa of intestine anatomical wall OBOL:automatic serosa of intestine wall OBOL:automatic serosa of wall of bowel OBOL:automatic serosa of wall of intestine OBOL:automatic serous membrane of anatomical wall of bowel OBOL:automatic serous membrane of anatomical wall of intestine OBOL:automatic serous membrane of bowel anatomical wall OBOL:automatic serous membrane of bowel wall OBOL:automatic serous membrane of intestinal wall OBOL:automatic serous membrane of intestine anatomical wall OBOL:automatic serous membrane of intestine wall OBOL:automatic serous membrane of wall of bowel OBOL:automatic serous membrane of wall of intestine OBOL:automatic wall of bowel serosa OBOL:automatic wall of bowel serous membrane OBOL:automatic wall of intestine serosa OBOL:automatic wall of intestine serous membrane OBOL:automatic Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. anal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00047153 FMA:15711 GAID:312 MA:0000331 NCIT:C43362 SCTID:181262009 TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 Wikipedia:Anus galen:Anus anal opening anal orifice opening of terminal part of digestive tract uberon proctodeum UBERON:0001245 anus http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. Wikipedia:Anus ZFIN:curator FBbt:00047153 UMLS:C0003461 ncithesaurus:Anus The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. FMA:15767 MA:0002668 NCIT:C32827 SCTID:83488001 UMLS:C0227515 Wikipedia:Interlobular_bile_ducts interlobular ductule uberon UBERON:0001246 interlobular bile duct FMA MA-part-of FMA MA MP The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. MP:0009500 UMLS:C0227515 ncithesaurus:Interlobular_Bile_Duct interlobular ductule MP:0009500 A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP]. in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament EHDAA2:0000499 EHDAA:4856 EMAPA:18288 FMA:15823 MA:0001622 NCIT:C32582 SCTID:362705001 UMLS:C0230240 VHOG:0000355 Wikipedia:Falciform_ligament falciform ligament of liver ligamentum falciforme (hepatis) ligamentum falciforme hepatis uberon UBERON:0001247 falciform ligament https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb MA A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP]. Wikipedia:Falciform_ligament in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament FMA UMLS:C0230240 ncithesaurus:Falciform_Ligament ligamentum falciforme hepatis FMA:15823 FMA:TA An adventitia that is part of a ureter. EMAPA:28114 FMA:15892 MA:0002652 SCTID:392273001 SCTID:47879001 external adventitia of ureter tunica adventitia (ureter) tunica adventitia ureteris ureter adventitia ureteral adventitia uberon UBERON:0001252 adventitia of ureter https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An adventitia that is part of a ureter. OBOL:automatic tunica adventitia (ureter) FMA:15892 FMA:TA tunica adventitia ureteris FMA:15892 FMA:TA A lamina propria that is part of a ureter [Automatically generated definition]. EMAPA:28841 FMA:15896 MA:0002653 SCTID:2771005 lamina propria mucosa of ureter lamina propria mucosae of ureter ureter lamina propria ureter lamina propria mucosa ureter lamina propria mucosae uberon UBERON:0001253 lamina propria of ureter true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a ureter [Automatically generated definition]. OBOL:automatic lamina propria mucosa of ureter OBOL:automatic lamina propria mucosae of ureter OBOL:automatic ureter lamina propria mucosa OBOL:automatic ureter lamina propria mucosae OBOL:automatic Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] vesical The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:D001743 MIAA:0000122 NCIT:C12414 SCTID:302512001 UMLS:C0005682 VHOG:0000740 Wikipedia:Urinary_bladder XAO:0000154 galen:UrinaryBladder vesica urinaria uberon urocyst vesica UBERON:0001255 urinary bladder https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg BTO FMA upper part of UG sinus Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. MGI:anna Wikipedia:Urinary_bladder https://orcid.org/0000-0003-3308-6245 GOTAX:0010073 https://github.com/obophenotype/uberon/issues/454 A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000740 VHOG http://bgee.unil.ch/ Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] 2012-06-20 AAO:0000623 AAO AAO:BJB In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] 2012-09-17 VHOG:0000740 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78 http://bgee.unil.ch/ bladder EHDAA2:0000174 UMLS:C0005682 ncithesaurus:Bladder vesica urinaria Wikipedia:Urinary_bladder urocyst Wikipedia:Urinary_bladder vesica BTO:0001418 An anatomical wall that lines the insider of a urinary bladder. BTO:0001462 EMAPA:35175 FMA:15902 MA:0002493 NCIT:C48941 SCTID:362225003 UMLS:C0458421 anatomical wall of bladder anatomical wall of urinary bladder bladder anatomical wall bladder wall urinary bladder anatomical wall urinary bladder wall wall of bladder uberon UBERON:0001256 wall of urinary bladder An anatomical wall that lines the insider of a urinary bladder. http://orcid.org/0000-0002-6601-2165 UMLS:C0458421 ncithesaurus:Bladder_Wall anatomical wall of bladder OBOL:automatic anatomical wall of urinary bladder OBOL:automatic bladder anatomical wall OBOL:automatic bladder wall OBOL:automatic urinary bladder anatomical wall OBOL:automatic wall of bladder OBOL:automatic The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. EMAPA:36078 FMA:15912 MA:0002491 NCIT:C12336 SCTID:362227006 UMLS:C0227716 Wikipedia:Neck_of_urinary_bladder galen:UrinaryBladderNeck bladder neck cervix vesicae collum vesicae neck of bladder urinary bladder neck vesical neck uberon cervix vesicae urinariae UBERON:0001258 neck of urinary bladder http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. MP:anna Wikipedia:Neck_of_urinary_bladder UMLS:C0227716 ncithesaurus:Bladder_Neck cervix vesicae FMA:15912 FMA:TA collum vesicae FMA:15912 FMA:TA cervix vesicae urinariae Wikipedia:Neck_of_urinary_bladder The mucous membrane lining the urinary bladder. EFO:0000293 EMAPA:35897 FMA:15928 MA:0001692 NCIT:C32205 SCTID:362224004 UMLS:C0227691 galen:MucousMembraneOfUrinaryBladder bladder mucosa bladder mucous membrane bladder organ mucosa mucosa of bladder mucous membrane of bladder mucous membrane of urinary bladder tunica mucosa (vesica urinaria) tunica mucosa vesicae tunica mucosa vesicae urinariae urinary bladder mucosa urinary bladder mucous membrane uberon UBERON:0001259 mucosa of urinary bladder The mucous membrane lining the urinary bladder. MGI:anna MP:0011766 UMLS:C0227691 ncithesaurus:Bladder_Mucosa bladder mucous membrane OBOL:automatic bladder organ mucosa OBOL:automatic mucosa of bladder OBOL:automatic tunica mucosa (vesica urinaria) FMA:15928 FMA:TA tunica mucosa vesicae FMA:15928 FMA:TA tunica mucosa vesicae urinariae MP:MP urinary bladder mucous membrane OBOL:automatic A serous membrane that is part of a urinary bladder [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:28661 FMA:15932 MA:0001696 SCTID:5868002 bladder serosa bladder serous membrane serosa of bladder serous coat of bladder serous coat of urinary bladder serous membrane of bladder serous membrane of urinary bladder tunica serosa (vesica urinaria) tunica serosa vesicae urinary bladder serosa urinary bladder serous membrane visceral peritoneum of urinary bladder uberon UBERON:0001260 serosa of urinary bladder https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A serous membrane that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic bladder serous membrane OBOL:automatic serous membrane of bladder OBOL:automatic serous membrane of urinary bladder OBOL:automatic tunica serosa (vesica urinaria) FMA:15932 FMA:TA tunica serosa vesicae FMA:15932 FMA:TA urinary bladder serous membrane OBOL:automatic A lamina propria that is part of a urinary bladder [Automatically generated definition]. Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue EMAPA:30088 FMA:15935 MA:0001695 NCIT:C48940 UMLS:C1706967 bladder lamina propria bladder lamina propria mucosa bladder lamina propria mucosae lamina propria mucosa of bladder lamina propria mucosa of urinary bladder lamina propria mucosae of bladder lamina propria mucosae of urinary bladder lamina propria of bladder urinary bladder lamina propria urinary bladder lamina propria mucosa urinary bladder lamina propria mucosae uberon UBERON:0001261 lamina propria of urinary bladder A lamina propria that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic UMLS:C1706967 ncithesaurus:Bladder_Lamina_Propria bladder lamina propria OBOL:automatic bladder lamina propria mucosa OBOL:automatic bladder lamina propria mucosae OBOL:automatic lamina propria mucosa of bladder OBOL:automatic lamina propria mucosa of urinary bladder OBOL:automatic lamina propria mucosae of bladder OBOL:automatic lamina propria mucosae of urinary bladder OBOL:automatic lamina propria of bladder OBOL:automatic urinary bladder lamina propria mucosa OBOL:automatic urinary bladder lamina propria mucosae OBOL:automatic An anatomical wall that is part of a intestine [Automatically generated definition]. we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different BTO:0000647 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 NCIT:C49478 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall intestinal wall intestine anatomical wall intestine wall wall of bowel uberon bowel wall UBERON:0001262 wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. OBOL:automatic UMLS:C1708548 ncithesaurus:Intestinal_Wall_Tissue anatomical wall of bowel OBOL:automatic anatomical wall of intestine OBOL:automatic bowel anatomical wall OBOL:automatic bowel wall OBOL:automatic intestine anatomical wall OBOL:automatic wall of bowel OBOL:automatic bowel wall MA:0001525 The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. BTO:0000028 EMAPA:35651 FMA:16011 MA:0002417 NCIT:C49268 SCTID:247604006 UMLS:C0227578 acinus pancreaticus pancreas acinus uberon pancreatic acinar pancreatic acini UBERON:0001263 pancreatic acinus FMA The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. MP:0009145 BTO:0000028 https://github.com/biopragmatics/biomappings UMLS:C0227578 ncithesaurus:Pancreatic_Acinus acinus pancreaticus FMA:16011 pancreatic acini An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] pancreatic As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans AAO:0010112 BTO:0000988 CALOHA:TS-0736 EFO:0000855 EHDAA2:0001367 EHDAA:6893 EMAPA:17503 EV:0100092 FMA:7198 GAID:334 MA:0000120 MAT:0000075 MESH:D010179 MIAA:0000075 NCIT:C12393 SCTID:181277001 TAO:0000140 UMLS:C0030274 VHOG:0000050 Wikipedia:Pancreas XAO:0000136 ZFA:0000140 galen:Pancreas uberon UBERON:0001264 pancreas https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png PMID:16417468 Wikipedia Wikipedia An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. GO:0031016 Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] 2012-06-20 AAO:0010112 AAO AAO:BJB In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000050 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) http://bgee.unil.ch/ As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) PMID:20959416 The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans PMID:16417468 UMLS:C0030274 ncithesaurus:Pancreas A trabecula that is part of a spleen. EMAPA:35808 FMA:16027 MA:0000758 NCIT:C33607 SCTID:61987002 UMLS:C0229688 Wikipedia:Trabeculae_of_spleen spleen trabeculum splenic trabecula trabeculae of spleen uberon UBERON:0001265 trabecula of spleen FMA A trabecula that is part of a spleen. OBOL:automatic UMLS:C0229688 ncithesaurus:Splenic_Trabecula trabeculae of spleen Transudate contained in the peritoneal cavity. BTO:0001031 EMAPA:35683 FMA:16515 MA:0002531 MESH:D001202 Wikipedia:Peritoneal_fluid ncithesaurus:Peritoneal_Fluid uberon UBERON:0001268 peritoneal fluid FMA Transudate contained in the peritoneal cavity. FMA:16515 MESH:D001202 https://github.com/biopragmatics/biomappings The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted]. Cavity for the articulation of the proximal bone of the hind limb.[AAO] During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG] In reptiles and in birds, the acetabula are deep sockets. whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface. AAO:0000770 EHDAA:10661 EMAPA:18346 FMA:16579 GAID:206 MA:0001335 MESH:D000077 NCIT:C32042 RETIRED_EHDAA2:0001427 SCTID:182027007 UMLS:C0000962 VHOG:0000974 Wikipedia:Acetabulum acetabular region acetabulum uberon UBERON:0001269 acetabular part of hip bone http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg FMA Phenoscape FMA The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted]. Wikipedia:Acetabulum Cavity for the articulation of the proximal bone of the hind limb.[AAO] 2012-06-20 AAO:0000770 AAO AAO:LAP During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG] 2012-09-17 VHOG:0000974 VHOG DOI:10.1038/nature04119 Boisvert CA, The pelvic fin and girdle of Panderichthys and the origin of tetrapod locomotion. Nature (2005) http://bgee.unil.ch/ In reptiles and in birds, the acetabula are deep sockets. WP whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface. MA UMLS:C0000962 ncithesaurus:Acetabulum acetabular region VHOG:0000974 acetabulum MA:0001335 A ring of bone formed by the sacrum and the first few coccygeal vertebrae as the roof, the pubis and ischia as the floor and the ilia and the acetabular part of the ischia as the walls. TODO add taxon-specific part of relations connecting sub-structures to this. in FMA, this is part of the axial skeletal system FMA:16580 SCTID:46633002 pelvis ossea skeletal system of pelvis uberon UBERON:0001270 bony pelvis https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb FMA A ring of bone formed by the sacrum and the first few coccygeal vertebrae as the roof, the pubis and ischia as the floor and the ilia and the acetabular part of the ischia as the walls. http://medical-dictionary.thefreedictionary.com/bony+pelvis in FMA, this is part of the axial skeletal system FMA skeletal system of pelvis FMA:16580 The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions. this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 SCTID:360010001 UMLS:C0684083 VSAO:0000304 uberon girdle - pelvic pelvic girdle UBERON:0001271 pelvic girdle region The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions. DOI:10.1002/dvdy.22617 FMA:16581 FMA:23217 UBERONREF:0000003 https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion https://orcid.org/0000-0002-6601-2165 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] 2012-08-14 VSAO:0000304 VSAO https://orcid.org/0000-0002-6601-2165 EMAPA:37862 MA:th UMLS:C0684083 ncithesaurus:Pelvic_Girdle pelvic girdle A fused bone consisting of the ilium, ischium and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified]. currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra. bone of pelvic girdle innominate FMA:16585 GAID:205 SCTID:361776002 Wikipedia:Hip_bone coxal bone hip bone innominate bone os coxa os coxae pelvic bone uberon basipterygium os innominatum UBERON:0001272 innominate bone http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png FMA FMA A fused bone consisting of the ilium, ischium and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified]. Wikipedia:Hip_bone https://github.com/obophenotype/uberon/issues/290 https://orcid.org/0000-0002-6601-2165 The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column WP in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra. FMA bone of pelvic girdle FMA:16585 coxal bone FMA:16585 hip bone FMA:16585 innominate bone FMA:16585 os coxa os coxae FMA:16585 FMA:TA pelvic bone FMA:16585 os innominatum Wikipedia:Hip_bone Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad]. Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO] iliac All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium this is_a hip bone in MA. AAO:0000772 CALOHA:TS-2200 EFO:0003049 EMAPA:18726 FMA:16589 GAID:207 MA:0001336 MESH:D007085 NCIT:C32765 SCTID:182029005 UMLS:C0020889 Wikipedia:Ilium_(bone) galen:Ilium iliac bone ilium bone os iliacum os ilii os ilium uberon illium UBERON:0001273 ilium https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb FMA cjm Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad]. PHENOSCAPE:ad https://github.com/obophenotype/uberon/issues/105 https://github.com/obophenotype/uberon/issues/60 Wikipedia Wikipedia Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO] 2012-06-20 AAO:0000772 AAO AAO:LAP All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium WP this is_a hip bone in MA. MA UMLS:C0020889 ncithesaurus:Ilium iliac bone EMAPA:18726 os ilium FMA:16589 FMA:TA Endochondral bone that is paired, forming the posterior part of the pelvis, articulating with the pubis and ilium. Paired bones of endochondral origin that constitute the posterior elements of the pelvic girdle. They are synostotically fused to each other and form the posterior part of the acetabulum.[AAO] ischial this is_a hip bone in MA; in FMA it is a zone of bone organ. AAO:0000860 EMAPA:18727 FMA:16592 GAID:208 MA:0001337 MESH:D007512 NCIT:C32884 SCTID:182025004 UMLS:C0022122 VSAO:0005006 Wikipedia:Ischium galen:Ischium ischial bone ischium bone uberon os ischii UBERON:0001274 ischium http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb VSAO MA MA cjm Endochondral bone that is paired, forming the posterior part of the pelvis, articulating with the pubis and ilium. VSAO:0005006 VSAO:NI Wikipedia:Ischium Paired bones of endochondral origin that constitute the posterior elements of the pelvic girdle. They are synostotically fused to each other and form the posterior part of the acetabulum.[AAO] 2012-06-20 AAO:0000860 AAO AAO:LAP this is_a hip bone in MA; in FMA it is a zone of bone organ. MA UMLS:C0022122 ncithesaurus:Ischium ischial bone EMAPA:18727 os ischii AAO:0000860 Wikipedia:Ischium A paired endochondral bone making up the anteroventral region of the tripartite pelvic girdle forming part of the ventral edge of the acetabulum. The origin site of many proximal hindlimb muscles. [PHENOSCAPE:ad]. Paired, cartilaginous (ocassionally calcified) elements that form the ventral portion of the pelvic girdle. Each is located ventral to the acetabulum between the anteroventral margin of the ischium and the posteroventral margin of the illium. When the element calcifies or ossifies, its articulation with adjacent elements is difficult to distinguish. Both pubes are synchondrotically fused to one another.[AAO] isa bone zone in FMA AAO:0000861 EMAPA:18728 FMA:16595 MA:0001338 MESH:D011630 NCIT:C33423 SCTID:182035005 UMLS:C0034014 Wikipedia:Pubis_(bone) galen:Pubis uberon os pubis pubic bone pubis bone UBERON:0001275 pubis https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb VSAO MA MA FMA A paired endochondral bone making up the anteroventral region of the tripartite pelvic girdle forming part of the ventral edge of the acetabulum. The origin site of many proximal hindlimb muscles. [PHENOSCAPE:ad]. PHENOSCAPE:ad https://github.com/obophenotype/uberon/issues/68 Paired, cartilaginous (ocassionally calcified) elements that form the ventral portion of the pelvic girdle. Each is located ventral to the acetabulum between the anteroventral margin of the ischium and the posteroventral margin of the illium. When the element calcifies or ossifies, its articulation with adjacent elements is difficult to distinguish. Both pubes are synchondrotically fused to one another.[AAO] 2012-06-20 AAO:0000861 AAO AAO:LAP isa bone zone in FMA FMA UMLS:C0034014 ncithesaurus:Pubic_Bone os pubis Wikipedia:Pubis_(bone) pubic bone Wikipedia:Pubis_(bone) pubis bone Wikipedia:Pubis_(bone) The epithelial layer of the stomach . in FMA this is classified as simple columnar, MA divides this into squamous and glandular BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 SCTID:64977002 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus stomach epithelial tissue stomach epithelium ventriculus epithelial tissue ventriculus epithelium uberon gastric epithelium UBERON:0001276 epithelium of stomach The epithelial layer of the stomach . MP:0000471 in FMA this is classified as simple columnar, MA divides this into squamous and glandular FMA epithelial tissue of stomach OBOL:automatic epithelial tissue of ventriculus OBOL:automatic epithelium of ventriculus OBOL:automatic stomach epithelial tissue OBOL:automatic stomach epithelium OBOL:automatic ventriculus epithelial tissue OBOL:automatic ventriculus epithelium OBOL:automatic gastric epithelium BTO:0000500 Epithelial layer that lines the intestine. Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] BTO:0000781 EMAPA:32873 FMA:17229 MA:0001536 NCIT:C49240 SCTID:266135004 TAO:0005124 UMLS:C0226890 Wikipedia:Intestinal_epithelium ZFA:0005124 bowel epithelial tissue bowel epithelium epithelial tissue of bowel epithelial tissue of intestine epithelium of bowel epithelium of intestine intestine epithelial tissue villous epithelium uberon intestine epithelium UBERON:0001277 intestinal epithelium Epithelial layer that lines the intestine. UBERON:cjm Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005124 TAO ZFIN:curator UMLS:C0226890 ncithesaurus:Intestinal_Epithelium bowel epithelial tissue OBOL:automatic bowel epithelium OBOL:automatic epithelial tissue of bowel OBOL:automatic epithelial tissue of intestine OBOL:automatic epithelium of bowel OBOL:automatic epithelium of intestine OBOL:automatic intestine epithelial tissue OBOL:automatic villous epithelium ZFA:0005124 An epithelium that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2105 EMAPA:35466 FMA:17301 MA:0001545 epithelial tissue of large intestine large intestinal epithelium large intestine epithelial tissue large intestine epithelium uberon UBERON:0001278 epithelium of large intestine An epithelium that is part of a large intestine [Automatically generated definition]. OBOL:automatic epithelial tissue of large intestine OBOL:automatic large intestine epithelial tissue OBOL:automatic A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver. FMA:17523 MA:0002499 NCIT:C33342 SCTID:362192000 UMLS:C0227514 Wikipedia:Portal_triad trias hepatica uberon trias hepatica UBERON:0001279 portal triad https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. ISBN:0-683-40008-8 MGI:csmith MP:0008993 http://orcid.org/0000-0002-6601-2165 UMLS:C0227514 ncithesaurus:Portal_Triad trias hepatica Wikipedia:Portal_triad The functional units of the liver including the lobules. the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] UBERON:0003223 AAO:0010405 EHDAA2:0001004 EHDAA:2201 EMAPA:17203 FMA:17540 MA:0000366 NCIT:C32735 SCTID:363535004 UMLS:C0736268 VHOG:0000539 XAO:0000454 hepatic parenchyma liver parenchyme parenchyma of liver uberon hepatic parenchyme UBERON:0001280 liver parenchyma XAO The functional units of the liver including the lobules. MP:0008986 the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] 2012-09-17 VHOG:0000539 VHOG DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007) http://bgee.unil.ch/ hepatic parenchyma FMA:17540 liver parenchyme XAO:0000454 parenchyma of liver FMA:17540 hepatic parenchyme VHOG:0000539 Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] UBERON:0003275 EHDAA2:0000999 EMAPA:17365 FMA:17543 MA:0000367 NCIT:C32733 SCTID:67435004 TAO:0005091 UMLS:C0227523 VHOG:0000708 Wikipedia:Hepatic_sinusoid ZFA:0005091 liver hepatic sinusoids liver sinusoid liver sinusoidal blood vessel sinusoid of liver sinusoidal blood vessel of liver vas capillare sinusoideum vas sinusoideum uberon hepatic sinusoids UBERON:0001281 hepatic sinusoid https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. Wikipedia:Hepatic_sinusoid ZFIN:curator (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] 2012-09-17 VHOG:0000708 VHOG DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) http://bgee.unil.ch/ UMLS:C0227523 ncithesaurus:Hepatic_Sinusoid liver hepatic sinusoids EHDAA2:0000999 liver sinusoidal blood vessel OBOL:automatic sinusoid of liver OBOL:automatic sinusoidal blood vessel of liver OBOL:automatic vas sinusoideum Wikipedia:Hepatic_sinusoid The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule. Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct) FMA:17545 MA:0002669 NCIT:C32255 SCTID:227002 SCTID:269922006 UMLS:C0227517 Wikipedia:Canals_of_Hering canal of Herring cholangiole ductus interlobularis bilifer uberon canal of Hering canals of Hering duct of Herring intrahepatic bile ductule UBERON:0001282 intralobular bile duct FMA FMA FMA The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule. MGI:csmith MP:0009499 UMLS:C0227517 ncithesaurus:Canal_of_Hering canal of Herring FMA:17545 cholangiole FMA:17545 ductus interlobularis bilifer FMA:17545 FMA:TA canals of Hering Wikipedia:Canals_of_Hering duct of Herring Wikipedia:Canals_of_Hering intrahepatic bile ductule Wikipedia:Canals_of_Hering The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. Functional unit of the kidney that filters waste.[TAO] In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) BTO:0000924 CALOHA:TS-1312 EMAPA:28491 EMAPA:35592 EV:0100384 FMA:17640 GAID:428 MA:0000375 MESH:D009399 NCIT:C13048 SCTID:361337001 TAO:0002153 UMLS:C0027713 Wikipedia:Nephron ZFA:0005282 mature nephron uberon nephroneum tubulus renalis UBERON:0001285 nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png FMA definitional Bgee:AN The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. PMID:9268568 Wikipedia:Nephron Functional unit of the kidney that filters waste.[TAO] 2012-08-14 TAO:0002153 TAO ZFIN:curator In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) GO UMLS:C0027713 ncithesaurus:Nephron mature nephron EMAPA:28491 nephroneum Wikipedia:Nephron tubulus renalis Wikipedia:Nephron The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy. The mucous membrane lining the uterus. [TFD][VHOG] The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] endometrial Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead in FMA this is subdivided into basal and outer BTO:0001422 CALOHA:TS-0276 EFO:0000980 EMAPA:29917 EV:0100115 FMA:17742 GAID:377 MA:0000390 MAT:0000319 MESH:D004717 MIAA:0000319 NCIT:C12313 SCTID:278867007 UMLS:C0014180 VHOG:0001285 Wikipedia:Endometrium tunica mucosa (endometrium) tunica mucosa uteri uterine endometrium uberon uterine mucosa uterine mucous membrane UBERON:0001295 endometrium https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg FMA The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy. MESH:A05.360.319.679.490 MGI:smb MP:0004896 The mucous membrane lining the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001285 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Endometrium The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] 2012-09-17 VHOG:0001285 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 http://bgee.unil.ch/ in FMA this is subdivided into basal and outer FMA UMLS:C0014180 ncithesaurus:Endometrium tunica mucosa (endometrium) FMA:17742 tunica mucosa uteri Wikipedia:Endometrium uterine endometrium BTO:0001422 uterine mucous membrane BTO:0001422 Outer serosa layer of the uterus. TODO - check for parallel structure with peritoneum EMAPA:37792 FMA:17744 MA:0001729 NCIT:C33298 SCTID:253705006 UMLS:C0227824 Wikipedia:Perimetrium perimetrium serous coat of uterus serous membrane of uterus tunica serosa (perimetrium) tunica serosa uteri uterine serosa uterus serosa uterus serous membrane visceral peritoneum of uterus uberon UBERON:0001297 serosa of uterus https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Outer serosa layer of the uterus. Wikipedia:Perimetrium EMAPA:37792 MA:th UMLS:C0227824 ncithesaurus:Perimetrium perimetrium Wikipedia:Perimetrium serous coat of uterus Wikipedia:Perimetrium serous membrane of uterus OBOL:automatic tunica serosa uteri FMA:17744 FMA:TA uterus serous membrane OBOL:automatic The conic expansion of the corpus spongiosum that forms the head of the penis. glans BTO:0003118 EMAPA:18988 EV:0100108 FMA:18247 GAID:0000012 MA:0002726 NCIT:C12324 SCTID:263378009 UMLS:C0227948 VHOG:0001475 Wikipedia:Glans_penis uberon balanus coronal sulcus UBERON:0001299 glans penis http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png Bgee:AN The conic expansion of the corpus spongiosum that forms the head of the penis. MGI:anna MP:0009102 glans EV:0100108 UMLS:C0227948 ncithesaurus:Glans_Penis balanus BTO:0003118 coronal sulcus Wikipedia:Glans_penis The external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. scrotal In elephants the testes remain in the abdomen In hedgehogs the testes remain in the inguinal canal In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field The scrotum of marsupials is not homologous with the scrotum of mammals[ISBN:113945742X] BTO:0003098 CALOHA:TS-2341 EMAPA:19296 FMA:18252 GAID:393 MA:0000409 MESH:D012611 NCIT:C12785 SCTID:265794003 UMLS:C0036471 Wikipedia:Scrotum galen:Scrotum uberon UBERON:0001300 scrotum http://upload.wikimedia.org/wikipedia/commons/a/a6/Scrotum_warm_and_cold.jpg http://upload.wikimedia.org/wikipedia/en/thumb/3/3e/HairedHumanScrotum.png/200px-HairedHumanScrotum.png Wikipedia The external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. ISBN:0-683-40008-8 MP:0002669 Wikipedia:Scrotum In elephants the testes remain in the abdomen PMC1570914 NCBITaxon:9780 In hedgehogs the testes remain in the inguinal canal PMC1570914 NCBITaxon:9363 In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty NCBITaxon:9606 In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens PMID:10984412 NCBITaxon:9263 In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field ISBN:113945742X NCBITaxon:9263 UMLS:C0036471 ncithesaurus:Scrotum The elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens. Kardong has epididymis in elasmobranch epididymal A similar, but probably non-homologous, structure is found in cartilaginous fishes Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells. BTO:0000408 CALOHA:TS-0285 EFO:0000982 EMAPA:19290 EV:0100103 FMA:18255 GAID:397 MA:0000397 MAT:0000130 MESH:D004822 MIAA:0000130 NCIT:C12328 SCTID:181432000 UMLS:C0014533 VHOG:0001265 Wikipedia:Epididymis galen:Epididymis uberon UBERON:0001301 epididymis http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg FMA Wikipedia The elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens. MGI:pvb MP:0002631 A similar, but probably non-homologous, structure is found in cartilaginous fishes WP UMLS:C0014533 ncithesaurus:Epididymis A fallopian tube that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern non-functional in monotremes[ISBN:978-0226870137] EMAPA:37369 FMA:18483 MA:0001717 NCIT:C33475 SCTID:280106006 UMLS:C0227900 right fallopian tube right oviduct uberon UBERON:0001302 right uterine tube https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_R.glb A fallopian tube that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37369 MA:th UMLS:C0227900 ncithesaurus:Right_Fallopian_Tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37368 FMA:18484 MA:0001716 NCIT:C32959 SCTID:280107002 UMLS:C0227902 left fallopian tube left oviduct uberon UBERON:0001303 left uterine tube https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_L.glb A fallopian tube that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37368 MA:th UMLS:C0227902 ncithesaurus:Left_Fallopian_Tube Layer of simple cuboidal cells covering surface of ovary[WP]. BTO:0004483 EHDAA:8126 EMAPA:17963 FMA:18629 MA:0001711 NCIT:C61518 RETIRED_EHDAA2:0001361 SCTID:258308007 UMLS:C0227875 VHOG:0000630 Wikipedia:Germinal_epithelium_(female) epithelium superficiale (ovarium) germinal epithelium (female) ovarian surface epithelium ovary germinal epithelium surface epithelium of ovary uberon female coelomic epithelium ovary surface epithelium UBERON:0001304 Controversial - see article. Requires expert input. Also check BTO placement germinal epithelium of ovary Layer of simple cuboidal cells covering surface of ovary[WP]. PMID:16923182 Wikipedia:Germinal_epithelium_(female) Wikipedia:Talk:Germinal_epithelium_(female) UMLS:C0227875 ncithesaurus:Ovarian_Surface_Epithelium germinal epithelium (female) Wikipedia:Germinal_epithelium_(female) ovarian surface epithelium BTO:0004483 female coelomic epithelium EMAPA:17384 ovary surface epithelium EMAPA:17963 A capsule that surrounds a female gonad. EMAPA:35626 FMA:18662 MA:0001706 NCIT:C49265 SCTID:258491008 UMLS:C0227877 ovarian capsule ovary capsule uberon UBERON:0001307 capsule of ovary A capsule that surrounds a female gonad. OBOL:automatic UMLS:C0227877 ncithesaurus:Ovarian_Capsule The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted]. BTO:0004666 EHDAA2:0000463 EHDAA:4337 EMAPA:17614 FMA:18805 MA:0001973 NCIT:C32558 SCTID:181352000 UMLS:C0226398 Wikipedia:External_iliac_artery galen:ExternalIliacArtery uberon arteria iliaca externa UBERON:0001308 external iliac artery http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray539.png MA The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted]. Wikipedia:External_iliac_artery UMLS:C0226398 ncithesaurus:External_Iliac_Artery arteria iliaca externa Wikipedia:External_iliac_artery The internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted]. BTO:0004667 EMAPA:17860 FMA:18808 MA:0001974 NCIT:C32845 SCTID:181346001 UMLS:C0226364 Wikipedia:Internal_iliac_artery galen:InternalIliacArtery uberon arteria iliaca interna hypogastric artery UBERON:0001309 internal iliac artery http://upload.wikimedia.org/wikipedia/commons/d/d3/Iliac_artery_bifurcation.PNG MA The internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted]. Wikipedia:Internal_iliac_artery UMLS:C0226364 ncithesaurus:Internal_Iliac_Artery arteria iliaca interna Wikipedia:Internal_iliac_artery hypogastric artery BTO:0004667 The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]. todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships BTO:0000841 CALOHA:TS-1077 EHDAA:1026 EHDAA:410 EMAPA:16331 EMAPA:16372 FMA:18820 GAID:516 MA:0002072 MESH:D014469 NCIT:C33827 RETIRED_EHDAA2:0002106 SCTID:261404000 UMLS:C0041632 Wikipedia:Umbilical_artery uberon a. umbilicalis UBERON:0001310 umbilical artery https://github.com/obophenotype/uberon/issues/328 http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]. Wikipedia:Umbilical_artery https://github.com/obophenotype/uberon/issues/328 UMLS:C0041632 ncithesaurus:Umbilical_Artery a. umbilicalis Wikipedia:Umbilical_artery An artery that supplies blood to the upper urinary bladder. The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP] EMAPA:37123 FMA:18839 MA:0002080 NCIT:C52686 SCTID:113268007 UMLS:C0226376 Wikipedia:Superior_vesical_artery arteria vesicali superior arteria vesicalis superior uberon arteriae vesicales superiores UBERON:0001312 superior vesical artery https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG An artery that supplies blood to the upper urinary bladder. http://orcid.org/0000-0002-6601-2165 EMAPA:37123 MA:th UMLS:C0226376 ncithesaurus:Superior_Vesical_Artery arteria vesicali superior Wikipedia:Superior_vesical_artery arteria vesicalis superior Wikipedia:Superior_vesical_artery arteriae vesicales superiores Wikipedia:Superior_vesical_artery A large vein that connects the femoral vein to the common iliac vein. Their origin is at the inferior margin of the inguinal ligaments and they terminate when they join the internal iliac veins (to form the common iliac veins). Both external iliac veins are accompanied along their course by external iliac arteries. [WP,modified]. EHDAA2:0000464 EMAPA:37144 FMA:18883 MA:0002144 NCIT:C32560 SCTID:181400000 UMLS:C0226761 Wikipedia:External_iliac_vein galen:ExternalIliacVein uberon vena iliaca externa UBERON:0001316 external iliac vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif MA A large vein that connects the femoral vein to the common iliac vein. Their origin is at the inferior margin of the inguinal ligaments and they terminate when they join the internal iliac veins (to form the common iliac veins). Both external iliac veins are accompanied along their course by external iliac arteries. [WP,modified]. Wikipedia:External_iliac_vein EMAPA:37144 MA:th UMLS:C0226761 ncithesaurus:External_Iliac_Vein vena iliaca externa Wikipedia:External_iliac_vein A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EHDAA2:0000874 EMAPA:37148 FMA:18884 MA:0002139 MA:0002145 NCIT:C32847 SCTID:181399007 UMLS:C0226764 VHOG:0000749 Wikipedia:Internal_iliac_vein galen:InternalIliacVein uberon hypogastric vein v. hypogastrica v. iliaca interna UBERON:0001317 internal iliac vein http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb MA A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. Wikipedia:Internal_iliac_vein EMAPA:37148 MA:th UMLS:C0226764 ncithesaurus:Internal_Iliac_Vein hypogastric vein MA:0002139 Wikipedia:Internal_iliac_vein v. hypogastrica Wikipedia:Internal_iliac_vein v. iliaca interna Wikipedia:Internal_iliac_vein One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 FMA:18899 MA:0002251 SCTID:424336009 vagina vein vein of vagina uberon UBERON:0001319 vaginal vein http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png FMA/obol One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. Wikipedia:Vaginal_venous_plexus EMAPA:37796 MA:th vagina vein OBOL:automatic vein of vagina OBOL:automatic Muscle (organ) which is a part of the pelvis. Examples: levator ani,. EMAPA:18184 EMAPA:37481 FMA:19086 MA:0000534 muscle organ of pelvis pelvic muscle pelvis muscle pelvis muscle organ uberon UBERON:0001325 muscle of pelvis FMAdef MA Muscle (organ) which is a part of the pelvis. Examples: levator ani,. FMA:19086 EMAPA:37481 MA:th muscle organ of pelvis OBOL:automatic pelvic muscle FMA:19086 pelvis muscle organ OBOL:automatic A portion of a prostate that forms a lobe. Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue BTO:0000548 EMAPA:35712 FMA:19570 MA:0001738 NCIT:C52726 SCTID:279692004 UMLS:C0227970 lobe of prostate gland prostate gland lobe prostatic lobe uberon UBERON:0001328 lobe of prostate A portion of a prostate that forms a lobe. https://github.com/obophenotype/uberon/issues/665 Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue PMID:15163300 https://github.com/obophenotype/uberon/issues/665 UMLS:C0227970 ncithesaurus:Prostate_Gland_Lobe The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]. EMAPA:37385 FMA:19607 MA:0001866 SCTID:279661001 Wikipedia:Pampiniform_venous_plexus pampiniform venous plexus plexus of veins of fascia of prostate plexus venosus pampiniformis venous plexus of fascia of prostate venous plexus of fascia of prostate gland uberon UBERON:0001330 pampiniform plexus http://upload.wikimedia.org/wikipedia/commons/a/af/Gray1147.png The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]. Wikipedia:Pampiniform_venous_plexus EMAPA:37385 MA:th plexus venosus pampiniformis FMA:19607 FMA:TA A zone of skin that is part of a penis [Automatically generated definition]. EMAPA:35675 FMA:19638 MA:0002727 SCTID:35900000 penile skin penis skin penis zone of skin zone of skin of penis uberon UBERON:0001331 skin of penis A zone of skin that is part of a penis [Automatically generated definition]. OBOL:automatic penile skin FMA:19638 penis zone of skin OBOL:automatic zone of skin of penis OBOL:automatic A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. prepuce preputium BTO:0001113 CALOHA:TS-0383 EFO:0001664 EMAPA:18989 EV:0100109 FMA:19639 MA:0000407 NCIT:C33049 SCTID:181426005 UMLS:C0227952 Wikipedia:Foreskin penile prepuce prepuce of male preputium penis uberon foreskin praeputium prepucium UBERON:0001332 prepuce of penis http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg https://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. Wikipedia:Foreskin http://orcid.org/0000-0002-6601-2165 prepuce MA:0000407 Wikipedia:Foreskin preputium HP:0100587 UMLS:C0227952 ncithesaurus:Male_Prepuce penile prepuce FMA:19639 prepuce of male EMAPA:18989 preputium penis FMA:19639 FMA:TA foreskin FMA:19639 praeputium Wikipedia:Foreskin prepucium Wikipedia:Foreskin A urethra that is part of a male reproductive system. BTO:0004089 EMAPA:18692 FMA:19668 MA:0002640 NCIT:C33050 SCTID:264085007 UMLS:C0458452 Wikipedia:Male_urethra uberon UBERON:0001333 male urethra https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png A urethra that is part of a male reproductive system. http://orcid.org/0000-0002-6601-2165 UMLS:C0458452 ncithesaurus:Male_Urethra A urethra that is part of a female reproductive system. BTO:0004088 EMAPA:28747 FMA:19669 MA:0002637 NCIT:C32591 SCTID:264469008 UMLS:C0458485 Wikipedia:Female_urethra uberon urethra feminina urethra muliebris UBERON:0001334 female urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png A urethra that is part of a female reproductive system. http://orcid.org/0000-0002-6601-2165 UMLS:C0458485 ncithesaurus:Female_Urethra urethra feminina BTO:0004088 urethra muliebris BTO:0004088 Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine. NCIT:C12339 paraurethral gland belongs here EMAPA:37784 FMA:19683 MA:0001688 SCTID:279477005 gland of urethra urethra gland urethra gland (male or female) urethral mucuous gland uberon UBERON:0001338 urethral gland MP Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine. MP:anna NCIT:C12339 paraurethral gland belongs here NCIT EMAPA:37784 MA:th gland of urethra OBOL:automatic The tubules in the testes where spermatogenesis occurs. Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO] One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG] Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG] AAO:0010399 BTO:0001235 CALOHA:TS-1239 EFO:0001404 EMAPA:18685 EMAPA:31476 EV:0100380 FMA:19825 GAID:400 MA:0000412 MAT:0000503 MESH:D012671 NCIT:C13047 NCIT:C34293 SCTID:279614002 UMLS:C0036630 UMLS:C1519236 VHOG:0001363 Wikipedia:Seminiferous_tubule XAO:0003088 seminiferous cord seminiferous tubule testis - seminiferous tubule tubuli seminiferi uberon tubuli seminiferi UBERON:0001343 seminiferous tubule of testis http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png Wikipedia The tubules in the testes where spermatogenesis occurs. ISBN:0-683-40008-8 MGI:csmith MP:0002216 https://github.com/obophenotype/uberon/issues/1381 Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO] 2012-06-20 AAO:0010399 AAO AAO:BJB One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG] 2012-09-17 VHOG:0001363 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/SEMINIFEROUS+TUBULE Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG] 2012-09-17 VHOG:0001363 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28 http://bgee.unil.ch/ UMLS:C0036630 ncithesaurus:Seminiferous_Tubule UMLS:C1519236 ncithesaurus:Seminiferous_Cord seminiferous cord EMAPA:18685 tubuli seminiferi Wikipedia:Seminiferous_tubule The epithelial layer of the vagina. FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) BTO:0000422 CALOHA:TS-1325 EMAPA:30991 FMA:19978 MA:0001730 NCIT:C49313 UMLS:C0920840 epithelial tissue of vagina vagina epithelial tissue vagina epithelium vaginal epithelium uberon epithelium, vaginal UBERON:0001344 epithelium of vagina The epithelial layer of the vagina. MP:0001140 FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) FMA UMLS:C0920840 ncithesaurus:Vaginal_Epithelium epithelial tissue of vagina OBOL:automatic vagina epithelial tissue OBOL:automatic epithelium, vaginal BTO:0000422 A collection of caudal vertebrae in the coccygeal region that are fused and part of the bony pelvis. Small, bony element consisting of several fused, rudimentary caudal vertebrae; near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle.[AAO] coccygeal In humans: The coccyx, commonly referred to as the tailbone, is the final segment of the human vertebral column. Comprising three to five separate or fused vertebrae (the coccygeal vertebrae) below the sacrum, it is attached to the sacrum by a fibrocartilaginous joint, the sacrococcygeal symphysis, which permits limited movement between the sacrum and the coccyx. AAO:0000731 EHDAA2:0000259 FMA:20229 GAID:239 MESH:D003050 NCIT:C12696 SCTID:182028002 UMLS:C0009194 Wikipedia:Coccyx galen:Coccyx coccygeal skeleton coccygeal vertebrae I-IV coccyx [coccygeal vertebrae I-IV] coccyx [vertebrae coccygeae I-IV] fused caudal vertebrae fused caudal vertebral column os coccygis uberon os coccygis tailbone UBERON:0001350 coccyx http://upload.wikimedia.org/wikipedia/commons/9/91/Gray100.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb FMA FMA A collection of caudal vertebrae in the coccygeal region that are fused and part of the bony pelvis. https://orcid.org/0000-0002-6601-2165 Small, bony element consisting of several fused, rudimentary caudal vertebrae; near metamorphosis the hypochord fuses to the coccyx, thereby forming the urostyle.[AAO] 2012-06-20 AAO:0000731 AAO AAO:Pugener_2002 AAO:Pugener_and_Maglia_2008 In humans: The coccyx, commonly referred to as the tailbone, is the final segment of the human vertebral column. Comprising three to five separate or fused vertebrae (the coccygeal vertebrae) below the sacrum, it is attached to the sacrum by a fibrocartilaginous joint, the sacrococcygeal symphysis, which permits limited movement between the sacrum and the coccyx. WP,unvetted UMLS:C0009194 ncithesaurus:Coccyx coccygeal skeleton EHDAA2:0000259 coccygeal vertebrae I-IV FMA:20229 coccyx [coccygeal vertebrae I-IV] FMA:20229 coccyx [vertebrae coccygeae I-IV] FMA:20229 FMA:TA fused caudal vertebrae http://orcid.org/0000-0002-6601-2165 fused caudal vertebral column http://orcid.org/0000-0002-6601-2165 os coccygis FMA:20229 FMA:TA os coccygis Wikipedia:Coccyx tailbone FMA:20229 The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue. FMA:20289 MA:0001298 NCIT:C32909 SCTID:362534009 UMLS:C0229289 Wikipedia:Lacrimal_sac lachrymal sac lacrymal sac saccus lacrimalis uberon UBERON:0001351 lacrimal sac http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue. MGI:anna UMLS:C0229289 ncithesaurus:Lacrimal_Sac saccus lacrimalis Wikipedia:Lacrimal_sac A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter. consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct. tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469] subdivision of head in FMA. EHDAA2:0000460 EHDAA:8975 EMAPA:17588 EV:0100356 FMA:61734 GAID:864 MA:0000260 MESH:D004424 NCIT:C12498 SCTID:181178004 UMLS:C0013444 VHOG:0000977 Wikipedia:External_acoustic_meatus galen:ExternalAuditoryMeatus auditory canal ear canal external acoustic tube external auditory canal external auditory tube uberon auditory meatus external auditory meatus UBERON:0001352 external acoustic meatus FMA PMID:11237469 EHDAA2 A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter. Wikipedia:External_acoustic_meatus subdivision of head in FMA. FMA UMLS:C0013444 ncithesaurus:External_Acoustic_Meatus ear canal Wikipedia:Ear_canal external acoustic tube FMA:61734 external auditory tube FMA:61734 auditory meatus EHDAA2:0000460 The anus and surrounding regions. Encompasses both internal and external regions, where present. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 NCIT:C32069 SCTID:362680001 UMLS:C0230120 VHOG:0000395 WBbt:0006919 uberon posterior posterior end of organism UBERON:0001353 anal region https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png cjm The anus and surrounding regions. Encompasses both internal and external regions, where present. https://orcid.org/0000-0002-6601-2165 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000395 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0230120 ncithesaurus:Anal_Region The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted]. EMAPA:37216 FMA:20741 MA:0002027 NCIT:C32436 SCTID:181348000 UMLS:C0226455 Wikipedia:Deep_femoral_artery arteria profunda femoris profunda femoris artery uberon UBERON:0001355 deep femoral artery http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted]. Wikipedia:Deep_femoral_artery EMAPA:37216 MA:th UMLS:C0226455 ncithesaurus:Deep_Femoral_Artery The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted]. EMAPA:37670 FMA:20799 MA:0001996 SCTID:244326008 Wikipedia:Medial_circumflex_femoral_artery medial femoral circumflex artery uberon arteria circumflexa femoris medialis UBERON:0001356 medial circumflex femoral artery http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png FMA The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted]. Wikipedia:Medial_circumflex_femoral_artery EMAPA:37670 MA:th arteria circumflexa femoris medialis Wikipedia:Medial_circumflex_femoral_artery A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6] Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] EHDAA2 models this as developing from CP, which is wrong the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:D002555 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 Wikipedia:Cerebrospinal_fluid ZFA:0001626 CSF cerebral spinal fluid uberon liquor cerebrospinalis spinal fluid UBERON:0001359 cerebrospinal fluid Wikipedia EHDAA2 see notes EHDAA2 A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. Wikipedia:Cerebrospinal_fluid Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] 2012-08-14 TAO:0002184 TAO ZFIN:curator In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] 2012-09-17 VHOG:0001278 VHOG DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005) http://bgee.unil.ch/ EHDAA2 models this as developing from CP, which is wrong EHDAA2 the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. FMA UMLS:C0007806 BIRNLEX:1798 ncithesaurus:Cerebrospinal_Fluid cerebral spinal fluid ZFA:0001626 liquor cerebrospinalis Wikipedia:Cerebrospinal_fluid spinal fluid BTO:0000237 In the human body, the femoral vein is a blood vessel that accompanies the femoral artery in the femoral sheath. It begins at the adductor canal (also known as Hunter's canal) and is a continuation of the popliteal vein. It ends at the inferior margin of the inguinal ligament, where it becomes the external iliac vein. [WP,unvetted]. Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO] AAO:0010237 EMAPA:17876 FMA:21185 GAID:533 MA:0002118 MESH:D005268 NCIT:C12716 SCTID:362071002 UMLS:C0015809 Wikipedia:Femoral_vein galen:FemoralVein uberon vena femoralis UBERON:0001361 femoral vein In the human body, the femoral vein is a blood vessel that accompanies the femoral artery in the femoral sheath. It begins at the adductor canal (also known as Hunter's canal) and is a continuation of the popliteal vein. It ends at the inferior margin of the inguinal ligament, where it becomes the external iliac vein. [WP,unvetted]. Wikipedia:Femoral_vein Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO] 2012-06-20 AAO:0010237 AAO AAO:BJB UMLS:C0015809 ncithesaurus:Femoral_Vein vena femoralis Wikipedia:Femoral_vein The great saphenous vein (GSV), also greater saphenous vein, is the large (subcutaneous) superficial vein of the leg and thigh. The terms 'safaina' (Greek) and 'el safin' (Arabic) have both been claimed as the origin for the word 'saphenous'. [WP,unvetted]. BTO:0003271 EMAPA:37147 FMA:21376 MA:0002216 NCIT:C33004 SCTID:181402008 UMLS:C0392907 Wikipedia:Great_saphenous_vein galen:GreatSaphenousVein galen:GreaterSaphenousVein greater saphenous vein uberon large saphenous vein long saphenous vein vena saphena magna UBERON:0001363 great saphenous vein http://upload.wikimedia.org/wikipedia/commons/5/51/Great_saphenous_vein.png FMA/obol The great saphenous vein (GSV), also greater saphenous vein, is the large (subcutaneous) superficial vein of the leg and thigh. The terms 'safaina' (Greek) and 'el safin' (Arabic) have both been claimed as the origin for the word 'saphenous'. [WP,unvetted]. Wikipedia:Great_saphenous_vein EMAPA:37147 MA:th UMLS:C0392907 ncithesaurus:Long_Saphenous_Vein large saphenous vein BTO:0003271 vena saphena magna Wikipedia:Great_saphenous_vein The joint in the bony pelvis between the sacrum and the ilium of the pelvis, which are joined by strong ligaments. In humans, the sacrum supports the spine and is supported in turn by an ilium on each side EMAPA:19300 FMA:21440 GAID:268 MA:0001506 MESH:D012446 NCIT:C33507 SCTID:182199004 UMLS:C0036036 Wikipedia:Sacroiliac_joint articulatio sacro-iliaca sacroiliac joint uberon UBERON:0001365 sacro-iliac joint http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray319.png FMA The joint in the bony pelvis between the sacrum and the ilium of the pelvis, which are joined by strong ligaments. Wikipedia:Sacroiliac_joint UMLS:C0036036 ncithesaurus:Sacroiliac_Joint The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Peritoneum attached to the abdominal wall.[AAO] UBERON:0004459 AAO:0010816 EMAPA:16591 FMA:21451 SCTID:362700006 TAO:0005131 VHOG:0001527 Wikipedia:Parietal_peritoneum ZFA:0005131 parietal serous membrane of peritoneum uberon peritoneal cavity lining UBERON:0001366 parietal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Wikipedia:Peritoneum#Types http://orcid.org/0000-0002-6601-2165 Peritoneum attached to the abdominal wall.[AAO] 2012-06-20 AAO:0010816 AAO AAO:JMG parietal serous membrane of peritoneum UBERON:cjm A muscle that is part of the region of the hindlimb between the pelvis and ankle. see notes on UBERON:0000978 for possible confusion over the term 'leg'. UBERON:0003270 BTO:0000722 EHDAA:8291 EMAPA:19144 EMAPA:19318 MA:0000672 RETIRED_EHDAA2:0000974 Wikipedia:Leg_muscle leg muscle leg muscle organ leg skeletal muscle leg skeletal muscle tissue muscle of hindlimb zeugopod or stylopod muscle of thigh or crus muscle of upper or lower hindlimb segment muscle of upper/lower leg muscle organ of leg skeletal muscle of leg uberon UBERON:0001383 muscle of leg prolog A muscle that is part of the region of the hindlimb between the pelvis and ankle. Wikipedia:Leg_muscle https://orcid.org/0000-0002-6601-2165 leg muscle organ OBOL:automatic leg skeletal muscle OBOL:automatic leg skeletal muscle tissue OBOL:automatic muscle of hindlimb zeugopod or stylopod OBOL:automatic https://orcid.org/0000-0002-6601-2165 muscle of thigh or crus OBOL:automatic https://orcid.org/0000-0002-6601-2165 muscle of upper or lower hindlimb segment OBOL:automatic https://orcid.org/0000-0002-6601-2165 muscle organ of leg OBOL:automatic skeletal muscle of leg OBOL:automatic Artery that supplies the axilla. In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery. EMAPA:18749 FMA:22654 GAID:473 MA:0002573 MESH:D001366 NCIT:C32169 SCTID:181321001 UMLS:C0004455 Wikipedia:Axillary_artery galen:AxillaryArtery arteria axillaris axillary part of subclavian artery axillary part of trunk of subclavian artery uberon UBERON:0001394 axillary artery https://upload.wikimedia.org/wikipedia/commons/8/88/Axillary_limits.PNG Artery that supplies the axilla. http://orcid.org/0000-0002-6601-2165 UMLS:C0004455 ncithesaurus:Axillary_Artery arteria axillaris Wikipedia:Axillary_artery axillary part of subclavian artery FMA:22654 The subscapular artery, the largest branch of the axillary artery, arises at the lower border of the Subscapularis, which it follows to the inferior angle of the scapula, where it anastomoses with the lateral thoracic and intercostal arteries and with the descending branch of the transverse cervical, and ends in the neighboring muscles. About 4 cm. from its origin it gives off two branches, first the scapular circumflex artery and then the thoracodorsal artery. [WP,unvetted]. EMAPA:37116 FMA:22677 MA:0002050 NCIT:C33650 SCTID:244311006 UMLS:C0226422 Wikipedia:Subscapular_artery uberon arteria subscapularis UBERON:0001397 subscapular artery https://upload.wikimedia.org/wikipedia/commons/4/4c/Axillary_branches.PNG The subscapular artery, the largest branch of the axillary artery, arises at the lower border of the Subscapularis, which it follows to the inferior angle of the scapula, where it anastomoses with the lateral thoracic and intercostal arteries and with the descending branch of the transverse cervical, and ends in the neighboring muscles. About 4 cm. from its origin it gives off two branches, first the scapular circumflex artery and then the thoracodorsal artery. [WP,unvetted]. Wikipedia:Subscapular_artery EMAPA:37116 MA:th UMLS:C0226422 ncithesaurus:Subscapular_Artery arteria subscapularis Wikipedia:Subscapular_artery A zone of skin that is part of a pelvis [Automatically generated definition]. EMAPA:37282 FMA:22984 MA:0000546 SCTID:181517009 pelvic skin pelvis skin pelvis zone of skin zone of skin of pelvis uberon UBERON:0001415 skin of pelvis A zone of skin that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37282 MA:th pelvis zone of skin OBOL:automatic zone of skin of pelvis OBOL:automatic A zone of skin that is part of an abdomen [Automatically generated definition]. EFO:0000214 FMA:22988 FMA:23000 MA:0000523 NCIT:C52758 SCTID:361707007 UMLS:C0222166 abdomen skin abdomen zone of skin abdominal skin skin of abdomen proper zone of skin of abdomen uberon UBERON:0001416 skin of abdomen A zone of skin that is part of an abdomen [Automatically generated definition]. OBOL:automatic UMLS:C0222166 ncithesaurus:Abdominal_Skin abdomen zone of skin OBOL:automatic skin of abdomen proper FMA:22988 zone of skin of abdomen OBOL:automatic A zone of skin that is part of a neck [Automatically generated definition]. EMAPA:37277 FMA:23021 FMA:23022 MA:0000590 NCIT:C52756 SCTID:361705004 UMLS:C0205030 neck (volume) zone of skin neck skin neck zone of skin zone of skin of neck zone of skin of neck (volume) uberon UBERON:0001417 skin of neck A zone of skin that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37277 MA:th UMLS:C0205030 ncithesaurus:Neck_Skin neck (volume) zone of skin OBOL:automatic neck zone of skin OBOL:automatic zone of skin of neck OBOL:automatic zone of skin of neck (volume) OBOL:automatic A zone of skin that is part of a thorax [Automatically generated definition]. EMAPA:37765 FMA:23028 FMA:23029 MA:0000564 SCTID:281723000 thoracic skin thorax skin thorax zone of skin zone of skin of thorax uberon upper body skin UBERON:0001418 skin of thorax A zone of skin that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37765 MA:th thorax zone of skin OBOL:automatic zone of skin of thorax OBOL:automatic A zone of skin that is part of a limb [Automatically generated definition]. EMAPA:32726 FMA:23100 MA:0000694 NCIT:C53276 SCTID:314403009 UMLS:C1282135 limb skin limb zone of skin zone of skin of limb uberon UBERON:0001419 skin of limb A zone of skin that is part of a limb [Automatically generated definition]. OBOL:automatic UMLS:C1282135 ncithesaurus:Skin_of_the_Extremity limb zone of skin OBOL:automatic zone of skin of limb OBOL:automatic An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] EMAPA:37856 FMA:23217 SCTID:229759004 VSAO:0000305 galen:ShoulderGirdle cingulum membri superioris girdle - pectoral cingulum membri superioris shoulder girdle upper limb girdle uberon pectoral girdle pectoral region UBERON:0001421 pectoral girdle region An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. FMA:23217 UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] 2012-08-14 VSAO:0000305 VSAO https://orcid.org/0000-0002-6601-2165 Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] 2012-09-06 VSAO:0000305 VSAO Curator EMAPA:37856 MA:th cingulum membri superioris FMA:23217 FMA:TA cingulum membri superioris FMA:TA shoulder girdle FMA:23217 upper limb girdle FMA:23217 A lymphatic vessel that is part of a face [Automatically generated definition]. FMA:233946 TAO:0005108 ZFA:0005108 buccal lymphatic vessel face lymph vessel face lymphatic vessel lymph vessel of face lymphatic vessel of face uberon FL UBERON:0001422 facial lymphatic vessel A lymphatic vessel that is part of a face [Automatically generated definition]. OBOL:automatic face lymph vessel OBOL:automatic face lymphatic vessel OBOL:automatic lymph vessel of face OBOL:automatic lymphatic vessel of face OBOL:automatic FMA:234865 TAO:0005107 ZFA:0005107 uberon PL UBERON:0001425 pectoral lymphatic vessel PL Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] System that provides physical support to the organism.[AAO] By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] skeletal GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 MA:0000018 NCIT:C12788 TAO:0000434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 skeleton system set of all bones and joints uberon Skelettsystem UBERON:0001434 skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. GO_REF:0000034 VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] 2012-08-14 TAO:0000434 TAO TAO:wd Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] 2012-08-14 VSAO:0000027 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 System that provides physical support to the organism.[AAO] 2012-06-20 AAO:0000566 AAO AAO:LAP By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] 2012-09-17 VHOG:0001254 VHOG DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) http://bgee.unil.ch/ GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates GO UMLS:C0037253 ncithesaurus:Skeletal_System set of all bones and joints Skelettsystem BTO:0001486 A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm]. In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist. EMAPA:25056 FMA:23889 GAID:179 MA:0000296 MESH:D002348 NCIT:C12688 SCTID:83936004 UMLS:C0007285 Wikipedia:Carpus galen:CarpalBone bone of carpus carpal carpal skeleton bone uberon carpus bone UBERON:0001435 carpal bone http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm]. https://orcid.org/0000-0002-6601-2165 In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist. Wikipedia:Carpus UMLS:C0007285 ncithesaurus:Carpal_Bone carpal PHENOSCAPE:ad carpus bone EMAPA:25056 A phalanx that is part of a forelimb autopod[Automatically generated definition]. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO] AAO:0000947 EMAPA:32650 FMA:23914 MA:0000306 NCIT:C52771 SCTID:181976001 SCTID:361100001 UMLS:C0223792 Wikipedia:Phalanges_of_the_hand http://mbe.oxfordjournals.org/content/26/3/613/F1.large.jpg digitus manus phalanx finger phalanx hand digit phalanx hand phalanx manual phalanx phalanx of digit of hand phalanx of digitus manus phalanx of finger phalanx of fore digit phalanx of hand phalanx of hand digit phalanx of manual digit digital bone of manus uberon bone of finger phalanges of fore digit UBERON:0001436 phalanx of manus A phalanx that is part of a forelimb autopod[Automatically generated definition]. Wikipedia:Phalanges_of_the_hand https://orcid.org/0000-0002-6601-2165 Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO] 2012-06-20 AAO:0000947 AAO AAO:LAP UMLS:C0223792 ncithesaurus:Hand_Phalanx digitus manus phalanx OBOL:automatic finger phalanx OBOL:automatic hand digit phalanx OBOL:automatic hand phalanx MA:0000306 phalanx of digit of hand OBOL:automatic phalanx of digitus manus OBOL:automatic phalanx of finger FMA:23914 phalanx of hand digit OBOL:automatic digital bone of manus OBOL:automatic bone of finger FMA:23914 phalanges of fore digit AAO:0000947 The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified]. Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO] Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur. epiphyseal epiphysial AAO:0000742 BTO:0000413 EMAPA:35508 FMA:24012 MA:0001362 MESH:D004838 NCIT:C32529 NCIT:C52722 SCTID:244701002 UMLS:C1708734 Wikipedia:Epiphysis bone epiphysis end of long bone epiphyses long bone epiphysis uberon UBERON:0001437 epiphysis http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified]. MESH:A02.835.232.251 http://orcid.org/0000-0002-6601-2165 Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO] 2012-06-20 AAO:0000742 AAO AAO:Pugener_2002 Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur. FMA:24012 UMLS:C1708734 ncithesaurus:Long_Bone_Epiphysis epiphyses Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]. todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA] EMAPA:35509 FMA:24014 MA:0001363 NCIT:C52723 SCTID:304581004 UMLS:C0222671 Wikipedia:Metaphysis diaphyseal end of long bone long bone metaphysis metaphyses uberon UBERON:0001438 metaphysis Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]. FMA:24014 Wikipedia:Metaphysis Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA] FMA:24014 UMLS:C0222671 ncithesaurus:Metaphysis metaphyses The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle. TODO - find a home for: FMA:24139 ! skeleton of upper limb Skeletal structure of the paired, anterior appendages.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] AAO:0000202 EHDAA2:0002222 EMAPA:32623 FMA:24142 VHOG:0001256 VSAO:0000151 XAO:0003061 bones of upper limb fore limb skeleton forelimb skeleton free upper limb skeleton ossa membri superioris pectoral limb skeleton set of bones of upper limb skeleton of forelimb skeleton of free upper limb skeleton of pectoral limb skeleton of upper limb upper limb skeleton wing skeleton uberon UBERON:0001440 forelimb skeleton FMA The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle. https://orcid.org/0000-0002-6601-2165 Skeletal structure of the paired, anterior appendages.[AAO] 2012-06-20 AAO:0000202 AAO AAO:LAP relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0000202 AAO Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001256 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ forelimb skeleton VHOG:0001256 free upper limb skeleton FMA:24142 ossa membri superioris FMA:24139 FMA:TA skeleton of free upper limb FMA:24142 skeleton of upper limb FMA:24139 upper limb skeleton EHDAA2:0002222 wing skeleton NCBITaxon:8782 OBOL:automatic Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. Skeletal structure of the paired, posterior appendages.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] AAO:0000217 EHDAA2:0002226 EMAPA:32633 FMA:24144 VHOG:0001255 VSAO:0000152 XAO:0003062 bones of lower limb free lower limb skeleton hind limb skeleton hind-limb skeleton hindlimb skeleton lower limb skeleton ossa membri inferioris set of bones of lower limb skeleton of free lower limb skeleton of lower limb uberon UBERON:0001441 TOOD - find a home for: FMA:24140 hindlimb skeleton FMA Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. https://orcid.org/0000-0002-6601-2165 Skeletal structure of the paired, posterior appendages.[AAO] 2012-06-20 AAO:0000217 AAO AAO:LAP relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0000217 AAO Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001255 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ free lower limb skeleton FMA:24144 hind limb skeleton XAO:0003062 hind-limb skeleton VSAO:0000152 hindlimb skeleton VHOG:0001255 ossa membri inferioris FMA:24140 FMA:TA skeleton of free lower limb FMA:24144 skeleton of lower limb FMA:24140 Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EHDAA2:0002227 EMAPA:32643 FMA:24159 VSAO:0005020 anterior autopodium skeleton bones of hand fore autopod skeleton forelimb autopod skeleton hand region skeleton hand skeleton manual skeleton manus skeleton ossa manus set of bones of hand skeleton of hand uberon anterior autopodium manus UBERON:0001442 here 'manus' includes both the wrist region, metatarsal region and acropodial region skeleton of manus EHDAA2 lexical Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape]. PHENOSCAPE:MAH https://github.com/obophenotype/uberon/issues/74 https://orcid.org/0000-0002-6601-2165 bones of hand FMA:24159 hand region skeleton EHDAA2:0002227 hand skeleton FMA:24159 ossa manus FMA:24159 FMA:TA set of bones of hand FMA:24159 skeleton of hand FMA:24159 anterior autopodium VSAO:0005020 VSAO:NI manus VSAO:0005020 VSAO:NI Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. FMA:24216 present in FMA1, but gone in subsequent versions pectoral thoracic BTO:0001368 CALOHA:TS-1039 EFO:0000965 EMAPA:37232 EV:0100010 FMA:9576 GAID:91 MA:0000031 MAT:0000295 MESH:D013909 MIAA:0000295 NCIT:C12799 NCIT:C25389 UMLS:C0817096 UMLS:C1527391 Wikipedia:Chest galen:Chest galen:Thorax anterolateral part of thorax front of thorax pectus ventral part of thoracic region uberon thoracic body wall thorax UBERON:0001443 chest http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg FMA-modified FMA MA Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. FMA:9576 Wikipedia:Chest EMAPA:37232 MA:th UMLS:C0817096 ncithesaurus:Thorax UMLS:C1527391 ncithesaurus:Chest pectus FMA:24816 FMA:TA thoracic body wall MA:0000031 thorax FMA:9576 Wikipedia:Chest FMA:24218 SCTID:123852005 XAO:0000040 head subdivision uberon head region region of head UBERON:0001444 subdivision of head Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EHDAA2:0002228 FMA:24222 VSAO:0005021 foot region skeleton foot skeleton pedal skeleton pes skeleton posterior autopodium skeleton set of bones of foot skeleton of foot uberon pes posterior autopodium UBERON:0001445 here 'pes' includes both the ankle region, metatarsals and acropodial region skeleton of pes EHDAA2 Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]. PHENOSCAPE:MAH https://github.com/obophenotype/uberon/issues/75 https://orcid.org/0000-0002-6601-2165 foot region skeleton EHDAA2:0002228 foot skeleton FMA:24222 set of bones of foot FMA:24222 skeleton of foot FMA:24222 pes VSAO:0005021 VSAO:NI posterior autopodium VSAO:0005021 VSAO:NI The major postaxial endochondral bone in the posterior zeugopod[Phenoscape]. One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO] fibular AAO:0000891 BTO:0002346 CALOHA:TS-2203 EFO:0003052 EMAPA:19141 FMA:24479 GAID:202 MA:0001360 MESH:D005360 NCIT:C12718 SCTID:302529003 UMLS:C0016068 Wikipedia:Fibula galen:Fibula uberon UBERON:0001446 fibula http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg The major postaxial endochondral bone in the posterior zeugopod[Phenoscape]. PHENOSCAPE:mah One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO] 2012-06-20 AAO:0000891 AAO AAO:LAP UMLS:C0016068 ncithesaurus:Fibula A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia. In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment BTO:0002343 EMAPA:25072 FMA:24491 GAID:194 MA:0000297 MESH:D013639 NCIT:C12796 SCTID:108372004 UMLS:C0039316 galen:TarsalBone ankle bone bone of ankle bone of tarsal skeleton bone of tarsus ossa tarsalia ossa tarsi uberon bony tarsus hind mesopodium tarsal tarsus osseus UBERON:0001447 tarsal bone https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia. https://orcid.org/0000-0002-6601-2165 In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment Wikipedia:Tarsus_(skeleton) UMLS:C0039316 ncithesaurus:Tarsal_Bone ankle bone FMA:24491 bone of ankle FMA:24491 bone of tarsal skeleton http://orcid.org/0000-0002-6601-2165 bone of tarsus FMA:24491 ossa tarsalia FMA:71339 FMA:TA ossa tarsi FMA:71339 FMA:TA bony tarsus BTO:0002343 hind mesopodium AAO:0000220 tarsal BTO:0002343 tarsus osseus BTO:0002343 The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted]. BTO:0002347 EMAPA:32940 EMAPA:36159 FMA:24492 GAID:193 MA:0000303 MESH:D008682 NCIT:C12752 SCTID:302532000 UMLS:C0025584 Wikipedia:Metatarsal_bone galen:Metatarsal metatarsal uberon ossa metatarsalia ossa metatarsi UBERON:0001448 metatarsal bone http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png true The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted]. Wikipedia:Metatarsal_bone UMLS:C0025584 ncithesaurus:Metatarsal_Bone ossa metatarsalia BTO:0002347 ossa metatarsi BTO:0002347 A phalanx that is part of a hindlimb autopod[Automatically generated definition]. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO] UBERON:0004272 digital bone of pes AAO:0000930 EMAPA:32941 FMA:24493 MA:0000305 NCIT:C52772 SCTID:302533005 UMLS:C0584876 Wikipedia:Phalanges_of_the_foot ncithesaurus:Phalanx_of_the_Foot digitus pedis phalanx foot digit phalanx foot phalanx pedal phalanx phalanx of digit of foot phalanx of digitus pedis phalanx of foot digit phalanx of hind digit phalanx of pes phalanx of toe toe phalanx uberon bone of toe phalanges of hind digit UBERON:0001449 phalanx of pes A phalanx that is part of a hindlimb autopod[Automatically generated definition]. Wikipedia:Phalanges_of_the_foot https://orcid.org/0000-0002-6601-2165 Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO] 2012-06-20 AAO:0000930 AAO AAO:LAP digital bone of pes OBOL:automatic UMLS:C0584876 ncithesaurus:Foot_Phalanx digitus pedis phalanx OBOL:automatic foot digit phalanx OBOL:automatic foot phalanx MA:0000305 phalanx of digit of foot OBOL:automatic phalanx of digitus pedis OBOL:automatic phalanx of foot digit OBOL:automatic phalanx of toe FMA:24493 toe phalanx OBOL:automatic bone of toe FMA:24493 phalanges of hind digit AAO:0000930 A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. facial The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 NCIT:C13071 SCTID:302549007 UMLS:C0015450 Wikipedia:Face galen:Face uberon facia/facies visage UBERON:0001456 face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). http://orcid.org/0000-0002-6601-2165 Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 http://api.hymao.org/api/ref/67791 NCBITaxon:7399 The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf UMLS:C0015450 ncithesaurus:Face facia/facies Wikipedia:Face visage BTO:0003369 A zone of skin that is part of a lip [Automatically generated definition]. EMAPA:37643 FMA:24764 MA:0001579 NCIT:C12291 SCTID:244092005 UMLS:C0222101 lip skin lip zone of skin zone of skin of lip uberon skin of lips UBERON:0001458 skin of lip A zone of skin that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37643 MA:th UMLS:C0222101 ncithesaurus:Skin_of_the_Lip lip zone of skin OBOL:automatic zone of skin of lip OBOL:automatic skin of lips A zone of skin that is part of a external ear [Automatically generated definition]. EMAPA:35301 FMA:24775 MA:0001233 NCIT:C49481 SCTID:244073008 UMLS:C0222110 auricular region of head zone of skin auricular region zone of skin ear skin external ear skin external ear zone of skin outer ear zone of skin zone of skin of auricular region zone of skin of auricular region of head zone of skin of external ear zone of skin of outer ear uberon UBERON:0001459 skin of external ear A zone of skin that is part of a external ear [Automatically generated definition]. OBOL:automatic UMLS:C0222110 ncithesaurus:Ear_Skin auricular region of head zone of skin OBOL:automatic auricular region zone of skin OBOL:automatic external ear zone of skin OBOL:automatic outer ear zone of skin OBOL:automatic zone of skin of auricular region OBOL:automatic zone of skin of auricular region of head OBOL:automatic zone of skin of external ear OBOL:automatic zone of skin of outer ear OBOL:automatic The part of the forelimb extending from the shoulder to the autopod[cjm]. currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] BTO:0001435 CALOHA:TS-2204 EFO:0001410 EHDAA2:0000140 EHDAA:4164 EHDAA:6210 EHDAA:8275 EMAPA:17413 GAID:52 MA:0000033 MESH:D001132 VHOG:0000339 Wikipedia:Arm uberon brachium upper extremity UBERON:0001460 arm http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg The part of the forelimb extending from the shoulder to the autopod[cjm]. Wikipedia:Arm Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000339 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ brachium Wikipedia:Arm upper extremity MESH:A01.378.800 The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific]. cubital Naming conventions for pod terms under discussion within phenoscape group CALOHA:TS-2222 EFO:0003069 EHDAA2:0000429 EHDAA:4166 EHDAA:6212 EMAPA:17414 FMA:24901 GAID:54 MA:0000036 MESH:D004550 SCTID:76248009 VHOG:0000340 Wikipedia:Elbow galen:Elbow cubital region elbow limb segment elbow region uberon articulatio cubiti UBERON:0001461 elbow https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG EHDAA2 The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific]. Wikipedia:Elbow articulatio cubiti Wikipedia:Elbow 1st (preaxial) digit of the manus[Wikipedia]. Not present in Anurans (Phenotype RCN Oct 2012) This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit). digitus 1 digitus I digitus primus digitus primus [I] AAO:0010639 EHDAA2:0000511 EMAPA:17429 FMA:24938 GAID:58 MA:0000454 MESH:D013933 NCIT:C52834 SCTID:302540006 SCTID:69603001 UMLS:C0040067 Wikipedia:Thumb digit 1 of fore-paw digit 1 of manus finger 1 first digit of hand fore digit I fore limb digit 1 hand digit 1 manual digit 1 manual digit I pollex alula forelimb dewclaw hand digit 1 thumb uberon first finger UBERON:0001463 manual digit 1 http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg https://upload.wikimedia.org/wikipedia/commons/2/2c/Thumbs_up.jpg 1st (preaxial) digit of the manus[Wikipedia]. PMCID:PMC2553264 Wikipedia:Thumb This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit). NCBITaxon:8782 PMID:10220427 PhenoscapeRCN UBERON:0012260 digitus I Wikipedia:Thumb digitus primus Wikipedia:Thumb UMLS:C0040067 ncithesaurus:Hand_Digit_1 digit 1 of fore-paw EMAPA:17429 finger 1 EHDAA2:0000511 fore digit I AAO:0010639 fore limb digit 1 OBOL:accepted hand digit 1 MA:0000454 manual digit I https://github.com/obophenotype/uberon/issues/458 pollex Wikipedia:Thumb alula Wikipedia:Alula forelimb dewclaw Wikipedia:Dewclaw hand digit 1 NCBITaxon:9606 OBOL:accepted thumb first finger EMAPA:17429 The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] coxal See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint BTO:0001457 CALOHA:TS-2226 EFO:0001929 EHDAA2:0000783 EHDAA:5153 EHDAA:6178 EMAPA:17490 FMA:24964 GAID:47 MA:0000045 MESH:D006615 NCIT:C64193 SCTID:302543008 UMLS:C0019552 VHOG:0000346 Wikipedia:Hip galen:Hip hip region regio coxae uberon coxa UBERON:0001464 hip http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg FMA-modified The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. Wikipedia:Hip The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000346 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 http://bgee.unil.ch/ See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint BTO UMLS:C0019552 ncithesaurus:Hip hip region FMA:24964 regio coxae FMA:24964 coxa Wikipedia:Hip A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. BTO:0003595 CALOHA:TS-2220 EHDAA2:0000895 EHDAA:5159 EHDAA:6184 EMAPA:17493 FMA:24974 GAID:48 MA:0000046 MESH:D007717 SCTID:361291001 VHOG:0000347 galen:Knee knee region uberon UBERON:0001465 knee http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. https://orcid.org/0000-0002-6601-2165 A digit that is part of a pes (foot). UBERON:0000027 AAO:0000888 BTO:0002348 EMAPA:32649 FMA:25046 GAID:44 MA:0000048 NCIT:C33788 SCTID:116667001 UMLS:C0040357 Wikipedia:Toe XAO:0003035 galen:Toe digit of foot digit of terminal segment of lower limb digiti pedis digitus pedis foot digit hind digit hind_digit hindlimb digit pedal digit (phalangeal portion) plus soft tissue pes digit toe uberon digiti pedis digitipedis UBERON:0001466 pedal digit http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg PHENOSCAPE:ni A digit that is part of a pes (foot). https://orcid.org/0000-0002-6601-2165 UMLS:C0040357 ncithesaurus:Toe digit of terminal segment of lower limb OBOL:automatic digiti pedis FMA:70664 FMA:TA foot digit MA:0000048 hind digit XAO:0003035 hind_digit AAO:0000888 pedal digit (phalangeal portion) plus soft tissue http://orcid.org/0000-0002-6601-2165 toe FMA:25046 digiti pedis Wikipedia:Toe digitipedis BTO:0002348 A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG] In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone CALOHA:TS-2229 EFO:0003068 EHDAA2:0001834 EHDAA:4180 EHDAA:6228 EMAPA:17421 FMA:25202 GAID:60 MA:0000038 MESH:D012782 NCIT:C25203 SCTID:361103004 UMLS:C0037004 VHOG:0000342 Wikipedia:Shoulder galen:Shoulder shoulder region uberon articulatio humeri UBERON:0001467 shoulder http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG FMA-modified A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). http://orcid.org/0000-0002-6601-2165 (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG] 2012-09-17 VHOG:0000342 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332 http://bgee.unil.ch/ In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone FMA UMLS:C0037004 ncithesaurus:Shoulder articulatio humeri Wikipedia:Shoulder 2 The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments. FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra vertebral joint EMAPA:37622 FMA:25511 MA:0001514 NCIT:C49577 SCTID:244512000 UMLS:C1182940 inter-centrum joint inter-vertebral joint intervertebral symphysis joint of vertebral body uberon UBERON:0001468 intervertebral joint FMA FMA connects successive pairs of centra The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments. http://www.medilexicon.com/medicaldictionary.php?t=87401 FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra FMA EMAPA:37622 MA:th UMLS:C1182940 ncithesaurus:Vertebral_Joint intervertebral symphysis FMA:25511 joint of vertebral body FMA:25511 The sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted]. sternoclavicular EMAPA:19203 FMA:25883 GAID:270 MA:0001507 MESH:D013247 NCIT:C33615 SCTID:182165002 UMLS:C0038291 Wikipedia:Sternoclavicular_articulation sterno clavicular joint sternoclavicular articulation uberon articulatio sternoclavicularis UBERON:0001469 sternoclavicular joint http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png FMA clavicular notch of the manubrium sterni sternal end of the clavicle and first rib The sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted]. Wikipedia:Sternoclavicular_articulation sternoclavicular Wikipedia:Sternoclavicular_articulation UMLS:C0038291 ncithesaurus:Sternoclavicular_Joint sternoclavicular articulation Wikipedia:Sternoclavicular_articulation articulatio sternoclavicularis Wikipedia:Sternoclavicular_articulation The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted]. note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle joint of shoulder shoulder joint EMAPA:19105 FMA:25912 GAID:269 MA:0000459 MESH:D012785 NCIT:C33548 SCTID:182168000 UMLS:C0037009 VHOG:0001002 Wikipedia:Glenohumeral_joint galen:ShoulderJoint articulatio humeri humeral joint uberon humeroscapular joint UBERON:0001470 glenohumeral joint http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png FMA The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted]. Wikipedia:Glenohumeral_joint in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle FMA joint of shoulder OBOL:automatic shoulder joint MA:0000459 UMLS:C0037009 ncithesaurus:Shoulder_Joint articulatio humeri FMA:25912 FMA:TA humeral joint FMA:25912 humeroscapular joint Wikipedia:Glenohumeral_joint The loose fold of skin that covers the penis. EV:0100109 FMA:27648 MA:0001744 SCTID:39059001 VHOG:0001342 foreskin of penis penis foreskin preputial skin uberon UBERON:0001471 skin of prepuce of penis The loose fold of skin that covers the penis. MP:0003553 NCBI:matt The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]. EMAPA:37801 FMA:29713 MA:0002257 SCTID:294653003 Wikipedia:Vaginal_venous_plexus venous vaginal plexus uberon plexus venosus vaginalis UBERON:0001472 vaginal venous plexus http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]. Wikipedia:Vaginal_venous_plexus EMAPA:37801 MA:th plexus venosus vaginalis Wikipedia:Vaginal_venous_plexus A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] A vessel that contains or conveys lymph.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] AAO:0011005 BTO:0000752 CALOHA:TS-2102 EFO:0000873 EMAPA:35532 FMA:30315 MA:0000138 MAT:0000443 MESH:D042601 NCIT:C33038 SCTID:279089004 TAO:0005105 UMLS:C0229889 VHOG:0001249 Wikipedia:Lymphatic_vessel XAO:0000375 lymph vessel uberon vas lymphaticum UBERON:0001473 lymphatic vessel http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. BTO:0000752 Wikipedia:Lymphatic_vessel DOI:10.1152/japplphysiol.00201.2013 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] 2012-08-14 TAO:0005105 TAO ZFIN:curator A vessel that contains or conveys lymph.[AAO] 2012-06-20 AAO:0011005 AAO AAO:EJS Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] 2012-09-17 VHOG:0001249 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627 http://bgee.unil.ch/ MESH:D042601 https://github.com/biopragmatics/biomappings UMLS:C0229889 ncithesaurus:Lymphatic_Vessel vas lymphaticum Wikipedia:Lymphatic_vessel Skeletal element that is composed of bone tissue. Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 SCTID:90780006 TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 Wikipedia:Bone XAO:0000169 ZFA:0001514 galen:Bone bone organ uberon bone bones UBERON:0001474 bone element VSAO-modified Skeletal element that is composed of bone tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000057 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] 2012-06-20 AAO:0000047 AAO AAO:LAP Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] 2012-08-14 TAO:0001514 TAO ZFIN:curator Skeletal element that is composed of bone tissue.[VSAO] 2012-08-14 VSAO:0000057 VSAO PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000047 AAO The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] 2012-09-17 VHOG:0001190 VHOG DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) http://bgee.unil.ch/ UMLS:C0262950 ncithesaurus:Bone bone organ FMA:5018 bone AEO:0000082 BTO:0000140 MA:0001459 VHOG:0001190 bones ZFA:0001514 A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized]. Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO] AAO:0010716 EFO:0001412 EHDAA2:0000339 EMAPA:18177 FMA:32521 MA:0002286 NCIT:C32446 SCTID:181620007 UMLS:C0224234 VHOG:0000846 Wikipedia:Deltoid_muscle deltoid muscle m. deltoideus musculus deltoideus uberon common shoulder muscle deltoideus deltoideus muscle musculus deltoideus UBERON:0001476 We use a generic definition that includes the deltoideus as represented in AAO: 'Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus'. Kardong: Dorsal group deltoid http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png FMA EHDAA2 dbpedia EHDAA2 FMA the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula dbpedia the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula dbpedia the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula dbpedia deltoid tuberosity of humerus dbpedia dbpedia A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized]. FMA:32521 http://orcid.org/0000-0002-6601-2165 Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO] 2012-06-20 AAO:0010716 AAO AAO:MEJ UMLS:C0224234 ncithesaurus:Deltoid deltoid muscle Wikipedia:Deltoid_muscle m. deltoideus AAO:0010716 musculus deltoideus Wikipedia:Deltoid_muscle common shoulder muscle Wikipedia:Deltoid_muscle deltoideus Wikipedia:Deltoid_muscle deltoideus muscle Wikipedia:Deltoid_muscle musculus deltoideus Wikipedia:Deltoid_muscle A sesamoid element that is composed of bone tissue. sesamoid AEO:0000086 EHDAA2:0003086 EMAPA:36620 FMA:32672 GAID:210 MA:0001375 MESH:D012716 NCIT:C33541 SCTID:362914002 UMLS:C0036846 Wikipedia:Sesamoid_bone galen:SessamoidBone ossa sesamoidea uberon UBERON:0001479 Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage.[VSAO] sesamoid bone http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png UBERON:cjm A sesamoid element that is composed of bone tissue. http://orcid.org/0000-0002-6601-2165 UMLS:C0036846 ncithesaurus:Sesamoid_Bone ossa sesamoidea Wikipedia:Sesamoid_bone A carpal bone that proximally_connected_to a forelimb zeugopod skeleton. EMAPA:36164 FMA:33302 MA:0002557 SCTID:306715004 uberon UBERON:0001480 proximal carpal bone A carpal bone that proximally_connected_to a forelimb zeugopod skeleton. OBOL:automatic Any muscle organ that is part of a shoulder [Automatically generated definition]. EMAPA:36154 FMA:33531 MA:0000633 muscle organ of shoulder shoulder muscle shoulder muscle organ uberon UBERON:0001482 muscle of shoulder prolog Any muscle organ that is part of a shoulder [Automatically generated definition]. OBOL:automatic muscle organ of shoulder OBOL:automatic shoulder muscle organ OBOL:automatic A zone of skin that is part of a shoulder region. in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon EMAPA:18059 FMA:34830 MA:0000635 SCTID:244131002 shoulder skin shoulder zone of skin zone of skin of shoulder uberon UBERON:0001483 skin of shoulder A zone of skin that is part of a shoulder region. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon MA shoulder zone of skin OBOL:automatic zone of skin of shoulder OBOL:automatic An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita EMAPA:37621 FMA:34836 GAID:263 MA:0001519 MESH:D017746 NCIT:C32259 NCIT:C84388 SCTID:182238002 UMLS:C0206207 Wikipedia:Articular_capsule galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. Wikipedia:Articular_capsule check ncita ncit EMAPA:37621 MA:th UMLS:C0206207 ncithesaurus:Joint_Capsule capsula articularis FMA:34836 FMA:TA capsulae articulares Wikipedia:Articular_capsule The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. EFO:0001957 EMAPA:19137 FMA:35175 GAID:114 MA:0000471 MESH:D007719 NCIT:C32898 SCTID:182204005 UMLS:C0022745 VHOG:0001003 Wikipedia:Knee galen:KneeJoint joint of knee uberon articulatio genus UBERON:0001485 knee joint http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg definitional The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. Wikipedia:Knee UMLS:C0022745 ncithesaurus:Knee_Joint joint of knee OBOL:automatic articulatio genus Wikipedia:Knee A synovial joint that connects the femur to the acetbulum of the innominate bone. BTO:0001502 EMAPA:19136 FMA:35178 GAID:262 MA:0000470 MESH:D006621 NCIT:C32742 SCTID:182201002 UMLS:C0019558 VHOG:0001001 Wikipedia:Hip#Articulation galen:HipJoint articulatio coxofemoralis femoro-iliac joint uberon coxal articulation UBERON:0001486 hip joint FMA FMA definitional A synovial joint that connects the femur to the acetbulum of the innominate bone. http://orcid.org/0000-0002-6601-2165 UMLS:C0019558 ncithesaurus:Hip_Joint articulatio coxofemoralis FMA:35178 coxal articulation Wikipedia:Hip A skeletal joint that is part of a pes [Automatically generated definition]. TODO check FMA - use the set class for now EMAPA:32949 FMA:35194 GAID:256 MA:0000464 MESH:D033023 SCTID:244555001 Wikipedia:Joints_of_foot articulationes pedis foot joint hind limb autopod joint joint of pes joint of terminal segment of free lower limb joints of foot pedal joint uberon UBERON:0001487 pes joint A skeletal joint that is part of a pes [Automatically generated definition]. OBOL:automatic articulationes pedis FMA:71349 FMA:TA hind limb autopod joint OBOL:automatic joint of terminal segment of free lower limb OBOL:automatic joints of foot FMA:71349 A joint that connects the hindlimb autopod and zeugopod skeletons. todo - accurately represent different types of ankle joint BTO:0004706 EMAPA:35126 FMA:35195 GAID:257 MA:0000463 MESH:D000843 NCIT:C32078 SCTID:182212002 UMLS:C0003087 Wikipedia:Ankle galen:AnkleJoint gambrel hock hock joint talotibial joint uberon mortise joint talocrural articulation talocrural joint UBERON:0001488 ankle joint https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg A joint that connects the hindlimb autopod and zeugopod skeletons. MESH:A02.835.583.378.062 Wikipedia:Ankle https://orcid.org/0000-0002-6601-2165 UMLS:C0003087 ncithesaurus:Ankle_Joint gambrel Wikipedia:Hock_(anatomy) hock Wikipedia:Hock_(anatomy) hock joint Wikipedia:Hock_(anatomy) talotibial joint Wikipedia:Ankle mortise joint BTO:0004706 talocrural articulation Wikipedia:Ankle talocrural joint Wikipedia:Ankle A skeletal joint that is part of a manus (hand) [Automatically generated definition]. TODO check FMA - use the set class for now EMAPA:32641 MA:0000452 SCTID:244546004 Wikipedia:Joints_of_hand articulationes manus hand joint joint of hand joint of manus joint of terminal segment of free upper limb manual joint uberon UBERON:0001489 manus joint A skeletal joint that is part of a manus (hand) [Automatically generated definition]. OBOL:automatic articulationes manus FMA:71345 FMA:TA joint of terminal segment of free upper limb OBOL:automatic A joint that connects the forelimb zeugopod and stylopod skeletons[Obol]. In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis EMAPA:19102 FMA:35289 GAID:253 MA:0000451 MESH:D004551 NCIT:C32497 SCTID:182169008 UMLS:C0013770 VHOG:0000997 Wikipedia:Elbow galen:ElbowJoint articulatio cubiti cubital region joint joint of cubital region joint of elbow uberon UBERON:0001490 elbow joint definitional A joint that connects the forelimb zeugopod and stylopod skeletons[Obol]. Wikipedia:Elbow https://orcid.org/0000-0002-6601-2165 In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis HP UMLS:C0013770 ncithesaurus:Elbow_Joint articulatio cubiti cubital region joint OBOL:automatic joint of cubital region OBOL:automatic joint of elbow OBOL:automatic A joint connecting the forelimb zeugopod skeleton with the carpal skeleton. in FMA this includes radio-carpal and radio-ulnar *ligaments* EMAPA:19205 FMA:321842 GAID:274 MA:0000460 MESH:D014955 NCIT:C33894 SCTID:182178002 UMLS:C1322271 Wikipedia:Wrist galen:WristJoint carpal region joint joint of carpal region joint of wrist radiocarpal joint uberon UBERON:0001491 wrist joint https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png A joint connecting the forelimb zeugopod skeleton with the carpal skeleton. Wikipedia:Wrist https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/?group_id=76834&atid=1205376 in FMA this includes radio-carpal and radio-ulnar *ligaments* FMA UMLS:C1322271 ncithesaurus:Wrist_Joint carpal region joint OBOL:automatic joint of carpal region OBOL:automatic radiocarpal joint FMA:35291 The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted]. EMAPA:18802 FMA:37072 MA:0001166 NCIT:C52817 SCTID:181009006 UMLS:C0228885 Wikipedia:Axillary_nerve circumflex humeral nerve uberon auxillery nerve circumflex nerve nervus axillaris UBERON:0001493 axillary nerve http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg MA The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted]. Wikipedia:Axillary_nerve UMLS:C0228885 ncithesaurus:Axillary_Nerve auxillery nerve Wikipedia:Axillary_nerve circumflex nerve Wikipedia:Axillary_nerve nervus axillaris Wikipedia:Axillary_nerve The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]. EHDAA2:0000147 EHDAA:9828 EMAPA:17014 FMA:3736 MA:0002570 NCIT:C32150 SCTID:181299009 UMLS:C0003956 Wikipedia:Ascending_aorta ascending thoracic aorta pars ascendens aortae uberon aorta ascendens pars ascendens aortae UBERON:0001496 ascending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb EHDAA2 The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]. GO:0035905 Wikipedia:Ascending_aorta UMLS:C0003956 ncithesaurus:Ascending_Aorta ascending thoracic aorta EMAPA:17014 aorta ascendens Wikipedia:Ascending_aorta pars ascendens aortae Wikipedia:Ascending_aorta Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 EHDAA:8326 EMAPA:18184 EMAPA:18185 FMA:37367 MA:0000537 RETIRED_EHDAA2:0001430 girdle-pelvic muscle organ muscle organ of girdle-pelvic muscle organ of pelvic girdle muscle organ of pelvic girdle bone pelvic girdle muscle pelvic girdle muscle organ pelvic girdle skeletal muscle uberon UBERON:0001497 muscle of pelvic girdle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. MA girdle-pelvic muscle organ OBOL:automatic muscle organ of girdle-pelvic OBOL:automatic muscle organ of pelvic girdle OBOL:automatic muscle organ of pelvic girdle bone OBOL:automatic pelvic girdle muscle organ OBOL:automatic pelvic girdle skeletal muscle EMAPA:18185 Any muscle organ that is part of a pes [Automatically generated definition]. BTO:0000477 EMAPA:36160 FMA:37369 MA:0000652 SCTID:67240005 foot muscle foot muscle organ muscle of foot muscle organ of foot uberon UBERON:0001498 muscle of pes prolog Any muscle organ that is part of a pes [Automatically generated definition]. OBOL:automatic foot muscle organ OBOL:automatic muscle of foot FMA:37369 muscle organ of foot OBOL:automatic A muscle organ that is part of an arm [Automatically generated definition]. See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand) UBERON:0003272 EHDAA:8277 EMAPA:36053 MA:0000594 RETIRED_EHDAA2:0000142 arm muscle arm skeletal muscle arm skeletal muscle tissue muscle of upper arm or lower arm upper arm / lower arm muscle uberon arm muscle system UBERON:0001499 muscle of arm https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A muscle organ that is part of an arm [Automatically generated definition]. OBOL:automatic arm muscle MA:0000594 arm skeletal muscle OBOL:automatic arm skeletal muscle tissue OBOL:automatic muscle of upper arm or lower arm https://orcid.org/0000-0002-6601-2165 upper arm / lower arm muscle https://orcid.org/0000-0002-6601-2165 arm muscle system EHDAA2:0000141 Any muscle organ that is part of a manus [Automatically generated definition]. EMAPA:32644 FMA:37372 MA:0000628 SCTID:110540008 hand muscle manus muscle manus muscle organ muscle of hand muscle organ of manus uberon UBERON:0001500 muscle of manus prolog Any muscle organ that is part of a manus [Automatically generated definition]. OBOL:automatic hand muscle MA:0000628 manus muscle organ OBOL:automatic muscle of hand FMA:37372 muscle organ of manus OBOL:automatic The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery. Do not confuse with aortic arch The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] birds have right aortic arch, mammals left. BTO:0000157 EFO:0002526 EHDAA2:0000132 EMAPA:17613 FMA:3768 GAID:471 MA:0000475 SCTID:181300001 VHOG:0001196 Wikipedia:Arch_of_aorta arcus aortae uberon aortic arch thoracic aorta UBERON:0001508 arch of aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb left arch 4 in human embryology.ch The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery. ISBN:0-683-40008-8 MP:0004113 The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] 2012-09-17 VHOG:0001196 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/arch+of+aorta The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] 2012-09-17 VHOG:0001196 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20 http://bgee.unil.ch/ arcus aortae FMA:3768 FMA:TA aortic arch FMA:3768 thoracic aorta GAID:471 A zone of skin that is part of a knee [Automatically generated definition]. EMAPA:18151 FMA:37800 MA:0000668 NCIT:C64859 SCTID:181552001 UMLS:C0222275 knee skin knee zone of skin zone of skin of knee uberon UBERON:0001510 skin of knee A zone of skin that is part of a knee [Automatically generated definition]. OBOL:automatic UMLS:C0222275 ncithesaurus:Knee_Skin knee zone of skin OBOL:automatic zone of skin of knee OBOL:automatic A zone of skin that is part of a leg [Automatically generated definition]. EMAPA:18156 EMAPA:18159 EMAPA:37352 FMA:37828 MA:0000674 NCIT:C52749 UMLS:C0222279 leg skin leg zone of skin zone of skin of leg uberon UBERON:0001511 skin of leg A zone of skin that is part of a leg [Automatically generated definition]. OBOL:automatic EMAPA:37352 MA:th UMLS:C0222279 ncithesaurus:Leg_Skin leg zone of skin OBOL:automatic zone of skin of leg OBOL:automatic A zone of skin that is part of an ankle [Automatically generated definition]. EMAPA:37353 FMA:37831 MA:0000641 NCIT:C52751 SCTID:181560000 UMLS:C0222286 ankle skin ankle zone of skin tarsal region skin zone of skin of ankle uberon UBERON:0001512 skin of ankle A zone of skin that is part of an ankle [Automatically generated definition]. OBOL:automatic EMAPA:37353 MA:th UMLS:C0222286 ncithesaurus:Ankle_Skin ankle zone of skin OBOL:automatic tarsal region skin https://orcid.org/0000-0002-6601-2165 zone of skin of ankle OBOL:automatic A zone of skin that is part of a pes [Automatically generated definition]. EMAPA:18504 FMA:37834 MA:0000654 NCIT:C52750 SCTID:181529000 UMLS:C0222289 foot skin skin of foot skin of hind-paw uberon UBERON:0001513 skin of pes MA A zone of skin that is part of a pes [Automatically generated definition]. OBOL:automatic UMLS:C0222289 ncithesaurus:Foot_Skin skin of foot FMA:37834 skin of hind-paw EMAPA:18504 The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. results from fusion of left and right dorsal aortae EMAPA:18606 FMA:3784 MA:0002571 NCIT:C32455 SCTID:261399002 UMLS:C0011666 Wikipedia:Descending_aorta pars descendens aortae uberon aorta descendens pars descendens aortae UBERON:0001514 descending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA Wikipedia The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. GO:0035906 Wikipedia:Descending_aorta UMLS:C0011666 ncithesaurus:Descending_Aorta pars descendens aortae FMA:3784 aorta descendens Wikipedia:Descending_aorta pars descendens aortae Wikipedia:Descending_aorta The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. BTO:0000157 EFO:0002525 EMAPA:18603 FMA:3786 GAID:471 MA:0002569 MESH:D001013 NCIT:C33766 SCTID:302510009 UMLS:C1522460 Wikipedia:Thoracic_aorta galen:ThoracicAorta aorta thoracica thoracic part of aorta uberon aorta thoracalis pars thoracica aortae UBERON:0001515 thoracic aorta http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png FMA The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. MP:0010468 http://www.medterms.com UMLS:C1522460 ncithesaurus:Thoracic_Aorta aorta thoracica FMA:3786 FMA:TA aorta thoracalis Wikipedia:Thoracic_aorta pars thoracica aortae Wikipedia:Thoracic_aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates BTO:0002976 EFO:0002524 EMAPA:17856 FMA:3789 GAID:470 MA:0000474 MESH:D001012 NCIT:C32038 SCTID:244231007 UMLS:C0003484 Wikipedia:Abdominal_aorta galen:AbdominalAorta abdominal part of aorta descending abdominal aorta pars abdominalis aortae uberon abdominal part of aorta aorta abdominalis pars abdominalis aortae UBERON:0001516 abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png FMA Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. BTO:0002976 Wikipedia:Abdominal_aorta UMLS:C0003484 ncithesaurus:Abdominal_Aorta abdominal part of aorta FMA:3789 descending abdominal aorta FMA:3789 pars abdominalis aortae FMA:3789 abdominal part of aorta BTO:0002976 aorta abdominalis BTO:0002976 Wikipedia:Abdominal_aorta pars abdominalis aortae BTO:0002976 Wikipedia:Abdominal_aorta A zone of skin that is part of a elbow [Automatically generated definition]. UBERON:0003399 EMAPA:18051 FMA:38250 MA:0000610 NCIT:C52755 SCTID:181534001 UMLS:C0222213 cubital region zone of skin elbow skin elbow zone of skin zone of skin of cubital region zone of skin of elbow uberon UBERON:0001517 skin of elbow A zone of skin that is part of a elbow [Automatically generated definition]. OBOL:automatic UMLS:C0222213 ncithesaurus:Elbow_Skin cubital region zone of skin OBOL:automatic elbow zone of skin OBOL:automatic zone of skin of cubital region OBOL:automatic zone of skin of elbow OBOL:automatic A zone of skin that is part of a wrist [Automatically generated definition]. EMAPA:37351 FMA:38280 MA:0000638 NCIT:C52752 SCTID:181540008 UMLS:C0222223 carpal region zone of skin wrist skin wrist zone of skin zone of skin of carpal region zone of skin of wrist uberon UBERON:0001518 skin of wrist A zone of skin that is part of a wrist [Automatically generated definition]. OBOL:automatic EMAPA:37351 MA:th UMLS:C0222223 ncithesaurus:Wrist_Skin carpal region zone of skin OBOL:automatic wrist zone of skin OBOL:automatic zone of skin of carpal region OBOL:automatic zone of skin of wrist OBOL:automatic A zone of skin that is part of a manus [Automatically generated definition]. EMAPA:18486 FMA:38295 MA:0000630 NCIT:C52753 SCTID:181527003 UMLS:C0222224 hand skin manus skin skin of hand skin of fore-paw uberon UBERON:0001519 skin of manus A zone of skin that is part of a manus [Automatically generated definition]. OBOL:automatic UMLS:C0222224 ncithesaurus:Hand_Skin hand skin MA:0000630 skin of hand FMA:38295 skin of fore-paw EMAPA:18486 The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery. innominate EFO:0002550 EHDAA2:0000835 EMAPA:17615 FMA:3932 GAID:476 MA:0001922 MESH:D016122 NCIT:C32814 SCTID:244244002 UMLS:C0006094 Wikipedia:Brachiocephalic_artery galen:BrachioCephalicArtery brachiocephalic trunk innominate artery truncus brachiocephalicus uberon truncus brachiocephalicus UBERON:0001529 brachiocephalic artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery. MGI:csmith MP:0010663 innominate Wikipedia:Brachiocephalic_artery UMLS:C0006094 ncithesaurus:Innominate_Artery brachiocephalic trunk MA:0001922 innominate artery Wikipedia:Brachiocephalic_artery truncus brachiocephalicus FMA:3932 FMA:TA truncus brachiocephalicus Wikipedia:Brachiocephalic_artery A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery' This class represents the adult and developing structures' in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae carotid artery CALOHA:TS-0116 EHDAA2:0000217 EHDAA:7331 EMAPA:17855 FMA:3939 GAID:479 MA:0001926 MESH:D017536 NCIT:C32352 SCTID:362041005 UMLS:C0162859 VHOG:0000272 Wikipedia:Common_carotid_artery carotid artery system common carotid artery trunk of common carotid tree uberon a. carotis communis UBERON:0001530 common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA Wikipedia A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. Wikipedia:Common_carotid_artery carotid artery FMA:3939 UMLS:C0162859 ncithesaurus:Common_Carotid_Artery carotid artery system EHDAA2:0000217 common carotid artery FMA:3939 trunk of common carotid tree FMA:3939 a. carotis communis Wikipedia:Common_carotid_artery The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35749 FMA:3941 MA:0001928 NCIT:C33473 SCTID:362042003 UMLS:C0226086 Wikipedia:Right_common_carotid_artery right common carotid artery trunk of right common carotid tree uberon right common carotid artery UBERON:0001531 right common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. UBERON:cjm UMLS:C0226086 ncithesaurus:Right_Common_Carotid_Artery right common carotid artery MA:0001928 trunk of right common carotid tree FMA:3941 right common carotid artery FMA:3941 A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP]. Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] AAO:0010219 AAO:0011054 BTO:0004697 EFO:0001952 EHDAA2:0000873 EHDAA:408 EHDAA:6389 EMAPA:16328 FMA:3947 GAID:481 MA:0001930 MESH:D002343 NCIT:C32836 SCTID:362045001 TAO:0005081 UMLS:C0007276 VHOG:0000267 Wikipedia:Internal_carotid_artery XAO:0000366 ZFA:0005081 cranial carotid artery internal carotid uberon ICA arteria carotis interna UBERON:0001532 internal carotid artery http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png MA cjm FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP]. MGI:anna Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] 2012-09-17 VHOG:0000267 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Internal+carotid+artery One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] 2012-06-20 AAO:0011054 AAO PMID:12606281 UMLS:C0007276 ncithesaurus:Internal_Carotid_Artery cranial carotid artery ZFA:0005081 internal carotid AAO:0010219 ICA arteria carotis interna Wikipedia:Internal_carotid_artery One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta. Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO] In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP] The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO] AAO:0010232 EHDAA2:0001933 EHDAA:4357 EMAPA:17617 FMA:3951 GAID:511 MA:0002045 MESH:D013348 NCIT:C33643 SCTID:265790007 TAO:0005086 UMLS:C0038530 Wikipedia:Subclavian_artery XAO:0000365 ZFA:0005086 arteria subclavia arterial tree of upper limb pectoral artery subclavian arterial tree uberon PA arteria subclavia UBERON:0001533 subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg EHDAA2 EHDAA2 One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta. ISBN:0073040584 https://orcid.org/0000-0002-6601-2165 Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO] 2012-06-20 AAO:0010232 AAO AAO:BJB In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP] Wikipedia:Subclavian_artery The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO] 2012-08-14 TAO:0005086 TAO ZFIN:curator UMLS:C0038530 ncithesaurus:Subclavian_Artery arteria subclavia XAO:0000365 PA arteria subclavia Wikipedia:Subclavian_artery The subclavian artery that supplies the right pectoral appendage. in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery proximal part arises from right 4th aortic arch in humans EHDAA2:0004514 EMAPA:37384 FMA:3953 MA:0002047 NCIT:C33490 SCTID:244246000 UMLS:C0226261 Wikipedia:Subclavian_artery arteria subclavia dextra uberon UBERON:0001534 right subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg The subclavian artery that supplies the right pectoral appendage. http://orcid.org/0000-0002-6601-2165 EMAPA:37384 MA:th UMLS:C0226261 ncithesaurus:Right_Subclavian_Artery arteria subclavia dextra FMA:3953 FMA:TA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35491 FMA:4058 MA:0001927 NCIT:C32956 SCTID:362043008 UMLS:C0226087 Wikipedia:Left_common_carotid_artery left common carotid artery trunk of left common carotid tree uberon left common carotid artery UBERON:0001536 left common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. UBERON:cjm UMLS:C0226087 ncithesaurus:Left_Common_Carotid_Artery left common carotid artery MA:0001927 trunk of left common carotid tree FMA:4058 left common carotid artery FMA:4058 The popliteal vein course runs alongside the popliteal artery but carries the blood from the knee joint and muscles in the thigh and calf back to the heart. Its origin is defined by the junction of the posterior tibial vein and anterior tibial vein. It drains the peroneal vein before reaching the knee joint and turns into the femoral vein when leaving the adductor canal (also known as Hunter's canal). The popliteal artery extends from the femoral artery behind the popliteal fossa which is the space behind the knee. [WP,unvetted]. EMAPA:37181 FMA:44327 GAID:537 MA:0002197 MESH:D011152 NCIT:C33339 SCTID:281065001 UMLS:C0032652 Wikipedia:Popliteal_vein galen:PoplitealVein uberon vena poplitea UBERON:0001544 popliteal vein http://upload.wikimedia.org/wikipedia/commons/6/66/Gray609.png FMA/obol The popliteal vein course runs alongside the popliteal artery but carries the blood from the knee joint and muscles in the thigh and calf back to the heart. Its origin is defined by the junction of the posterior tibial vein and anterior tibial vein. It drains the peroneal vein before reaching the knee joint and turns into the femoral vein when leaving the adductor canal (also known as Hunter's canal). The popliteal artery extends from the femoral artery behind the popliteal fossa which is the space behind the knee. [WP,unvetted]. Wikipedia:Popliteal_vein EMAPA:37181 MA:th UMLS:C0032652 ncithesaurus:Popliteal_Vein vena poplitea Wikipedia:Popliteal_vein A vein of the lower limb that carries blood from the anterior compartment of the leg to the popliteal vein which is forms when it joins with the posterior tibial vein. Like most deep veins, the anterior tibial vein is accompanied by an artery of the same name, the anterior tibial artery, along its course. [WP,unvetted]. EMAPA:37135 FMA:44331 MA:0002244 NCIT:C32115 SCTID:281066000 UMLS:C0226833 Wikipedia:Anterior_tibial_vein galen:AnteriorTibialVein uberon venae tibiales anteriores UBERON:0001545 anterior tibial vein https://upload.wikimedia.org/wikipedia/commons/4/4e/Gray440_color.png MA FMA/obol FMA/obol A vein of the lower limb that carries blood from the anterior compartment of the leg to the popliteal vein which is forms when it joins with the posterior tibial vein. Like most deep veins, the anterior tibial vein is accompanied by an artery of the same name, the anterior tibial artery, along its course. [WP,unvetted]. Wikipedia:Anterior_tibial_vein EMAPA:37135 MA:th UMLS:C0226833 ncithesaurus:Anterior_Tibial_Vein venae tibiales anteriores Wikipedia:Anterior_tibial_vein The small saphenous vein (also lesser saphenous vein), is a relatively large vein of the superficial posterior leg. [WP,unvetted]. BTO:0003272 EMAPA:37187 FMA:44333 MA:0002217 NCIT:C33546 SCTID:181404009 UMLS:C0226827 Wikipedia:Small_saphenous_vein galen:LesserSaphenousVein lesser saphenous vein short saphenous vein vena saphena parva uberon UBERON:0001547 small saphenous vein http://upload.wikimedia.org/wikipedia/commons/6/62/Gray582.png FMA The small saphenous vein (also lesser saphenous vein), is a relatively large vein of the superficial posterior leg. [WP,unvetted]. Wikipedia:Small_saphenous_vein EMAPA:37187 MA:th UMLS:C0226827 ncithesaurus:Short_Saphenous_Vein vena saphena parva Wikipedia:Small_saphenous_vein The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted]. EMAPA:37143 FMA:44377 MA:0002105 NCIT:C52689 UMLS:C0835053 Wikipedia:Dorsal_metatarsal_veins metatarsal vein uberon venae metatarsales dorsales UBERON:0001549 dorsal metatarsal vein The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted]. Wikipedia:Dorsal_metatarsal_veins EMAPA:37143 MA:th UMLS:C0835053 ncithesaurus:Dorsal_Metatarsal_Vein venae metatarsales dorsales Wikipedia:Dorsal_metatarsal_veins A continuation of the Dorsal venous arch of the foot and is the origin of the long saphenous vein. EMAPA:37170 FMA:44420 MA:0002171 Wikipedia:Medial_marginal_vein medial marginal vein of foot vena marginalis medialis vena marginalis medialis pedis uberon UBERON:0001550 medial marginal vein FMA/obol A continuation of the Dorsal venous arch of the foot and is the origin of the long saphenous vein. Wikipedia:Medial_marginal_vein EMAPA:37170 MA:th vena marginalis medialis pedis FMA:44420 FMA:TA One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries. arcuate artery EMAPA:28215 FMA:70497 MA:0002583 Wikipedia:Arcuate_arteries_of_the_kidney renal arcuate artery uberon UBERON:0001552 kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg MA One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries. MP:0011315 Wikipedia:Arcuate_artery_of_the_foot arcuate artery MA:0002583 A zone of skin that is part of a hip region. in MA this isa hindlimb skin EMAPA:18148 FMA:45282 MA:0000658 SCTID:181518004 hip region zone of skin hip skin hip zone of skin regio coxae zone of skin zone of skin of hip zone of skin of hip region zone of skin of regio coxae uberon UBERON:0001554 skin of hip A zone of skin that is part of a hip region. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 in MA this isa hindlimb skin MA hip region zone of skin OBOL:automatic hip zone of skin OBOL:automatic regio coxae zone of skin OBOL:automatic zone of skin of hip OBOL:automatic zone of skin of hip region OBOL:automatic zone of skin of regio coxae OBOL:automatic A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] FMA also has a term 'gastrointestinal tract', but this includes the liver. we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA:45615 MA:0000917 MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 galen:AlimentaryTract digestive tube enteric tract alimentary canal alimentary tract uberon digestive canal gut tube UBERON:0001555 digestive tract NCBIBook:NBK10107 A tube extending from the mouth to the anus. Wikipedia:Talk:Human_gastrointestinal_tract https://github.com/geneontology/go-ontology/issues/7549 Wikipedia:Acoelomorpha DOI:10.1371/journal.pone.0016309 The alimentary or digestive tract, and associated organs.[TAO] 2012-08-14 TAO:0000112 TAO ZFIN:curator The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000309 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 MA FBbt:00003125 MESH:D041981 https://github.com/biopragmatics/biomappings UMLS:C0017189 ncithesaurus:Gastrointestinal_Tract enteric tract ZFA:0000112 digestive canal BTO:0000058 Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 MA:0002636 SCTID:181420004 galen:LowerUrinaryTract uberon UBERON:0001556 lower urinary tract Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 SCTID:361381009 VHOG:0000406 Wikipedia:Upper_respiratory_tract uberon UBERON:0001557 upper respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. http://orcid.org/0000-0002-6601-2165 Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] FMA The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 SCTID:281488008 VHOG:0000382 Wikipedia:Lower_respiratory_tract lower respiratory system uberon UBERON:0001558 lower respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. Wikipedia:Lower_respiratory_tract http://orcid.org/0000-0002-6601-2165 FMA:45733 organ neck uberon UBERON:0001560 neck of organ FMA A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO] buccal In many animals the inside of the cheek is lined with mucous membrane covered with stratified squamous epithelium and supplied with secretions from buccal glands. BTO:0001754 EMAPA:37451 FMA:46476 GAID:65 MA:0002475 MESH:D002610 NCIT:C13070 SCTID:182325008 TAO:0002113 UMLS:C0007966 Wikipedia:Cheek galen:Cheek uberon buccae jowl UBERON:0001567 cheek https://upload.wikimedia.org/wikipedia/commons/a/a9/Chica_cachetona.jpg FMA-abduced-lr A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. Wikipedia:Cheek http://orcid.org/0000-0002-6601-2165 Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO] 2012-08-14 TAO:0002113 TAO TAO:wd EMAPA:37451 MA:th UMLS:C0007966 ncithesaurus:Cheek buccae Wikipedia:Cheek jowl Wikipedia:Cheek The muscles associated with the larynx. BTO:0001626 EMAPA:35473 FMA:46562 GAID:144 MA:0001768 MESH:D007821 NCIT:C32934 SCTID:181744001 UMLS:C0023054 Wikipedia:Muscles_of_larynx laryngeal muscle larynx muscle larynx muscle organ muscle organ of larynx musculi laryngeales uberon UBERON:0001568 muscle of larynx prolog The muscles associated with the larynx. MP:0002263 UMLS:C0023054 ncithesaurus:Laryngeal_Muscle larynx muscle organ OBOL:automatic muscle organ of larynx OBOL:automatic Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG] Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO] see Intrinsic Tongue.[FEED] relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. AAO:0010660 EHDAA2:0000704 EHDAA:9150 EMAPA:18276 FMA:46690 MA:0002307 NCIT:C52928 SCTID:244784007 UMLS:C0224194 VHOG:0000847 Wikipedia:Genioglossus_muscle genioglossus m. genioglossus musculus genioglossus uberon UBERON:0001571 genioglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png FMA EHDAA2 Wikipedia Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. VHOG:0000847 Wikipedia:Genioglossus_muscle Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG] 2012-09-17 VHOG:0000847 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/genioglossus Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO] 2012-06-20 AAO:0010660 AAO AAO:BMZ see Intrinsic Tongue.[FEED] 2012-07-02 FEED http://www.feedexp.org relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] 2012-06-20 AAO:0010660 AAO The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000847 VHOG DOI:10.1002/dvdy.20587, DOI:10.1186/1471-213X-8-24 Table 7 http://bgee.unil.ch/ Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. AAO:0010660 UMLS:C0224194 ncithesaurus:Genioglossus A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII. Makes up part of the tongue in frogs and salamanders.[AAO] The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED] relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] AAO:0010663 EMAPA:18277 FMA:46691 MA:0002317 MFMO:0000064 NCIT:C53161 SCTID:244785008 UMLS:C0224196 Wikipedia:Hyoglossus_muscle hyoglossus m. hyoglossus uberon UBERON:0001572 hyoglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png FMA lingual process in horse dbpedia A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII. FEED:rd Makes up part of the tongue in frogs and salamanders.[AAO] 2012-06-20 AAO:0010663 AAO AAO:BMZ The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED] 2012-07-02 FEED http://www.feedexp.org relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] 2012-06-20 AAO:0010663 AAO UMLS:C0224196 ncithesaurus:Hyoglossus_Muscle hyoglossus Wikipedia:Hyoglossus A muscle organ that attaches the tongue to some other structure. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus. EHDAA2:0002063 EHDAA:9148 EMAPA:18275 FMA:46699 MA:0002296 SCTID:244782006 VHOG:0000825 extrinsic lingual muscle extrinsic tongue muscle uberon UBERON:0001575 extrinsic muscle of tongue true check palatoglossus Wikipedia A muscle organ that attaches the tongue to some other structure. Wikipedia:Muscles_of_tongue https://github.com/obophenotype/uberon/issues/331 The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000825 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) http://bgee.unil.ch/ main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement WP All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus. WP The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII. The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED] The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone EHDAA2:0002064 EHDAA:9152 EMAPA:18280 FMA:46701 MA:0002327 SCTID:244788005 VHOG:0000748 intrinsic lingual muscle intrinsic tongue muscle uberon UBERON:0001576 intrinsic muscle of tongue true FEED Wikipedia EHDAA2 The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII. http://www.feedexp.org/wiki/Mammalian_Muscle_Ontology_Workshop The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED] 2012-07-02 FEED http://www.feedexp.org The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000748 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) http://bgee.unil.ch/ The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone WP A muscle innervated by a facial nerve. FMA:46751 GAID:143 MA:0003160 MESH:D005152 MFMO:0000005 NCIT:C13073 SCTID:25903009 UMLS:C0015460 Wikipedia:Facial_muscles XAO:0001013 face muscle face muscle organ facial muscle facial muscle proper facial nerve innervated muscle facial nerve muscle muscle of face muscle organ of face uberon cranial-facial muscle cranio-facial muscle craniofacial muscle mimetic muscles muscle of facil expression muscles of facial expression musculi faciei UBERON:0001577 facial muscle http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png FEED Wikipedia A muscle innervated by a facial nerve. FEED:rd UMLS:C0015460 ncithesaurus:Facial_Muscle face muscle FMA:46751 face muscle organ OBOL:automatic facial muscle FMA:46751 XAO:0001013 facial nerve innervated muscle https://orcid.org/0000-0002-6601-2165 muscle of face FMA:46751 muscle organ of face OBOL:automatic cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 mimetic muscles Wikipedia:Facial_muscles muscle of facil expression Wikipedia:Facial_muscles muscles of facial expression Wikipedia:Facial_muscles musculi faciei Wikipedia:Facial_muscles The subclavian artery that supplies the left pectoral appendage. in humans, branches off the arch of aorta arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans EMAPA:37100 FMA:4694 MA:0002046 NCIT:C32972 SCTID:244245001 UMLS:C0226262 Wikipedia:Subclavian_artery arteria subclavia (sinistra) uberon UBERON:0001584 left subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The subclavian artery that supplies the left pectoral appendage. http://orcid.org/0000-0002-6601-2165 EMAPA:37100 MA:th UMLS:C0226262 ncithesaurus:Left_Subclavian_Artery arteria subclavia (sinistra) FMA:4694 FMA:TA A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green). BTO:0002683 EHDAA2:0001962 EHDAA:8726 EMAPA:18417 FMA:4720 GAID:549 MA:0000481 MESH:D014683 NCIT:C12816 SCTID:181368006 UMLS:C0042459 VHOG:0001195 Wikipedia:Superior_vena_cava galen:SuperiorVenaCava superior caval vein superior vena cava uberon cranial vena cava precava vena cava superior vena maxima UBERON:0001585 anterior vena cava http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Wikipedia:Superior_vena_cava http://orcid.org/0000-0002-6601-2165 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001195 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 http://bgee.unil.ch/ UMLS:C0042459 ncithesaurus:Superior_Vena_Cava superior caval vein http://orcid.org/0000-0002-6601-2165 superior vena cava FMA:4720 cranial vena cava VHOG:0001195 vena cava superior BTO:0002683 Wikipedia:Superior_vena_cava vena maxima Wikipedia:Superior_vena_cava One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] AAO:0010236 EHDAA2:0000877 EHDAA:5407 EMAPA:17620 FMA:4724 MA:0002157 NCIT:C32849 RETIRED_EHDAA2:0000878 SCTID:181372005 UMLS:C0226550 Wikipedia:Internal_jugular_vein XAO:0000382 galen:InternalJugularVein internal jugular internal jugular venous tree uberon vena jugularis interna UBERON:0001586 internal jugular vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Wikipedia:Internal_jugular_vein Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] 2012-06-20 AAO:0010236 AAO AAO:BJB UMLS:C0226550 ncithesaurus:Internal_Jugular_Vein internal jugular EHDAA2:0000877 vena jugularis interna Wikipedia:Internal_jugular_vein The subclavian vein is a paired large vein, one on either side of the body. Their diameter is approximately that of the smallest finger. Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO] AAO:0010510 EHDAA2:0001934 EHDAA:4455 EMAPA:17621 FMA:4725 GAID:546 MA:0002221 MESH:D013350 NCIT:C12794 SCTID:181388005 UMLS:C0038532 Wikipedia:Subclavian_vein galen:SubclavianVein subclavian venous tree vena subclavia uberon UBERON:0001587 subclavian vein http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png The subclavian vein is a paired large vein, one on either side of the body. Their diameter is approximately that of the smallest finger. Wikipedia:Subclavian_vein Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO] 2012-06-20 AAO:0010510 AAO AAO:BJB UMLS:C0038532 ncithesaurus:Subclavian_Vein vena subclavia Wikipedia:Subclavian_vein A vein that drains blood from the thymus. EMAPA:36325 FMA:4747 MA:0002246 NCIT:C53143 SCTID:303432009 UMLS:C0226698 Wikipedia:Thymic_veins thymic tributary of brachiocephalic vein vena thymica uberon venae thymicae UBERON:0001591 thymic vein A vein that drains blood from the thymus. http://orcid.org/0000-0002-6601-2165 UMLS:C0226698 ncithesaurus:Thymic_Vein vena thymica Wikipedia:Thymic_veins venae thymicae Wikipedia:Thymic_veins The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. EMAPA:36284 FMA:4749 MA:0002088 NCIT:C53031 SCTID:198293000 UMLS:C0226650 Wikipedia:Bronchial_veins bronchial venous tree uberon UBERON:0001592 bronchial vein The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. Wikipedia:Bronchial_veins UMLS:C0226650 ncithesaurus:Bronchial_Vein A congregation of multiple veins. EMAPA:36327 FMA:4767 MA:0000069 SCTID:322151008 Wikipedia:Venous_plexus venous network uberon plexus venosus rete venosum UBERON:0001593 venous plexus http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png A congregation of multiple veins. Wikipedia:Venous_plexus plexus venosus Wikipedia:Venous_plexus rete venosum Wikipedia:Venous_plexus The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 EMAPA:35240 FMA:49151 MA:0001269 NCIT:C32315 SCTID:280862009 UMLS:C0559230 Wikipedia:Ciliary_muscle musculus ciliarus uberon Bowman`s muscles ciliaris musculus ciliaris UBERON:0001605 ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png MA FMA FMA The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. Wikipedia:Ciliary_muscle UMLS:C0559230 ncithesaurus:Ciliary_Muscle musculus ciliarus BTO:0000654 Bowman`s muscles BTO:0000654 ciliaris Wikipedia:Ciliary_muscle musculus ciliaris Wikipedia:Ciliary_muscle revisit this, see issue #331 The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP] in aves, stromal mesenchymal cells may migrate to the iris and become skeletal EMAPA:35448 FMA:49154 MA:0001287 SCTID:280888007 Wikipedia:Iris_muscle iris muscle iris muscle organ muscle organ of iris uberon UBERON:0001606 muscle of iris FMA iris muscle organ OBOL:automatic muscle organ of iris OBOL:automatic A sphincter muscle that is part of the iris. In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted] WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure constricts iris BTO:0000656 EMAPA:35788 FMA:49157 MA:0001289 NCIT:C33586 SCTID:280889004 UMLS:C0229189 Wikipedia:Iris_sphincter_muscle M. sphincter pupillae iris sphincter muscle musculus sphincter pupillae sphincter muscle of pupil uberon circular fibers constrictor pupillae iris constrictor iris constrictor muscle iris sphincter m. sphincter pupillae pupillary constrictor muscle pupillary sphincter pupillary sphincter muscle sphincter pupillae sphincter pupillae muscle spincter pupillae UBERON:0001607 sphincter pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png BTO ISBN:0781772214 encircles iris dbpedia encircles iris dbpedia dbpedia A sphincter muscle that is part of the iris. Wikipedia:Iris_sphincter_muscle UMLS:C0229189 ncithesaurus:Sphincter_Pupillae_Muscle iris sphincter muscle BTO:0000656 musculus sphincter pupillae BTO:0000656 sphincter muscle of pupil BTO:0000656 circular fibers Wikipedia:Iris_sphincter_muscle constrictor pupillae Wikipedia:Iris_sphincter_muscle iris constrictor muscle Wikipedia:Iris_sphincter_muscle iris sphincter Wikipedia:Iris_sphincter_muscle m. sphincter pupillae Wikipedia:Iris_sphincter_muscle pupillary constrictor muscle Wikipedia:Iris_sphincter_muscle pupillary sphincter Wikipedia:Iris_sphincter_muscle pupillary sphincter muscle Wikipedia:Iris_sphincter_muscle sphincter pupillae Wikipedia:Iris_sphincter_muscle sphincter pupillae muscle Wikipedia:Iris_sphincter_muscle spincter pupillae Wikipedia:Iris_sphincter_muscle A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina BTO:0001371 EMAPA:35286 FMA:49158 MA:0001288 NCIT:C32463 SCTID:280890008 UMLS:C0229190 Wikipedia:Iris_dilator_muscle dilator muscle of pupil dilator of pupil dilator pupillae dilator pupillae muscle iris dilator muscle musculus dilatator pupillae pupillary dilator muscle radial muscle of iris uberon dilator pupillae muscle iris dilator musculus dilatator pupillae musculus dilator pupillae pupil dilator pupil dilator muscle pupillary dilator pupillary muscle radial muscle radiating fibers UBERON:0001608 dilatator pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png BTO ISBN:0781772214 outer margins of iris dbpedia inner margins of iris dbpedia dbpedia A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. Wikipedia:Iris_dilator_muscle UMLS:C0229190 ncithesaurus:Dilator_Pupillae_Muscle dilator pupillae muscle Wikipedia:Iris_dilator_muscle iris dilator muscle BTO:0001371 musculus dilatator pupillae FMA:49158 FMA:TA pupillary dilator muscle Wikipedia:Iris_dilator_muscle radial muscle of iris Wikipedia:Iris_dilator_muscle dilator pupillae muscle BTO:0001371 iris dilator Wikipedia:Iris_dilator_muscle musculus dilatator pupillae Wikipedia:Iris_dilator_muscle musculus dilator pupillae BTO:0001371 pupil dilator Wikipedia:Iris_dilator_muscle pupil dilator muscle Wikipedia:Iris_dilator_muscle pupillary dilator Wikipedia:Iris_dilator_muscle pupillary muscle Wikipedia:Iris_dilator_muscle radial muscle Wikipedia:Iris_dilator_muscle radiating fibers Wikipedia:Iris_dilator_muscle The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]. Part of the external carotid which supplies blood to the tongue.[AAO] relationship loss: part_of external carotid (AAO:0010218)[AAO] AAO:0010492 EMAPA:36324 FMA:49526 MA:0001992 NCIT:C52961 SCTID:181327002 UMLS:C0226104 Wikipedia:Lingual_artery lingual branch of external carotid artery uberon arteria lingualis UBERON:0001610 lingual artery https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG FMA-abduced-lr The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]. Wikipedia:Lingual_artery Part of the external carotid which supplies blood to the tongue.[AAO] 2012-06-20 AAO:0010492 AAO AAO:BJB relationship loss: part_of external carotid (AAO:0010218)[AAO] 2012-06-20 AAO:0010492 AAO UMLS:C0226104 ncithesaurus:Lingual_Artery arteria lingualis Wikipedia:Lingual_artery A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. EMAPA:19213 FMA:49549 MA:0001950 NCIT:C32578 SCTID:181328007 UMLS:C0226109 Wikipedia:Facial_artery uberon arteria maxillaris externa external maxillary artery UBERON:0001612 facial artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. Wikipedia:Facial_artery UMLS:C0226109 ncithesaurus:Facial_Artery arteria maxillaris externa Wikipedia:Facial_artery An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries EHDAA2:0001069 EHDAA:7357 EMAPA:17311 FMA:49675 GAID:498 MA:0001919 MESH:D008438 NCIT:C34205 SCTID:181326006 UMLS:C0024949 Wikipedia:Maxillary_artery uberon arteria maxillaris internal maxillary artery UBERON:0001616 maxillary artery http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. Wikipedia:Maxillary_artery ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries http://download.videohelp.com/vitualis/med/Vascular_Devt.html UMLS:C0024949 ncithesaurus:Maxillary_Artery arteria maxillaris Wikipedia:Maxillary_artery The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] AAO:0010497 EHDAA2:0001300 EHDAA:7363 EMAPA:17007 FMA:49868 GAID:503 MA:0002011 MESH:D009880 NCIT:C33216 SCTID:181310005 UMLS:C0029078 Wikipedia:Ophthalmic_artery XAO:0000368 uberon arteria ophthalmica opthalmic artery UBERON:0001619 ophthalmic artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. Wikipedia:Ophthalmic_artery Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] 2012-06-20 AAO:0010497 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010497 AAO UMLS:C0029078 ncithesaurus:Opthalmic_Artery arteria ophthalmica Wikipedia:Ophthalmic_artery opthalmic artery Wikipedia:Ophthalmic_artery An artery that supplies the myocardium. BTO:0000290 CALOHA:TS-0176 EFO:0002551 EMAPA:19160 EV:0100383 FMA:49893 MA:0002453 NCIT:C12843 SCTID:181294004 UMLS:C0205042 VHOG:0001557 Wikipedia:Coronary_circulation#Coronary_anatomy ZFA:0005812 galen:CoronaryArtery coronary arterial tree uberon coronary vessel UBERON:0001621 coronary artery http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png An artery that supplies the myocardium. Wikipedia:Coronary_circulation#Coronary_anatomy http://orcid.org/0000-0002-6601-2165 UMLS:C0205042 ncithesaurus:Coronary_Artery coronary vessel ZFA:0005812 The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. EMAPA:37094 FMA:49927 MA:0001988 NCIT:C52948 SCTID:369324002 UMLS:C0226171 Wikipedia:Lacrimal_artery uberon a. lacrimalis UBERON:0001622 lacrimal artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png FMA The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. Wikipedia:Lacrimal_artery EMAPA:37094 MA:th UMLS:C0226171 ncithesaurus:Lacrimal_Artery a. lacrimalis Wikipedia:Lacrimal_artery One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery EHDAA2:0004518 EHDAA:3352 EMAPA:18600 FMA:50084 MA:0002023 NCIT:C33357 RETIRED_EHDAA2:0001487 SCTID:181314001 TAO:0005001 UMLS:C0149559 Wikipedia:Posterior_communicating_artery ZFA:0005001 caudal communicating segment posterior communicating segment of the basilar artery uberon PCA PCS arteria cerebri communicans posterior UBERON:0001628 posterior communicating artery http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg FMA-abduced-lr FMA ZFA One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. Wikipedia:Posterior_communicating_artery An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005001 TAO ZFIN:curator UMLS:C0149559 ncithesaurus:Posterior_Communicating_Artery caudal communicating segment ZFA:0005001 posterior communicating segment of the basilar artery ZFA:0005001 arteria cerebri communicans posterior Wikipedia:Posterior_communicating_artery Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Portion of tissue composed of contractile fibers.[TAO] It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] muscular muscle AAO:0011066 EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 GAID:131 MA:0000015 SCTID:71616004 TAO:0005145 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle uberon UBERON:0001630 muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 Portion of tissue composed of contractile fibers.[TAO] 2012-08-14 TAO:0005145 TAO ZFIN:curator It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] 2012-09-17 VHOG:0001245 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 http://bgee.unil.ch/ muscle ZFA:0005145 EMAPA:37474 MA:th An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] arterial Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system. AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 FMA:50720 GAID:468 MA:0000064 MAT:0000034 MESH:D001158 MIAA:0000034 NCIT:C12372 SCTID:362877004 TAO:0000005 UMLS:C0003842 VHOG:0001251 Wikipedia:Artery XAO:0000114 ZFA:0000005 galen:Artery arterial subtree arterial tree organ part arteries uberon arterial system arterial vessel UBERON:0001637 artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] 2012-06-20 AAO:0010211 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001251 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0003842 ncithesaurus:Artery arteries TAO:0000005 Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] venous venous subtree venous vessel AAO:0010212 AEO:0000209 BTO:0000234 CALOHA:TS-1108 EFO:0000816 EHDAA2:0003254 EMAPA:35906 EV:0100031 FMA:50723 GAID:492 MA:0000067 MAT:0000037 MESH:D014680 MIAA:0000037 NCIT:C12814 SCTID:181367001 TAO:0000082 UMLS:C0042449 VHOG:0001743 Wikipedia:Vein XAO:0000115 ZFA:0000082 galen:Vein venous tree organ part uberon vascular element vena venae UBERON:0001638 vein http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Wikipedia:Vein Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] 2012-06-20 AAO:0010212 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001743 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0042449 ncithesaurus:Vein vascular element EMAPA:th vena Wikipedia:Vein venae VHOG:0001743 A portal vein that transports nutrients from the digestive tract to the liver[Kardong]. Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG] In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted] AAO:0010214 FMA:50735 MA:0002132 TAO:0005090 VHOG:0000642 Wikipedia:Hepatic_portal_vein ZFA:0005090 hepatic portal tree liver portal vein portal vein of liver uberon HPV portal vein primary hepatic portal vein primary hepatic portal veins vena portae hepatis UBERON:0001639 hepatic portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb MA A portal vein that transports nutrients from the digestive tract to the liver[Kardong]. ISBN:0073040584 Wikipedia:Hepatic_portal_vein http://sourceforge.net/tracker/?func=detail&aid=3091300&group_id=76834&atid=1205376 Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG] 2012-09-17 VHOG:0000642 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265 http://bgee.unil.ch/ liver portal vein OBOL:automatic portal vein of liver OBOL:automatic portal vein primary hepatic portal vein ZFA:0005090 vena portae hepatis Wikipedia:Hepatic_portal_vein The first major branch of the abdominal aorta. EHDAA2:0004519 EMAPA:35202 FMA:50737 GAID:483 MA:0001931 MESH:D002445 NCIT:C52846 SCTID:181340007 UMLS:C0007569 Wikipedia:Celiac_artery celiac tree coeliac artery uberon arteria coeliaca arteria cœliaca celiac trunk coeliac axis coeliac trunck coeliac trunk truncus coeliacus truncus cœliacus UBERON:0001640 dorsal aorta in Kardong celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 The first major branch of the abdominal aorta. Wikipedia:Celiac_artery UMLS:C0007569 ncithesaurus:Coeliac_Artery coeliac artery Wikipedia:Celiac_artery arteria coeliaca Wikipedia:Celiac_artery arteria cœliaca Wikipedia:Celiac_artery celiac trunk Wikipedia:Celiac_artery coeliac axis Wikipedia:Celiac_artery coeliac trunck Wikipedia:Celiac_artery coeliac trunk Wikipedia:Celiac_artery truncus coeliacus Wikipedia:Celiac_artery truncus cœliacus Wikipedia:Celiac_artery Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls 5n AAO:0010470 BAMS:5n BAMS:Vn BAMS:nV BIRNLEX:869 BM:VN BTO:0001072 EFO:0001402 EHDAA2:0002084 EHDAA:3738 EMAPA:17576 FMA:50866 GAID:726 HBA:9322 MA:0001100 MBA:901 MESH:D014276 MFMO:0000093 NCIT:C12806 SCTID:362459002 TAO:0000697 UMLS:C0040996 VHOG:0000704 Wikipedia:Trigeminal_nerve XAO:0003092 ZFA:0000697 neuronames:549 fifth cranial nerve nervus trigeminus nervus trigeminus [v] trigeminal V trigeminal nerve [V] trigeminal nerve tree trigeminal v nerve uberon CN-V cranial nerve V nerve V nervus trigeminus trigeminus UBERON:0001645 trigeminal nerve https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png Wikipedia Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). ISBN:0471209627 Wikipedia:Trigeminal_nerve Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] 2012-06-20 AAO:0010470 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000704 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls ISBN:0471888893 5n BIRNLEX:869 NIFSTD:NeuroNames_abbrevSource UMLS:C0040996 BIRNLEX:869 ncithesaurus:Trigeminal_Nerve neuronames:549 BIRNLEX:869 nervus trigeminus Wikipedia:Trigeminal_nerve nervus trigeminus [v] FMA:50866 FMA:TA trigeminal V EHDAA2:0002084 nerve V NeuroNames:549 nervus trigeminus BTO:0001072 trigeminus BTO:0001072 Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 7n AAO:0010472 BAMS:7n BAMS:VIIn BAMS:Viin BAMS:nVII BIRNLEX:827 BM:Pons-VIIN EHDAA2:0000489 EHDAA:3729 EMAPA:17796 FMA:50868 GAID:719 HBA:9328 MA:0001091 MBA:798 MESH:D005154 NCIT:C12714 SCTID:362460007 TAO:0000664 UMLS:C0015462 VHOG:0000706 Wikipedia:Facial_nerve XAO:0003094 ZFA:0000664 neuronames:551 branchiomeric cranial nerve face nerve facial VII facial VII nerve facial nerve [VII] facial nerve tree nerve of face nervus facialis nervus facialis [vii] seventh cranial nerve uberon CN-VII cranial nerve VII facial nerve or its root facial nerve/root nerve VII nervus facialis UBERON:0001647 facial nerve http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg ZFA Wikipedia Wikipedia Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). ISBN:0471209627 Wikipedia:Facial_nerve Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] 2012-06-20 AAO:0010472 AAO AAO:DSM We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000706 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ 7n BIRNLEX:827 NIFSTD:NeuroNames_abbrevSource UMLS:C0015462 BIRNLEX:827 ncithesaurus:Facial_Nerve neuronames:551 BIRNLEX:827 face nerve OBOL:automatic facial VII EHDAA2:0000489 nerve of face OBOL:automatic nervus facialis ZFA:0000664 nervus facialis [vii] FMA:50868 FMA:TA facial nerve or its root BAMS:7n facial nerve/root BAMS:7n nerve VII NeuroNames:551 nervus facialis Wikipedia:Facial_nerve Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 9n AAO:0010474 BAMS:9n BAMS:IXn BIRNLEX:899 BTO:0004979 EHDAA2:0000709 EHDAA:3733 EMAPA:17268 FMA:50870 GAID:827 HBA:9334 MA:0001093 MBA:808 MESH:D005930 NCIT:C12723 SCTID:362465002 TAO:0000668 UMLS:C0017679 UMLS:C1305752 VHOG:0000701 Wikipedia:Glossopharyngeal_nerve XAO:0003096 ZFA:0000668 neuronames:701 glossopharyngeal IX glossopharyngeal IX nerve glossopharyngeal nerve [IX] glossopharyngeal nerve tree nervus glossopharyngeus nervus glossopharyngeus [ix] ninth cranial nerve uberon CN-IX cranial nerve IX nerve IX nervus glossopharyngeus UBERON:0001649 glossopharyngeal nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png motor Wikipedia Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). ISBN:0471209627 Wikipedia:Glossopharyngeal_nerve Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] 2012-06-20 AAO:0010474 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000701 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ 9n BIRNLEX:899 NIFSTD:NeuroNames_abbrevSource UMLS:C0017679 BIRNLEX:899 ncithesaurus:Glossopharyngeal_Nerve UMLS:C1305752 BIRNLEX:899 neuronames:701 BIRNLEX:899 glossopharyngeal IX EHDAA2:0000709 nervus glossopharyngeus ZFA:0000668 nervus glossopharyngeus [ix] FMA:50870 FMA:TA CN-IX nerve IX NeuroNames:701 nervus glossopharyngeus Wikipedia:Glossopharyngeal_nerve Cranial nerve that innervates the muscles of the tongue. Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves 12n AAO:0010477 BAMS:12n BAMS:XIIn BAMS:nXII BIRNLEX:820 BTO:0003386 EHDAA2:0000798 EHDAA:2859 EMAPA:17269 FMA:50871 GAID:828 HBA:9343 MA:0001094 MBA:813 MESH:D007002 NCIT:C12732 SCTID:362471008 UMLS:C0020614 VHOG:0000693 Wikipedia:Hypoglossal_nerve XAO:0004215 neuronames:704 cranial nerve XII hypoglossal XII hypoglossal XII nerve hypoglossal nerve [XII] hypoglossal nerve tree nervus hypoglossus [xii] twelfth cranial nerve uberon CN-XII hypoglossal nerve/ root nerve XII nervi hypoglossalis nervus hypoglossus UBERON:0001650 hypoglossal nerve http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png Cranial nerve that innervates the muscles of the tongue. ISBN:080184780X VHOG:0000693 http://orcid.org/0000-0002-6601-2165 Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000693 VHOG http://bgee.unil.ch/ In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis ISBN:080184780X Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO] 2012-06-20 AAO:0010477 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000693 VHOG Wikipedia:Cranial_nerves http://bgee.unil.ch/ 12n BIRNLEX:820 NIFSTD:NeuroNames_abbrevSource UMLS:C0020614 BIRNLEX:820 ncithesaurus:Hypoglossal_Nerve neuronames:704 BIRNLEX:820 cranial nerve XII BIRNLEX:820 hypoglossal XII EHDAA2:0000798 nervus hypoglossus [xii] FMA:50871 FMA:TA CN-XII VHOG:0000693 hypoglossal nerve/ root BAMS:12n nerve XII NeuroNames:704 nervi hypoglossalis NeuroNames:704 nervus hypoglossus Wikipedia:Hypoglossal_nerve The pulmonary artery that supplies the right lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37378 FMA:50872 MA:0002500 NCIT:C33489 SCTID:244235003 UMLS:C0923924 Wikipedia:Right_pulmonary_artery galen:RightPulmonaryArtery right main pulmonary artery right pulmonary arterial tree uberon arteria pulmonalis dextra UBERON:0001651 right pulmonary artery http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png The pulmonary artery that supplies the right lung. UBERON:cjm EMAPA:37378 MA:th UMLS:C0923924 ncithesaurus:Right_Pulmonary_Artery arteria pulmonalis dextra Wikipedia:Right_pulmonary_artery The pulmonary artery that supplies the left lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37097 FMA:50873 MA:0002032 NCIT:C32971 SCTID:244234004 UMLS:C0923925 Wikipedia:Left_pulmonary_artery galen:LeftPulmonaryArtery left main pulmonary artery left pulmonary arterial tree uberon arteria pulmonalis sinistra UBERON:0001652 left pulmonary artery http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png The pulmonary artery that supplies the left lung. UBERON:cjm EMAPA:37097 MA:th UMLS:C0923925 ncithesaurus:Left_Pulmonary_Artery arteria pulmonalis sinistra Wikipedia:Left_pulmonary_artery The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] MA and NCITA also has 'anterior facial vein' AAO:0010513 EMAPA:19220 FMA:50874 MA:0002115 NCIT:C32579 SCTID:181374006 UMLS:C0226532 Wikipedia:Facial_vein face vein vein of face uberon anterior facial vein vena facialis anterior UBERON:0001653 facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png FMA The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Wikipedia:Facial_vein Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] 2012-06-20 AAO:0010513 AAO AAO:BJB MA and NCITA also has 'anterior facial vein' MA UMLS:C0226532 ncithesaurus:Facial_Vein face vein OBOL:automatic vein of face OBOL:automatic anterior facial vein Wikipedia:Facial_vein vena facialis anterior Wikipedia:Facial_vein The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. EMAPA:37140 FMA:50981 GAID:530 MA:0002096 MESH:D002550 NCIT:C53037 SCTID:244392000 UMLS:C0007797 Wikipedia:Cerebral_veins XAO:0004160 uberon venae cerebri venae encephali UBERON:0001663 cerebral vein http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. Wikipedia:Cerebral_veins EMAPA:37140 MA:th UMLS:C0007797 ncithesaurus:Cerebral_Vein venae cerebri Wikipedia:Cerebral_veins venae encephali Wikipedia:Cerebral_veins A vein that drains the cerebellum. EMAPA:37139 FMA:51227 MA:0002093 NCIT:C53032 SCTID:40693009 UMLS:C0226601 Wikipedia:Cerebellar_veins cerebellum vein epencephalon-1 vein vein of cerebellum vein of epencephalon-1 uberon UBERON:0001668 cerebellar vein A vein that drains the cerebellum. http://orcid.org/0000-0002-6601-2165 EMAPA:37139 MA:th UMLS:C0226601 ncithesaurus:Cerebellar_Vein cerebellum vein OBOL:automatic epencephalon-1 vein OBOL:automatic vein of cerebellum OBOL:automatic vein of epencephalon-1 OBOL:automatic The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks) A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. AAO:0011107 BAMS:5Gn BAMS:GV BTO:0001231 EFO:0000903 EHDAA2:0002085 EHDAA:2113 EMAPA:16797 FMA:52618 GAID:725 MA:0001080 MAT:0000511 MESH:D012668 NCIT:C62642 SCTID:244449009 TAO:0000295 UMLS:C0040995 VHOG:0000694 Wikipedia:Trigeminal_ganglion XAO:0000427 XAO:0000428 ZFA:0000295 neuronames:1402 5th ganglion Gasserian ganglion fifth ganglion ganglion of trigeminal complex semilunar ganglion trigeminal V ganglion fused trigeminal ganglion uberon Gasser's ganglion Gasserian ganglia gV ganglion of trigeminal nerve ganglion semilunare ganglion trigeminale trigeminal ganglia trigeminus ganglion UBERON:0001675 trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png ncithesaurus Bgee:AN The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. http://orcid.org/0000-0002-6601-2165 http://www.ncbi.nlm.nih.gov/books/NBK53171 https://github.com/obophenotype/uberon/issues/693 A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000295 TAO ZFIN:curator In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. PMID:21452441 XAO:0004093 UMLS:C0040995 ncithesaurus:Trigeminal_Ganglion 5th ganglion ZFA:0000295 Gasserian ganglion Wikipedia:Trigeminal_ganglion fifth ganglion ZFA:0000295 ganglion of trigeminal complex http://orcid.org/0000-0002-6601-2165 semilunar ganglion ISBN:0471888893 trigeminal V ganglion MA:0001080 fused trigeminal ganglion NCBITaxon:32524 Gasser's ganglion BTO:0001231 Gasserian ganglia Wikipedia:Trigeminal_ganglion ganglion of trigeminal nerve BTO:0001231 ganglion semilunare Wikipedia:Trigeminal_ganglion ganglion trigeminale BTO:0001231 Wikipedia:Trigeminal_ganglion trigeminal ganglia The bone at the lower, posterior part of the skull. formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) EMAPA:25112 FMA:52735 GAID:227 MA:0001468 MESH:D009777 NCIT:C12757 SCTID:181796003 UMLS:C0028784 Wikipedia:Occipital_bone uberon occipital complex occipital squama os occipitale UBERON:0001676 occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png FMA FMA basi paired exo and supra occipital bones MA-modified interparietal (postparietal) WP PMID:11523816 The bone at the lower, posterior part of the skull. ISBN:0-683-40008-8 MP:0005269 formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII PMID:11523816 fusion of basi-, exo- and supra-occipitals (and maybe tabular) Kardong UMLS:C0028784 ncithesaurus:Occipital_Bone occipital complex http://palaeos.com/vertebrates/bones/braincase/occiput.html os occipitale Wikipedia:Occipital_bone An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. part of viscerocranium (facial skeleton) in FMA CALOHA:TS-2343 EMAPA:18340 FMA:52736 GAID:230 MA:0001472 MESH:D013100 NCIT:C12790 SCTID:272676008 UMLS:C0037884 Wikipedia:Sphenoid_bone os sphenoidale sphenoid sphenoidal bone uberon butterfly bone os sphenoidale os sphenoidum sphenoid complex UBERON:0001677 sphenoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg FMA orbito pre and basi sphenoid pterygoid process alisphenoid cjm An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended. Wikipedia:Sphenoid_bone part of viscerocranium (facial skeleton) in FMA FMA UMLS:C0037884 ncithesaurus:Sphenoid_Bone os sphenoidale FMA:52736 FMA:TA butterfly bone Wikipedia:Sphenoid_bone os sphenoidale Wikipedia:Sphenoid_bone os sphenoidum Wikipedia:Sphenoid_bone The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous. In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA EHDAA:6035 EMAPA:17682 FMA:52737 GAID:232 MA:0001476 MESH:D013701 NCIT:C12797 SCTID:181795004 UMLS:C0039484 VHOG:0000800 Wikipedia:Temporal_bone uberon os temporale UBERON:0001678 temporal bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg FMA petrosal squamosal plus angular temporal series styloid process The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous. ISBN:0-683-40008-8 MP:0005272 fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) chond. The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. [WP] Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA FMA UMLS:C0039484 ncithesaurus:Temporal_Bone os temporale Wikipedia:Temporal_bone A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP]. A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG] The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG] ethmoidal todo - homology e.g. mesethmoid of teleost Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA BTO:0004140 EMAPA:19018 FMA:52740 GAID:212 MA:0001483 MESH:D005004 NCIT:C12711 SCTID:272674006 UMLS:C0015027 VHOG:0001317 Wikipedia:Ethmoid_bone ethmoid ethmoidal bone os ethmoidale uberon UBERON:0001679 ethmoid bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg ISBN:0073040584 definitional A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP]. Wikipedia:Ethmoid_bone A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG] 2012-09-17 VHOG:0001317 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/ethmoid+bone The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG] 2012-09-17 VHOG:0001317 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259 http://bgee.unil.ch/ Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA MA UMLS:C0015027 ncithesaurus:Ethmoid_Bone ethmoid FMA:52740 ethmoidal bone MP:0000101 os ethmoidale FMA:52740 FMA:TA Wikipedia:Ethmoid A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]. Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO] relationship loss: part_of hyoid plate (AAO:0000664)[AAO] The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia. AAO:0000684 EMAPA:18650 FMA:52749 GAID:197 MA:0001484 MESH:D006928 NCIT:C32752 SCTID:263352000 UMLS:C0020417 VHOG:0001325 Wikipedia:Hyoid_bone uberon hyoid hyoid bone hyoideum lingual bone os hyoideum UBERON:0001685 hyoid bone http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png FMA Wikipedia Wikipedia A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]. Wikipedia:Hyoid_bone Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO] 2012-06-20 AAO:0000684 AAO AAO:LAP relationship loss: part_of hyoid plate (AAO:0000664)[AAO] 2012-06-20 AAO:0000684 AAO The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia. WP https://github.com/obophenotype/uberon/issues/548 UMLS:C0020417 ncithesaurus:Hyoid_Bone hyoid Wikipedia:Hyoid_bone hyoid bone Wikipedia:Hyoid_bone hyoideum Wikipedia:Hyoid_bone lingual bone Wikipedia:Hyoid_bone os hyoideum Wikipedia:Hyoid_bone One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted]. This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5. The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG] Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG] Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry. ossicle AAO:0011015 EHDAA2:0001183 EHDAA:5697 EMAPA:17824 EV:0100360 FMA:52750 MA:0000254 NCIT:C32164 SCTID:181184001 UMLS:C0013450 VHOG:0000461 Wikipedia:Auditory_ossicle XAO:0000214 auditory bone middle ear ossicle uberon auditory ossicle ear bone ear ossicle ear ossicles middle ear bone ossicle of ear ossicle of inner ear ossicular chain UBERON:0001686 auditory ossicle bone http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted]. Wikipedia:Auditory_ossicle https://github.com/obophenotype/uberon/issues/91 The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG] 2012-09-17 VHOG:0000461 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/auditory+ossicles Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG] 2012-09-17 VHOG:0000461 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695 http://bgee.unil.ch/ Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry. WP ossicle EMAPA:17824 Wikipedia:Auditory_ossicle UMLS:C0013450 ncithesaurus:Auditory_Ossicle middle ear ossicle MP:0005105 auditory ossicle MA:0000254 ear bone MA:0000254 ear ossicles ossicular chain Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. The organ of hearing and of equilibrium. [TFD][VHOG] Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] auricular AAO:0011014 BIRNLEX:1062 BTO:0000368 CALOHA:TS-1165 EFO:0000826 EHDAA2:0000423 EHDAA:502 EMAPA:16193 EV:0100353 FMA:52780 GAID:62 MA:0000236 MAT:0000138 MESH:D004423 MIAA:0000138 NCIT:C12394 SCTID:1910005 UMLS:C0013443 UMLS:C0521421 VHOG:0000330 Wikipedia:Ear XAO:0000189 galen:Ear uberon auditory apparatus auris UBERON:0001690 ear http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. GO:0042471 Wikipedia:Ear The organ of hearing and of equilibrium. [TFD][VHOG] 2012-09-17 VHOG:0000330 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/ear Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] 2012-09-17 VHOG:0000330 VHOG DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005) http://bgee.unil.ch/ UMLS:C0013443 BIRNLEX:1062 ncithesaurus:Ear UMLS:C0521421 BIRNLEX:1062 auris BTO:0000368 Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]. The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG] in XAO this includes and is only the tympanum auricular region AAO:0011037 BIRNLEX:1705 BTO:0002100 EFO:0004221 EHDAA2:0000462 EHDAA:3786 EMAPA:16991 EV:0100354 FMA:52781 GAID:104 MA:0000258 MAT:0000147 MESH:D004431 MIAA:0000147 NCIT:C12292 SCTID:420893000 UMLS:C0013453 UMLS:C1269548 VHOG:0000311 Wikipedia:External_ear XAO:0000190 auricular region of head outer ear uberon auris externa UBERON:0001691 external ear http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]. GO:0042473 Wikipedia:External_ear Wikipedia The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000311 VHOG http://bgee.unil.ch/ Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG] 2012-09-17 VHOG:0000311 VHOG DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008) http://bgee.unil.ch/ in XAO this includes and is only the tympanum XAO UMLS:C0013453 BIRNLEX:1705 ncithesaurus:External_Ear UMLS:C1269548 BIRNLEX:1705 outer ear MA:0000258 auris externa BTO:0002100 The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]. The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG] derivative of prootic and opisthotic petrosal EHDAA2:0001452 EMAPA:17683 FMA:52871 GAID:234 MA:0001477 MESH:D010579 NCIT:C32316 SCTID:361733004 UMLS:C1261761 VHOG:0001553 Wikipedia:Petrous_part_of_the_temporal_bone pars petrosa (os temporale) pars petrosa ossis temporalis petromastoid part of temporal bone temporal bone petrous part uberon petrosal bone petrous bone UBERON:0001694 petrous part of temporal bone http://upload.wikimedia.org/wikipedia/commons/9/96/Gray137.png FMA The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]. Wikipedia:Petrous_part_of_the_temporal_bone The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG] 2012-09-17 VHOG:0001553 VHOG http://bgee.unil.ch/ petrosal VHOG:0001553 UMLS:C1261761 ncithesaurus:Ciliary_Process pars petrosa (os temporale) FMA:52871 petromastoid part of temporal bone FMA:52871 petrosal bone FMA:52871 petrous bone FMA:52871 Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball. Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO] in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit BTO:0004687 FMA:53074 GAID:223 MA:0002482 MESH:D009915 NCIT:C12347 TAO:0001410 UMLS:C0029180 Wikipedia:Orbit_(anatomy) XAO:0003171 ZFA:0001410 galen:Orbit bony orbit eye socket orbit of skull uberon orbit UBERON:0001697 orbit of skull FMA-abduced-lr Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball. TAO:0001410 Wikipedia:Orbit_(anatomy) http://orcid.org/0000-0002-6601-2165 Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO] 2012-08-14 TAO:0001410 TAO TAO:MAH in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit FMA UMLS:C0029180 ncithesaurus:Orbit orbit of skull FMA:53074 orbit ZFA:0001410 The group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve). resolve facial VII vs geniculate (see EHDAA2) These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] geniculate BAMS:GgVII EFO:0003669 EHDAA2:0000491 EHDAA2:0004623 EHDAA:5567 EHDAA:6644 EMAPA:17569 FMA:53414 GAID:718 MA:0001076 MESH:D005830 NCIT:C12721 SCTID:279076005 TAO:0001291 UMLS:C0017406 VHOG:0000707 Wikipedia:Geniculate_ganglion ZFA:0001291 neuronames:1535 facial VII ganglion gVII ganglion genicularum genicular ganglion uberon facial ganglion ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion internal genu UBERON:0001700 geniculate ganglion http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png ncithesaurus EHDAA2:0004623 ZFA EHDAA2:0004623 EHDAA2:0000491 The group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve). ISBN:0-683-40008-8 MP:0001082 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000707 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ geniculate Wikipedia:Geniculate_ganglion UMLS:C0017406 ncithesaurus:Geniculate_Ganglion facial VII ganglion MA:0001076 gVII ZFA:0001291 ganglion genicularum FMA:53414 genicular ganglion FMA:53414 Wikipedia:Geniculate_ganglion facial ganglion ZFA:0001291 ganglion geniculi Wikipedia:Geniculate_ganglion ganglion geniculi nervi facialis Wikipedia:Geniculate_ganglion geniculate ganglion MA:0001076 internal genu Wikipedia:Geniculate_ganglion The group of neuron cell bodies associated with the ninth cranial nerve. These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] EHDAA2:0000710 EHDAA:2838 EMAPA:16795 FMA:53471 MA:0001077 SCTID:244451008 TAO:0001301 VHOG:0000702 ZFA:0001301 ganglion of glossopharyngeal nerve ganglion of glosspharyngeal nerve glossopharyngeal IX ganglion petrosal ganglion uberon gIX UBERON:0001701 glossopharyngeal ganglion ZFA dorsal EHDAA2 ISBN:0471888893 ZFA ventrolateral EHDAA2 ISBN:0471888893 ZFA The group of neuron cell bodies associated with the ninth cranial nerve. MP:0001096 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000702 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ ganglion of glosspharyngeal nerve FMA:53471 glossopharyngeal IX ganglion MA:0001077 petrosal ganglion ZFA:0001301 Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] neurocranial It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... AAO:0010153 EHDAA2:0000243 EMAPA:17681 FMA:53672 MA:0000317 SCTID:361731002 TAO:0001580 Wikipedia:Neuroranium XAO:0003170 ZFA:0001580 brain box uberon brain case brain pan braincase UBERON:0001703 neurocranium FMA Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. PMID:11523816 TAO:MAH Wikipedia:Neuroranium ZFA:0001580 Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] 2012-08-14 TAO:0001580 TAO TAO:MAH The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. WP It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... MA brain case ZFA:0001580 brain pan http://www.thefreedictionary.com/braincase braincase ZFA:0001580 The nasal septum separates the left and right airways in the nose, dividing the two nostrils. It is depressed by the Depressor septi nasi muscle. [WP,unvetted]. We follow AAO in making this part of the nasal skeleton A median dividing wall, sagittally directed, which divides the nasal cavity into the right and the left nasal fossae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Medial vertical wall between nasal capsules.[AAO] Medial, vertical plate that separates the nasal capsules.[AAO] Whatever the common ancestor of the lamprey and gnathostomes may have looked like, it most likely possessed a neural-crest-derived premandibular ectomesenchyme closely associated with the NHP. Invention of the jaw subsequently required a space for the nasal septum and maxillary process to develop, which might have been provided by subdivision of the NHP into the nasal placode and the hypophysis (diplorhiny, the state of bilaterally separated nasal openings, would also have been a prerequisite for this).[well established][VHOG] AAO:0000559 AAO:0010135 EHDAA2:0001234 EHDAA2:0004104 EHDAA:6809 EMAPA:17608 FMA:54375 GAID:115 MA:0000285 MESH:D009300 NCIT:C33160 SCTID:181197004 UMLS:C0027432 VHOG:0000017 Wikipedia:Nasal_septum uberon septal cartilage septum mobile nasi septum nasi septum of the nose UBERON:0001706 nasal septum http://upload.wikimedia.org/wikipedia/commons/6/65/Gray854.png AAO AAO EHDAA2-abduced The nasal septum separates the left and right airways in the nose, dividing the two nostrils. It is depressed by the Depressor septi nasi muscle. [WP,unvetted]. Wikipedia:Nasal_septum A median dividing wall, sagittally directed, which divides the nasal cavity into the right and the left nasal fossae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000017 VHOG http://bgee.unil.ch/ Medial vertical wall between nasal capsules.[AAO] 2012-06-20 AAO:0010135 AAO AAO:EJS Medial, vertical plate that separates the nasal capsules.[AAO] 2012-06-20 AAO:0000559 AAO AAO:LAP Whatever the common ancestor of the lamprey and gnathostomes may have looked like, it most likely possessed a neural-crest-derived premandibular ectomesenchyme closely associated with the NHP. Invention of the jaw subsequently required a space for the nasal septum and maxillary process to develop, which might have been provided by subdivision of the NHP into the nasal placode and the hypophysis (diplorhiny, the state of bilaterally separated nasal openings, would also have been a prerequisite for this).[well established][VHOG] 2012-09-17 VHOG:0000017 VHOG DOI:10.1098/rstb.2001.0976 Kuratani S, Nobusada Y, Horigome N, Shigetani Y, Embryology of the lamprey and evolution of the vertebrate jaw: insights from molecular and developmental perspectives. Philosophical transactions of the Royal Society of London (2001) http://bgee.unil.ch/ UMLS:C0027432 ncithesaurus:Nasal_Septum septal cartilage Wikipedia:Nasal_septum septum mobile nasi Wikipedia:Nasal_septum septum nasi Wikipedia:Nasal_septum septum of the nose Wikipedia:Nasal_septum An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures AAO:0000314 BTO:0002096 EHDAA2:0001226 EHDAA:6801 EMAPA:17604 FMA:54378 GAID:350 MA:0000284 MESH:D009296 NCIT:C12424 SCTID:263481003 TAO:0000130 UMLS:C0027423 VHOG:0000271 Wikipedia:Nasal_cavity ZFA:0000130 cavity of nose cavity of olfactory apparatus nasal canal nasal conduit space nasal fossa olfactory chamber cavity uberon cavitas nasalis cavitas nasi cavum nasi nasal pit olfactory cavity olfactory chamber olfactory pit UBERON:0001707 nasal cavity http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg cjm An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. http://orcid.org/0000-0002-6601-2165 Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] 2012-06-20 AAO:0000314 AAO AAO:LAP a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Wikipedia:Nasal_cavity Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] 2012-09-17 VHOG:0000271 VHOG DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006) http://bgee.unil.ch/ in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures HP UMLS:C0027423 ncithesaurus:Nasal_Cavity cavity of olfactory apparatus http://orcid.org/0000-0002-6601-2165 nasal canal ZFA:0000130 nasal conduit space http://orcid.org/0000-0002-6601-2165 nasal fossa Wikipedia:Nasal_cavity olfactory chamber cavity http://orcid.org/0000-0002-6601-2165 cavitas nasalis BTO:0002096 cavitas nasi BTO:0002096 Wikipedia:Nasal_cavity cavum nasi Wikipedia:Nasal_cavity olfactory chamber http://orcid.org/0000-0002-6601-2165 olfactory pit ZFA:0000130 Subdivision of skeleton which includes upper and lower jaw skeletons. TODO - move ZFA:0001227 (it is the entire jaw skeleton). Skeletal and cartilage elements of the first pharyngeal arch.[TAO] There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates AAO:0000988 BTO:0001749 EMAPA:35455 FMA:54396 GAID:214 MA:0001905 MESH:D007568 NCIT:C48821 SCTID:181811001 TAO:0001227 UMLS:C0022359 Wikipedia:Jaw ZFA:0001227 galen:Jaw jaw jaw cartilage mandibular arch skeleton uberon anterior splanchnocranium jaws mandibular arch oral jaw skeleton pharyngeal arch 1 skeleton visceral arch 1 UBERON:0001708 jaw skeleton cjm Subdivision of skeleton which includes upper and lower jaw skeletons. Wikipedia:Jaw https://orcid.org/0000-0002-6601-2165 Skeletal and cartilage elements of the first pharyngeal arch.[TAO] 2012-08-14 TAO:0001227 TAO ZFIN:curator in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates FMA UMLS:C0022359 ncithesaurus:Jaw jaw MA:0001905 jaw cartilage ZFA:0001227 mandibular arch skeleton ZFA:0001227 mandibular arch TAO:0001227 Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000620 EHDAA2:0002118 EHDAA2:0004607 EHDAA:8025 EMAPA:17924 FMA:59399 SCTID:362636001 VHOG:0000454 Wikipedia:Upper_jaw ncithesaurus:Upper_Jaw maxillary part of mouth uberon alveolodental arch of bimaxilla dorsal mandibular arch dorsal pharyngeal arch 1 maxillary part of mouth proper palatoquadrate arch upper pharyngeal jaws UBERON:0001709 See notes for jaw w.r.t skeletal element vs subdivision of head. upper jaw region http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Wikipedia:Upper_jaw http://orcid.org/0000-0002-6601-2165 Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000620 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000454 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Note isa/partof difference MA/FMA MA maxillary part of mouth FMA:59399 alveolodental arch of bimaxilla FMA:59399 dorsal pharyngeal arch 1 maxillary part of mouth proper FMA:59399 palatoquadrate arch Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000272 EFO:0003660 EHDAA2:0001018 EHDAA:7995 EMAPA:17906 FMA:59398 MESH:D008334 SCTID:362637005 VHOG:0000453 Wikipedia:Lower_jaw ncithesaurus:Lower_Jaw mandibular part of mouth uberon lower part of mouth mandibular series UBERON:0001710 See notes for jaw w.r.t skeletal element vs subdivision of head lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png Wikipedia:Mandibular_prominence Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Wikipedia:Lower_jaw Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000272 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000453 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Note isa/partof difference MA/FMA MA mandibular part of mouth FMA:59398 The groups of nerve cell bodies associated with the twelve cranial nerves. Ganglion which is located in the head.[TAO] UBERON:0003213 UBERON:0026601 BIRNLEX:2597 BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 SCTID:244448001 TAO:0000013 VHOG:0000076 Wikipedia:Cranial_nerve_ganglion XAO:0000027 ZFA:0000013 cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ uberon cranial ganglia head ganglion presumptive cranial ganglia UBERON:0001714 cranial ganglion The groups of nerve cell bodies associated with the twelve cranial nerves. ISBN:0-683-40008-8 MGI:csmith MP:0001081 PMID:9362461 Ganglion which is located in the head.[TAO] 2012-08-14 TAO:0000013 TAO ZFIN:curator cranial ganglion part of peripheral nervous system BIRNLEX:2597 cranial neural tree organ ganglion OBOL:automatic ganglion of cranial nerve FMA:54502 ganglion of cranial neural tree organ OBOL:automatic presumptive cranial ganglia ZFA:0000013 The part of the palate formed from the fusion of the two palatine shelves, extensions of the maxillary prominences. palatal present in mammals and some reptiles. A similar structure is found in crocodilians, but, in most other tetrapods, the oral and nasal cavities are not truly separate. The secondary palate is formed by bilateral medial extensions of maxillary processes. The extensions (palatine processes) meet at the midline, merging dorsally with nasal septum and rostrally with primary palate. The secondary palate (hard palate) separates nasal and oral cavities. Caudal extension of the secondary palate into the pharynx, forms a soft palate which divides the rostral pharynx into dorsal (nasopharynx) and ventral (oropharynx) chamber. separates respiratory and oral passages palate palatum BTO:0001779 EMAPA:18948 FMA:54549 GAID:152 MA:0002476 MESH:D010159 NCIT:C12229 NCIT:C34292 SCTID:181227004 UMLS:C0700374 UMLS:C1519217 Wikipedia:Secondary_palate galen:Palate definitive palate oral roof palatum definitivum palatum secundarium uberon palatum roof of mouth UBERON:0001716 secondary palate http://upload.wikimedia.org/wikipedia/commons/3/31/Pig_snout_sagittal_cut.jpg http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg EMAPA fusion http://www.indiana.edu/~anat550/hnanim/face/face.html The part of the palate formed from the fusion of the two palatine shelves, extensions of the maxillary prominences. Wikipedia:Secondary_palate http://www.indiana.edu/~anat550/hnanim/face/face.html palate EMAPA:18948 GO:0060021 MA:0002476 UMLS:C0700374 ncithesaurus:Palate UMLS:C1519217 ncithesaurus:Secondary_Palate definitive palate EMAPA:18948 palatum definitivum Wikipedia:Secondary_palate palatum secundarium Wikipedia:Secondary_palate palatum Wikipedia:Palate A muscular organ in the floor of the mouth. in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence. A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] Muscular organ in the floor of the mouth.[FEED] The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] glossal lingual Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions AAO:0010360 BTO:0001385 CALOHA:TS-1050 EFO:0000833 EHDAA2:0002062 EHDAA:9144 EMAPA:17185 EV:0100058 FMA:54640 GAID:816 MA:0000347 MAT:0000040 MESH:D014059 MIAA:0000040 NCIT:C12422 SCTID:181226008 TAO:0005333 UMLS:C0040408 VHOG:0000419 Wikipedia:Tongue XAO:0000446 ZFA:0005333 uberon glossus UBERON:0001723 tongue http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg GO BTO EHDAA2 FMA ZFA MA anterior 2/3 Wikipedia Wikipedia definitional A muscular organ in the floor of the mouth. FEED:rd https://github.com/obophenotype/uberon/issues/256 A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] 2012-09-17 VHOG:0000419 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/tongue Muscular organ in the floor of the mouth.[FEED] 2012-07-02 FEED http://www.feedexp.org The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. GO:0043586 Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000419 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) http://bgee.unil.ch/ UMLS:C0040408 ncithesaurus:Tongue glossus Wikipedia:Tongue The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis. EMAPA:35264 FMA:54816 MA:0001502 SCTID:314228003 uberon UBERON:0001725 cranial synchondrosis FMA The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis. http://www.medilexicon.com/medicaldictionary.php?t=87514 BIRNLEX:4102 EMAPA:32777 FMA:54819 MA:0001593 NCIT:C33258 SCTID:368728006 UMLS:C0226964 UMLS:C1289183 lingual papilla tongue papilla uberon UBERON:0001726 papilla of tongue FMA-modified UMLS:C0226964 BIRNLEX:4102 ncithesaurus:Papilla_of_the_Tongue UMLS:C1289183 BIRNLEX:4102 A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish. arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL) AAO:0010573 BIRNLEX:4101 BTO:0000989 CALOHA:TS-1015 EMAPA:35850 FMA:54825 GAID:815 MA:0001591 MESH:D013650 NCIT:C96518 SCTID:362099006 TAO:0001074 UMLS:C0039337 VHOG:0000130 Wikipedia:Taste_bud XAO:0000445 ZFA:0001074 http://uri.neuinfo.org/nif/nifstd/nifext_14 tastebud uberon caliculus gustatorius taste buds taste-bud tastebuds UBERON:0001727 taste bud http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png NIF FMA http://dev.biologists.org/content/128/22/4573.full A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. http://periowiki.wikispot.org/Taste_bud_histology http://periowiki.wikispot.org/Taste_bud_histology A chemoreceptive organ.[AAO] 2012-06-20 AAO:0010573 AAO AAO:EJS One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] 2012-09-17 VHOG:0000130 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/taste+bud Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000130 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ UMLS:C0039337 BIRNLEX:4101 ncithesaurus:Taste_Bud tastebud Wikipedia:Taste_bud caliculus gustatorius Wikipedia:Taste_bud taste buds Wikipedia:Taste_bud taste-bud Wikipedia:Taste_bud tastebuds Wikipedia:Taste_bud The section of the pharynx that lies above the soft palate. The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG] nasopharyngeal In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane BTO:0000662 CALOHA:TS-0663 EHDAA2:0001239 EHDAA:7086 EMAPA:17670 EV:0100066 FMA:54878 GAID:339 MA:0000443 MAT:0000447 MESH:D009305 NCIT:C12423 SCTID:181200003 UMLS:C0027442 VHOG:0000375 Wikipedia:Nasopharynx nasal part of pharynx rhinopharynx uberon Nasenrachenraum epipharynx pars nasalis pharyngis UBERON:0001728 nasopharynx https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg The section of the pharynx that lies above the soft palate. MGI:cwg MP:0002251 The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG] 2012-09-17 VHOG:0000375 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/nasopharynx UMLS:C0027442 ncithesaurus:Nasopharynx Nasenrachenraum BTO:0000662 epipharynx Wikipedia:Pharynx pars nasalis pharyngis Wikipedia:Nasopharynx The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. One of the three anatomic divisions of the pharynx that lies posterior to the mouth and is continuous above with the nasopharynx and below with the laryngopharynx. It extends behind the mouth from the soft palate above to the level of the hyoid bone below and contains the palatine and lingual tonsils. [TFD][VHOG] oropharyngeal BTO:0005257 CALOHA:TS-0718 EFO:0001976 EHDAA2:0004082 EMAPA:25094 EV:0100067 FMA:54879 GAID:340 MA:0000351 MAT:0000446 MESH:D009960 NCIT:C12762 SCTID:263376008 UMLS:C0521367 VHOG:0000457 VSAO:0000034 Wikipedia:Oropharynx XAO:0004048 oral part of pharynx uberon mesopharynx pars oralis pharyngis UBERON:0001729 oropharynx https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg ISBN:0073040584-table13.1 The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. MGI:cwg MP:0002252 One of the three anatomic divisions of the pharynx that lies posterior to the mouth and is continuous above with the nasopharynx and below with the laryngopharynx. It extends behind the mouth from the soft palate above to the level of the hyoid bone below and contains the palatine and lingual tonsils. [TFD][VHOG] 2012-09-17 VHOG:0000457 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/oropharynx UMLS:C0521367 ncithesaurus:Oropharynx mesopharynx Wikipedia:Pharynx pars oralis pharyngis Wikipedia:Oropharynx An anatomical space that is enclosed by a pharynx. See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship TOODO check AAO:0010435 BSA:0000113 BTO:0002097 EMAPA:18381 FMA:54935 SCTID:180543003 XAO:0000105 lumen of pharynx pharyngeal cavity uberon cavitas pharyngealis cavitas pharyngis UBERON:0001731 cavity of pharynx XAO An anatomical space that is enclosed by a pharynx. OBOL:automatic cavitas pharyngealis cavitas pharyngis BTO:0002097 The lymph tissue in the roof and posterior wall of the nasopharynx. BTO:0000777 EV:0100054 FMA:54970 GAID:1288 MA:0000774 MESH:D000234 NCIT:C33318 SCTID:181199001 UMLS:C0001428 Wikipedia:Pharyngeal_tonsil adenoid nasopharyngeal tonsil tonsil of Luschka tonsilla pharyngealis uberon Rachenmandel tonsilla pharyngea UBERON:0001732 pharyngeal tonsil http://upload.wikimedia.org/wikipedia/commons/b/be/Gray994-adenoid.png cjm The lymph tissue in the roof and posterior wall of the nasopharynx. MGI:cwg MP:0002384 UMLS:C0001428 ncithesaurus:Pharyngeal_Tonsil tonsilla pharyngealis FMA:54970 FMA:TA Rachenmandel BTO:0000777 tonsilla pharyngea Wikipedia:Pharyngeal_tonsil The circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils. FMA:55070 MA:0000752 NCIT:C73468 SCTID:56411004 UMLS:C0459892 Wikipedia:Waldeyer's_ring Waldeyer's ring Waldeyer's tonsillar ring anulus lymphoideus pharyngis oropharyngeal lymphoid tissue pharyngeal lymphatic ring pharyngeal lymphoid ring uberon UBERON:0001735 tonsillar ring The circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils. MGI:cwg MP:0002379 UMLS:C0459892 ncithesaurus:Waldeyers_Tonsillar_Ring anulus lymphoideus pharyngis FMA:55070 FMA:TA Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG] The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted] In mouse, multilobed and lobulated, on the ventral midline of the neck in mice, submandibular gland development initiates as a thickening of the oral epithelium; around E12 an initial (single) epithelial bud on a stalk grows into a condensing neural crest-derived mesenchyme; clefts in the epithelium result in 3-5 epithelial buds at E13.5, and branching morphogenesis occurs with continued proliferation, successive rounds of cleft formation, duct elongation, and duct lumen formation, so that by E14 the gland is highly branched (multi-lobed); functional differentiation, with the appearance of proacinar cells and secretory products begins after E15 and continues to birth; acinar differentiation continues postnatally with final differentiation of the granular convoluted tubules at puberty[MGI:anna] The submandibular is the first major salivary gland to develop in the embryo, followed by the neighbouring sublingual and then the parotid.[PMID:17336109] The term submandibular as used in humans, is incorrect due the difference in topography of these structures[http://www.avdc.org] BTO:0001316 CALOHA:TS-0988 EFO:0001387 EMAPA:18812 EV:0100061 FMA:55093 GAID:942 MA:0001589 MESH:D013363 NCIT:C12233 SCTID:181235001 UMLS:C0038556 VHOG:0000364 Wikipedia:Submandibular_gland mandibular gland mandibular salivary gland submandibular salivary gland uberon glandula submandibularis maxillary gland submaxillary gland UBERON:0001736 lobular, sexually dimorphic in mouse submandibular gland http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg FMA-abduced-lr https://orcid.org/0000-0003-3308-6245 Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. DOI:10.1111/j.1432-0436.2006.00088.x MGI:anna Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG] 2012-09-17 VHOG:0000364 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/submandibular+gland The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] 2012-09-17 VHOG:0000364 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.525 http://bgee.unil.ch/ In mouse, multilobed and lobulated, on the ventral midline of the neck ISBN:0123813611 UMLS:C0038556 ncithesaurus:Submandibular_Gland mandibular gland http://www.avdc.org/Nomenclature.pdf mandibular salivary gland http://www.avdc.org/Nomenclature.pdf glandula submandibularis Wikipedia:Submandibular_gland A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] laryngeal AAO:0000268 BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 NCIT:C12420 SCTID:181212004 UMLS:C0023078 VHOG:0001279 Wikipedia:Larynx XAO:0003081 galen:Larynx uberon UBERON:0001737 larynx http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb EHDAA2 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. Wikipedia:Larynx http://orcid.org/0000-0002-6601-2165 An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] 2012-07-02 FEED http://www.feedexp.org Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] 2012-06-20 AAO:0000268 AAO AAO:BJB (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001279 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 http://bgee.unil.ch/ UMLS:C0023078 ncithesaurus:Larynx The cartilaginous structures that support the larynx. (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] BTO:0003660 EHDAA:8157 EMAPA:18697 FMA:55108 GAID:107 MA:0001758 MESH:D007817 NCIT:C12281 SCTID:263482005 UMLS:C0023050 VHOG:0001550 cartilage of larynx cartilagines laryngeales larynx cartilage uberon UBERON:0001739 laryngeal cartilage https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb The cartilaginous structures that support the larynx. MP:0002256 (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001550 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 http://bgee.unil.ch/ UMLS:C0023050 ncithesaurus:Laryngeal_Cartilage cartilage of larynx FMA:55108 cartilagines laryngeales larynx cartilage VHOG:0001550 A ligament that is part of a larynx and connexts the cartilages of the larynx. EMAPA:37626 FMA:55131 MA:0001755 NCIT:C32933 SCTID:279508004 UMLS:C0458519 laryngeal ligament larynx ligament uberon UBERON:0001743 ligament of larynx FMA A ligament that is part of a larynx and connexts the cartilages of the larynx. http://education.yahoo.com/reference/gray/subjects/subject/236 EMAPA:37626 MA:th UMLS:C0458519 ncithesaurus:Laryngeal_Ligament larynx ligament MA:0001755 Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. BTO:0000753 CALOHA:TS-0584 FMA:55220 GAID:342 MA:0002436 MESH:D008221 NCIT:C13049 SCTID:181768009 UMLS:C0024296 Wikipedia:Lymphoid_tissue galen:LymphoidTissue lymphatic tissue lymphocytic tissue uberon UBERON:0001744 lymphoid tissue FMA NCBIBook:NBK27108 Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. Wikipedia:Lymphoid_tissue lampreys lack organized lymphoid tissue NCBIBook:NBK27108 UMLS:C0024296 ncithesaurus:Lymphoid_Tissue EMAPA:37767 FMA:55513 MA:0002675 NCIT:C33781 SCTID:176859009 UMLS:C0229575 capsula fibrosa glandulae thyroideae fibrous capsule of thyroid gland thyroid capsule thyroid gland capsule uberon UBERON:0001746 capsule of thyroid gland EMAPA:37767 MA:th UMLS:C0229575 ncithesaurus:Thyroid_Gland_Capsule capsula fibrosa glandulae thyroideae FMA:55513 FMA:TA fibrous capsule of thyroid gland FMA:55513 thyroid gland capsule MA:0002675 A parenchyma that is part of a thyroid follicle [Automatically generated definition]. BTO:0004579 EMAPA:37769 FMA:55515 MA:0000730 SCTID:371402001 parenchyma of thyroid parenchyma of thyroid follicle parenchyma of thyroid gland follicle thyroid follicle parenchyma thyroid gland follicle parenchyma thyroid gland parenchyma thyroid parenchyma uberon parenchyma glandulae thyroideae UBERON:0001747 parenchyma of thyroid gland FMA FMA A parenchyma that is part of a thyroid follicle [Automatically generated definition]. OBOL:automatic EMAPA:37769 MA:th parenchyma of thyroid OBOL:accepted parenchyma of thyroid follicle OBOL:automatic parenchyma of thyroid gland follicle OBOL:automatic thyroid follicle parenchyma OBOL:automatic thyroid gland follicle parenchyma OBOL:automatic thyroid parenchyma OBOL:accepted parenchyma glandulae thyroideae BTO:0004579 The dense and irregular connective tissue capsule surrounding a parathyroid gland. EMAPA:35663 FMA:55566 MA:0002676 NCIT:C33265 UMLS:C0927176 parathyroid gland capsule uberon UBERON:0001748 capsule of parathyroid gland MA The dense and irregular connective tissue capsule surrounding a parathyroid gland. MGI:anna UMLS:C0927176 ncithesaurus:Parathyroid_Gland_Capsule A parenchyma that is part of a parathyroid gland [Automatically generated definition]. EMAPA:35664 FMA:55569 MA:0002677 parathyroid gland parenchyma parathyroid parenchyma parenchyma of parathyroid uberon UBERON:0001749 parenchyma of parathyroid gland FMA FMA A parenchyma that is part of a parathyroid gland [Automatically generated definition]. OBOL:automatic parathyroid parenchyma OBOL:automatic parenchyma of parathyroid OBOL:automatic A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta. TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye EMAPA:35462 FMA:55605 GAID:901 MA:0000274 MESH:D007765 NCIT:C32905 UMLS:C0022903 Wikipedia:Lacrimal_apparatus apparatus lacrimalis lacrymal system uberon lacrimal drainage system nasolacrimal drainage system nasolacrimal system UBERON:0001750 lacrimal apparatus http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png MA HPO:pr ISBN:0781772214 A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta. MGI:anna this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye ncit UMLS:C0022903 ncithesaurus:Lacrimal_Apparatus apparatus lacrimalis Wikipedia:Lacrimal_apparatus lacrymal system MGI:anna lacrimal drainage system https://orcid.org/0000-0002-6601-2165 nasolacrimal drainage system https://orcid.org/0000-0002-6601-2165 nasolacrimal system HPO:pr Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular. Mineralized collagen containing substance that forms the tooth structure.[TAO] Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG] dentinal Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP] BTO:0003453 EMAPA:35281 FMA:55628 GAID:1272 MA:0002542 MESH:D003804 NCIT:C32453 SCTID:362112004 TAO:0005143 UMLS:C0011429 VHOG:0001589 VSAO:0000069 Wikipedia:Dentin XAO:0004051 ZFA:0005143 dentin dentine of tooth predentin uberon UBERON:0001751 . dentine VSAO VSAO Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular. GO_REF:0000034 PSPUB:0000170 VSAO:0000069 http://dx.plos.org/10.1371/journal.pone.0051070 Mineralized collagen containing substance that forms the tooth structure.[TAO] 2012-08-14 TAO:0005143 TAO ZFIN:curator Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG] 2012-09-17 VHOG:0001589 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) http://bgee.unil.ch/ UMLS:C0011429 ncithesaurus:Dentin dentin MA:0002542 ZFA:0005143 predentin GO:0070468 A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP]. current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles) Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO] part_of tooth enamel organ in MA BTO:0001844 CALOHA:TS-1057 EMAPA:35303 FMA:55629 MA:0002543 MESH:D003743 NCIT:C32505 SCTID:362113009 UMLS:C0011350 VSAO:0000065 Wikipedia:Enamel_organ XAO:0004198 enamel of tooth enamel tissue tooth enamel uberon enameloid UBERON:0001752 enamel http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg VSAO VSAO 85 Wikipedia:ENAM A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP]. Wikipedia:Enamel_organ ZFIN:curator PMID:19730686 PMID:19730686 Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO] 2012-08-14 VSAO:0000065 VSAO PSPUB:0000170 part_of tooth enamel organ in MA MA UMLS:C0011350 ncithesaurus:Enamel enamel tissue VSAO:curator The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP]. Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO] The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG] BTO:0000339 CALOHA:TS-0195 EMAPA:35274 FMA:55631 GAID:1270 MA:0001599 MESH:D003782 NCIT:C32451 SCTID:362110007 TAO:0005141 UMLS:C0011399 VHOG:0001469 Wikipedia:Dental_pulp ZFA:0005141 pulp of tooth tooth pulp uberon dental pulp cell UBERON:0001754 dental pulp https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg FMA ZFA The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP]. Wikipedia:Dental_pulp Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO] 2012-08-14 TAO:0005141 TAO ZFIN:curator The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0001469 VHOG DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011) http://bgee.unil.ch/ UMLS:C0011399 ncithesaurus:Dental_Pulp tooth pulp ZFA:0005141 dental pulp cell BTO:0000339 The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]. The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG] AAO:0011065 BIRNLEX:1695 BTO:0002099 CALOHA:TS-2233 EHDAA2:0001181 EHDAA:5693 EMAPA:17000 EV:0100357 FMA:56513 GAID:165 MA:0000253 MAT:0000146 MESH:D004432 MIAA:0000146 NCIT:C12274 SCTID:181185000 UMLS:C0013455 UMLS:C1268972 VHOG:0000312 Wikipedia:Middle_ear XAO:0000191 uberon auris media UBERON:0001756 middle ear The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]. GO:0042474 Wikipedia:Middle_ear The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000312 VHOG http://bgee.unil.ch/ The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG] 2012-09-17 VHOG:0000312 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417 http://bgee.unil.ch/ UMLS:C0013455 BIRNLEX:1695 ncithesaurus:Middle_Ear UMLS:C1268972 BIRNLEX:1695 auris media BTO:0002099 Wikipedia:Middle_ear The part of the ear that projects from the head, connecting to the external acoustic meatus. The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG] In various species, the pinna can also signal mood and radiate heat The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch). EHDAA2:0001467 EMAPA:17589 EV:0100355 FMA:56580 MA:0000259 NCIT:C32165 SCTID:421159007 UMLS:C0928075 VHOG:0000460 Wikipedia:Pinna_(anatomy) galen:Auricle auricle auricle of ear auricle of external ear auricula auricula (auris externa) pinna of ear uberon pinnae UBERON:0001757 pinna The part of the ear that projects from the head, connecting to the external acoustic meatus. Wikipedia:Pinna_(anatomy) http://orcid.org/0000-0002-6601-2165 The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000460 VHOG http://bgee.unil.ch/ Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG] 2012-09-17 VHOG:0000460 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420 http://bgee.unil.ch/ UMLS:C0928075 ncithesaurus:Auricle auricula Wikipedia:Auricula pinnae The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]. FMA treats periodontium and periodontal ligament as the same BTO:0001021 CALOHA:TS-2380 GAID:216 MESH:D010519 NCIT:C33304 UMLS:C0031093 Wikipedia:Periodontium uberon paradentium periodontal ligament periodontal membrane tooth supporting structure UBERON:0001758 periodontium https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg cjm cjm FMA The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]. BTO:0001021 Wikipedia:Periodontium FMA treats periodontium and periodontal ligament as the same FMA UMLS:C0031093 ncithesaurus:Periodontium paradentium MESH:A14.254.646 periodontal ligament FMA:56665 periodontal membrane MA:0002467 tooth supporting structure MESH:A14.254.646 Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 10n AAO:0010475 BAMS:10n BAMS:Xn BIRNLEX:801 BTO:0003472 EFO:0002549 EMAPA:37797 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 NCIT:C12812 SCTID:362466001 TAO:0000453 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 Wikipedia:Vagus_nerve XAO:0003097 ZFA:0000453 galen:VagusNerve neuronames:702 nervus vagus [x] tenth cranial nerve vagus vagus X nerve vagus nerve [X] vagus nerve tree uberon CN-X cranial nerve X nerve X nervus vagus pneuomgastric nerve vagal nerve vagus nerve or its root UBERON:0001759 vagus nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png motor Wikipedia Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). ISBN:0471209627 Wikipedia:Vagus_nerve Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] 2012-06-20 AAO:0010475 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000737 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ 10n BIRNLEX:801 NIFSTD:NeuroNames_abbrevSource EMAPA:37797 MA:th UMLS:C0042276 BIRNLEX:801 ncithesaurus:Vagus_Nerve UMLS:C1305910 BIRNLEX:801 neuronames:702 BIRNLEX:801 nervus vagus [x] FMA:5731 FMA:TA vagus X nerve MA:0001106 nerve X NeuroNames:702 nervus vagus BTO:0003472 Wikipedia:Vagus_nerve pneuomgastric nerve BTO:0003472 vagus nerve or its root BAMS:10n The small curved bones that extends horizontally along the lateral wall of the nasal passage. In humans, the turbinates divide the nasal airway into three groove-like air passages -and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue. Turbinals are only ossified in birds and derived synapsids. FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here EHDAA2:0004101 EMAPA:25093 GAID:224 MA:0000286 MESH:D014420 NCIT:C49594 SCTID:361931007 UMLS:C1266928 Wikipedia:Nasal_concha ossified nasal turbinal ossified nasal turbinate ossified turbinate turbinal bone turbinate bone uberon concha UBERON:0001762 turbinate bone http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray153.png The small curved bones that extends horizontally along the lateral wall of the nasal passage. ISBN:0-683-40008-8 MP:0002244 disputed http://palaeos.com/vertebrates/bones/braincase/ethmoid.html In humans, the turbinates divide the nasal airway into three groove-like air passages -and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue. WP,unvetted FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here FMA UMLS:C1266928 ncithesaurus:Nasal_Turbinate turbinate bone EMAPA:25093 concha EMAPA:25093 A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ. Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO] Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO] Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG] In humans, the dental papilla appears after 8-10 weeks intra uteral life BTO:0001839 EMAPA:32892 FMA:57662 GAID:1277 MA:0001598 MESH:D003771 TAO:0005140 VHOG:0001465 VSAO:0000025 Wikipedia:Dental_papilla XAO:0004045 ZFA:0005140 odontogenic condensation pharyngeal tooth mesenchyme uberon dental papilla dentinal papilla dermal papilla papilla dentis tooth mesenchyme UBERON:0001763 odontogenic papilla http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png ZFA A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ. Wikipedia:Dental_papilla ZFA:0005140 Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO] 2012-08-14 VSAO:0000025 VSAO PSPUB:0000170 Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO] 2012-08-14 TAO:0005140 TAO ZFIN:curator Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG] 2012-09-17 VHOG:0001465 VHOG DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011) http://bgee.unil.ch/ odontogenic condensation VSAO:0000025 pharyngeal tooth mesenchyme ZFA:0005140 dental papilla MA:0001598 dentinal papilla BTO:0001839 dermal papilla ISBN:0073040584 papilla dentis Wikipedia:Dental_papilla tooth mesenchyme ZFA:0005140 Epithelial tube that transports milk[GO]. BTO:0002845 CALOHA:TS-2385 EMAPA:35538 FMA:58006 MA:0000791 NCIT:C32910 SCTID:361719004 UMLS:C0222613 Wikipedia:Lactiferous_duct lactiferous duct lactiferous gland duct mammary gland duct uberon ductus lactiferi galactophorous duct galactophorous tubule lactiferous tubule mammilary duct UBERON:0001765 This structure regresses in most males mammary duct http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg Epithelial tube that transports milk[GO]. GO:0060603 Wikipedia:Lactiferous_duct UMLS:C0222613 ncithesaurus:Lactiferous_Duct lactiferous duct FMA:58006 lactiferous gland duct OBOL:automatic mammary gland duct MA:0000791 ductus lactiferi BTO:0002845 Wikipedia:Lactiferous_duct galactophorous duct Wikipedia:Lactiferous_duct galactophorous tubule BTO:0002845 lactiferous tubule BTO:0002845 mammilary duct Wikipedia:Lactiferous_duct The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 EMAPA:18231 FMA:58078 GAID:889 MA:0000262 MESH:D000867 NCIT:C12667 SCTID:181160009 UMLS:C0003151 VHOG:0001431 Wikipedia:Anterior_chamber_of_eyeball anterior chamber anterior chamber of eye camera anterior eye anterior chamber uberon camera anterior bulbi camera anterior bulbi oculi camera oculi anterior UBERON:0001766 anterior chamber of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. MESH:A09.371.060.067 MP:0005205 The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] 2012-09-17 VHOG:0001431 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/anterior+chamber space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball EHDAA2 UMLS:C0003151 ncithesaurus:Anterior_Chamber_of_the_Eye anterior chamber HP:0000593 MP:0010709 camera anterior bulbi BTO:0002084 camera anterior bulbi oculi Wikipedia:Anterior_chamber_of_eyeball camera oculi anterior BTO:0002084 The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 NCIT:C12811 SCTID:280648000 UMLS:C0042160 Wikipedia:Uvea tunica vasculosa of eyeball uvea uveal tract uberon pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball UBERON:0001768 uvea http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png FMA The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. MP:0005197 Wikipedia:Uvea DOI:10.1177/0192623311409597 UMLS:C0042160 ncithesaurus:Uvea tunica vasculosa of eyeball FMA:58103 uvea FMA:58103 uveal tract FMA:58103 pars iridica retinae Wikipedia:Uvea tunica vasculatis oculi Wikipedia:Uvea tunica vasculosa bulbi Wikipedia:Uvea vascular layer of eyeball FMA:58103 The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] iridial The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 NCIT:C12737 SCTID:181164000 TAO:0001238 UMLS:C0022077 VHOG:0000101 Wikipedia:Iris_(anatomy) XAO:0000185 ZFA:0001238 uberon anterior uvea irides irises UBERON:0001769 iris XAO The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. ISBN:0-683-40008-8 MP:0001322 The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000101 VHOG http://bgee.unil.ch/ The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000101 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0022077 ncithesaurus:Iris irides irises VHOG:0000101 The smooth stratified squamous epithelium that covers the outer surface of the cornea. Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 MA:0001243 MESH:D019573 NCIT:C12928 SCTID:368825001 TAO:0002187 UMLS:C0459875 Wikipedia:Corneal_epithelium ZFA:0001683 anterior corneal epithelium cornea epithelial tissue cornea epithelium epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea external epithelium of cornea uberon anterior endothelium of cornea e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelium posterius corneae UBERON:0001772 corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png ISBN:0781772214 The smooth stratified squamous epithelium that covers the outer surface of the cornea. MESH:A09.371.060.217.325 MGI:smb MP:0006000 Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] 2012-08-14 TAO:0002187 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0459875 ncithesaurus:Corneal_Epithelium cornea epithelial tissue OBOL:automatic cornea epithelium OBOL:automatic epithelial tissue of cornea OBOL:automatic epithelium anterius corneae FMA:58263 FMA:TA anterior endothelium of cornea BTO:0000287 e. anterius corneae Wikipedia:Corneal_epithelium endothelium anterius corneae BTO:0000287 endothelium camerae anterioris bulbi BTO:0000287 endothelium corneale BTO:0000287 epithelium posterius corneae BTO:0000287 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] scleral in fish, reptiles and monotremes the connective tissue of the sclera is skeletal continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 NCIT:C12784 SCTID:181163006 UMLS:C0036410 VHOG:0001274 Wikipedia:Sclera XAO:0000183 ZFA:0005563 uberon scleral capsule UBERON:0001773 Disease notes: implicated in rheumatoid arthritis. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA ZFA ISBN:0781772214 cjm ISBN:0781772214 Wikipedia Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. Wikipedia:Sclera ZFIN:ZDB-PUB-050701-15 The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. Wikipedia:Sclera The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] 2012-09-17 VHOG:0001274 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/sclera UMLS:C0036410 ncithesaurus:Sclera A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. AAO:0000611 EMAPA:35888 FMA:58274 MA:0000514 TAO:0000473 XAO:0003230 ZFA:0000473 body musculature muscle of trunk muscle organ of torso muscle organ of trunk torso muscle organ trunk muscle trunk muscle organ trunk musculature uberon UBERON:0001774 skeletal muscle of trunk prolog A skeletal muscle organ that is part of the trunk region. http://orcid.org/0000-0002-6601-2165 body musculature ZFA:0000473 muscle of trunk FMA:58274 muscle organ of torso OBOL:automatic muscle organ of trunk OBOL:automatic torso muscle organ OBOL:automatic trunk muscle organ OBOL:automatic The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 NCIT:C12345 SCTID:263340007 UMLS:C0008779 VHOG:0000102 Wikipedia:Ciliary_body XAO:0000186 neuronames:1571 ocular ciliary body uberon anterior uvea ciliary bodies corpus ciliare UBERON:0001775 ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg ISBN:0781772214 The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes. ISBN:0-683-40008-8 MP:0005099 Wikipedia:Ciliary_body The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000102 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0008779 ncithesaurus:Ciliary_Body ciliary bodies VHOG:0000102 corpus ciliare Wikipedia:Ciliary_body Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA choroidal MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 NCIT:C12344 SCTID:181172003 TAO:0005229 UMLS:C0008520 VHOG:0001568 Wikipedia:Choroid ZFA:0005229 choroid choroid coat choroidea eye choroid posterior uvea uberon chorioid choroidea optic choroid UBERON:0001776 optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg MA Wikipedia lexical Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. Wikipedia:Choroid MP treats posterior uvea and optic choroid as distinct MP UMLS:C0008520 ncithesaurus:Choroid choroid MA:0000263 choroid coat Wikipedia:Choroid choroidea Wikipedia:Choroid eye choroid VHOG:0001568 posterior uvea Wikipedia:Uvea#Regions chorioid BTO:0001829 choroidea Wikipedia:Choroid optic choroid ZFA:0005229 The lamellated connective tissue of the cornea between the Bowman and Descemet membranes. Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] substantia propria CALOHA:TS-1138 EFO:0002514 EMAPA:17602 FMA:58306 GAID:893 MA:0001245 MESH:D003319 NCIT:C12699 SCTID:362511000 TAO:0002189 UMLS:C0010040 Wikipedia:Corneal_stroma ZFA:0001685 corneal stroma stroma of cornea substantia propria corneae uberon UBERON:0001777 substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png cjm ISBN:0781772214 Wikipedia The lamellated connective tissue of the cornea between the Bowman and Descemet membranes. ISBN:0-683-40008-8 MESH:A09.371.060.217.228 MP:0005300 Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] 2012-08-14 TAO:0002189 TAO ZFIN:ZDB-PUB-061010-3 relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO UMLS:C0010040 ncithesaurus:Corneal_Stroma corneal stroma MA:0001245 substantia propria corneae FMA:58306 FMA:TA A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 CALOHA:TS-0695 EMAPA:35239 FMA:58464 MA:0001238 NCIT:C32314 SCTID:280870004 UMLS:C0459736 Wikipedia:Ciliary_body#Ciliary_epithelium ciliary body epithelium epithelium of ciliary body ocular ciliary epithelium uberon UBERON:0001778 ciliary epithelium FMA MA MP Wikipedia A double layer covering the ciliary body that produces aqueous humor. Wikipedia:Ciliary_body#Ciliary_epithelium UMLS:C0459736 ncithesaurus:Ciliary_Epithelium ciliary body epithelium FMA:58464 epithelium of ciliary body FMA:58464 The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. EMAPA:35451 FMA:58526 MA:0002777 SCTID:280882008 Wikipedia:Iris_stroma ZFA:0005569 iridial stroma stroma of iris uberon UBERON:0001779 iris stroma http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. Wikipedia:Iris_stroma http://www.drugs.com/dict/stroma-of-iris.html The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]. Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] AAO:0011101 BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 NCIT:C12792 SCTID:361099009 UMLS:C0037941 VHOG:0000824 Wikipedia:Spinal_nerve XAO:0003101 neuronames:1228 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column spinal column nerve spinal nerve tree spine nerve vertebral column nerve uberon nervi spinales spinal nerves UBERON:0001780 spinal nerve https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]. MESH:A08.800.800.720 MP:0001077 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] 2012-09-17 VHOG:0000824 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/spinal+nerve UMLS:C0037941 ncithesaurus:Spinal_Nerve backbone nerve OBOL:automatic nerve of backbone OBOL:automatic nerve of spinal column OBOL:automatic nerve of spine OBOL:automatic nerve of vertebral column OBOL:automatic spinal column nerve OBOL:automatic spine nerve OBOL:automatic vertebral column nerve OBOL:automatic nervi spinales Wikipedia:Spinal_nerve spinal nerves BAMS:spin Any of the layers that make up the retina[MP]. MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 MA:0001319 NCIT:C49328 SCTID:280657006 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon UBERON:0001781 layer of retina Any of the layers that make up the retina[MP]. MP:0003727 MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers MA UMLS:C0459649 ncithesaurus:Retina_Layer retina neuronal layer MP:0006069 retinal neuronal layer MP:0006069 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 AAO:0000108 BAMS:cran BIRNLEX:1623 BTO:0001104 EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 NCIT:C12700 SCTID:244447006 TAO:0000641 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 Wikipedia:Cranial_nerve XAO:0000429 XAO:0003089 ZFA:0000641 neuronames:1227 cranial neural tree organ uberon cranial nerves nervus cranialis UBERON:0001785 cranial nerve http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. Wikipedia:Cranial_nerve Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] 2012-08-14 TAO:0000641 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] 2012-09-17 VHOG:0000279 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ UMLS:C0010268 BIRNLEX:1623 ncithesaurus:Cranial_Nerve UMLS:C1269897 BIRNLEX:1623 nervus cranialis Wikipedia:Cranial_nerve A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 ENVO:02000024 FMA:58819 GAID:890 MA:0001236 MESH:D001082 NCIT:C13190 SCTID:280587006 UMLS:C0003662 VHOG:0000548 Wikipedia:Aqueous_humor ZFA:0005564 aqueous humor aqueous humour humor aquosus uberon UBERON:0001796 aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA def states A and P located_in in EHDAA2 VHOG A thick watery refractive medium that fills the space between the lens and the cornea[WP]. Wikipedia:Aqueous_humor The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] 2012-09-17 VHOG:0000548 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/aqueous+humour (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000548 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 http://bgee.unil.ch/ FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. FMA UMLS:C0003662 ncithesaurus:Aqueous_Humor aqueous humour EHDAA2:0000139 humor aquosus FMA:58819 FMA:TA A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. portion of vitreous humor BTO:0001451 CALOHA:TS-0308 EMAPA:17837 ENVO:02000032 EV:0100344 FMA:58822 MA:0001286 MESH:D014822 NCIT:C13323 UMLS:C0229096 VHOG:0000795 Wikipedia:Vitreous_humour ZFA:0005561 humor vitreous humor vitreus vitreous whole portion of vitreous humor uberon humoral fluid ocular fluid vitreous fluid vitreous humour UBERON:0001797 vitreous humor http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. MP:0002699 portion of vitreous humor FMA:67388 MESH:D014822 https://github.com/biopragmatics/biomappings UMLS:C0229096 ncithesaurus:Vitreous_Humor humor vitreus FMA:58822 FMA:TA vitreous ZFA:0005561 whole portion of vitreous humor FMA:58822 humoral fluid BTO:0001451 ocular fluid BTO:0001451 vitreous fluid BTO:0001451 Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified]. distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body CALOHA:TS-0308 FMA:58827 GAID:919 MA:0002462 MESH:D014822 NCIT:C33884 SCTID:181170006 UMLS:C0042905 uberon UBERON:0001798 vitreous body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA neural ectoderm of optic cup ISBN:0781772214 Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified]. MP:0002699 UMLS:C0042905 ncithesaurus:Vitreous_Body The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified]. BTO:0002087 EMAPA:37805 FMA:58848 MA:0002461 NCIT:C33885 UMLS:C0229095 Wikipedia:Vitreous_chamber camera postrema camera postrema bulbi oculi camera vitrea camera vitrea bulbi postremal chamber postremal chamber of eyeball vitreous chamber uberon UBERON:0001799 vitreous chamber of eyeball The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified]. BTO:0002087 EMAPA:37805 MA:th UMLS:C0229095 ncithesaurus:Vitreous_Chamber camera postrema FMA:58848 camera postrema bulbi oculi FMA:58848 FMA:TA camera vitrea FMA:58848 camera vitrea bulbi FMA:58848 postremal chamber FMA:58848 postremal chamber of eyeball FMA:58848 vitreous chamber FMA:58848 The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. AEO:0001000 BTO:0005630 EMAPA:36596 FMA:5885 MA:0002566 MESH:D017950 NCIT:C13060 UMLS:C0206429 ganglion sensorium uberon UBERON:0001800 sensory ganglion The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. MP:0000960 UMLS:C0206429 ncithesaurus:Sensory_Ganglion ganglion sensorium Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive). EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 NCIT:C12668 SCTID:280658001 UMLS:C0003153 Wikipedia:Anterior_segment_of_eyeball ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye eye anterior segment segmentum anterius (bulbus oculi) uberon segmentum anterius bulbi oculi UBERON:0001801 anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png FMA cjm lexical Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive). ISBN:0-683-40008-8 MESH:A09.371.060 MP:0005193 ZFA https://github.com/obophenotype/uberon/issues/378 pending UMLS:C0003153 ncithesaurus:Anterior_Eye_Segment anterior segment eye ZFA:0005566 segmentum anterius bulbi oculi Wikipedia:Anterior_segment_of_eyeball Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive). EMAPA:36595 FMA:58868 MA:0002485 NCIT:C12906 SCTID:280659009 UMLS:C0278450 Wikipedia:Posterior_segment_of_eyeball ZFA:0005567 eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) uberon segmentum posterius bulbi oculi UBERON:0001802 posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA cjm Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive). ISBN:0-683-40008-8 MP:0005195 UMLS:C0278450 ncithesaurus:Posterior_Eye_Segment posterior segment eye ZFA:0005567 segmentum posterius bulbi oculi Wikipedia:Posterior_segment_of_eyeball A layer of epithelial cells that is part of the eye. this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former BTO:0001873 CALOHA:TS-0543 EMAPA:32871 FMA:58871 MA:0001301 SCTID:362523006 TAO:0001326 Wikipedia:Lens_(anatomy)#Lens_Epithelium XAO:0004094 ZFA:0001326 epithelial tissue of eye lens epithelial tissue of lens epithelium lentis epithelium of eye lens eye lens epithelial tissue eye lens epithelium lens epithelial tissue lens epithelium uberon UBERON:0001803 epithelium of lens A layer of epithelial cells that is part of the eye. http://orcid.org/0000-0002-6601-2165 epithelial tissue of eye lens OBOL:automatic epithelial tissue of lens OBOL:automatic epithelium lentis FMA:58871 FMA:TA epithelium of eye lens OBOL:automatic eye lens epithelial tissue OBOL:automatic eye lens epithelium OBOL:automatic lens epithelial tissue OBOL:automatic The elastic, clear, membrane-like structure, that is outer most layer of the lens. The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular EHDAA2:0000977 EMAPA:18237 FMA:58881 MA:0001300 NCIT:C32975 SCTID:244500004 UMLS:C0229232 VHOG:0000550 Wikipedia:Lens_(anatomy)#Lens_capsule ZFA:0005574 capsula lentis lens capsule uberon UBERON:0001804 capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png EHDAA2 The elastic, clear, membrane-like structure, that is outer most layer of the lens. MGI:smb MP:0003236 PMID:15483628 The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000550 VHOG http://bgee.unil.ch/ (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000550 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 http://bgee.unil.ch/ FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular FMA UMLS:C0229232 ncithesaurus:Lens_Capsule capsula lentis Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. AEO:0001001 CALOHA:TS-2340 EMAPA:17157 EMAPA:18221 FMA:5889 MA:0000220 MESH:D005725 NCIT:C12720 UMLS:C0017068 Wikipedia:Autonomic_ganglion autonomic nervous system ganglion ganglion of autonomic nervous system ganglion of visceral nervous system visceral nervous system ganglion uberon ganglion autonomicum UBERON:0001805 autonomic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. Wikipedia:Autonomic_ganglion UMLS:C0017068 ncithesaurus:Autonomic_Ganglion autonomic nervous system ganglion OBOL:automatic ganglion of autonomic nervous system OBOL:automatic ganglion of visceral nervous system OBOL:automatic visceral nervous system ganglion OBOL:automatic ganglion autonomicum Wikipedia:Autonomic_ganglion A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia. AAO:0010773 BTO:0001333 CALOHA:TS-0994 EHDAA2:0001969 EMAPA:17157 FMA:5890 MA:0000226 MESH:D005728 NCIT:C12467 SCTID:362485003 UMLS:C0017071 Wikipedia:Sympathetic_ganglion ganglion of sympathetic nervous system ganglion of sympathetic part of autonomic division of nervous system ganglion sympatheticum sympathetic nervous system ganglion sympathetic part of autonomic division of nervous system ganglion uberon ganglion sympathicum UBERON:0001806 sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png DOI:10.1101/gr.157586.113 ISBN:0073040584 A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia. MP:0001008 http://orcid.org/0000-0002-6601-2165 MESH:D005728 https://github.com/biopragmatics/biomappings UMLS:C0017071 ncithesaurus:Sympathetic_Ganglion ganglion of sympathetic nervous system OBOL:automatic ganglion of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system ganglion OBOL:automatic sympathetic part of autonomic division of nervous system ganglion OBOL:automatic ganglion sympathicum BTO:0001333 Wikipedia:Sympathetic_ganglion Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. BTO:0001256 EHDAA2:0001400 EMAPA:32813 FMA:5894 MA:0002469 MESH:D005726 NCIT:C52557 NLXANAT:100303 SCTID:279284004 UMLS:C0017069 Wikipedia:Parasympathetic_ganglion uberon ganglion parasympathicum UBERON:0001808 parasympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. NLXANAT:100303 MESH:D005726 https://github.com/biopragmatics/biomappings UMLS:C0017069 ncithesaurus:Parasympathetic_Ganglion ganglion parasympathicum BTO:0001256 Wikipedia:Parasympathetic_ganglion Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. Made to be a subtype of junction rather than tissue to be consistent with FMA plexus AEO:0000138 BTO:0000205 EHDAA2:0003138 EHDAA:3780 EMAPA:37683 FMA:5901 MA:0002407 NCIT:C12929 SCTID:122455009 UMLS:C0501403 Wikipedia:Nervous_system_plexus uberon UBERON:0001810 nerve plexus AEO AEO Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. FMA:5901 Wikipedia:Nervous_system_plexus https://github.com/obophenotype/cell-ontology/issues/1306 Made to be a subtype of junction rather than tissue to be consistent with FMA FMA EMAPA:37683 MA:th UMLS:C0501403 ncithesaurus:Nerve_Plexus An intermingling of fiber fascicles from adjacent spinal nerves to form a network. To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] EHDAA2:0001899 EMAPA:16987 FMA:5903 MA:0000235 NCIT:C49601 SCTID:42280003 UMLS:C0228603 VHOG:0000925 plexus nervorum spinalium plexus of spinal nerves somatic nerve plexus spinal nerve plexus uberon UBERON:0001813 spinal nerve plexus An intermingling of fiber fascicles from adjacent spinal nerves to form a network. http://www.medilexicon.com/medicaldictionary.php?t=70024 To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] 2012-09-17 VHOG:0000926 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436 http://bgee.unil.ch/ UMLS:C0228603 ncithesaurus:Spinal_Nerve_Plexus plexus nervorum spinalium FMA:5903 FMA:TA plexus of spinal nerves FMA:5903 somatic nerve plexus FMA:5903 spinal nerve plexus FMA:5903 An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified]. check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus' A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG] To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] EHDAA2:0000180 EHDAA:3782 EMAPA:16988 FMA:5906 GAID:842 MA:0001180 MESH:D001917 NCIT:C12682 SCTID:181002002 UMLS:C0006090 VHOG:0000372 Wikipedia:Brachial_plexus brachial plexus uberon plexus brachialis UBERON:0001814 brachial nerve plexus http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified]. UBERON:cjm Wikipedia:Brachial_plexus A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG] 2012-09-17 VHOG:0000372 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/brachial+plexus To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] 2012-09-17 VHOG:0000372 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436 http://bgee.unil.ch/ UMLS:C0006090 ncithesaurus:Brachial_Plexus brachial plexus MA:0001180 plexus brachialis Wikipedia:Brachial_plexus A nerve plexus that is part of an autonomic nervous system [Automatically generated definition]. EMAPA:18224 FMA:5910 MA:0000221 SCTID:362482000 autonomic plexus plexus autonomicus plexus nervosus visceralis plexus visceralis visceral nerve plexus visceral plexus uberon UBERON:0001816 autonomic nerve plexus A nerve plexus that is part of an autonomic nervous system [Automatically generated definition]. OBOL:automatic plexus autonomicus FMA:5910 FMA:TA plexus nervosus visceralis FMA:5910 FMA:TA plexus visceralis FMA:5910 FMA:TA The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands. The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, they are situated in the upper, outer portion of each orbit Innervation is highly complex and species-specific BTO:0000044 CALOHA:TS-0512 EFO:0001389 EMAPA:35463 EV:0100339 FMA:59101 MA:0001296 NCIT:C12346 SCTID:181147003 UMLS:C0022907 VHOG:0001476 Wikipedia:Lacrimal_gland Wikipedia:Preorbital_gland glandula lacrimalis lacrimal-preorbital gland uberon glandula praeorbitalis preorbital gland tear gland UBERON:0001817 lacrimal gland http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. Wikipedia:Lacrimal_gland http://orcid.org/0000-0002-6601-2165 PMID:7559104 Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands. FMA:59101 The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]. Wikipedia:Preorbital_gland UMLS:C0022907 ncithesaurus:Lacrimal_Gland glandula lacrimalis Wikipedia:Lacrimal_gland lacrimal-preorbital gland http://orcid.org/0000-0002-6601-2165 glandula praeorbitalis NCBITaxon:91561 Wikipedia:Preorbital_gland preorbital gland NCBITaxon:91561 Wikipedia:Preorbital_gland tear gland BTO:0000044 Any of the coil glands of the skin that secrete sweat. TODO - check if all sweat glands are epidermal - see EMAPA:29743 A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG] Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG] In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation BTO:0001331 CALOHA:TS-0993 EMAPA:35844 EV:0100160 FMA:59152 GAID:943 MA:0000150 MESH:D013545 NCIT:C33712 SCTID:361700009 UMLS:C0038989 VHOG:0001467 Wikipedia:Sweat_gland uberon glandula sudorifera sudoriferous gland sudoriparous gland UBERON:0001820 sweat gland http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg coiled tubular Wikipedia:Tubular_gland definitional Any of the coil glands of the skin that secrete sweat. ISBN:0-683-40008-8 MP:0000674 A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG] 2012-09-17 VHOG:0001467 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/sweat+gland Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG] 2012-09-17 VHOG:0001467 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101 http://bgee.unil.ch/ UMLS:C0038989 ncithesaurus:Sweat_Gland glandula sudorifera BTO:0001331 sudoriferous gland BTO:0001331 sudoriparous gland BTO:0001331 A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass. Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] Sebaceous glands are also limited to mammals.[well established][VHOG] BTO:0001980 CALOHA:TS-2384 EMAPA:35754 EV:0100161 FMA:59160 GAID:900 MA:0002565 MESH:D012627 NCIT:C33519 SCTID:361697005 UMLS:C0036505 VHOG:0001468 Wikipedia:Sebaceous_gland uberon glandula sebacea glandula sebaceae sebaceous follicle UBERON:0001821 sebaceous gland http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png Wikipedia VHOG definitional A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. MP:0000647 Wikipedia:Sebaceous_gland Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] 2012-09-17 VHOG:0001468 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/sebaceous+gland Sebaceous glands are also limited to mammals.[well established][VHOG] 2012-09-17 VHOG:0001468 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102 http://bgee.unil.ch/ UMLS:C0036505 ncithesaurus:Sebaceous_Gland glandula sebacea Wikipedia:Sebaceous_gland glandula sebaceae BTO:0001980 sebaceous follicle BTO:0001980 One of the cartilage structures in the nose that provide form and support[WP]. CALOHA:TS-0655 EMAPA:37681 FMA:59502 MA:0001883 MESH:D055171 NCIT:C49593 SCTID:278941001 UMLS:C0225415 Wikipedia:Nasal_cartilage cartilage of nose uberon UBERON:0001823 nasal cartilage http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png MA One of the cartilage structures in the nose that provide form and support[WP]. Wikipedia:Nasal_cartilage EMAPA:37681 MA:th MESH:D055171 https://github.com/biopragmatics/biomappings UMLS:C0225415 ncithesaurus:Nasal_Cartilage The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. EMAPA:18334 FMA:59662 GAID:301 MA:0001766 MESH:D007820 NCIT:C49246 SCTID:361940006 UMLS:C0023053 laryngeal mucosa larynx mucosa larynx mucosa of organ larynx mucous membrane larynx organ mucosa mucosa of organ of larynx mucous membrane of larynx organ mucosa of larynx tunica mucosa laryngis uberon laryngeal mucous membrane UBERON:0001824 mucosa of larynx The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. MP:0002261 UMLS:C0023053 ncithesaurus:Laryngeal_Mucosa larynx mucosa of organ OBOL:automatic larynx mucous membrane OBOL:automatic larynx organ mucosa OBOL:automatic mucosa of organ of larynx OBOL:automatic organ mucosa of larynx OBOL:automatic tunica mucosa laryngis FMA:59662 FMA:TA laryngeal mucous membrane EMAPA:18334 The mucous membrane that lines the nasal cavity[MP]. TODO - check lining vs part of. split olfactory and nasal mucosa? BTO:0000912 CALOHA:TS-0657 EMAPA:36026 FMA:59684 GAID:302 SCTID:310211009 Wikipedia:Mucous_membrane_of_nose mucosa of nose mucous membrane of nose tunica mucosa nasalis tunica mucosa nasi uberon nasal mucosa UBERON:0001826 nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. MP:0002238 mucosa of nose FMA:59684 mucous membrane of nose FMA:59684 tunica mucosa nasi FMA:59684 FMA:TA Aqueous substance secreted by the lacrimal gland. BTO:0001499 CALOHA:TS-1016 EMAPA:36537 ENVO:02000034 FMA:59756 GAID:1173 MA:0002508 MESH:D013666 NCIT:C33739 UMLS:C0039409 Wikipedia:Tear galen:Tear galen:Tears lacrimal fluid lacrimal gland secretion lacrimal secretion tear tears uberon tear fluid UBERON:0001827 secretion of lacrimal gland Aqueous substance secreted by the lacrimal gland. Wikipedia:Tear http://orcid.org/0000-0002-6601-2165 UMLS:C0039409 ncithesaurus:Tear tear FMA:59756 tears tear fluid BTO:0001499 The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001]. FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton. gingival BTO:0000519 CALOHA:TS-2074 EFO:0001925 EMAPA:35945 EV:0100064 FMA:59762 GAID:1257 MA:0000342 MESH:D005881 NCIT:C32677 SCTID:181224006 UMLS:C0017562 VHOG:0001269 Wikipedia:Gingiva galen:Gingiva gum gum tissue gums uberon gingival mucosa UBERON:0001828 gingiva https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg Carranza ISBN:0013002015 The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001]. ISBN:0013002015 Wikipedia:Gingiva UMLS:C0017562 ncithesaurus:Gingiva gum FMA:59762 gum tissue https://orcid.org/0000-0002-6601-2165 One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. There are 3 pairs of major salivary glands in human and mouse FMA:59788 MA:0002478 NCIT:C12999 SCTID:303049006 UMLS:C0930553 galen:MajorSalivaryGland uberon UBERON:0001829 major salivary gland One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. MP:0003792 There are 3 pairs of major salivary glands in human and mouse ISBN:0123813611 UMLS:C0930553 ncithesaurus:Major_Salivary_Gland One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] labial BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 NCIT:C12220 SCTID:181221003 TAO:0007006 UMLS:C0023759 VHOG:0000677 Wikipedia:Lip ZFA:0007006 galen:Lip uberon labia oris lips UBERON:0001833 lip http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg ZFA BTO FMA-implicit VHOG ZFA cjm One of the two fleshy folds which surround the opening of the mouth. Wikipedia:Lip http://www.medterms.com/script/main/art.asp?articlekey=9458 Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] 2012-08-14 TAO:0007006 TAO ZFIN:curator http//:www.medterms.com/script/main/art.asp?articlekey=9458 UMLS:C0023759 ncithesaurus:Lip labia oris Wikipedia:Lip Lip that covers the upper portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG] Lip that covers the upper portion of the mouth.[TAO] UBERON:0003391 EMAPA:17925 FMA:59817 MA:0000919 SCTID:245776003 TAO:0001970 VHOG:0001750 Wikipedia:Upper_lip ZFA:0005226 upper jaw lip uberon labium superius oris UBERON:0001834 upper lip http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg Lip that covers the upper portion of the mouth.[TAO]. TAO:0001970 Wikipedia:Upper_lip Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG] 2012-09-17 VHOG:0001750 VHOG http://bgee.unil.ch/ Lip that covers the upper portion of the mouth.[TAO] 2012-08-14 TAO:0001970 TAO TAO:wd upper jaw lip https://orcid.org/0000-0002-6601-2165 labium superius oris Wikipedia:Upper_lip Lip that covers the lower portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth.[TAO] UBERON:0003392 EHDAA2:0001020 EMAPA:17909 FMA:59818 MA:0000921 NCIT:C94572 SCTID:245777007 TAO:0002060 UMLS:C0458583 Wikipedia:Lower_lip ZFA:0005225 lower jaw lip uberon labium inferius oris UBERON:0001835 lower lip http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg Lip that covers the lower portion of the mouth.[TAO]. TAO:0002060 Wikipedia:Lower_lip Lip that covers the lower portion of the mouth.[TAO] 2012-08-14 TAO:0002060 TAO TAO:wd UMLS:C0458583 ncithesaurus:Lower_Lip lower jaw lip https://orcid.org/0000-0002-6601-2165 labium inferius oris Wikipedia:Lower_lip A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. salivary We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin BTO:0001202 CALOHA:TS-0891 EMAPA:36536 ENVO:02000036 FMA:59862 GAID:1167 MA:0002507 MAT:0000444 MESH:D012463 NCIT:C13275 UMLS:C0036087 Wikipedia:Saliva galen:Saliva salivary gland secretion uberon sailva normalis saliva atomaris saliva molecularis UBERON:0001836 saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. GO:0046541 Wikipedia:Saliva We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin GO UMLS:C0036087 ncithesaurus:Saliva salivary gland secretion FMA:59862 sailva normalis Wikipedia:Saliva saliva atomaris Wikipedia:Saliva saliva molecularis Wikipedia:Saliva The duct of a salivary gland. BTO:0005115 EMAPA:35750 FMA:59908 GAID:939 MA:0001586 MESH:D018987 NCIT:C32486 SCTID:181238004 Wikipedia:Salivary_duct salivary duct salivary gland duct uberon secretory duct UBERON:0001837 duct of salivary gland The duct of a salivary gland. http://orcid.org/0000-0002-6601-2165 secretory duct BTO:0005115 A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]. AAO:0011078 BTO:0004685 CALOHA:TS-2080 EMAPA:36580 EV:0100362 FMA:60179 MA:0000238 NCIT:C33227 SCTID:279727008 UMLS:C0458699 VHOG:0001219 Wikipedia:Bony_labyrinth XAO:0000193 osseous labyrinth uberon labyrinthus osseus osseus labyrinth UBERON:0001839 Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved. bony labyrinth http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png FMA MA FMA A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]. Wikipedia:Bony_labyrinth UMLS:C0458699 ncithesaurus:Osseous_Labyrinth labyrinthus osseus Wikipedia:Bony_labyrinth The spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]. A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG] Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG] cochlear The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)' the cochlea is coiled in most mammals, monotremes being the exceptions. sources vary in connection to bony labyrinth AAO:0000253 BIRNLEX:1190 BTO:0000267 CALOHA:TS-0151 EFO:0000357 EMAPA:17597 EV:0100363 FMA:60201 GAID:724 MA:0000240 MAT:0000144 MESH:D003051 MIAA:0000144 NCIT:C12395 NIFSTD_RETIRED:birnlex_883 SCTID:181187008 TAO:0000374 UMLS:C0009195 UMLS:C1278895 VHOG:0000691 Wikipedia:Cochlea XAO:0000197 ZFA:0000374 cochlear part of bony labyrinth lagena uberon cochleae cochlear duct cochlear organ lagenas UBERON:0001844 cochlea http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg FMA VHOG XAO ncit The spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]. ISBN:0-683-40008-8 MP:0000031 Wikipedia:Cochlea A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG] 2012-09-17 VHOG:0000691 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/cochlea Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG] 2012-09-17 VHOG:0000691 VHOG DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998) http://bgee.unil.ch/ sources vary in connection to bony labyrinth XAO UMLS:C0009195 BIRNLEX:1190 ncithesaurus:Cochlea UMLS:C1278895 BIRNLEX:1190 lagena XAO:0000197 cochleae cochlear organ BTO:0000267 lagenas ZFA:0000374 Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] AAO:0000238 BIRNLEX:1196 BTO:0000630 CALOHA:TS-0478 EFO:0001363 EHDAA2:0000831 EHDAA:504 EMAPA:16194 EV:0100361 FMA:60909 GAID:871 MA:0000237 MAT:0000145 MESH:D007758 MIAA:0000145 NCIT:C12499 SCTID:181189006 SCTID:304982002 TAO:0000217 UMLS:C0022889 UMLS:C1268973 VHOG:0000284 Wikipedia:Internal_ear XAO:0000192 ZFA:0000217 galen:InnerEar inner ear uberon auris interna labyrinth otocyst UBERON:0001846 internal ear http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png definitional Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. PMID:16217737 Wikipedia:Internal_ear ZFIN:curator The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000217 TAO ZFIN:curator The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000284 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366 http://bgee.unil.ch/ UMLS:C0022889 BIRNLEX:1196 ncithesaurus:Internal_Ear UMLS:C1268973 BIRNLEX:1196 auris interna BTO:0000630 Cartilage of the pinna and much of the external ear canal. EMAPA:35158 FMA:61013 MA:0001227 SCTID:279627003 cartilage of pinna pinna cartilage uberon UBERON:0001848 auricular cartilage Cartilage of the pinna and much of the external ear canal. http://medical-dictionary.thefreedictionary.com/auricular+cartilage cartilage of pinna FMA:61013 A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct. chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104] EMAPA:19245 FMA:61063 MA:0001295 SCTID:280426002 uberon lacrimal duct tear duct UBERON:0001850 lacrimal drainage system FMA FMA ISBN:9780674021839 A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct. http://orcid.org/0000-0002-6601-2165 PMID:7559104 lacrimal duct FMA:61063 MA:0001295 tear duct MA:0001295 Outermost layer of an organ[WP]. cortical this class is used more generically than in FMA, and includes e.g. cortex of hair EFO:0000383 EHDAA:9344 FMA:61109 Wikipedia:Cortex_(anatomy) galen:Cortex cortex cortex of organ uberon UBERON:0001851 cortex Outermost layer of an organ[WP]. Wikipedia:Cortex_(anatomy) this class is used more generically than in FMA, and includes e.g. cortex of hair FMA cortex FMA:61109 Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]. The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans. waterproofs skin BTO:0001981 ENVO:02000037 FMA:61304 GAID:1168 MA:0002538 MESH:D012629 NCIT:C13276 UMLS:C0036511 Wikipedia:Sebaceous_glands#Sebum uberon UBERON:0001866 sebum Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]. BTO:0001981 Wikipedia:Sebaceous_glands#Sebum UMLS:C0036511 ncithesaurus:Sebum A cartilage that is part of a external ear [Automatically generated definition]. EMAPA:37706 FMA:61339 GAID:103 MA:0001886 MESH:D004425 NCIT:C49225 UMLS:C0013445 external ear cartilage uberon UBERON:0001867 cartilage of external ear A cartilage that is part of a external ear [Automatically generated definition]. OBOL:automatic EMAPA:37706 MA:th UMLS:C0013445 ncithesaurus:External_Ear_Cartilage A zone of skin that is part of a chest [Automatically generated definition]. check FMA:61415 EMAPA:37279 FMA:61416 MA:0000553 SCTID:181496004 anterior thoracic region zone of skin anterolateral part of thorax zone of skin chest skin chest zone of skin front of thorax zone of skin zone of skin of anterior chest zone of skin of anterior part of thorax zone of skin of anterior thoracic region zone of skin of anterolateral part of thorax zone of skin of chest zone of skin of front of thorax uberon zone of skin of pectoral part of chest UBERON:0001868 skin of chest A zone of skin that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37279 MA:th anterior thoracic region zone of skin OBOL:automatic anterolateral part of thorax zone of skin OBOL:automatic chest zone of skin OBOL:automatic front of thorax zone of skin OBOL:automatic zone of skin of anterior chest FMA:61416 zone of skin of anterior part of thorax FMA:61416 zone of skin of anterior thoracic region OBOL:automatic zone of skin of anterolateral part of thorax OBOL:automatic zone of skin of chest OBOL:automatic zone of skin of front of thorax OBOL:automatic zone of skin of pectoral part of chest FMA:61417 One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]. Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] AAO:0010480 BAMS:HEM BIRNLEX:1042 BTO:0000231 CALOHA:TS-2007 DMBA:15739 EFO:0002521 EMAPA:16653 FMA:61817 MA:0000133 MBA:403 NCIT:C12351 SCTID:278251007 UMLS:C0228174 UMLS:C0242202 VHOG:0001639 Wikipedia:Cerebral_hemisphere galen:CerebralHemisphere neuronames:241 uberon cerebrum hemisphere hemispheric regions hemispherium cerebri medial amygdalar nucleus nucleus amygdaloideus medialis nucleus medialis amygdalae UBERON:0001869 cerebral hemisphere http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png FMA-abduced-lr One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]. FMA:61817 Wikipedia:Cerebral_hemisphere Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] 2012-06-20 AAO:0010480 AAO AAO:BJB The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] 2012-09-17 VHOG:0001639 VHOG DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981) http://bgee.unil.ch/ UMLS:C0228174 ncithesaurus:Cerebral_Hemisphere UMLS:C0242202 BIRNLEX:1042 neuronames:241 BIRNLEX:1042 cerebrum MA:0000133 VHOG:0001639 https://github.com/obophenotype/uberon/issues/1208 hemisphere VHOG:0001639 hemispheric regions BAMS:HEM hemispherium cerebri Wikipedia:Cerebral_hemisphere medial amygdalar nucleus NeuroNames:241 nucleus amygdaloideus medialis NeuroNames:241 nucleus medialis amygdalae NeuroNames:241 Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally. BTO:0000484 DHBA:10161 DMBA:16002 EMAPA:35357 FMA:242199 GAID:674 MA:0000905 MESH:D005625 NLXANAT:20090601 Wikipedia:Frontal_lobe cortex of frontal lobe frontal lobe cortex gray matter of frontal lobe grey matter of frontal lobe uberon frontal neocortex UBERON:0001870 frontal cortex http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. NLXANAT:20090601 Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally. NLXANAT:20090601 MESH:D005625 https://github.com/biopragmatics/biomappings cortex of frontal lobe FMA:242199 frontal lobe cortex FMA:242199 gray matter of frontal lobe FMA:242199 frontal neocortex DHBA:10161 Lower lateral part of the cerebral hemisphere. (MSH). BAMS:TL BAMS:Temporal_lobe BIRNLEX:1160 BTO:0001355 CALOHA:TS-1020 DHBA:12139 EFO:0000917 EMAPA:18797 EV:0100169 FMA:61825 GAID:635 HBA:4132 MAT:0000508 MESH:D013702 NCIT:C12353 SCTID:180921000 UMLS:C0039485 UMLS:C1268978 Wikipedia:Temporal_lobe neuronames:125 lobus temporalis temporal cortex uberon UBERON:0001871 Boundary notes: It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. [Wikipedia:Temporal_lobe] temporal lobe http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png FMA Lower lateral part of the cerebral hemisphere. (MSH). BIRNLEX:1160 UMLS:C0039485 BIRNLEX:1160 ncithesaurus:Temporal_Lobe UMLS:C1268978 BIRNLEX:1160 neuronames:125 BIRNLEX:1160 lobus temporalis Wikipedia:Temporal_lobe Upper central part of the cerebral hemisphere. (MSH). parietal region BAMS:Parietal_lobe BIRNLEX:1148 BTO:0001001 CALOHA:TS-0747 DHBA:12131 EFO:0000914 EV:0100168 FMA:61826 GAID:680 HBA:4084 MAT:0000506 MESH:D010296 NCIT:C12354 SCTID:180922007 UMLS:C0030560 Wikipedia:Parietal_lobe neuronames:95 regio parietalis uberon lobus parietalis UBERON:0001872 parietal lobe http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png FMA Upper central part of the cerebral hemisphere. (MSH). BIRNLEX:1148 UMLS:C0030560 BIRNLEX:1148 ncithesaurus:Parietal_Lobe_of_the_Brain neuronames:95 BIRNLEX:1148 regio parietalis FMA:61826 FMA:TA lobus parietalis Wikipedia:Parietal_lobe A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] BAMS:phn BTO:0001063 EHDAA:4677 EMAPA:17813 FMA:6191 GAID:848 MA:0001170 MESH:D010791 NCIT:C52813 SCTID:280344009 UMLS:C0031774 VHOG:0000728 Wikipedia:Phrenic_nerve uberon diaphragmatic nerve nervus phrenicus phrenic UBERON:0001884 phrenic nerve http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. VHOG:0000728 A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] 2012-09-17 VHOG:0000728 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/phrenic+nerve UMLS:C0031774 ncithesaurus:Phrenic_Nerve diaphragmatic nerve BTO:0001063 nervus phrenicus BTO:0001063 Wikipedia:Phrenic_nerve phrenic BTO:0001063 A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] Fringe of the tela choroidea of the brain ventricles[MP] choroidal CP BAMS:CHP BAMS:GHP BAMS:chp BAMS:chpl BTO:0000258 CALOHA:TS-0145 EFO:0001915 EMAPA:32741 FMA:61934 GAID:607 MA:0000823 MBA:108 MESH:D002831 NCIT:C12694 SCTID:264450003 TAO:0001443 UMLS:C0008524 VHOG:0001377 Wikipedia:Choroid_plexus ZFA:0001443 neuronames:1377 chorioid plexus plexus choroideus uberon choroid plexus of cerebral hemisphere plexus choroideus ventricular choroid plexus UBERON:0001886 choroid plexus http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. ISBN:0471888893 Wikipedia:Choroid_plexus A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] 2012-08-14 TAO:0001443 TAO ZFIN:curator Fringe of the tela choroidea of the brain ventricles[MP] MP:0000820 CP PMID:23375746 UMLS:C0008524 ncithesaurus:Choroid_Plexus chorioid plexus FMA:61934 plexus choroideus FMA:61934 FMA:TA choroid plexus of cerebral hemisphere FMA:61934 plexus choroideus Wikipedia:Choroid_plexus EHDAA2:0001463 EMAPA:37718 FMA:6198 MA:0001177 phrenic nerve trunk phrenic neural trunk uberon UBERON:0001889 trunk of phrenic nerve EMAPA:37718 MA:th The most anterior region of the brain including both the telencephalon and diencephalon. Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] prosencephalic FB AAO:0010147 BAMS:FB BAMS:Forebrain BIRNLEX:1509 BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FMA:61992 MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 NCIT:C40185 SCTID:362291003 TAO:0000109 UMLS:C0085140 VHOG:0000383 Wikipedia:Forebrain XAO:0000011 ZFA:0000109 neuronames:27 uberon prosencephalon UBERON:0001890 forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The most anterior region of the brain including both the telencephalon and diencephalon. Wikipedia:Forebrain ZFIN:ZDB-PUB-961014-576 Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] 2012-06-20 AAO:0010147 AAO AAO:BJB The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000109 TAO ZFIN:curator relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] 2012-08-14 TAO:0000109 TAO In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] 2012-09-17 VHOG:0000383 VHOG PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996) http://bgee.unil.ch/ FB BIRNLEX:1509 NIFSTD:NeuroNames_abbrevSource UMLS:C0085140 BIRNLEX:1509 ncithesaurus:Fore-Brain neuronames:27 BIRNLEX:1509 The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised Middle part of the brain composed of the optic tectum and penducular region.[AAO] The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] mesencephalic part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES BIRNLEX:1667 BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 HBA:9001 MA:0000207 MAT:0000106 MBA:313 MESH:D008636 MIAA:0000106 NCIT:C12510 RETIRED_EHDAA2:0001104 SCTID:279099009 TAO:0000128 UMLS:C0025462 VHOG:0000069 Wikipedia:Midbrain XAO:0000014 ZFA:0000128 neuronames:462 uberon mesencephalon UBERON:0001891 midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG definitional Bgee:AN The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 ZFA https://github.com/obophenotype/uberon/issues/378 ABA pending ZFA ABA pending Middle part of the brain composed of the optic tectum and penducular region.[AAO] 2012-06-20 AAO:0010149 AAO AAO:BJB The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000128 TAO ZFIN:curator Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000069 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships ABA MB BIRNLEX:1667 NIFSTD:NeuroNames_abbrevSource UMLS:C0025462 BIRNLEX:1667 ncithesaurus:Mesencephalon neuronames:462 BIRNLEX:1667 mesencephalon Wikipedia:Midbrain A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] In human embryonic development, the rhombomeres are present by day 29 DHBA divides this into A(1-3),B(4),C(5-7) and D(8) hindbrain segment segment of hindbrain DHBA:12664 EFO:0003617 EMAPA:16148 FMA:295666 MAT:0000272 MIAA:0000272 RETIRED_EHDAA2:0000669 TAO:0001064 VHOG:0000672 Wikipedia:Rhombomere XAO:0004079 ZFA:0001064 hindbrain neuromere hindbrain neuromeres rhombomere uberon future rhombencephalon rhombomeres UBERON:0001892 rhombomere A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. Wikipedia:Rhombomere ZFIN:curator A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001064 TAO ZFIN:curator Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] 2012-09-17 VHOG:0000672 VHOG DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002) http://bgee.unil.ch/ hindbrain segment ZFA:0001064 segment of hindbrain ZFA:0001064 hindbrain neuromeres DHBA:HNM future rhombencephalon MIAA:0000272 rhombomeres VHOG:0000672 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] cerebral telencephalic telenencephalic In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209] In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. supratentorial region AAO:0010479 BAMS:CB BAMS:CH BAMS:IV BAMS:Tel BIRNLEX:1115 BM:Tel BTO:0000239 CALOHA:TS-1018 DHBA:10158 EFO:0000912 EHDAA2:0001982 EMAPA:16910 EV:0100165 FMA:62000 GAID:621 HBA:4007 MA:0000183 MAT:0000421 MBA:567 MESH:D013687 MIAA:0000421 PBA:128011350 SCTID:263353005 TAO:0000079 UMLS:C0039452 VHOG:0000283 Wikipedia:Telencephalon XAO:0000012 ZFA:0000079 neuronames:31 cerebrum endbrain uberon UBERON:0001893 telencephalon Bgee:AN Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. AAO:0010479 XAO:0000012 ABA Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. FMA:62000 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] 2012-06-20 AAO:0010479 AAO AAO:BJB The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000079 TAO ZFIN:curator relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] 2012-08-14 TAO:0000079 TAO From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000283 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ In mammals the cortex covers almost the whole of the cerebral hemispheres. Wikipedia:Telencephalon#Variation_among_species In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. Wikipedia:Telencephalon#Variation_among_species In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. Wikipedia:Telencephalon#Variation_among_species In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. Wikipedia:Telencephalon#Variation_among_species The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. Wikipedia:Telencephalon#Variation_among_species dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. Wikipedia:Telencephalon#Variation_among_species supratentorial region Wikipedia:Tentorium_cerebelli UMLS:C0039452 BIRNLEX:1115 neuronames:31 BIRNLEX:1115 cerebrum BTO:0000239 EMAPA:16910 FMA:62000 Wikipedia:Talk:Cerebrum/Archive_1 https://github.com/obophenotype/uberon/issues/1208 endbrain Swanson:2004 neuronames:31 The division of the forebrain that develops from the foremost primary cerebral vesicle. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] diencephalic in ABA, this is part of the brain stem DiE AAO:0010481 BAMS:DI BAMS:Di BAMS:DiE BAMS:IB BAMS:Zh. BIRNLEX:1503 BM:Die BTO:0000342 CALOHA:TS-0199 DHBA:10389 DMBA:16308 EFO:0000911 EHDAA2:0000385 EHDAA:1969 EHDAA:2645 EHDAA:3472 EMAPA:16896 EV:0100194 FMA:62001 GAID:618 HBA:4391 MA:0000171 MAT:0000420 MBA:1129 MESH:D004027 MIAA:0000420 NCIT:C12456 PBA:128013010 SCTID:279328001 TAO:0000101 UMLS:C0012144 VHOG:0000318 Wikipedia:Diencephalon XAO:0000013 ZFA:0000101 neuronames:288 between brain interbrain mature diencephalon thalamencephalon uberon betweenbrain diencephalon UBERON:0001894 diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional definitional The division of the forebrain that develops from the foremost primary cerebral vesicle. Wikipedia:Diencephalon ZFA ABA https://github.com/obophenotype/uberon/issues/378 pending ABA not well differentiated from the cerebrum. (Ariens, p. 868) PMID:8932866 The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000101 TAO ZFIN:curator Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] 2012-06-20 AAO:0010481 AAO AAO:BJB Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000318 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ in ABA, this is part of the brain stem ABA DiE BIRNLEX:1503 NIFSTD:NeuroNames_abbrevSource UMLS:C0012144 BIRNLEX:1503 ncithesaurus:Diencephalon neuronames:288 BIRNLEX:1503 interbrain Swanson:2004 mature diencephalon FMA:62001 thalamencephalon MGI:anna betweenbrain BTO:0000342 diencephalon Wikipedia:Diencephalon Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] epencephalon BAMS:Met BIRNLEX:965 BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 NCIT:C32741 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 Wikipedia:Metencephalon neuronames:543 epencephalon-2 uberon UBERON:0001895 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Wikipedia:Metencephalon https://github.com/obophenotype/uberon/issues/300 Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. BIRNLEX:965 The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] 2012-09-17 VHOG:0000741 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/metencephalon The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000741 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ epencephalon ncithesaurus:Epencephalon UMLS:C0376353 BIRNLEX:965 UMLS:C1516904 ncithesaurus:Epencephalon neuronames:543 BIRNLEX:965 epencephalon-2 FMA:62003 Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 BAMS:MY BAMS:Md BIRNLEX:957 BM:Me BTO:0000041 CALOHA:TS-0607 DMBA:17352 EFO:0000924 EHDAA2:0001088 EHDAA:7588 EMAPA:17550 EV:0100275 FMA:62004 GAID:590 MA:0000206 MAT:0000111 MAT:0000367 MBA:354 MESH:D008526 MIAA:0000111 NCIT:C12442 SCTID:279104005 TAO:0000545 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 Wikipedia:Bone_marrow_of_ovary_oblongata XAO:0003100 ZFA:0000545 neuronames:698 bulbus uberon medulla oblonzata metepencephalon UBERON:0001896 medulla oblongata http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. FMA:62004 GO:0021550 Wikipedia:Bone_marrow_of_ovary_oblongata Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] 2012-06-20 AAO:0010486 AAO AAO:BJB The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000181 VHOG http://bgee.unil.ch/ Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000181 VHOG DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) http://bgee.unil.ch/ medulla ABA:MY UMLS:C0025148 BIRNLEX:957 ncithesaurus:Medulla_Oblongata UMLS:C1269575 BIRNLEX:957 neuronames:698 BIRNLEX:957 bulbus FMA:62004 FMA:TA medulla oblonzata Wikipedia:Medulla_oblongata metepencephalon FMA:62004 Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG] Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO] (...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG] thalamic Th thalamus AAO:0010483 BAMS:TH BAMS:Th BIRNLEX:954 BTO:0001365 CALOHA:TS-1031 DHBA:10390 DMBA:16376 EFO:0000910 EMAPA:17540 EV:0100195 GAID:656 HBA:4392 MA:0000179 MAT:0000109 MBA:549 MIAA:0000109 NCIT:C12459 PBA:128013014 SCTID:244433007 TAO:0001215 UMLS:C0039729 VHOG:0000657 Wikipedia:Thalamus ZFA:0001215 galen:Thalamus neuronames:300 wider thalamus uberon thalamencephalon thalami thalamus opticus UBERON:0001897 dorsal plus ventral thalamus http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg FMA-abduced-lr Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). BIRNLEX:954 ABA One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG] 2012-09-17 VHOG:0000657 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/thalamus Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO] 2012-06-20 AAO:0010483 AAO AAO:BJB (...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG] 2012-09-17 VHOG:0000657 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484 http://bgee.unil.ch/ Th BIRNLEX:954 NIFSTD:NeuroNames_abbrevSource PMID:23375746 thalamus FMA:62007 MA:0000179 UMLS:C0039729 BIRNLEX:954 ncithesaurus:Thalamus neuronames:300 BIRNLEX:954 wider thalamus PMCID:PMC3345571 thalamencephalon NeuroNames:300 thalami VHOG:0000657 thalamus opticus NeuroNames:300 A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO] Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO] For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG] hypothalamic all vertebrates contain a hypothalamus Hy AAO:0010484 BAMS:HY BAMS:Hy BIRNLEX:734 BM:Die-Hy BTO:0000614 CALOHA:TS-0469 DHBA:10467 EFO:0000107 EHDAA2:0000802 EHDAA:5446 EMAPA:17536 EV:0100225 FMA:62008 GAID:460 HBA:4540 MA:0000173 MAT:0000112 MBA:1097 MESH:D007031 MIAA:0000112 NCIT:C12458 SCTID:264483005 TAO:0000032 UMLS:C0020663 VHOG:0000179 Wikipedia:Hypothalamus XAO:0004070 ZFA:0000032 galen:Hypothalamus neuronames:292 preoptico-hypothalamic area preoptico-hypothalamic region uberon hypothalamus UBERON:0001898 hypothalamus http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb FMA EHDAA2 Wikipedia WP A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. Wikipedia:Hypothalamus ZFIN:curator ABA Lancelets possess a region similar to the hypothalamus (Murakami, 2005) Ariens, p. 1192 A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000032 TAO ZFIN:curator Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO] 2012-06-20 AAO:0010484 AAO AAO:BJB For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000179 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ all vertebrates contain a hypothalamus WP Hy BIRNLEX:734 NIFSTD:NeuroNames_abbrevSource UMLS:C0020663 BIRNLEX:734 ncithesaurus:Hypothalamus neuronames:292 BIRNLEX:734 hypothalamus Wikipedia:Hypothalamus Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346. Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO] The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG] epithalamic ETh AAO:0010482 BAMS:EPI BAMS:ETh BAMS:EpT BAMS:Epi BIRNLEX:1710 BM:Die-Epi BTO:0000175 CALOHA:TS-2060 DHBA:10451 EFO:0000918 EHDAA2:0000448 EHDAA:5433 EMAPA:17532 EV:0100220 FMA:62009 GAID:455 HBA:4520 MA:0000172 MAT:0000422 MBA:958 MESH:D019261 MIAA:0000422 NCIT:C12457 PBA:128013147 SCTID:281487003 TAO:0000509 UMLS:C0152361 VHOG:0000178 Wikipedia:Epithalamus ZFA:0000509 neuronames:292 uberon epithalamus UBERON:0001899 epithalamus http://upload.wikimedia.org/wikipedia/commons/c/cb/Epithalamus.png Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346. BIRNLEX:1710 ABA ABA ABA Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO] 2012-06-20 AAO:0010482 AAO AAO:BJB The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000178 VHOG http://bgee.unil.ch/ The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG] 2012-09-17 VHOG:0000178 VHOG DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001) http://bgee.unil.ch/ ETh BIRNLEX:1710 NIFSTD:NeuroNames_abbrevSource UMLS:C0152361 BIRNLEX:1710 ncithesaurus:Epithalamus neuronames:292 BIRNLEX:1710 epithalamus Wikipedia:Epithalamus The epithelial lining of the trachea which contains numerous ciliated cells. UBERON:0003227 BTO:0001389 CALOHA:TS-1061 EHDAA2:0002069 EHDAA:5007 EMAPA:16855 EMAPA:18409 FMA:62015 MA:0001862 NCIT:C33797 UMLS:C1179002 VHOG:0001045 epithelial tissue of trachea epithelial tissue of windpipe epithelium of windpipe trachea epithelial tissue trachea epithelium tracheal epithelium windpipe epithelial tissue windpipe epithelium uberon UBERON:0001901 epithelium of trachea The epithelial lining of the trachea which contains numerous ciliated cells. ISBN:0-397-51047-0 MGI:cwg MP:0002285 UMLS:C1179002 ncithesaurus:Tracheal_Epithelium epithelial tissue of trachea OBOL:automatic epithelial tissue of windpipe OBOL:automatic epithelium of windpipe OBOL:automatic trachea epithelial tissue OBOL:automatic windpipe epithelial tissue OBOL:automatic windpipe epithelium OBOL:automatic An epithelium that is part of a small intestine [Automatically generated definition]. Intestinal epithelium which lines the lumen of the mid intestine.[TAO] BTO:0001258 CALOHA:TS-2104 EMAPA:35778 FMA:62017 MA:0001553 SCTID:45480009 TAO:0005127 ZFA:0005127 epithelial tissue of small bowel epithelial tissue of small intestine epithelium of small bowel mid intestine epithelium small bowel epithelial tissue small bowel epithelium small intestinal epithelium small intestine epithelial tissue small intestine epithelium uberon UBERON:0001902 epithelium of small intestine FMA An epithelium that is part of a small intestine [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the mid intestine.[TAO] 2012-08-14 TAO:0005127 TAO ZFIN:curator epithelial tissue of small bowel OBOL:automatic epithelial tissue of small intestine OBOL:automatic epithelium of small bowel OBOL:automatic mid intestine epithelium ZFA:0005127 small bowel epithelial tissue OBOL:automatic small bowel epithelium OBOL:automatic small intestine epithelial tissue OBOL:automatic A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399). A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO] Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO] relationship loss: part_of pineal complex (TAO:0001359)[TAO] The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG] epiphyseal epiphysial lobulated in humans, homogeneous in mouse. Calcifies with age in humans. Pi AAO:0010549 BAMS:PIN BAMS:Pi BIRNLEX:1184 BM:P BTO:0001067 CALOHA:TS-0789 DHBA:10460 EFO:0000865 EHDAA2:0001466 EHDAA:7523 EMAPA:18778 EV:0100131 EV:0100221 FMA:62033 GAID:453 HBA:4532 MA:0000175 MAT:0000448 MBA:953 MESH:D010870 NCIT:C12398 NLXANAT:1010009 SCTID:181126002 TAO:0000019 UMLS:C0031939 VHOG:0000051 Wikipedia:Pineal_gland XAO:0000160 ZFA:0000019 galen:PinealGland neuronames:297 corpus pineale glandula pinealis pineal gland pineal organ uberon conarium epiphysis epiphysis cerebri frontal organ pineal pineal gland (Galen) stirnorgan UBERON:0001905 pineal body http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb MA ZFA various EDITOR_NOTE add secretion A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399). BIRNLEX:1184 ABA ABA Hardisty, p. 310 A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000019 TAO ZFIN:curator Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO] 2012-06-20 AAO:0010549 AAO AAO:BJB relationship loss: part_of pineal complex (TAO:0001359)[TAO] 2012-08-14 TAO:0000019 TAO The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG] 2012-09-17 VHOG:0000051 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516 http://bgee.unil.ch/ Pi BIRNLEX:1184 NIFSTD:NeuroNames_abbrevSource UMLS:C0031939 BIRNLEX:1184 ncithesaurus:Pineal_Gland neuronames:297 BIRNLEX:1184 glandula pinealis FMA:62033 FMA:TA pineal gland FMA:62033 pineal organ ZFA:0000019 conarium BIRNLEX:1184 epiphysis ZFA:0000019 epiphysis cerebri Wikipedia:Epiphysis_cerebri frontal organ VHOG:0000051 pineal VHOG:0000051 pineal gland (Galen) NeuroNames:297 stirnorgan VHOG:0000051 A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. Originally this was classified as a female reproductive structure, as it was in the MP in 2011 Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG] The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] mammary A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts The male Dayak fruit bat has lactating mammary glands The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges. The BTO class represents the combination of nipple plus lobe The FMA class represents an individule lobe. The nipple is not a part The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts BTO:0000817 CALOHA:TS-0595 EFO:0000854 EMAPA:17759 EV:0100125 FMA:286452 MA:0000145 MAT:0000073 MESH:D008321 MIAA:0000073 NCIT:C12367 SCTID:361720005 UMLS:C0929301 VHOG:0000398 Wikipedia:Mammary_gland glandula mammaria lactiferous gland lobe of breast milk patch uberon Brustdruese dug glandula mammaria lobe of mammary gland mamma mammae UBERON:0001911 mammary gland http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. BTO:0000817 Wikipedia:Mammary_gland http://orcid.org/0000-0002-6601-2165 Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG] 2012-09-17 VHOG:0000398 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mammary+gland The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] 2012-09-17 VHOG:0000398 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224 http://bgee.unil.ch/ UMLS:C0929301 ncithesaurus:Mammary_Gland glandula mammaria FMA:57983 FMA:TA lactiferous gland FMA:62088 milk patch NCBITaxon:9255 Brustdruese BTO:0000817 dug Wikipedia:Mammary_gland glandula mammaria Wikipedia:Mammary_gland lobe of mammary gland FMA:62088 mamma BTO:0000817 mammae Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA]. TODO - ensure correct terminology for lobes/lobules. In mouse there are no distinct lobes (ISBN:0123813611), here lobule appears to be synonymous with acinus EMAPA:36634 FMA:62090 MA:0000793 acinus of mammary gland lactiferous acinus lactiferous gland lobule lactiferous lobule lobule of lactiferous gland lobule of mammary gland mammary acinus mammary gland lobule uberon UBERON:0001912 lobule of mammary gland FMA Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA]. FMA:62090 acinus of mammary gland FMA:62090 lactiferous acinus FMA:62090 lactiferous gland lobule FMA:62090 lactiferous lobule FMA:62090 lobule of lactiferous gland FMA:62090 lobule of mammary gland FMA:62090 mammary acinus FMA:62090 mammary gland lobule MA:0000793 An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular. The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] ncit:Milk refers specifically to cow milk BTO:0000868 CALOHA:TS-0636 EMAPA:36540 ENVO:02000031 EV:0100126 FMA:62100 GAID:1230 MA:0002552 MAT:0000056 MESH:D008892 MIAA:0000056 NCIT:C13401 UMLS:C1511310 VHOG:0001263 Wikipedia:Breast_milk galen:Milk mammary gland milk uberon UBERON:0001913 milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. http://orcid.org/0000-0002-6601-2165 The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] 2012-09-17 VHOG:0001263 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224 http://bgee.unil.ch/ ncit:Milk refers specifically to cow milk ncit UMLS:C1511310 ncithesaurus:Breast_Fluid_or_Secretion An endothelium that is part of a capillary [Automatically generated definition]. BTO:0004954 CALOHA:TS-0112 EMAPA:36292 FMA:62114 MA:0000711 NCIT:C49215 UMLS:C0006904 blood capillary endothelium capillary endothelium capillary vessel endothelium endothelium of blood capillary endothelium of capillary vessel uberon UBERON:0001915 endothelium of capillary An endothelium that is part of a capillary [Automatically generated definition]. OBOL:automatic UMLS:C0006904 ncithesaurus:Capillary_Endothelium blood capillary endothelium OBOL:automatic capillary vessel endothelium OBOL:automatic endothelium of blood capillary OBOL:automatic endothelium of capillary vessel OBOL:automatic An endothelium that is part of an arteriole [Automatically generated definition]. EMAPA:36286 FMA:62115 MA:0000705 NCIT:C49192 UMLS:C1179024 arteriole endothelium uberon UBERON:0001916 endothelium of arteriole An endothelium that is part of an arteriole [Automatically generated definition]. OBOL:automatic UMLS:C1179024 ncithesaurus:Arteriole_Endothelium An endothelium that is part of an artery [Automatically generated definition]. The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011013 BTO:0004757 EMAPA:35148 FMA:62116 MA:0000707 NCIT:C49194 UMLS:C1179025 VHOG:0001215 XAO:0000357 arterial endothelium artery endothelium uberon UBERON:0001917 endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. OBOL:automatic The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] 2012-06-20 AAO:0011013 AAO XAO:curator Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001215 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C1179025 ncithesaurus:Artery_Endothelium An endothelium that is part of a venule [Automatically generated definition]. EMAPA:36290 FMA:62117 MA:0000716 NCIT:C49319 UMLS:C1179026 venule endothelium uberon UBERON:0001918 endothelium of venule An endothelium that is part of a venule [Automatically generated definition]. OBOL:automatic UMLS:C1179026 ncithesaurus:Venule_Endothelium An endothelium that is part of a vein [Automatically generated definition]. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011110 BTO:0004756 EMAPA:36288 FMA:62118 MA:0000712 NCIT:C49317 UMLS:C1179027 VHOG:0001216 XAO:0000358 vein endothelium venous endothelium uberon veinous endothelium UBERON:0001919 endothelium of vein An endothelium that is part of a vein [Automatically generated definition]. OBOL:automatic Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001216 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C1179027 ncithesaurus:Vein_Endothelium veinous endothelium VHOG:0001216 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg BIRNLEX:1200 BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 MESH:D013681 SCTID:362392007 TAO:0000160 UMLS:C0039441 VHOG:0001367 Wikipedia:Midbrain_tegmentum XAO:0004271 ZFA:0000160 neuronames:491 tegmentum mesencephali tegmentum of midbrain uberon mesencephalic tegmentum tegmentum mesencephalicum UBERON:0001943 'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png ZFA Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. FMA:FMA ISBN:0471888893 Wikipedia:Midbrain_tegmentum Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] 2012-09-17 VHOG:0001367 VHOG DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) http://bgee.unil.ch/ MTg BIRNLEX:1200 NIFSTD:NeuroNames_abbrevSource tegmentum ISBN:0471888893 MESH:D013681 https://github.com/biopragmatics/biomappings UMLS:C0039441 BIRNLEX:1200 neuronames:491 BIRNLEX:1200 tegmentum mesencephali Wikipedia:Midbrain_tegmentum mesencephalic tegmentum VHOG:0001367 tegmentum mesencephalicum NeuroNames:491 A multi-tissue structure that is part of a spinal cord. BIRNLEX:1496 NCIT:C33969 SCTID:244437008 UMLS:C1268166 uberon spinal cord part UBERON:0001948 regional part of spinal cord A multi-tissue structure that is part of a spinal cord. OBOL:automatic UMLS:C1268166 ncithesaurus:Spinal_Cord_Part A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO]. In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva BTO:0004998 FMA:62423 MA:0001576 NCIT:C49239 UMLS:C1179154 epithelial tissue of gingiva epithelium of gingiva gingiva epithelial tissue gingiva epithelium uberon UBERON:0001949 gingival epithelium A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO]. BTO:0004998 UMLS:C1179154 ncithesaurus:Gingival_Epithelium epithelial tissue of gingiva OBOL:automatic gingiva epithelial tissue OBOL:automatic gingiva epithelium OBOL:automatic An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN). The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils BAMS:ISO BAMS:Iso-cortex BAMS:NCX BIRNLEX:2547 BTO:0000920 DHBA:10160 EHDAA2:0004662 EMAPA:32842 EMAPA:35589 FMA:62429 GAID:677 MA:0002754 MBA:315 MESH:D019579 PBA:294021746 UMLS:C0175173 Wikipedia:Neocortex neuronames:757 cerebral neocortex homogenetic cortex homotypical cortex isocortex (sensu lato) neocortex (isocortex) neopallial cortex neopallium isocortex uberon iso-cortex nonolfactory cortex nucleus hypoglossalis UBERON:0001950 neocortex http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg Wikipedia An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN). BIRNLEX:2547 OldNeuroNames:754 ABA The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils PMID:23027930 UMLS:C0175173 BIRNLEX:2547 neuronames:757 BIRNLEX:2547 homogenetic cortex ISBN:0471888893 homotypical cortex BIRNLEX:2547 isocortex (sensu lato) FMA:62429 neocortex (isocortex) DHBA:10160 isocortex BRAINSPAN:BRAINSPAN iso-cortex BAMS:iso-cortex nonolfactory cortex BTO:0000920 nucleus hypoglossalis NeuroNames:757 An epithelium that is part of a nasopharynx [Automatically generated definition]. UBERON:0003237 BTO:0004480 CALOHA:TS-0662 EHDAA2:0001241 EHDAA:7090 EMAPA:17672 FMA:62452 MA:0001865 NCIT:C49263 UMLS:C1179157 VHOG:0001038 epithelial tissue of nasal part of pharynx epithelial tissue of nasopharynx epithelial tissue of rhinopharynx epithelium of nasal part of pharynx epithelium of rhinopharynx nasal part of pharynx epithelial tissue nasal part of pharynx epithelium nasopharynx epithelial tissue nasopharynx epithelium rhinopharynx epithelial tissue rhinopharynx epithelium uberon nasopharyngeal epithelium UBERON:0001951 epithelium of nasopharynx EHDAA2 An epithelium that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic UMLS:C1179157 ncithesaurus:Nasopharynx_Epithelium epithelial tissue of nasal part of pharynx OBOL:automatic epithelial tissue of nasopharynx OBOL:automatic epithelial tissue of rhinopharynx OBOL:automatic epithelium of nasal part of pharynx OBOL:automatic epithelium of rhinopharynx OBOL:automatic nasal part of pharynx epithelial tissue OBOL:automatic nasal part of pharynx epithelium OBOL:automatic nasopharynx epithelial tissue OBOL:automatic rhinopharynx epithelial tissue OBOL:automatic rhinopharynx epithelium OBOL:automatic nasopharyngeal epithelium BTO:0004480 An epithelium that is part of a oropharynx [Automatically generated definition]. Composition varies with species and time. This is classified as nonkeratinizing stratified squamous in FMA, unilaminar in EHDAA2; the majority of the pharyngeal epithelium is unilaminar in zebrafish EHDAA2:0004083 EMAPA:37705 FMA:62453 MA:0001605 NCIT:C49264 UMLS:C1179158 oropharyngeal epithelium oropharynx epithelial tissue oropharynx epithelium uberon UBERON:0001952 epithelium of oropharynx EHDAA2 An epithelium that is part of a oropharynx [Automatically generated definition]. OBOL:automatic Composition varies with species and time. This is classified as nonkeratinizing stratified squamous in FMA, unilaminar in EHDAA2; the majority of the pharyngeal epithelium is unilaminar in zebrafish FMA EMAPA:37705 MA:th UMLS:C1179158 ncithesaurus:Oropharynx_Epithelium oropharynx epithelial tissue OBOL:automatic oropharynx epithelium MA:0001605 The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. EMAPA:35192 FMA:62649 MA:0001835 NCIT:C49209 SCTID:278980009 UMLS:C0225604 bronchi cartilage bronchial cartilage bronchial cartilage ring bronchial trunk cartilage bronchus cartilage cartilage of bronchi cartilage of bronchial trunk cartilagines bronchiales uberon UBERON:0001956 cartilage of bronchus MP The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. MP:0010988 UMLS:C0225604 ncithesaurus:Bronchus_Cartilage bronchi cartilage OBOL:automatic bronchial cartilage ring MP:0010988 bronchial trunk cartilage OBOL:automatic cartilage of bronchi OBOL:automatic cartilage of bronchial trunk OBOL:automatic cartilagines bronchiales A submucosa that is part of a bronchus [Automatically generated definition]. BTO:0002108 EMAPA:37449 FMA:62653 MA:0001837 NCIT:C49214 SCTID:85546005 UMLS:C0225601 bronchi submucosa bronchial submucosa bronchial trunk submucosa bronchus submucosa submucosa of bronchi submucosa of bronchial trunk tela submucosa bronchi uberon submucous layer of bronchi UBERON:0001957 submucosa of bronchus A submucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic EMAPA:37449 MA:th UMLS:C0225601 ncithesaurus:Bronchus_Submucosa bronchi submucosa OBOL:automatic bronchial trunk submucosa OBOL:automatic submucosa of bronchi OBOL:automatic submucosa of bronchial trunk OBOL:automatic tela submucosa bronchi FMA:62653 FMA:TA submucous layer of bronchi BTO:0002108 Diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. todo - add part relationships to specific layers FMA:62819 MA:0000140 NCIT:C12910 UMLS:C0599921 Wikipedia:Mucosa-associated_lymphoid_tissue MALT epithelio-lymphoid tissue mucosa associated lymphatic tissue mucosa associated lymphoid tissue mucosa-associated lymphoid tissue mucosal-associated lymphatic tissue mucosal-associated lymphoid tissue uberon UBERON:0001961 mucosa-associated lymphoid tissue FMA Diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. Wikipedia:Mucosa-associated_lymphoid_tissue UMLS:C0599921 ncithesaurus:Mucosa-Associated_Lymphoid_Tissue epithelio-lymphoid tissue FMA:62819 mucosa-associated lymphoid tissue GO:0048537 mucosal-associated lymphatic tissue GO:0048537 mucosal-associated lymphoid tissue GO:0048537 Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. phylogenetic relationships to be added guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002). FMA:62820 MA:0000136 NCIT:C12936 UMLS:C0596638 Wikipedia:Gut-associated_lymphoid_tissue gut associated lymphoid tissue uberon GALT UBERON:0001962 gut-associated lymphoid tissue Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. Wikipedia:Gut-associated_lymphoid_tissue UMLS:C0596638 ncithesaurus:Gut_Associated_Lymphoid_Tissue A diffuse collection of lymphpoid cells that participate in airway immune responses. FMA:62821 MA:0000135 NCIT:C32234 UMLS:C1179418 bronchus associated lymphoid tissue uberon BALT UBERON:0001963 Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN:0123813611] Notes: FMA classifies this as organized, not diffuse bronchial-associated lymphoid tissue ISBN:0123813611 A diffuse collection of lymphpoid cells that participate in airway immune responses. ISBN:0123813611 UMLS:C1179418 ncithesaurus:Bronchus-Associated_Lymphoid_Tissue Organism substance that is composed of sperm cells suspended in seminal fluid. seminal Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530). BTO:0001230 CALOHA:TS-0917 EMAPA:31488 FMA:62966 GAID:1169 MA:0002522 MESH:D012661 NCIT:C13277 NCIT:C13713 UMLS:C1518159 UMLS:C2756969 Wikipedia:Semen uberon ejaculate sperm UBERON:0001968 semen http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg Organism substance that is composed of sperm cells suspended in seminal fluid. http://orcid.org/0000-0002-6601-2165 UMLS:C1518159 ncithesaurus:Male_Genital_System_Fluid_or_Secretion UMLS:C2756969 ncithesaurus:Semen sperm BTO:0001230 The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 UMLS:C0032105 Wikipedia:Blood_plasma blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The liquid component of blood, in which erythrocytes are suspended. http://orcid.org/0000-0002-6601-2165 plasma MA:0002501 portion of plasma FMA:62970 UMLS:C0032105 ncithesaurus:Plasma Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. aids the process of digestion of lipids in the small intestine bile salts function to emulsify dietary fats and facilitate their intestinal absorption elimination of cholesterol major excretory route for potentially harmful exogenous lipophilic substances many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine BTO:0000121 CALOHA:TS-1172 ENVO:02000023 FMA:62971 GAID:1157 MA:0002513 MESH:D001646 NCIT:C13192 UMLS:C0005388 Wikipedia:Bile ZFA:0005857 galen:Bile uberon fel gall UBERON:0001970 bile 0.3% in humans Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. DOI:10.1002/cphy.c120027 Wikipedia:Bile UMLS:C0005388 ncithesaurus:Bile fel BTO:0000121 gall BTO:0000121 BTO:0000501 FMA:62972 GAID:1160 MA:0002519 MESH:D005750 NCIT:C32661 UMLS:C0017133 Wikipedia:Gastric_juice galen:GastricJuice stomach secretion uberon succus gastricus UBERON:0001971 gastric juice UMLS:C0017133 ncithesaurus:Gastric_Secretion succus gastricus BTO:0000501 A submucosa that is part of a esophagus [Automatically generated definition]. BTO:0002109 EMAPA:35325 FMA:62997 MA:0002724 SCTID:362128009 esophageal submucosa esophagus submucosa gullet submucosa oesophagus submucosa submucosa of esophagus submucosa of gullet submucosa of oesophagus tela submucosa (oesophagus) tela submucosa esophagi tela submucosa oesophageae tela submucosa of esophagus uberon submucous layer of esophagus tela submucosa oesophagi UBERON:0001972 submucosa of esophagus A submucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic gullet submucosa OBOL:automatic oesophagus submucosa OBOL:automatic submucosa of gullet OBOL:automatic submucosa of oesophagus OBOL:automatic tela submucosa (oesophagus) FMA:62997 FMA:TA tela submucosa esophagi BTO:0002109 tela submucosa oesophageae FMA:62997 FMA:TA submucous layer of esophagus BTO:0002109 tela submucosa oesophagi BTO:0002109 A lamina propria that is part of a esophagus [Automatically generated definition]. EMAPA:26987 FMA:63050 MA:0001568 NCIT:C49223 UMLS:C1707949 esophagus lamina propria esophagus lamina propria mucosa esophagus lamina propria mucosae gullet lamina propria gullet lamina propria mucosa gullet lamina propria mucosae lamina propria mucosa of esophagus lamina propria mucosa of gullet lamina propria mucosa of oesophagus lamina propria mucosae of esophagus lamina propria mucosae of gullet lamina propria mucosae of oesophagus lamina propria of gullet lamina propria of oesophagus oesophagus lamina propria mucosa oesophagus lamina propria mucosae uberon esophageal lamina propria oesophagus lamina propria UBERON:0001974 lamina propria of esophagus FMA A lamina propria that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C1707949 ncithesaurus:Esophageal_Lamina_Propria esophagus lamina propria mucosa OBOL:automatic esophagus lamina propria mucosae OBOL:automatic gullet lamina propria OBOL:automatic gullet lamina propria mucosa OBOL:automatic gullet lamina propria mucosae OBOL:automatic lamina propria mucosa of esophagus OBOL:automatic lamina propria mucosa of gullet OBOL:automatic lamina propria mucosa of oesophagus OBOL:automatic lamina propria mucosae of gullet OBOL:automatic lamina propria mucosae of oesophagus OBOL:automatic lamina propria of gullet OBOL:automatic lamina propria of oesophagus OBOL:automatic oesophagus lamina propria mucosa OBOL:automatic oesophagus lamina propria mucosae OBOL:automatic esophageal lamina propria EMAPA:26987 A serous membrane that is part of a esophagus [Automatically generated definition]. EMAPA:35322 FMA:63057 MA:0001571 esophagus serosa esophagus serous membrane gullet serosa gullet serous membrane oesophagus serous membrane serosa of abdominal part of esophagus serosa of gullet serosa of oesophagus serous coat of oesophagus serous membrane of esophagus serous membrane of gullet serous membrane of oesophagus tunica serosa oesophageae uberon oesophagus serosa UBERON:0001975 serosa of esophagus A serous membrane that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus serous membrane OBOL:automatic gullet serosa OBOL:automatic gullet serous membrane OBOL:automatic oesophagus serous membrane OBOL:automatic serosa of gullet OBOL:automatic serous membrane of esophagus OBOL:automatic serous membrane of gullet OBOL:automatic serous membrane of oesophagus OBOL:automatic tunica serosa oesophageae FMA:63057 FMA:TA The epithelial layer that lines the luminal space of the esophagus. TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] BTO:0001578 CALOHA:TS-0698 EFO:0003041 EHDAA2:0001287 EMAPA:16835 FMA:63063 MA:0001565 NCIT:C49221 TAO:0001499 UMLS:C1179544 ZFA:0001499 epithelial tissue of esophagus epithelial tissue of gullet epithelial tissue of oesophagus epithelium of gullet epithelium of oesophagus esophageal epithelium esophagus epithelial tissue esophagus epithelium gullet epithelial tissue gullet epithelium oesophagus epithelial tissue uberon oesophagus epithelium UBERON:0001976 epithelium of esophagus FMA The epithelial layer that lines the luminal space of the esophagus. ISBN:0-683-40008-8 MP:0000468 Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001499 TAO ZFIN:curator UMLS:C1179544 ncithesaurus:Esophageal_Epithelium epithelial tissue of esophagus OBOL:automatic epithelial tissue of gullet OBOL:automatic epithelial tissue of oesophagus OBOL:automatic epithelium of gullet OBOL:automatic epithelium of oesophagus OBOL:automatic esophagus epithelial tissue OBOL:automatic gullet epithelial tissue OBOL:automatic gullet epithelium OBOL:automatic oesophagus epithelial tissue OBOL:automatic The portion of blood plasma that excludes clotting factors. BTO:0000133 BTO:0001239 CALOHA:TS-0923 EHDAA2:0004728 EMAPA:35770 FMA:63083 MA:0002502 MESH:D044967 NCIT:C13325 UMLS:C0229671 Wikipedia:Serum_(blood) serum uberon UBERON:0001977 blood serum The portion of blood plasma that excludes clotting factors. Wikipedia:Serum_(blood) http://orcid.org/0000-0002-6601-2165 MESH:D044967 https://github.com/biopragmatics/biomappings UMLS:C0229671 ncithesaurus:Serum EMAPA:32925 FMA:63120 MA:0000724 SCTID:371401008 VHOG:0001430 pancreas parenchyma pancreatic parenchyma uberon UBERON:0001978 parenchyma of pancreas One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins. Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:D014699 NCIT:C12818 SCTID:341687009 TAO:0005315 UMLS:C0042520 VHOG:0001765 Wikipedia:Venule ZFA:0005315 uberon venula UBERON:0001979 venule https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins. MESH:A07.231.432.952 MP:0004125 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] 2012-08-14 TAO:0005315 TAO ZFIN:curator UMLS:C0042520 ncithesaurus:Venule venula Wikipedia:Venule The smallest division of the artery located between the muscular arteries and the capillaries[GO]. Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 NCIT:C12672 SCTID:337724002 TAO:0002138 UMLS:C0003847 VHOG:0001763 Wikipedia:Arteriole ZFA:0005255 uberon arteriola UBERON:0001980 arteriole https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg MA The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] 2012-08-14 TAO:0002138 TAO ZFIN:curator Small, terminal branch of an artery which generally connects to capillaries.[AAO] 2012-06-20 AAO:0010253 AAO AAO:BJB UMLS:C0003847 ncithesaurus:Arteriole arteriola Wikipedia:Arteriole A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] annelids have blood vessels, but this class is not applicable to annelids. FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 GAID:169 MA:0000060 MAT:0000393 MESH:D001808 NCIT:C12679 NLXANAT:090901 SCTID:361097006 TAO:0002137 UMLS:C0005847 VHOG:0001250 Wikipedia:Blood_vessel XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg AEO EHDAA2 GO:0072360 A vessel through which blood circulates in the body. BTO:0001102 Wikipedia:Blood_vessel Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] 2012-09-17 VHOG:0001250 VHOG http://bgee.unil.ch/ Any of the vessels through which blood circulates in the body.[AAO] 2012-06-20 AAO:0011004 AAO AAO:EJS The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001250 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX FMA vascular element EMAPA:35993 UMLS:C0005847 ncithesaurus:Blood_Vessel region of vascular tree organ FMA:50722 vascular tree organ region FMA:50722 vas sanguineum Wikipedia:Blood_vessel Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:D002196 NCIT:C12685 NLXANAT:090902 TAO:0005250 UMLS:C0935624 VHOG:0001253 Wikipedia:Capillary XAO:0000116 ZFA:0005250 blood capillary capillary vessel uberon UBERON:0001982 capillary https://github.com/obophenotype/uberon/issues/2186 http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg Any of the smallest blood vessels connecting arterioles with venules. ISBN:0073040584 Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] 2012-06-20 AAO:0010252 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001253 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0935624 ncithesaurus:Capillary A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. CALOHA:TS-0172 EMAPA:35935 FMA:63882 GAID:891 MA:0001242 MESH:D004728 NCIT:C12707 SCTID:368827009 TAO:0002186 UMLS:C0014259 Wikipedia:Corneal_endothelium ZFA:0001687 cornea endothelium endothelium of cornea uberon epithelium posterius corneae UBERON:0001985 corneal endothelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. Wikipedia:Corneal_endothelium UMLS:C0014259 ncithesaurus:Corneal_Endothelium cornea endothelium OBOL:automatic endothelium of cornea OBOL:automatic epithelium posterius corneae Wikipedia:Corneal_endothelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 FMA:63916 GAID:520 MESH:D004727 NCIT:C12481 SCTID:27168002 UMLS:C0014257 galen:Endothelium uberon UBERON:0001986 The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) endothelium FMA-text-def https://github.com/obophenotype/uberon/issues/225 A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. FMA:63916 MESH:A10.272.491 https://github.com/obophenotype/uberon/issues/225 UMLS:C0014257 ncithesaurus:Endothelium Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] placental Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011 BTO:0001078 CALOHA:TS-0799 EFO:0001407 EMAPA:35689 EV:0100119 FMA:63934 GAID:379 MA:0000386 MAT:0000279 MESH:D010920 MIAA:0000279 NCIT:C13272 SCTID:181455002 UMLS:C0032043 VHOG:0001266 Wikipedia:Placenta allantoic placenta eutherian placenta uberon UBERON:0001987 Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities. placenta http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb https://github.com/obophenotype/uberon/issues/1376 ISBN:0073040584 Wikipedia ISBN:0073040584 Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Wikipedia:Placenta http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/06placenta.htm Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] 2012-09-17 VHOG:0001266 VHOG DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001) http://bgee.unil.ch/ UMLS:C0032043 ncithesaurus:Placenta allantoic placenta ISBN:0073040584 Portion of semisolid bodily waste discharged through the anus[MW,modified]. Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 UMLS:C0015733 Wikipedia:Feces galen:Feces faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces Portion of semisolid bodily waste discharged through the anus[MW,modified]. Wikipedia:Feces http://www.merriam-webster.com/dictionary/feces Excretion in semisolid state processed by the intestine.[FMA] FMA:64183 UMLS:C0015733 ncithesaurus:Feces piece of shit PMID:23285307 portionem cacas cow dung Wikipedia:Cow_dung cow pat Wikipedia:Cow_dung fewmet Wikipedia:Fewmet frass Wikipedia:Frass guano Wikipedia:Guano spraint Wikipedia:Spraint excrement BTO:0000440 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] EMAPA:35414 FMA:64783 MA:0000109 NCIT:C32746 SCTID:39298000 UMLS:C0225362 VSAO:0000094 Wikipedia:Hyaline_cartilage XAO:0004029 hyaline cartilage uberon chondroid cartilage UBERON:0001994 hyaline cartilage tissue http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg FMA VSAO-text-def Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. GO_REF:0000034 PSPUB:0000170 VSAO:0000094 http://dx.plos.org/10.1371/journal.pone.0051070 Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. FMA:64783 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] 2012-08-14 VSAO:0000094 VSAO PSPUB:0000170 UMLS:C0225362 ncithesaurus:Hyaline_Cartilage hyaline cartilage MA:0000109 chondroid cartilage http://orcid.org/0000-0002-6601-2165 Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns. A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]. Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO] fibrocartilaginous FMA:64784 MA:0000108 MESH:D051445 NCIT:C32599 SCTID:91685003 UMLS:C0684077 VSAO:0000103 Wikipedia:Fibrocartilage XAO:0004028 galen:Fibrocartilage fibrocartilage tissue stratified cartilage tissue uberon UBERON:0001995 The white fibrocartilages admit of arrangement into four groups-interarticular, connecting, circumferential, and stratiform -- WP. EDITOR NOTE: TODO add mineralized fibrocartilage http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns. GO_REF:0000034 PSPUB:0000170 VSAO:0000103 http://dx.plos.org/10.1371/journal.pone.0051070 A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I Wikipedia:Fibrocartilage Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]. FMA:64784 Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO] 2012-08-14 VSAO:0000103 VSAO PSPUB:0000170 MESH:D051445 https://github.com/biopragmatics/biomappings UMLS:C0684077 ncithesaurus:Fibrocartilage fibrocartilage tissue http://orcid.org/0000-0002-6601-2165 stratified cartilage tissue http://orcid.org/0000-0002-6601-2165 Cartilage tissue that is flexible and contains abundant elastic fibers. Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785]. Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO] MA has a distinct class for yellow FMA:64785 MA:0000107 MA:0000485 NCIT:C32494 UMLS:C0682559 VSAO:0000091 Wikipedia:Elastic_cartilage XAO:0004197 elastic cartilage elastic cartilage tissue yellow elastic cartilage yellow elastic cartilage tissue uberon reticular cartilage yellow cartilage UBERON:0001996 elastic cartilage tissue http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray904.png VSAO Wikipedia VSAO Cartilage tissue that is flexible and contains abundant elastic fibers. GO_REF:0000034 PSPUB:0000170 VSAO:0000091 http://dx.plos.org/10.1371/journal.pone.0051070 Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785]. FMA:64785 Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO] 2012-08-14 VSAO:0000091 VSAO PSPUB:0000170 MA has a distinct class for yellow MA UMLS:C0682559 ncithesaurus:Elastic_Cartilage elastic cartilage MA:0000107 elastic cartilage tissue VSAO:0000091 yellow elastic cartilage Wikipedia:Elastic_cartilage reticular cartilage http://orcid.org/0000-0002-6601-2165 yellow cartilage http://orcid.org/0000-0002-6601-2165 Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints. FMA_RETIRED:64994 MA:0001508 NCIT:C49575 SCTID:263314001 UMLS:C1261194 rib joint uberon UBERON:0002001 joint of rib cjm Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints. https://orcid.org/0000-0002-6601-2165 UMLS:C1261194 ncithesaurus:Joint_of_the_Rib Peripheral portion of the lymph node, underneath the capsule[WP]. EMAPA:35525 FMA:66253 MA:0000740 NCIT:C33029 UMLS:C0933402 Wikipedia:Cortex_of_lymph_node lymph node cortex uberon cortex nodi lymphoidei UBERON:0002006 cortex of lymph node http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png Peripheral portion of the lymph node, underneath the capsule[WP]. Wikipedia:Cortex_of_lymph_node UMLS:C0933402 ncithesaurus:Lymph_Node_Cortex cortex nodi lymphoidei Wikipedia:Cortex_of_lymph_node The medullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells. EMAPA:35529 FMA:66254 MA:0000745 lymph node medulla uberon medulla nodi lymphoidei UBERON:0002007 medulla of lymph node https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb The medullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells. Wikipedia:Lymph_node#Medulla http://orcid.org/0000-0002-6601-2165 medulla nodi lymphoidei Wikipedia:Medulla_of_lymph_node A plexus of nerves situated at the base of the heart that innervate the heart. EMAPA:37460 FMA:6628 MA:0001138 NCIT:C52833 SCTID:280511002 UMLS:C0459528 Wikipedia:Cardiac_plexus autonomic nerve plexus of heart autonomic plexus of heart cardiac plexus heart autonomic nerve plexus heart autonomic plexus plexus cardiacus uberon UBERON:0002008 cardiac nerve plexus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png A plexus of nerves situated at the base of the heart that innervate the heart. Wikipedia:Cardiac_plexus EMAPA:37460 MA:th UMLS:C0459528 ncithesaurus:Cardiac_Nerve_Plexus autonomic nerve plexus of heart OBOL:automatic autonomic plexus of heart OBOL:automatic heart autonomic nerve plexus OBOL:automatic heart autonomic plexus OBOL:automatic plexus cardiacus Wikipedia:Cardiac_plexus The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted]. EMAPA:37129 FMA:66320 MA:0002065 NCIT:C53018 UMLS:C0933449 Wikipedia:Thoracodorsal_artery uberon arteria thoracodorsalis UBERON:0002011 thoracodorsal artery https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted]. Wikipedia:Thoracodorsal_artery EMAPA:37129 MA:th UMLS:C0933449 ncithesaurus:Thoracodorsal_Artery arteria thoracodorsalis Wikipedia:Thoracodorsal_artery An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP] AAO:0010221 BTO:0000778 CALOHA:TS-0839 EFO:0001399 EHDAA2:0001575 EHDAA:4351 EMAPA:17008 FMA:66326 GAID:505 MA:0002031 MESH:D011651 NCIT:C12774 SCTID:181380003 UMLS:C0034052 VHOG:0000982 Wikipedia:Pulmonary_artery XAO:0004162 galen:PulmonaryArtery pulmonary arterial tree pulmonary arterial tree organ part uberon arteria pulmonalis pulmonary arterial subtree truncus pulmonalis UBERON:0002012 pulmonary artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png Wikipedia EHDAA2 XAO EHDAA2 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Wikipedia:Pulmonary_artery http://orcid.org/0000-0002-6601-2165 Major artery which supplies blood to the lungs.[AAO] 2012-06-20 AAO:0010221 AAO AAO:BJB One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] 2012-09-17 VHOG:0000982 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+artery On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0000982 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0034052 ncithesaurus:Pulmonary_Artery pulmonary arterial tree FMA:66326 pulmonary arterial tree organ part FMA:66326 arteria pulmonalis Wikipedia:Pulmonary_artery pulmonary arterial subtree FMA:66326 truncus pulmonalis Wikipedia:Pulmonary_artery The tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage. provides some protection from trauma and damage. The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule] EMAPA:18679 FMA:66610 MA:0000370 NCIT:C12885 SCTID:243657006 UMLS:C0227637 Wikipedia:Kidney_capsule galen:CapsuleOfKidney capsula fibrosa renis capsule of kidney fibrous capsule of kidney renal capsule uberon UBERON:0002015 kidney capsule https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg The tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage. MGI:anna MP:0011383 UMLS:C0227637 ncithesaurus:Renal_Capsule capsula fibrosa renis FMA:66610 FMA:TA fibrous capsule of kidney FMA:66610 renal capsule GO:0072127 Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] the veins that return oxygenated blood from the lungs to the left atrium of the heart On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] AAO:0010521 BTO:0001799 CALOHA:TS-0840 EHDAA2:0001579 EHDAA:2629 EMAPA:18645 FMA:66643 GAID:543 MA:0002206 MESH:D011667 NCIT:C12776 SCTID:430160002 UMLS:C0034090 VHOG:0001133 Wikipedia:Pulmonary_vein XAO:0000394 galen:PulmonaryVein pulmonary venous tree organ part uberon venae pulmonales UBERON:0002016 pulmonary vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. GO:0060577 Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] 2012-06-20 AAO:0010521 AAO AAO:BJB One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] 2012-09-17 VHOG:0001133 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+vein the veins that return oxygenated blood from the lungs to the left atrium of the heart MP:0002726,MGI:cwg On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0001133 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0034090 ncithesaurus:Pulmonary_Vein venae pulmonales Wikipedia:Pulmonary_vein A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 CALOHA:TS-0814 EHDAA2:0001485 EHDAA:6510 EMAPA:17349 FMA:66645 GAID:540 MA:0002198 MESH:D011169 NCIT:C33343 SCTID:362064007 UMLS:C0032718 VHOG:0000656 XAO:0000392 galen:PortalVein portal venous tree organ part uberon UBERON:0002017 portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 UMLS:C0032718 ncithesaurus:Portal_Vein portal venous tree organ part FMA:66645 Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints). Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG] synovial layer synovial membrane synovium AEO:0000181 BTO:0001823 EFO:0001393 EHDAA2_RETIRED:0003181 EMAPA:37476 EV:0100143 FMA:9865 GAID:264 MA:0000114 MESH:D013583 NCIT:C12473 SCTID:361828005 UMLS:C0039099 VHOG:0001282 Wikipedia:Synovial_membrane galen:SynovialMembrane membrana synovialis (capsula articularis) membrana synovialis capsulae articularis stratum synoviale stratum synoviale (capsula articularis) uberon synovial layer of articular capsule of synovial joint synovial membrane of articular capsule of synovial joint synovium of articular capsule of synovial joint UBERON:0002018 synovial membrane of synovial joint http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png FMA EHDAA2 GAID Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints). Wikipedia:Synovial_membrane Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001282 VHOG PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000) http://bgee.unil.ch/ synovial layer FMA:66762 synovial membrane AEO:0000181 synovium BTO:0001823 VHOG:0001282 EMAPA:37476 MA:th UMLS:C0039099 ncithesaurus:Synovial_Membrane membrana synovialis (capsula articularis) FMA:9865 FMA:TA membrana synovialis capsulae articularis Wikipedia:Synovial_membrane stratum synoviale FMA:66762 FMA:TA stratum synoviale (capsula articularis) FMA:9865 FMA:TA synovial layer of articular capsule of synovial joint FMA:9865 synovial membrane of articular capsule of synovial joint FMA:9865 synovium of articular capsule of synovial joint FMA:9865 A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] AAO:0010476 BAMS:11n BAMS:XIn BIRNLEX:812 EHDAA2:0000106 EHDAA:2855 EMAPA:17265 FMA:6720 FMA:80284 GAID:825 HBA:9340 MA:0001088 MBA:717 MESH:D000055 NCIT:C32041 SCTID:362469008 UMLS:C0000905 UMLS:C1305777 VHOG:0000699 Wikipedia:Spinal_accessory_nerve XAO:0004214 neuronames:2085 Willis' nerve accessory XI accessory XI nerve accessory nerve accessory nerve [XI] cervical accessory nerve cranial nerve XI eleventh cranial nerve nervus accessorius [XI] pars spinalis nervus accessorius radix spinalis nervus accessorius spinal accessory nerve spinal accessory nerve tree spinal part of accessory nerve uberon CN-XI accessory spinal nerve UBERON:0002019 accessory XI nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. BIRNLEX:812 http://orcid.org/0000-0002-6601-2165 VHOG Wikipedia http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7 A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. ISBN:080184780X XAO:0004214 Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000699 VHOG http://bgee.unil.ch/ Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] 2012-06-20 AAO:0010476 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000699 VHOG Wikipedia:Cranial_nerves http://bgee.unil.ch/ In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve GO FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] FMA UMLS:C0000905 BIRNLEX:812 ncithesaurus:Accessory_Nerve UMLS:C1305777 BIRNLEX:812 accessory XI EHDAA2:0000106 cranial nerve XI BIRNLEX:812 eleventh cranial nerve BIRNLEX:812 nervus accessorius [XI] FMA:6720 FMA:TA pars spinalis nervus accessorius FMA:6720 FMA:TA radix spinalis nervus accessorius FMA:6720 FMA:TA spinal accessory nerve FMA:6720 CN-XI VHOG:0000699 accessory spinal nerve BAMS:XIn A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 EMAPA:37596 FMA:67242 HBA:4006 MA:0001112 MESH:D066128 NCIT:C32695 TAO:0002197 UMLS:C0018220 VHOG:0001768 Wikipedia:Gray_matter ZFA:0001681 neuronames:2869 gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance neuronal grey matter substantia grisea uberon gray mater grisea UBERON:0002020 gray matter https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Wikipedia:Gray_matter http://orcid.org/0000-0002-6601-2165 Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] 2012-08-14 TAO:0002197 TAO ZFIN:curator EMAPA:37596 MA:th MESH:D066128 https://github.com/biopragmatics/biomappings UMLS:C0018220 ncithesaurus:Gray_Matter gray matter of neuraxis FMA:67242 neuronal grey matter AEO:0001012 substantia grisea FMA:67242 FMA:TA gray mater ZFA:0001681 grisea The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] rhombencephalic in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BIRNLEX:942 BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 NCIT:C40336 SCTID:303456008 TAO:0000029 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 Wikipedia:Rhombencephalon XAO:0000015 ZFA:0000029 neuronames:540 uberon rhombencephalon UBERON:0002028 hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg modified-source-relation ABA Bgee:AN The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Wikipedia:Rhombencephalon ZFA:0000029 ZFIN:curator ZFA ABA https://github.com/obophenotype/uberon/issues/378 pending ABA PMID:8932866 Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] 2012-06-20 AAO:0010150 AAO AAO:BJB The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000029 TAO ZFIN:curator relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] 2012-08-14 TAO:0000029 TAO Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000070 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps MA UMLS:C0035507 BIRNLEX:942 ncithesaurus:Hind-Brain UMLS:C1522180 BIRNLEX:942 neuronames:540 BIRNLEX:942 The simple columnar epithelial lining of the gall bladder. BTO:0001449 CALOHA:TS-1304 EMAPA:35370 FMA:67711 MA:0001632 NCIT:C49227 UMLS:C1180206 epithelial tissue of gall bladder epithelial tissue of gallbladder epithelium of gallbladder gall bladder epithelial tissue gall bladder epithelium gallbladder epithelial tissue gallbladder epithelium uberon biliary epithelium UBERON:0002029 epithelium of gall bladder The simple columnar epithelial lining of the gall bladder. MP:0009492 UMLS:C1180206 ncithesaurus:Gallbladder_Epithelium epithelial tissue of gall bladder OBOL:automatic epithelial tissue of gallbladder OBOL:automatic epithelium of gallbladder OBOL:automatic gall bladder epithelial tissue OBOL:automatic gallbladder epithelial tissue OBOL:automatic gallbladder epithelium OBOL:automatic Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip. a male mouse has no nipples - mammary tissue regresses during embryonic development FMA makes this part of the breast, whereas in MA it is part of the mammary gland - BTO:0000821 CALOHA:TS-2234 EMAPA:36508 FMA:67771 GAID:35 MA:0000796 MESH:D009558 NCIT:C12299 SCTID:265780004 UMLS:C0028109 Wikipedia:Nipple galen:Nipple papilla mammae papilla of breast thele thelium papillary part of breast teat uberon papilla mammaria UBERON:0002030 Nipple being part_of mammary gland is due to a practical modelling in uberon that treats mammary gland as including adnexa. A GCI asserts that nipple is part of the breast in humans. For discussion of this, please refer to https://github.com/obophenotype/uberon/issues/1873. nipple https://github.com/obophenotype/uberon/issues/1873 http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg Stedmans Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip. FMA:67771 Wikipedia:Nipple FMA makes this part of the breast, whereas in MA it is part of the mammary gland - FMA UMLS:C0028109 ncithesaurus:Nipple papilla mammae MP:0009723 thele MP:0009723 thelium MP:0009723 papilla mammaria Wikipedia:Nipple An epithelium that is part of a bronchus [Automatically generated definition]. BTO:0001845 CALOHA:TS-1240 EFO:0000307 EMAPA:32691 FMA:67782 MA:0001839 NCIT:C32231 UMLS:C0599333 bronchi epithelial tissue bronchi epithelium bronchial epithelium bronchial trunk epithelial tissue bronchial trunk epithelium bronchus epithelial tissue bronchus epithelium epithelial tissue of bronchi epithelial tissue of bronchial trunk epithelial tissue of bronchus epithelium of bronchi epithelium of bronchial trunk uberon UBERON:0002031 epithelium of bronchus FMA An epithelium that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C0599333 ncithesaurus:Bronchial_Epithelium bronchi epithelial tissue OBOL:automatic bronchi epithelium OBOL:automatic bronchial trunk epithelial tissue OBOL:automatic bronchial trunk epithelium OBOL:automatic bronchus epithelial tissue OBOL:automatic epithelial tissue of bronchi OBOL:automatic epithelial tissue of bronchial trunk OBOL:automatic epithelial tissue of bronchus OBOL:automatic epithelium of bronchi OBOL:automatic epithelium of bronchial trunk OBOL:automatic A tiny smooth muscle that connects the hair follicle with the dermis. When contracted the arrector pili causes the raising of the hair BTO:0005132 EMAPA:26775 FMA:67821 MA:0000778 SCTID:319910005 Wikipedia:Arrector_pili_muscle arrector pili arrector pili muscle arrector pili smooth muscle arrector pilli arrector pilli muscle arrector pilorum arrector pilorum muscle of hair uberon arectores pilorum erector pili erectores pilorum pilomotor muscle UBERON:0002033 arrector muscle of hair FMA FMA A tiny smooth muscle that connects the hair follicle with the dermis. DOI:10.1016/j.cub.2008.12.005 arrector pili FMA:67821 MA:0000778 arrector pili muscle EMAPA:26779 MP:0010679 arrector pili smooth muscle MA:0000778 arrector pilli MP:0010679 arrector pilli muscle MP:0010679 arrector pilorum ISBN:0123813611 arrector pilorum muscle of hair ISBN:0123813611 arectores pilorum BTO:0005132 erector pili BTO:0005132 erectores pilorum BTO:0005132 pilomotor muscle BTO:0005132 Muscle tissue that contains fibers that are divided by transverse bands into striations. Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 NCIT:C12436 UMLS:C1331262 WBbt:0005779 Wikipedia:Striated_muscle galen:StriatedMuscle striated muscle uberon UBERON:0002036 striated muscle tissue Muscle tissue that contains fibers that are divided by transverse bands into striations. CL:0000737 GOC:dph GOC:mtg_muscle Voluntary muscle tissue arranged in bundles of fibers.[AAO] 2012-06-20 AAO:0010762 AAO AAO:CAM UMLS:C1331262 ncithesaurus:Striated_Muscle_Tissue Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] cerebellar The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full] almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem infratentorial region AAO:0010485 BAMS:CB BAMS:Cb BIRNLEX:1489 BM:CB BTO:0000232 CALOHA:TS-0125 DHBA:10656 EFO:0000327 EHDAA2:0000232 EMAPA:17787 EV:0100293 FMA:67944 GAID:595 HBA:4696 MA:0000198 MAT:0000110 MBA:512 MESH:D002531 MIAA:0000110 NCIT:C12445 SCTID:180924008 TAO:0000100 UMLS:C0007765 UMLS:C1268981 VHOG:0000024 Wikipedia:Cerebellum XAO:0003098 ZFA:0000100 neuronames:643 epencephalon-1 uberon corpus cerebelli parencephalon UBERON:0002037 cerebellum https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png FMA MA ISBN:0471888893 definitional Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. BTO:0000232 ISBN:3764351209 MESH:A08.186.211.132.810.428.200 ZFA:0000100 https://sourceforge.net/tracker/index.php?func=detail&aid=3291162&group_id=76834&atid=1205376 ISBN:0471888893 ABA ZFA ABA https://github.com/obophenotype/uberon/issues/378 pending http://icb.oxfordjournals.org/content/42/4/743.full ISBN:0471888893 Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] 2012-06-20 AAO:0010485 AAO AAO:BJB Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000100 TAO ZFIN:curator However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] 2012-09-17 VHOG:0000024 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem ABA infratentorial region Wikipedia:Tentorium_cerebelli UMLS:C0007765 BIRNLEX:1489 ncithesaurus:Cerebellum UMLS:C1268981 BIRNLEX:1489 neuronames:643 BIRNLEX:1489 epencephalon-1 FMA:67944 corpus cerebelli NeuroNames:643 parencephalon NeuroNames:643 A systemic artery that supplies the lung with with oxygenated blood. EMAPA:18608 FMA:68109 GAID:477 MA:0001923 MESH:D001981 NCIT:C32230 SCTID:244247009 UMLS:C0006257 Wikipedia:Bronchial_artery bronchial arterial tree uberon arteriae bronchiales rami bronchiales partis thoracicae aortae UBERON:0002040 Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. bronchial artery http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png A systemic artery that supplies the lung with with oxygenated blood. UBERON:cjm Wikipedia:Bronchial_artery UMLS:C0006257 ncithesaurus:Bronchial_Artery arteriae bronchiales Wikipedia:Bronchial_artery rami bronchiales partis thoracicae aortae Wikipedia:Bronchial_artery An endothelium that is part of a lymphatic vessel [Automatically generated definition]. The vascular endothelium that lines the lymph vessels.[TAO] BTO:0004303 CALOHA:TS-2156 EMAPA:35533 FMA:68444 MA:0000750 MESH:D004729 NCIT:C49258 TAO:0005258 UMLS:C1180786 ZFA:0005258 endothelium of lymph vessel endothelium of lymphatic vessel lymph vessel endothelium lymphatic endothelium lymphatic vessel endothelium uberon UBERON:0002042 lymphatic vessel endothelium FMA An endothelium that is part of a lymphatic vessel [Automatically generated definition]. OBOL:automatic The vascular endothelium that lines the lymph vessels.[TAO] 2012-08-14 TAO:0005258 TAO ZFIN:curator UMLS:C1180786 ncithesaurus:Lymphatic_Vessel_Endothelium endothelium of lymph vessel OBOL:automatic endothelium of lymphatic vessel FMA:68444 lymph vessel endothelium OBOL:automatic lymphatic endothelium BTO:0004303 A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species AAO:0010544 BTO:0001379 CALOHA:TS-1047 EFO:0000861 EHDAA2:0002028 EHDAA:2148 EHDAA:2975 EMAPA:17068 EV:0100133 FMA:9603 GAID:465 MA:0000129 MAT:0000081 MESH:D013961 MIAA:0000081 NCIT:C12400 SCTID:181117000 UMLS:C0040132 VHOG:0000418 Wikipedia:Thyroid XAO:0000162 galen:ThyroidGland thyroid uberon glandula thyroidea UBERON:0002046 thyroid gland http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg Wikipedia:Endostyle Wikipedia Wikipedia A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. BTO:0001379 Wikipedia:Thyroid Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] 2012-06-20 AAO:0010544 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] 2012-09-17 VHOG:0000418 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes NCBITaxon:32443 Romer Wikipedia:Thyroid_gland#Other_animals In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) NCBITaxon:7746 Romer Wikipedia:Thyroid_gland#Other_animals In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species NCBITaxon:32523 Romer Wikipedia:Thyroid_gland#Other_animals UMLS:C0040132 ncithesaurus:Thyroid_Gland glandula thyroidea Wikipedia:Thyroid The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. BAMS:PnR BAMS:RA-PONS BAMS:RPn BIRNLEX:1110 DHBA:12471 DHBA:12475 FMA:68875 HBA:9159 MA:0001022 MBA:238 UMLS:C0175423 Wikipedia:Pontine_raphe_nucleus neuronames:589 raphe of pons raphe pontis uberon nucleus raphe pontis nucleus raphes pontis raphe (mediana pontina) raphe pontis nucleus UBERON:0002047 pontine raphe nucleus Wikipedia The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. Wikipedia:Pontine_raphe_nucleus ABA ABA ABA ABA UMLS:C0175423 BIRNLEX:1110 neuronames:589 BIRNLEX:1110 raphe pontis FMA:68875 FMA:TA nucleus raphe pontis NeuroNames:589 nucleus raphes pontis Wikipedia:Pontine_raphe_nucleus raphe (mediana pontina) NeuroNames:589 Respiration organ that develops as an outpocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 SCTID:181216001 UMLS:C0024109 VHOG:0000310 Wikipedia:Lung XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung https://github.com/obophenotype/uberon/issues/701 https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb some species only have a single lung Respiration organ that develops as an outpocketing of the esophagus. http://orcid.org/0000-0002-6601-2165 https://orcid.org/0000-0002-9415-5104 https://github.com/obophenotype/uberon/issues/701 https://orcid.org/0000-0002-9415-5104 https://github.com/obophenotype/uberon/issues/701 Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] 2012-06-20 AAO:0010567 AAO AAO:SBH Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000310 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) http://bgee.unil.ch/ UMLS:C0024109 ncithesaurus:Lung pulmo An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? vascular BTO:0003718 FMA:69050 TAO:0005249 ZFA:0005249 vascular network uberon UBERON:0002049 vasculature http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg FMA An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. ZFA:0005249 vascular network FMA:69050 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 SCTID:667009 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure Anatomical structure that is part of an embryo. BTO:0000174 ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] 2012-06-20 AAO:0000138 AAO AAO:BJB Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] 2012-08-14 TAO:0001105 TAO ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] 2012-08-14 VSAO:0000178 VSAO ZFIN:curator in FMA embryo is_a embryonic structure FMA FBbt:00004208 UMLS:C0013948 ncithesaurus:Embryonic_Structure developing embryonic structure FBbt:00004208 embryonic anatomical structure RETIRED_EHDAA2:0003169 embryonale Struktur BTO:0000174 embryonic structures ZFA:0001105 The thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. FMA:69087 MA:0000117 NCIT:C32050 UMLS:C1181304 capsule of adrenal gland uberon adrenal capsule UBERON:0002052 adrenal gland capsule The thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. MP:0013565 UMLS:C1181304 ncithesaurus:Adrenal_Gland_Capsule capsule of adrenal gland FMA:69087 Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]. EMAPA:37088 FMA:69264 MA:0002056 NCIT:C52737 SCTID:303426004 UMLS:C0226334 Wikipedia:Inferior_suprarenal_artery uberon arteria suprarenalis inferior UBERON:0002056 inferior suprarenal artery http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]. Wikipedia:Inferior_suprarenal_artery EMAPA:37088 MA:th UMLS:C0226334 ncithesaurus:Inferior_Suprarenal_Artery arteria suprarenalis inferior Wikipedia:Inferior_suprarenal_artery An artery that supplies the diaphragm. In humans this includes the superior and inferior phrenic arteries EMAPA:37108 FMA:69330 MA:0002019 NCIT:C33320 UMLS:C1181536 uberon UBERON:0002057 phrenic artery An artery that supplies the diaphragm. https://orcid.org/0000-0002-6601-2165 EMAPA:37108 MA:th UMLS:C1181536 ncithesaurus:Phrenic_Artery The ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands. BTO:0001318 EHDAA2:0001942 EHDAA:6710 EMAPA:36276 FMA:6966 MA:0002470 NCIT:C52558 SCTID:279282000 UMLS:C0229063 Wikipedia:Submandibular_ganglion mandibular ganglion uberon Blandin`s ganglion ganglion submandibulare lingual ganglion maxillary ganglion submaxillary ganglion UBERON:0002059 submandibular ganglion http://upload.wikimedia.org/wikipedia/commons/8/83/Gray778.png http://upload.wikimedia.org/wikipedia/en/thumb/8/83/Gray778.png/200px-Gray778.png The ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands. ISBN:0-683-40008-8 MP:0001035 UMLS:C0229063 ncithesaurus:Submandibular_Ganglion mandibular ganglion UBERON:cjm Blandin`s ganglion BTO:0001318 ganglion submandibulare BTO:0001318 Wikipedia:Submandibular_ganglion lingual ganglion MA:0002470 https://sourceforge.net/tracker/index.php?func=detail&aid=2979467&group_id=76834&atid=1205376 maxillary ganglion MA:0002470 submaxillary ganglion MA:0002470 The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted]. Artery which supplies blood via branches to the hindlimbs.[AAO] AAO:0010222 BTO:0001624 CALOHA:TS-0321 EMAPA:35342 FMA:70248 GAID:494 MA:0001951 MESH:D005263 NCIT:C12715 SCTID:244332003 UMLS:C0015801 Wikipedia:Femoral_artery galen:FemoralArtery uberon arteria femoralis UBERON:0002060 femoral artery http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray546.png FMA WP The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted]. Wikipedia:Femoral_artery Artery which supplies blood via branches to the hindlimbs.[AAO] 2012-06-20 AAO:0010222 AAO AAO:BJB UMLS:C0015801 ncithesaurus:Femoral_Artery arteria femoralis Wikipedia:Femoral_artery The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 EMAPA:35887 FMA:70301 GAID:554 MA:0000103 MESH:D014338 NCIT:C34317 SCTID:308828009 UMLS:C1519589 Wikipedia:Truncus_arteriosus_(embryology) uberon UBERON:0002061 truncus arteriosus EHDAA2 FMA MA EHDAA2 EHDAA2 The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. Wikipedia:Truncus_arteriosus_(embryology) assume spelling error for ncit ncit UMLS:C1519589 ncithesaurus:Trancus_Arteriosus The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] EHDAA2:0000434 EHDAA2:0004028 EHDAA:2586 EMAPA:16696 FMA:70302 MA:0000078 MESH:D054089 TAO:0001317 VHOG:0000932 Wikipedia:Atrioventricular_cushions XAO:0004189 ZFA:0001317 AV cushion atrioventricular cushion cardiac cushion endocardial cushion tissue uberon atrioventricular canal cushion endocardial cushions UBERON:0002062 GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png ZFA The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. GO:0003197 Wikipedia:Atrioventricular_cushions ZFIN:curator Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] 2012-08-14 TAO:0001317 TAO ZFIN:curator relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] 2012-08-14 TAO:0001317 TAO (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] 2012-09-17 VHOG:0000932 VHOG DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3 http://bgee.unil.ch/ MESH:D054089 https://github.com/biopragmatics/biomappings atrioventricular cushion Wikipedia:Endocardial_cushion cardiac cushion PMID:15797462 endocardial cushion tissue EHDAA2:0000434 atrioventricular canal cushion FMA:70302 endocardial cushions The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616] In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract inflow tract AAO:0010505 EHDAA2:0001839 EHDAA:480 EMAPA:16237 FMA:70303 NCIT:C34299 NCIT:C34300 TAO:0000154 UMLS:C0225857 UMLS:C0231084 VHOG:0000177 Wikipedia:Sinus_venosus ZFA:0000154 uberon sinus venarum sinus venosus cordis venarum venarum sinus venosus UBERON:0002063 sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png VHOG Bgee:AN The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. PMID:20735616 Wikipedia:Sinus_venosus Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000154 TAO ZFIN:curator Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] 2012-06-20 AAO:0010505 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000177 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract ZFA:0000154 inflow tract ZFA:0000154 UMLS:C0225857 ncithesaurus:Sinus_Venarum UMLS:C0231084 ncithesaurus:Sinus_Venosus sinus venarum Wikipedia:Sinus_venosus sinus venosus cordis Wikipedia:Sinus_venosus venarum Wikipedia:Sinus_venosus venarum sinus Wikipedia:Sinus_venosus venosus Wikipedia:Sinus_venosus The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] dermal AAO:0000128 BTO:0000294 CALOHA:TS-2076 EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 NCIT:C12701 SCTID:361696001 TAO:0001119 UMLS:C0011646 VHOG:0000108 Wikipedia:Dermis XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg FMA definitional The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Wikipedia:Dermis ZFIN:curator A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001119 TAO ZFIN:curator When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] 2012-09-17 VHOG:0000108 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 http://bgee.unil.ch/ UMLS:C0011646 ncithesaurus:Dermis corium BTO:0000294 Wikipedia:Dermis cutis BTO:0000294 Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. hypodermal subcutaneous subcutaneus BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO:0001314 CALOHA:TS-2366 EMAPA:37505 FMA:70544 MESH:D040521 NCIT:C33645 TAO:0001136 UMLS:C0278403 Wikipedia:Hypodermis ZFA:0001136 hypoderm vertebrate hypodermis uberon sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea UBERON:0002072 hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg ZFA FMA-modified Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. Wikipedia:Hypodermis A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001136 TAO ZFIN:curator A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. FMA:70544 BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO EMAPA:37505 MA:th MESH:D040521 https://github.com/biopragmatics/biomappings UMLS:C0278403 ncithesaurus:Subcutis sub-tegumental tissue BTO:0004525 subcutaneous tissue Wikipedia:Hypodermis subtegumental tissue BTO:0004525 superficial fascia tela subcutanea Wikipedia:Hypodermis A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] BTO:0000554 CALOHA:TS-0432 EFO:0002464 EMAPA:18771 EMAPA:29741 EV:0100156 FMA:70660 GAID:934 MA:0000154 MESH:D018859 NCIT:C13317 SCTID:280830006 UMLS:C0221971 VHOG:0001268 Wikipedia:Hair_follicle uberon folliculus pili UBERON:0002073 Development notes:Formation largely takes place during fetal and perinatal skin development. However, after skin wounding de novo hair follicle formation may also occur in adult mouse and rabbit skin[DOI:10.1016/j.cub.2008.12.005]. hair follicle https://upload.wikimedia.org/wikipedia/commons/4/4d/Hair_follicle-en.svg FMA DOI:10.1016/j.cub.2008.12.005 A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. Wikipedia:Hair_follicle The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] 2012-09-17 VHOG:0001268 VHOG ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3 http://bgee.unil.ch/ UMLS:C0221971 ncithesaurus:Hair_Follicle folliculus pili Wikipedia:Hair_follicle The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. TODO - add distinct subclasses for coat hair vs vibrissa hair TODO - check definition of trichocyte in CL BTO:0004672 EMAPA:36498 FMA:70728 MA:0000159 NCIT:C33543 SCTID:361359004 UMLS:C0221961 shaft of hair uberon scapus pili UBERON:0002074 hair shaft DOI:10.1016/j.cub.2008.12.005 The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. DOI:10.1016/j.cub.2008.12.005 UMLS:C0221961 ncithesaurus:Shaft_of_the_Hair scapus pili BTO:0004672 An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 SCTID:118760003 UMLS:C0042779 Wikipedia:Viscus XAO:0003034 visceral organ visceral organ system uberon splanchnic tissue viscera visceral tissue UBERON:0002075 viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. BTO:0001491 Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] 2012-06-20 AAO:0010386 AAO BTO:0001491 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. FMA UMLS:C0042779 ncithesaurus:Viscera visceral organ RETIRED_EHDAA2:0002201 visceral organ system MA:0000019 splanchnic tissue BTO:0001491 visceral tissue BTO:0001491 A cortex that is part of a hair [Automatically generated definition]. EMAPA:35387 FMA:70934 MA:0000156 SCTID:318832008 coat hair cortex coat/hair cortex cortex of coat hair cortex of coat/hair hair cortex uberon UBERON:0002077 cortex of hair A cortex that is part of a hair [Automatically generated definition]. OBOL:automatic coat hair cortex OBOL:automatic coat/hair cortex OBOL:automatic cortex of coat hair OBOL:automatic cortex of coat/hair OBOL:automatic A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010248 BTO:0001703 EHDAA2:0000290 EMAPA:17321 FMA:7096 MA:0000075 NCIT:C12868 SCTID:244383003 UMLS:C0225844 VHOG:0000328 Wikipedia:Right_atrium XAO:0003192 galen:RightAtrium cardiac right atrium heart right atrium right atrium right atrium of heart right cardiac atrium uberon atrium dextrum UBERON:0002078 right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Wikipedia:Right_atrium http://orcid.org/0000-0002-6601-2165 Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] FMA:7096 The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000328 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225844 ncithesaurus:Right_Atrium heart right atrium MA:0000075 right atrium VHOG:0000328 atrium dextrum Wikipedia:Right_atrium A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] The chamber of the heart that receives blood from the lungs[XAO:EJS]. The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010247 BTO:0001702 EHDAA2:0000275 EMAPA:17315 FMA:7097 MA:0000074 NCIT:C12869 SCTID:244387002 UMLS:C0225860 VHOG:0000369 Wikipedia:Left_atrium XAO:0003191 galen:LeftAtrium atrium sinistrum cardiac left atrium heart left atrium left atrium left atrium of heart left cardiac atrium uberon UBERON:0002079 left cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Wikipedia:Left_atrium http://orcid.org/0000-0002-6601-2165 Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] FMA:7097 The chamber of the heart that receives blood from the lungs[XAO:EJS]. XAO:EJS The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000369 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225860 ncithesaurus:Left_Atrium atrium sinistrum Wikipedia:Left_atrium heart left atrium MA:0000074 left atrium VHOG:0000369 A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with the pulmonary arteries BTO:0001630 CALOHA:TS-0443 EHDAA2:0000196 EMAPA:17340 FMA:7098 MA:0000093 NCIT:C12870 SCTID:244384009 UMLS:C0225883 VHOG:0000717 Wikipedia:Right_ventricle galen:RightVentricle cardiac right ventricle right ventricle right ventricle of heart uberon right cardiac ventricle ventriculus dexter UBERON:0002080 heart right ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb PMID:17276708 cjm A cardiac ventricle that is in the right side of the heart. http://orcid.org/0000-0002-6601-2165 The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] 2012-09-17 VHOG:0000717 VHOG http://bgee.unil.ch/ UMLS:C0225883 ncithesaurus:Right_Ventricle right ventricle FMA:7098 right cardiac ventricle EMAPA:17340 ventriculus dexter Wikipedia:Right_ventricle Cardiac chamber in which blood enters the heart. One of four heart chambers.[TAO] One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] AAO:0010246 BTO:0000903 CALOHA:TS-0437 EFO:0000277 EHDAA2:0000154 EHDAA:1265 EMAPA:16688 EV:0100019 FMA:7099 GAID:555 MA:0000073 MAT:0000496 MESH:D006325 NCIT:C12728 SCTID:261405004 TAO:0000471 UMLS:C0018792 VHOG:0000175 Wikipedia:Heart_atrium ZFA:0000471 galen:Atrium atria atrium atrium of heart cardiac atria heart atrium uberon atrial tissue UBERON:0002081 cardiac atrium Cardiac chamber in which blood enters the heart. Wikipedia:Heart_atrium http://orcid.org/0000-0002-6601-2165 One of four heart chambers.[TAO] 2012-08-14 TAO:0000471 TAO ZFIN:curator One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] 2012-06-20 AAO:0010246 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000175 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ UMLS:C0018792 ncithesaurus:Cardiac_Atrium atria atrium ZFA:0000471 cardiac atria atrial tissue BTO:0000903 Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] ventricle AAO:0010249 BTO:0000862 CALOHA:TS-0444 EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 MA:0000091 MAT:0000497 MESH:D006352 NCIT:C12730 SCTID:277699000 TAO:0000009 UMLS:C0018827 VHOG:0000435 Wikipedia:Ventricle_(heart) XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart ventricle of heart uberon UBERON:0002082 cardiac ventricle Bgee:AN Cardiac chamber through which blood leaves the heart. Wikipedia:Ventricle_(heart) http://orcid.org/0000-0002-6601-2165 A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] 2012-06-20 AAO:0010249 AAO AAO:BJB One of four heart chambers.[TAO] 2012-08-14 TAO:0000009 TAO ZFIN:curator In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] 2012-09-17 VHOG:0000435 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ UMLS:C0018827 ncithesaurus:Cardiac_Ventricle A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with aorta BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 MA:0000092 NCIT:C12871 SCTID:244385005 UMLS:C0225897 VHOG:0000718 Wikipedia:Left_ventricle galen:LeftVentricle cardiac left ventricle left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis UBERON:0002084 heart left ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb GO A cardiac ventricle that is in the left side of the heart. http://orcid.org/0000-0002-6601-2165 Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000718 VHOG http://bgee.unil.ch/ The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] 2012-09-17 VHOG:0000718 VHOG DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010) http://bgee.unil.ch/ UMLS:C0225897 ncithesaurus:Left_Ventricle left ventricle FMA:7101 ventriculus sinister cordis Wikipedia:Left_ventricle A cardiac septum that divides the left and right atria of the heart. The partition separating the right and left atria of the heart. [TFD][VHOG] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] EHDAA2:0000838 EHDAA:1896 EMAPA:17011 FMA:7108 MA:0000084 NCIT:C32818 SCTID:362016003 UMLS:C0225836 VHOG:0000385 Wikipedia:Interatrial_septum galen:InteratrialSeptum atrial septum atrium septum interatrial septal wall uberon UBERON:0002085 interatrial septum http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png A cardiac septum that divides the left and right atria of the heart. http://orcid.org/0000-0002-6601-2165 The partition separating the right and left atria of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000385 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/interatrial+septum The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000385 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225836 ncithesaurus:Interatrial_Septum Companion vein of the thoracodorsal artery, draining the apical part of the latissimus dorsi and merging with the circumflex scapular vein to form a subscapular vein. EMAPA:37198 FMA:71213 MA:0002238 uberon UBERON:0002089 thoracodorsal vein FMA/obol Companion vein of the thoracodorsal artery, draining the apical part of the latissimus dorsi and merging with the circumflex scapular vein to form a subscapular vein. http://www.medilexicon.com/medicaldictionary.php?t=97559 EMAPA:37198 MA:th The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 post-cranial axial skeleton uberon UBERON:0002090 previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. postcranial axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. ZFA:0000317 https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000093 VSAO PSPUB:0000170 The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] 2012-06-20 AAO:0000034 AAO AAO:LAP The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] 2012-08-14 TAO:0000317 TAO ZFIN:curator The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0000317 VHOG DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) http://bgee.unil.ch/ axial skeleton FMA:71221 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton EMAPA:37721 MA:th MESH:D013131 https://github.com/biopragmatics/biomappings Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 NCIT:C49477 SCTID:322050006 UMLS:C0222646 VHOG:0001666 VSAO:0000076 Wikipedia:Appendicular_skeleton XAO:0003166 appendicular skeleton entire appendicular skeleton paired fin skeleton uberon skeleton appendiculare UBERON:0002091 appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. UBERONREF:0000003 Wikipedia:Appendicular_skeleton https://orcid.org/0000-0002-6601-2165 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] 2012-08-14 VSAO:0000076 VSAO PSPUB:0000170 https://orcid.org/0000-0002-6601-2165 Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] 2012-08-14 TAO:0000027 TAO TAO:wd The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] 2012-06-20 AAO:0000747 AAO AAO:LAP ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. FMA UMLS:C0222646 ncithesaurus:Appendicular_Skeleton entire appendicular skeleton https://github.com/obophenotype/uberon/issues/59 paired fin skeleton skeleton appendiculare Wikipedia:Appendicular_skeleton The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer. The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32668 EV:0100313 FMA:71236 MA:0000815 NCIT:C49332 SCTID:309321003 UMLS:C0459393 VHOG:0000270 cranial dura mater dura mater cranialis dura mater encephali dura mater of brain uberon UBERON:0002092 brain dura mater The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer. MP:0009025 The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000270 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000270 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ UMLS:C0459393 ncithesaurus:Cerebral_Dura_Mater cranial dura mater FMA:71236 dura mater cranialis FMA:71236 FMA:TA A dura mater that is part of a spinal cord [Automatically generated definition]. The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17806 FMA:71237 MA:0001132 NCIT:C49799 SCTID:362302001 UMLS:C0228124 VHOG:0000411 dura mater of neuraxis of spinal cord dura mater of spinal cord spinal cord dura mater spinal cord dura mater of neuraxis uberon UBERON:0002093 spinal dura mater A dura mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000411 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000411 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ UMLS:C0228124 ncithesaurus:Spinal_Cord_Dura_Mater dura mater of neuraxis of spinal cord OBOL:automatic spinal cord dura mater of neuraxis OBOL:automatic Cardiac septum which separates the right ventricle from the left ventricle.[FMA]. The partition separating the right and left ventricles of the heart. [TFD][VHOG] The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) BTO:0002483 EFO:0001956 EHDAA:2603 EMAPA:17333 FMA:7133 MA:0000085 NCIT:C32874 SCTID:362019005 UMLS:C0225870 VHOG:0000386 Wikipedia:Interventricular_septum galen:InterventricularSeptum heart interventricular septum heart ventricular septum uberon interventricular septum of heart interventriculare cordis intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricle septum ventricular septum UBERON:0002094 interventricular septum http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb Cardiac septum which separates the right ventricle from the left ventricle.[FMA]. FMA:7133 The partition separating the right and left ventricles of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000386 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/interventricular+septum The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] 2012-09-17 VHOG:0000386 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430 http://bgee.unil.ch/ involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) ISBN:0124020607 UMLS:C0225870 ncithesaurus:Interventricular_Septum heart interventricular septum MA:0000085 heart ventricular septum MA:0000085 interventricular septum of heart BTO:0002483 interventriculare cordis BTO:0002483 intraventricular septum Wikipedia:Interventricular_septum s. interventriculare cordis Wikipedia:Interventricular_septum septum inferius Wikipedia:Interventricular_septum septum membranaceum Wikipedia:Interventricular_septum ventricular septum MA:0000085 Wikipedia:Interventricular_septum Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon. mesenteric in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery. AAO:0011061 BTO:0001380 EV:0100083 FMA:7144 GAID:21 MESH:D008643 NCIT:C33103 SCTID:362707009 UMLS:C0025474 Wikipedia:Mesentery#Mesentery_.28general.29 galen:Mesentery generic mesentery mesentery (generic) uberon UBERON:0002095 mesentery http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon. FMA:7144 Wikipedia:Mesentery Wikipedia:Mesentery#Mesentery_.28general.29 https://github.com/obophenotype/uberon/issues/85 in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery. FMA UMLS:C0025474 ncithesaurus:Mesentery generic mesentery Wikipedia:Mesentery mesentery (generic) Wikipedia:Mesentery The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 SCTID:181469002 UMLS:C1123023 Wikipedia:Skin XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb Wikipathways:WP2062 The organ covering the body that consists of the dermis and epidermis. UBERON:cjm MA uses the term skin to refer to what is called here: zone of skin FMA UMLS:C1123023 ncithesaurus:Skin The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this EMAPA:35400 FMA:7180 GAID:562 MA:0000083 MESH:D006346 NCIT:C49485 SCTID:362014000 UMLS:C0018819 cardiac septa heart septa heart septum septum of heart uberon spiral septa UBERON:0002099 cardiac septum The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. MESH:A07.541.459 in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this GO UMLS:C0018819 ncithesaurus:Heart_Septum cardiac septa heart septa spiral septa XAO:0004141 Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 NCIT:C33816 SCTID:262225004 TAO:0001115 UMLS:C0460005 Wikipedia:Torso XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon Rumpf UBERON:0002100 trunk Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. TAO:0001115 UBERONREF:0000006 Wikipedia:Torso ZFA https://github.com/obophenotype/uberon/issues/378 pending Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] 2012-06-20 AAO:0010339 AAO AAO:BJB Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] 2012-08-14 TAO:0001115 TAO ZFIN:curator UMLS:C0460005 ncithesaurus:Trunk trunk region XAO:0000054 Rumpf BTO:0001493 A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] AAO:0010336 AEO:0000172 CALOHA:TS-0552 EFO:0000876 EHDAA2:0003172 EHDAA:1697 EHDAA:8273 EMAPA:16405 FMA:24875 GAID:36 MA:0000007 MAT:0000090 MESH:D005121 MIAA:0000090 NCIT:C12429 SCTID:243996003 UMLS:C0015385 VHOG:0000336 VSAO:0000121 Wikipedia:Limb XAO:0003027 galen:Extremity free limb limb sensu Vertebrata pentadactyl limb tetrapod limb flipper uberon extremities extremity UBERON:0002101 limb Sarcopterygians extends to stem tetrapods such as Eusthenopteron A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. UBERONREF:0000003 Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] 2012-06-20 AAO:0010336 AAO AAO:BJB Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000336 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ MESH:D005121 https://github.com/biopragmatics/biomappings UMLS:C0015385 ncithesaurus:Limb free limb FMA:24875 limb sensu Vertebrata MAT:0000090 flipper extremities A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts. Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm Upper limb, which connects the manus with the pectoral girdle.[AAO] note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb AAO:0000205 BTO:0001729 CALOHA:TS-2214 EFO:0000882 EHDAA2:0002133 EHDAA:6208 EMAPA:17412 EV:0100014 FMA:24878 GAID:1215 GAID:51 MA:0000025 MAT:0000394 MESH:D005552 MIAA:0000394 NCIT:C12671 SCTID:182245002 UMLS:C1140618 VHOG:0000338 VSAO:0000148 Wikipedia:Forelimb XAO:0003030 galen:UpperExtremity anteriormost limb fore limb forelimb free part of upper limb free upper limb membrum superius pectoral limb superior member upper extremity upper limb pectoral flipper uberon foreleg UBERON:0002102 forelimb A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts. UBERONREF:0000003 Upper limb, which connects the manus with the pectoral girdle.[AAO] 2012-06-20 AAO:0000205 AAO AAO:LAP note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb FMA UMLS:C1140618 ncithesaurus:Upper_Extremity free part of upper limb FMA:24878 free upper limb FMA:24878 UBERONREF:0000003 membrum superius FMA:7183 FMA:TA pectoral flipper A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. Lower limb, which connects the pes with the pelvic girdle.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] crural note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton AAO:0000219 BTO:0002345 CALOHA:TS-2215 EFO:0000883 EHDAA2:0001033 EHDAA:6094 EMAPA:17458 EV:0100015 FMA:24879 GAID:1221 GAID:38 MA:0000026 MAT:0000395 MESH:D006614 MIAA:0000395 NCIT:C12742 NCIT:C77625 SCTID:182281004 UMLS:C0023216 UMLS:C1522391 VHOG:0000337 VSAO:0000150 Wikipedia:Hindlimb XAO:0003031 galen:LowerExtremity free lower limb hind limb hind-limb hindlimb inferior member lower limb membrum inferius uberon free part of lower limb lower extremity membrum inferius pelvic appendage UBERON:0002103 hindlimb http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. UBERONREF:0000003 Wikipedia:Hindlimb Wikipedia:Lower_limb Lower limb, which connects the pes with the pelvic girdle.[AAO] 2012-06-20 AAO:0000219 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000337 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton FMA UMLS:C0023216 ncithesaurus:Lower_Extremity UMLS:C1522391 ncithesaurus:Hind_Limb free lower limb FMA:24879 UBERONREF:0000003 hind-limb VSAO:0000150 membrum inferius FMA:7184 FMA:TA free part of lower limb FMA:24879 membrum inferius Wikipedia:Lower_limb The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 NCIT:C12888 SCTID:281831001 TAO:0001127 UMLS:C0587900 Wikipedia:Visual_system XAO:0003198 ZFA:0001127 http://uri.neuinfo.org/nif/nifstd/FMAID_7191 photosensory system visual organ system uberon UBERON:0002104 visual system The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 The sensory system used for sight.[AAO] 2012-06-20 AAO:0000632 AAO AAO:EJS UMLS:C0587900 ncithesaurus:Visual_System photosensory system BILA:0000140 Sensory system responsible for the perception of spatial orientation and auditory stimuli. The sensory system used for balance and hearing.[AAO] AAO:0000631 EMAPA:36002 EMAPA:37985 FMA:78500 TAO:0001138 XAO:0003195 ZFA:0001138 auditory organ system vestibuloauditory system uberon auditory system auditory/vestibular system vestibuloauditory system UBERON:0002105 vestibulo-auditory system http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg Sensory system responsible for the perception of spatial orientation and auditory stimuli. ZFA:0001138 The sensory system used for balance and hearing.[AAO] 2012-06-20 AAO:0000631 AAO AAO:EJS EMAPA:37985 MA:th The organ that functions to filter blood and to store red corpuscles and platelets. An organ involved in red blood cell filtration and immune response.[AAO] With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] lienal splenic In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells AAO:0010395 BTO:0001281 CALOHA:TS-0956 EFO:0000869 EMAPA:18767 EV:0100055 FMA:7196 GAID:1289 MA:0000141 MAT:0000085 MESH:D013154 MIAA:0000085 NCIT:C12432 SCTID:181279003 TAO:0000436 UMLS:C0037993 VHOG:0000120 Wikipedia:Spleen XAO:0000328 ZFA:0000436 galen:Spleen uberon lien UBERON:0002106 spleen https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Spleen.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg multiple sources - true spleen appear in jawed vertebrates The organ that functions to filter blood and to store red corpuscles and platelets. ISBN:0-683-40008-8 MP:0000689 An organ involved in red blood cell filtration and immune response.[AAO] 2012-06-20 AAO:0010395 AAO AAO:BMZ With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] 2012-09-17 VHOG:0000120 VHOG ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94 http://bgee.unil.ch/ Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) PMID:20959416 UMLS:C0037993 ncithesaurus:Spleen lien Wikipedia:Spleen An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Organ which secretes bile and participates in formation of certain blood proteins.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] hepatic An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 SCTID:181268008 TAO:0000123 UMLS:C0023884 VHOG:0000257 Wikipedia:Liver XAO:0000133 ZFA:0000123 galen:Liver uberon iecur jecur UBERON:0002107 liver https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg BTO EHDAA2 GO-def ZFA ZFA-weakened EHDAA2 http://www.stembook.org/node/512 An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. BTO:0000759 Wikipedia:Liver Organ which secretes bile and participates in formation of certain blood proteins.[AAO] 2012-06-20 AAO:0010111 AAO AAO:BJB relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] 2012-06-20 AAO:0010111 AAO All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000257 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. ZFA UMLS:C0023884 ncithesaurus:Liver iecur Wikipedia:Liver jecur Wikipedia:Liver Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 MA:0000337 MAT:0000047 MESH:D007421 MIAA:0000047 NCIT:C12386 SCTID:181250005 TAO:0001323 UMLS:C0021852 VHOG:0000055 Wikipedia:Small_intestine XAO:0000130 ZFA:0001323 galen:SmallIntestine small bowel small intestine uberon anterior intestine intestinum tenue mid intestine UBERON:0002108 small intestine http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb 2 cjm Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. ISBN:0073040584 Wikipedia:Small_intestine The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0001323 TAO ZFIN:curator Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000055 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 http://bgee.unil.ch/ UMLS:C0021852 ncithesaurus:Small_Intestine intestinum tenue BTO:0000651 Wikipedia:Small_intestine 2 Pair of nostrils. this is a 'set of anatomical planes' in FMA FMA:72005 Wikipedia:Nares nares set nostrils pair of nostrils uberon nares set of nares UBERON:0002109 pair of nares Pair of nostrils. Wikipedia:Nares http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html this is a 'set of anatomical planes' in FMA FMA set of nares FMA:72005 An organ that aids digestion and stores bile produced by the liver[WP]. Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] AAO:0010114 BTO:0000493 CALOHA:TS-0394 EFO:0000853 EHDAA2:0000699 EHDAA:8062 EMAPA:17202 EV:0100090 FMA:7202 MA:0000356 MAT:0000072 MESH:D005704 MIAA:0000072 NCIT:C12377 SCTID:181269000 TAO:0000208 UMLS:C0016976 VHOG:0000221 Wikipedia:Gallbladder XAO:0000135 ZFA:0000208 galen:Gallbladder cholecyst gall bladder uberon vesica biliaris vesica fellea UBERON:0002110 Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988) gallbladder https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg BTO definitional An organ that aids digestion and stores bile produced by the liver[WP]. Wikipedia:Gallbladder ISBN:9780120749034 GOC:mr ISBN:9781840761122 GOC:mr ISBN:9781840761122 Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000221 VHOG http://bgee.unil.ch/ Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] 2012-06-20 AAO:0010114 AAO AAO:BJB relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] 2012-06-20 AAO:0010114 AAO The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] 2012-09-17 VHOG:0000221 VHOG DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997) http://bgee.unil.ch/ UMLS:C0016976 ncithesaurus:Gallbladder cholecyst WikipediaVersioned:Gallbladder&oldid=1092217922 vesica biliaris Wikipedia:Gallbladder vesica fellea Wikipedia:Gallbladder A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. BTO:0000087 CALOHA:TS-1198 EMAPA:36285 FMA:72024 MA:0000708 NCIT:C49195 UMLS:C1706851 arterial smooth muscle artery smooth muscle artery smooth muscle tissue smooth muscle of artery uberon arterial smooth muscle cell UBERON:0002111 artery smooth muscle tissue A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. OBOL:automatic UMLS:C1706851 ncithesaurus:Artery_Smooth_Muscle_Tissue arterial smooth muscle BTO:0000087 smooth muscle of artery FMA:72024 arterial smooth muscle cell BTO:0000087 A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:35323 FMA:72025 MA:0001573 esophageal smooth muscle esophagus involuntary muscle esophagus non-striated muscle esophagus smooth muscle esophagus smooth muscle tissue gullet involuntary muscle gullet non-striated muscle gullet smooth muscle gullet smooth muscle tissue involuntary muscle of esophagus involuntary muscle of gullet involuntary muscle of oesophagus non-striated muscle of esophagus non-striated muscle of gullet non-striated muscle of oesophagus oesophagus involuntary muscle oesophagus non-striated muscle oesophagus smooth muscle tissue smooth muscle of gullet smooth muscle of oesophagus smooth muscle tissue of esophagus smooth muscle tissue of gullet smooth muscle tissue of oesophagus uberon oesophagus smooth muscle UBERON:0002112 smooth muscle of esophagus A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus involuntary muscle OBOL:automatic esophagus non-striated muscle OBOL:automatic esophagus smooth muscle tissue OBOL:automatic gullet involuntary muscle OBOL:automatic gullet non-striated muscle OBOL:automatic gullet smooth muscle OBOL:automatic gullet smooth muscle tissue OBOL:automatic involuntary muscle of esophagus OBOL:automatic involuntary muscle of gullet OBOL:automatic involuntary muscle of oesophagus OBOL:automatic non-striated muscle of esophagus OBOL:automatic non-striated muscle of gullet OBOL:automatic non-striated muscle of oesophagus OBOL:automatic oesophagus involuntary muscle OBOL:automatic oesophagus non-striated muscle OBOL:automatic oesophagus smooth muscle tissue OBOL:automatic smooth muscle of gullet OBOL:automatic smooth muscle of oesophagus OBOL:automatic smooth muscle tissue of esophagus OBOL:automatic smooth muscle tissue of gullet OBOL:automatic smooth muscle tissue of oesophagus OBOL:automatic A paired organ of the urinary tract which has the production of urine as its primary function. One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] renal AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 NCIT:C12415 SCTID:181414000 UMLS:C0022646 Wikipedia:Kidney XAO:0003267 galen:Kidney reniculate kidney uberon UBERON:0002113 kidney FMA definitional A paired organ of the urinary tract which has the production of urine as its primary function. Wikipedia:Kidney http://anatomy.uams.edu/anatomyhtml/kidney.html One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] 2012-06-20 AAO:0000250 AAO AAO:BJB UMLS:C0022646 ncithesaurus:Kidney reniculate kidney Wikipedia:Reniculate_kidney The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] duodenal In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 MA:0000338 MAT:0000044 MESH:D004386 MIAA:0000044 NCIT:C12263 SCTID:181247007 UMLS:C0013303 VHOG:0000052 Wikipedia:Duodenum XAO:0000236 galen:Duodenum uberon proximal intestine upper intestine UBERON:0002114 duodenum http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb 3 cjm The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). ISBN:0815318960 Wikipedia:Duodenum ZFA:0000348 The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000052 VHOG http://bgee.unil.ch/ In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. NCBITaxon:32443 Wikipedia:Duodenum In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. NCBITaxon:9606 Wikipedia:Duodenum UMLS:C0013303 ncithesaurus:Duodenum proximal intestine BTO:0000365 upper intestine BTO:0000365 The portion of the small intestine that extends from the duodenum to the ileum. TODO consider ZFA:0001323 mid intestine, see also small intestine The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] jejunal The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum] BTO:0000657 CALOHA:TS-0496 EFO:0001333 EMAPA:18666 EV:0100074 FMA:7207 GAID:318 MA:0000340 MAT:0000045 MESH:D007583 MIAA:0000045 NCIT:C12388 SCTID:181248002 UMLS:C0022378 VHOG:0000053 Wikipedia:Jejunum galen:Jejunum uberon intestinum jejunum mid-intestine middle intestine UBERON:0002115 jejunum http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb 3 cjm Wikipedia The portion of the small intestine that extends from the duodenum to the ileum. MGI:monikat MP:0004002 The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000053 VHOG http://bgee.unil.ch/ UMLS:C0022378 ncithesaurus:Jejunum intestinum jejunum BTO:0000657 mid-intestine Wikipedia:Jejunum middle intestine BTO:0000657 The portion of the small intestine that extends from the jejunum to the colon. TODO consider ZFA:0000706 posterior intestine, see also colon Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] ileal The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum] AAO:0010403 BTO:0000620 CALOHA:TS-0472 EFO:0001334 EMAPA:32764 EV:0100075 FMA:7208 GAID:315 MA:0000339 MAT:0000282 MESH:D007082 MIAA:0000282 NCIT:C12387 SCTID:181249005 UMLS:C0020885 VHOG:0000647 Wikipedia:Ileum XAO:0000237 galen:Ileum uberon distal intestine intestinum ileum lower intestine posterior intestine UBERON:0002116 ileum http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb 3 cjm The portion of the small intestine that extends from the jejunum to the colon. ISBN:0-683-40008-8 MGI:csmith MP:0002581 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000647 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0020885 ncithesaurus:Ileum distal intestine BTO:0000620 intestinum ileum BTO:0000620 lower intestine BTO:0000620 posterior intestine Wikipedia:Ileum An ovary that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37367 FMA:7213 MA:0001705 NCIT:C33487 SCTID:280123002 UMLS:C0227873 uberon UBERON:0002118 right ovary An ovary that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37367 MA:th UMLS:C0227873 ncithesaurus:Right_Ovary An ovary that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 FMA:7214 MA:0001704 NCIT:C32969 SCTID:280124008 UMLS:C0227874 uberon UBERON:0002119 left ovary An ovary that is part of a left side of organism [Automatically generated definition]. OBOL:automatic In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo Wikipedia:Ovary#In_other_animals EMAPA:37366 MA:th UMLS:C0227874 ncithesaurus:Left_Ovary In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] pronephric UBERON:0005794 AAO:0011089 BTO:0001541 EFO:0000927 EHDAA2:0001570 EHDAA:1017 EMAPA:16579 FMA:72170 MAT:0000117 MESH:D060910 MIAA:0000117 NCIT:C34280 SCTID:308804007 TAO:0000151 UMLS:C0231048 VHOG:0000037 Wikipedia:Pronephros XAO:0002000 ZFA:0000151 pronephric kidney uberon archinephron embryonic kidney pronephron UBERON:0002120 Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros GO OG ZFA In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. GO:0048793 Wikipedia:Pronephros A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] 2012-09-17 VHOG:0000037 VHOG http://bgee.unil.ch/ Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] 2012-06-20 AAO:0011089 AAO XAO:curator The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000151 TAO ZFIN:curator In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000037 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637 http://bgee.unil.ch/ MESH:D060910 https://github.com/biopragmatics/biomappings UMLS:C0231048 ncithesaurus:Pronephros pronephric kidney XAO:0002000 archinephron BTO:0001541 embryonic kidney BTO:0001541 pronephron BTO:0001541 The fibrous connective tissue surrounding the thymus. EMAPA:19306 FMA:72204 MA:0000766 NCIT:C33770 SCTID:188181003 UMLS:C0229945 thymic capsule thymus capsule uberon UBERON:0002122 capsule of thymus The fibrous connective tissue surrounding the thymus. MP:0002368 UMLS:C0229945 ncithesaurus:Thymic_Capsule The outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes. Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP] BTO:0002934 EMAPA:35863 FMA:72205 MA:0000767 NCIT:C33774 SCTID:188262003 UMLS:C0229948 Wikipedia:Thymus#Cortex thymic cortex thymus cortex uberon UBERON:0002123 cortex of thymus The outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes. ISBN:0-683-40008-8 MP:0002371 DOI:10.1177/0192623311409597 UMLS:C0229948 ncithesaurus:Thymus_Cortex thymic cortex BTO:0002934 thymus cortex MA:0000767 Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. BTO:0004560 EFO:0001969 EMAPA:19305 FMA:72206 MA:0000771 NCIT:C33775 SCTID:188344009 UMLS:C0229949 Wikipedia:Thymus#Medulla medulla of thymus gland thymus gland medulla thymus medulla uberon UBERON:0002124 medulla of thymus Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. Wikipedia:Thymus#Medulla DOI:10.1177/0192623311409597 UMLS:C0229949 ncithesaurus:Thymus_Medulla medulla of thymus gland OBOL:automatic thymus gland medulla OBOL:automatic A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]. in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP] Lymphocytes, reticular cells and macrophages are found in the lobules FMA:72215 MA:0000770 NCIT:C33772 SCTID:187882006 UMLS:C1522462 lobule of thymus thymic lobule thymus lobule uberon UBERON:0002125 thymus lobule A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:Thymic_Lobule UMLS:C1522462 ncithesaurus:Thymic_Lobule lobule of thymus FMA:72215 thymus lobule MA:0000770 A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718] The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates. BAMS:SOC BIRNLEX:1307 DHBA:12462 EMAPA:35840 EV:0100263 FMA:72247 HBA:9177 MA:0001026 MBA:398 MESH:D065832 UMLS:C0175427 VHOG:0001381 Wikipedia:Superior_olivary_complex neuronames:569 nucleus olivaris superior superior olivary nuclei uberon regio olivaris superioris superior olivary nucleus superior olivary nucleus (Barr & Kiernan) superior olive UBERON:0002128 superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png NIFSTD A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. ISBN:0-19-502694-2 Wikipedia:Superior_olivary_complex ABA ABA ABA MESH:D065832 https://github.com/biopragmatics/biomappings UMLS:C0175427 BIRNLEX:1307 neuronames:569 BIRNLEX:1307 nucleus olivaris superior FMA:72247 FMA:TA superior olivary nuclei FMA:72247 regio olivaris superioris NeuroNames:569 superior olivary nucleus FMA:72247 superior olivary nucleus (Barr & Kiernan) NeuroNames:569 superior olive FMA:72247 ISBN:0-19-502694-2 The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]. BAMS:CB BAMS:CBX BAMS:CbCx BIRNLEX:1566 BM:CB-Cbx BTO:0000043 CALOHA:TS-2000 DHBA:10657 DMBA:16939 EMAPA:35211 EV:0100294 FMA:72248 GAID:596 HBA:4697 MA:0000199 MBA:528 MESH:D002525 NCIT:C49216 SCTID:361593004 UMLS:C0007759 UMLS:C1284087 VHOG:0001597 Wikipedia:Cerebellar_cortex neuronames:647 cortex of cerebellar hemisphere uberon cortex cerebellaris cortex cerebelli UBERON:0002129 The circuits in the cerebellar cortex look similar across all classes of vertebrates, including fish, reptiles, birds, and mammals (e.g., Fig. 2). This has been taken as evidence that the cerebellum performs functions important to all vertebrate species. (Wikipedia) cerebellar cortex https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png Wikipedia The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer. BIRNLEX:1566 ABA The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]. GO:0021695 UMLS:C0007759 BIRNLEX:1566 ncithesaurus:Cerebellar_Cortex UMLS:C1284087 BIRNLEX:1566 neuronames:647 BIRNLEX:1566 cortex of cerebellar hemisphere DMBA:CbHCx cortex cerebellaris BTO:0000043 cortex cerebelli NeuroNames:647 A cardial valve in the atrioventricular region that separates the atrium from the ventricle and prevent backflow from the ventricles into the atria during systole. The atrioventricular valve has four distinct leaflets oriented anterior, posterior, left, and right of the atrioventricular orifice. Hu et al. 2001.[TAO] Valve in the heart through which blood flows from the atria to the ventricles. [TFD][VHOG] The conus arteriosus is the most distal part of the primitive fish heart and forms the connection between the ventricle and the ventral aorta. At the sinoatrial, the atrioventricular, and the ventriculoconal junctions, valves developed to prevent backflow of blood during relaxation of the preceding compartment.[uncertain][VHOG] in ZFA this is part of both atrium and ventricle, but we use a connecting relationship here; see also notes for left and right. EHDAA2:0000153 EHDAA:7421 EMAPA:35154 FMA:7233 MA:0002789 SCTID:11124005 TAO:0005064 VHOG:0001472 Wikipedia:Heart_valve#Atrioventricular_valves ZFA:0005064 galen:AtrioventricularValve AV valve uberon atrio-ventricular valve UBERON:0002133 atrioventricular valve EHDAA2 FMA A cardial valve in the atrioventricular region that separates the atrium from the ventricle and prevent backflow from the ventricles into the atria during systole. Wikipedia:Heart_valve#Atrioventricular_valves http://orcid.org/0000-0002-6601-2165 The atrioventricular valve has four distinct leaflets oriented anterior, posterior, left, and right of the atrioventricular orifice. Hu et al. 2001.[TAO] 2012-08-14 TAO:0005064 TAO ZFIN:curator Valve in the heart through which blood flows from the atria to the ventricles. [TFD][VHOG] 2012-09-17 VHOG:0001472 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/atrioventricular+valve The conus arteriosus is the most distal part of the primitive fish heart and forms the connection between the ventricle and the ventral aorta. At the sinoatrial, the atrioventricular, and the ventriculoconal junctions, valves developed to prevent backflow of blood during relaxation of the preceding compartment.[uncertain][VHOG] 2012-09-17 VHOG:0001472 VHOG DOI:10.1152/physrev.00006.2003 http://bgee.unil.ch/ in ZFA this is part of both atrium and ventricle, but we use a connecting relationship here; see also notes for left and right. ZFA atrio-ventricular valve EMAPA:35154 An atrioventricular valve that is part of the outflow part of the right atrium. The three-segmented valve of the heart that keeps blood in the right ventricle from flowing back into the right atrium. [TFD][VHOG] The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG] FMA part_ofs changed to connects EHDAA2:0004029 EHDAA:7427 EMAPA:17873 FMA:7234 GAID:567 MA:0000090 MESH:D014261 NCIT:C12805 RETIRED_EHDAA2:0002081 SCTID:181288007 UMLS:C0040960 VHOG:0000816 Wikipedia:Tricuspid_valve galen:TricuspidValve right atrioventricular valve valva atrioventricularis dextra uberon valvula tricuspidalis UBERON:0002134 tricuspid valve http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb An atrioventricular valve that is part of the outflow part of the right atrium. http://orcid.org/0000-0002-6601-2165 The three-segmented valve of the heart that keeps blood in the right ventricle from flowing back into the right atrium. [TFD][VHOG] 2012-09-17 VHOG:0000816 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Tricuspid+valves The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG] 2012-09-17 VHOG:0000816 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ FMA part_ofs changed to connects FMA UMLS:C0040960 ncithesaurus:Tricuspid_Valve right atrioventricular valve FMA:7234 valva atrioventricularis dextra FMA:7234 FMA:TA valvula tricuspidalis Wikipedia:Tricuspid_valve An atrioventricular valve that is part of the outflow part of the left atrium. A valve of the heart, composed of two triangular flaps, that is located between the left atrium and left ventricle and regulates blood flow between these chambers. [TFD][VHOG] The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG] FMA part_ofs changed to connects EFO:0003933 EHDAA2:0000168 EMAPA:17871 FMA:7235 GAID:565 MA:0000088 MESH:D008943 NCIT:C12753 SCTID:181286006 UMLS:C0026264 VHOG:0000817 Wikipedia:Mitral_valve galen:MitralValve left atrioventricular valve valva atrioventricularis sinistra uberon bicuspid valve valva mitralis UBERON:0002135 mitral valve http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb FMA FMA FMA An atrioventricular valve that is part of the outflow part of the left atrium. http://orcid.org/0000-0002-6601-2165 A valve of the heart, composed of two triangular flaps, that is located between the left atrium and left ventricle and regulates blood flow between these chambers. [TFD][VHOG] 2012-09-17 VHOG:0000817 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mitral+valve The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG] 2012-09-17 VHOG:0000817 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ FMA part_ofs changed to connects FMA UMLS:C0026264 ncithesaurus:Mitral_Valve valva atrioventricularis sinistra FMA:7235 FMA:TA valva mitralis Wikipedia:Mitral_valve The semilunar valve of the heart that lies between the right ventricle and the pulmonary artery. The valve with semilunar cusps at the entrance to the pulmonary trunk from the right ventricle of the heart. [TFD][VHOG] EHDAA2:0001577 EHDAA:4412 EMAPA:17872 FMA:7246 GAID:566 MA:0000089 MESH:D011664 NCIT:C12775 SCTID:181289004 UMLS:C0034086 VHOG:0000814 Wikipedia:Pulmonary_valve galen:PulmonaryValve pulmonic valve uberon valva trunci pulmonalis UBERON:0002146 pulmonary valve http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb The semilunar valve of the heart that lies between the right ventricle and the pulmonary artery. Wikipedia:Pulmonary_valve The valve with semilunar cusps at the entrance to the pulmonary trunk from the right ventricle of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000814 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+valve UMLS:C0034086 ncithesaurus:Pulmonary_Valve valva trunci pulmonalis Wikipedia:Pulmonary_valve The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. TODO - check ZFA/pons. also GO says part of dorsorostral pons BAMS:CAE BAMS:LC BIRNLEX:905 BM:Pons-LC BTO:0001408 DHBA:12819 DMBA:16972 EFO:0001963 EMAPA:35502 FMA:72478 GAID:577 HBA:9148 MA:0001017 MBA:147 MESH:D008125 NCIT:C97333 SCTID:369016004 TAO:0000539 UMLS:C0023951 Wikipedia:Locus_ceruleus ZFA:0000539 neuronames:583 Noradrenergic cell group A6 blue nucleus caerulean nucleus locus caeruleus locus coeruleu locus coeruleus nucleus caeruleus nucleus of locus caeruleus nucleus pigmentosus pontis substantia ferruginea uberon loci coeruleus locus cinereus locus coeruleus (Vicq d'Azyr) nucleus loci caerulei UBERON:0002148 locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png check ZFA NIFSTD The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. GAID:577 GO:0021703 Wikipedia:Locus_ceruleus ABA ABA ABA ABA UMLS:C0023951 BIRNLEX:905 ncithesaurus:Locus_Coeruleus neuronames:583 BIRNLEX:905 Noradrenergic cell group A6 Noradrenergic_cell_group_A6&oldid=981960774 blue nucleus BIRNLEX:905 locus caeruleus BIRNLEX:905 nucleus caeruleus FMA:72478 FMA:TA nucleus pigmentosus pontis BIRNLEX:905 substantia ferruginea BIRNLEX:905 loci coeruleus ZFA:0000539 locus cinereus BTO:0001408 locus coeruleus (Vicq d'Azyr) NeuroNames:583 nucleus loci caerulei NeuroNames:583 Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BAMS:SSN BAMS:SuS BIRNLEX:1131 DHBA:12435 EHDAA2:0004646 EMAPA:37756 FMA:72482 HBA:9194 MA:0001027 MBA:462 SCTID:369028007 UMLS:C0175447 Wikipedia:Superior_salivatory_nucleus neuronames:590 superior salivary nucleus uberon nucleus salivarius superior nucleus salivatorius cranialis nucleus salivatorius rostralis nucleus salivatorius superior UBERON:0002149 superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png definitional Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BIRNLEX:1131 ABA ABA ABA ABA ABA ABA ABA ABA ABA EMAPA:37756 MA:th UMLS:C0175447 BIRNLEX:1131 neuronames:590 BIRNLEX:1131 superior salivary nucleus GO:0021753 nucleus salivarius superior NeuroNames:590 nucleus salivatorius cranialis NeuroNames:590 nucleus salivatorius rostralis NeuroNames:590 nucleus salivatorius superior NeuroNames:590 The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. UBERON:0006225 AAO:0010408 BTO:0000387 CALOHA:TS-2075 EFO:0000821 EHDAA2:0004153 EMAPA:17868 EMAPA:32686 EV:0100021 FMA:7280 GAID:550 MA:0000076 MAT:0000455 MESH:D004699 NCIT:C13004 SCTID:362013006 TAO:0001320 UMLS:C0014124 VHOG:0000084 Wikipedia:Endocardium XAO:0000066 ZFA:0001320 galen:Endocardium endocardial lining endocardial tissue heart endocardium uberon heart endocardial tissue UBERON:0002165 fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png Bgee:AN The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. GO:0003157 Layer that lines the lumen of the heart.[TAO] 2012-08-14 TAO:0001320 TAO ZFIN:curator Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] 2012-06-20 AAO:0010408 AAO AAO:BJB Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. FMA:7280 UMLS:C0014124 ncithesaurus:Endocardium endocardial lining EMAPA:32686 endocardial tissue EMAPA:17868 heart endocardial tissue VHOG:0000084 Endocardium that is part of the atrium. EMAPA:32745 FMA:7284 MA:0000077 SCTID:192001005 TAO:0002169 VHOG:0000606 ZFA:0001614 Cardiac atria endocardium atrial endocardium atrium endocardium atrium of heart endocardium cardiac atrium endocardium endocardium of Cardiac atria endocardium of atrium of heart endocardium of cardiac atrium endocardium of heart atrium heart atrium endocardium uberon atrium endocardial tissue UBERON:0002166 endocardium of atrium Endocardium that is part of the atrium. ZFIN:curator Cardiac atria endocardium OBOL:automatic atrium of heart endocardium OBOL:automatic cardiac atrium endocardium OBOL:automatic endocardium of Cardiac atria OBOL:automatic endocardium of atrium of heart OBOL:automatic endocardium of cardiac atrium OBOL:automatic endocardium of heart atrium OBOL:automatic heart atrium endocardium OBOL:automatic atrium endocardial tissue VHOG:0000606 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]. Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 SCTID:361967000 UMLS:C0225706 VHOG:0000301 Wikipedia:Right_lung uberon UBERON:0002167 right lung http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]. FMA:FMA Wikipedia:Right_lung Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000301 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 http://bgee.unil.ch/ UMLS:C0225706 ncithesaurus:Right_Lung Lung which consists of the left upper lobe and left lower lobe.[FMA]. Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 MA:0000425 NCIT:C32967 SCTID:361982005 UMLS:C0225730 VHOG:0000618 Wikipedia:Left_lung uberon UBERON:0002168 left lung http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb Lung which consists of the left upper lobe and left lower lobe.[FMA]. FMA:FMA Wikipedia:Left_lung Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000618 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 http://bgee.unil.ch/ UMLS:C0225730 ncithesaurus:Left_Lung The upper conducting airways of the lung; these airways arise from the terminus of the trachea. Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] bronchial In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 FMA:7409 GAID:346 MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 NCIT:C12683 SCTID:181215002 UMLS:C0006255 VHOG:0000262 Wikipedia:Bronchus XAO:0000121 bronchi bronchial trunk uberon bronchial tissue UBERON:0002185 bronchus http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb The upper conducting airways of the lung; these airways arise from the terminus of the trachea. ISBN:0-397-51047-0 MESH:A04.411.125 MGI:cwg MP:0002264 Wikipedia Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000262 VHOG http://bgee.unil.ch/ UMLS:C0006255 ncithesaurus:Bronchus bronchi bronchial trunk FMA:7409 bronchial tissue BTO:0001340 A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] UBERON:0008875 panniculus adiposus BTO:0004042 EMAPA:35829 FMA:74315 MA:0000473 MESH:D015434 fatty layer of subcutaneous tissue hypodermis fat layer panniculus adiposus (tela subcutanea) panniculus adiposus telae subcutaneae subcutaneous fat layer uberon fatty layer of superficial fascia subcutaneous fat UBERON:0002190 subcutaneous adipose tissue A portion of adipose tissue that is part of the hypodermis, beneath the dermis. http://orcid.org/0000-0002-6601-2165 the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] MP:0011156 panniculus adiposus MP:0011156 MESH:D015434 https://github.com/biopragmatics/biomappings fatty layer of subcutaneous tissue FMA:74315 hypodermis fat layer MP:0011156 panniculus adiposus (tela subcutanea) FMA:74315 FMA:TA panniculus adiposus telae subcutaneae FMA:74315 FMA:TA subcutaneous fat layer MP:0011156 fatty layer of superficial fascia FMA:74315 subcutaneous fat BTO:0004042 Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 hematolymphoid system lymphomyeloid complex uberon haemolymphoid system UBERON:0002193 hemolymphoid system MA Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. http://orcid.org/0000-0002-6601-2165 Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers. from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP] EMAPA:35524 FMA:74604 MA:0000739 NCIT:C33028 SCTID:327532004 UMLS:C0229699 Wikipedia:Lymph_node_capsule capsula nodi lymphoidei lymph node capsule uberon UBERON:0002194 capsule of lymph node https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb https://upload.wikimedia.org/wikipedia/commons/9/92/Lymphknoten_(Schwein).jpg Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers. Wikipedia:Lymph_node#Capsule UMLS:C0229699 ncithesaurus:Lymph_Node_Capsule capsula nodi lymphoidei FMA:74604 FMA:TA Membranous process coming from capsule of lymph node[WP]. FMA:74605 MA:0000746 NCIT:C33035 UMLS:C1184179 Wikipedia:Lymph_node_trabeculae lymph node trabecula lymph node trabeculae lymph node trabeculum trabeculae of lymph node uberon UBERON:0002195 trabecula of lymph node http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png Membranous process coming from capsule of lymph node[WP]. Wikipedia:Lymph_node_trabeculae UMLS:C1184179 ncithesaurus:Lymph_Node_Trabecula lymph node trabeculae trabeculae of lymph node The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]. Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO] The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175]. AHP AAO:0010540 BAMS:AHY BAMS:AL BAMS:APit BIRNLEX:1581 BM:AHy BTO:0000040 CALOHA:TS-0794 EFO:0000230 EHDAA2:0000109 EMAPA:17514 FMA:74627 MA:0000177 MESH:D010903 NCIT:C12772 SCTID:245532007 TAO:0001282 UMLS:C0032008 UMLS:C1280369 VHOG:0000141 Wikipedia:Adenohypophysis ZFA:0001282 neuronames:407 anterior hypophysis anterior lobe (hypophysis) anterior lobe of hypophysis anterior lobe of pituitary anterior lobe of pituitary gland anterior pituitary lobus anterior (glandula pituitaria) lobus anterior hypophysis pituitary gland, anterior lobe uberon anterior lobe of the pituitary anterior pituitary gland cranial lobe lobus anterior pituitary anterior lobe pituitary glandanterior lobe rostral lobe UBERON:0002196 adenohypophysis http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png ZFA ZFA PMID:19084529 NCBIBook:NBK53175 ZFA lexical The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]. Wikipedia:Adenohypophysis ZFIN:curator Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO] 2012-06-20 AAO:0010540 AAO AAO:BJB The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO] 2012-08-14 TAO:0001282 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 http://bgee.unil.ch/ In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish ZFA AHP BIRNLEX:1581 NIFSTD:NeuroNames_abbrevSource UMLS:C0032008 BIRNLEX:1581 ncithesaurus:Anterior_Lobe_of_the_Pituitary_Gland UMLS:C1280369 BIRNLEX:1581 neuronames:407 BIRNLEX:1581 anterior hypophysis ZFA:0001282 lobus anterior (glandula pituitaria) FMA:74627 FMA:TA lobus anterior hypophysis FMA:74627 FMA:TA anterior lobe of the pituitary BAMS:APit anterior pituitary gland BTO:0000040 cranial lobe BTO:0000496 lobus anterior NeuroNames:407 pituitary anterior lobe EMAPA:17514 pituitary glandanterior lobe BAMS:AL rostral lobe BTO:0000496 The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon. request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon' The infundibular part of the pituitary gland consisting of two regions.[AAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19) NHP AAO:0010537 BAMS:NHP BAMS:NHY BAMS:NL BAMS:PPit BIRNLEX:1586 BM:NY BTO:0000937 CALOHA:TS-0815 DMBA:15691 EHDAA2:0001271 EHDAA:7536 EMAPA:17519 FMA:74628 MA:0000178 MESH:D010904 NCIT:C12773 SCTID:245527006 TAO:0001271 UMLS:C0032009 UMLS:C1280368 VHOG:0000142 Wikipedia:Neurohypophysis ZFA:0001271 neuronames:401 infundibular process lobus nervosus neurohypophysis lobus posterior (glandula pituitaria) lobus posterior hypophysis neural lobe neural lobe of pituitary neural lobe of pituitary gland neuro hypophysis neurohypophysis pituitary gland, posterior lobe posterior lobe of pituitary posterior lobe of pituitary gland posterior pituitary uberon lobus nervosus lobus posterior pituitary gland neural lobe pituitary gland, neural lobe posterior lobe of hypophysis posterior pituitary gland UBERON:0002198 neurohypophysis http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG MA ZFA PMID:19084529 Wikipedia Wikipedia The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon. MP:0004164 request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon' http://syllabus.med.unc.edu/courseware/embryo_images/ Ariens, p. 1192 The infundibular part of the pituitary gland consisting of two regions.[AAO] 2012-06-20 AAO:0010537 AAO AAO:BJB It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 http://bgee.unil.ch/ todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19) EMAPA NHP BIRNLEX:1586 NIFSTD:NeuroNames_abbrevSource UMLS:C0032009 BIRNLEX:1586 ncithesaurus:Posterior_Lobe_of_the_Pituitary_Gland UMLS:C1280368 BIRNLEX:1586 neuronames:401 BIRNLEX:1586 infundibular process FMA:74628 lobus nervosus neurohypophysis FMA:74628 FMA:TA lobus posterior (glandula pituitaria) FMA:74628 FMA:TA lobus posterior hypophysis FMA:74628 FMA:TA neural lobe FMA:74628 neural lobe of pituitary BIRNLEX:1586 neural lobe of pituitary gland FMA:74628 posterior lobe of pituitary gland FMA:74628 lobus nervosus NeuroNames:401 lobus posterior NeuroNames:401 pituitary gland neural lobe BAMS:NL pituitary gland, neural lobe NeuroNames:401 posterior lobe of hypophysis NeuroNames:401 posterior pituitary gland BTO:0000937 The dermis, epidermis and hypodermis. in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] Surface structure that is the outer protective covering of the body.[VSAO] The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] integumental integumentary AAO:0000239 BTO:0000634 EMAPA:37504 FMA:74657 TAO:0000368 VSAO:0000029 Wikipedia:Integument ZFA:0000368 galen:Integument dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument uberon dermal system dermoid system skin tegument vertebrate integument UBERON:0002199 integument FMA FMA The dermis, epidermis and hypodermis. Wikipedia:Integument Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] 2012-06-20 AAO:0000239 AAO AAO:EJS Surface structure that is the outer protective covering of the body.[VSAO] 2012-08-14 VSAO:0000029 VSAO PSPUB:0000170 The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000368 TAO ZFIN:curator EMAPA:37504 MA:th integumentum commune FMA:74657 FMA:TA the integument FMA:74657 dermal system BTO:0000634 dermoid system BTO:0000634 tegument BTO:0000634 Vasculature that is part of a head [Automatically generated definition]. EFO:0003656 FMA:74710 TAO:0001267 XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network vascular network of adult head vascular network of head vasculature of adult head uberon head vasculature UBERON:0002200 vasculature of head Vasculature that is part of a head [Automatically generated definition]. OBOL:automatic adult head vascular network OBOL:automatic adult head vasculature OBOL:automatic head vascular network OBOL:automatic vascular network of adult head OBOL:automatic vascular network of head OBOL:automatic vasculature of adult head OBOL:automatic A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature vascular network of torso vascular network of trunk vasculature of torso uberon UBERON:0002201 vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. OBOL:automatic torso vascular network OBOL:automatic torso vasculature OBOL:automatic trunk vascular network OBOL:automatic vascular network of torso OBOL:automatic vascular network of trunk OBOL:automatic vasculature of torso OBOL:automatic A submucosa that is part of a trachea. BTO:0002115 EMAPA:35879 FMA:7472 MA:0001860 NCIT:C49307 SCTID:4419000 UMLS:C0225586 submucosa of windpipe trachea submucosa tracheal submucosa windpipe submucosa uberon submucous layer of trachea UBERON:0002202 submucosa of trachea A submucosa that is part of a trachea. OBOL:automatic UMLS:C0225586 ncithesaurus:Trachea_Submucosa submucosa of windpipe OBOL:automatic windpipe submucosa OBOL:automatic submucous layer of trachea BTO:0002115 Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 SCTID:123846009 TAO:0007057 ZFA:0007057 eye vascular network ocular blood vessel ocular vasculature vascular network of eye uberon eye vasculature optic vasculature UBERON:0002203 vasculature of eye https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb ISBN:0781772214 Vasculature that is part of the eye region. OBOL:automatic https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726 not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ZFA eye vascular network OBOL:automatic ocular blood vessel ZFA:0007057 vascular network of eye OBOL:automatic Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 NCIT:C12754 SCTID:278858007 UMLS:C0026860 VHOG:0001275 VSAO:0000031 Wikipedia:Musculoskeletal_system XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system check ctenophore Anatomical system that consists of the muscular and skeletal systems. VSAO:0000031 VSAO:curator https://github.com/obophenotype/uberon/issues/77 Anatomical system that provides locomotion and physical support to the organism.[AAO] 2012-06-20 AAO:0010546 AAO AAO:EJS There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] 2012-09-17 VHOG:0001275 VHOG DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) http://bgee.unil.ch/ UMLS:C0026860 ncithesaurus:Musculoskeletal_System Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA]. A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO] AEO:0000178 EHDAA2:0003178 EMAPA:35344 FMA:7492 MA:0000321 SCTID:37772004 TAO:0005156 Wikipedia:Fibrous_joint ZFA:0005156 articulatio fibrosa uberon junctura fibrosa UBERON:0002209 fibrous joint FMA AEO Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA]. FMA:FMA Wikipedia:Fibrous_joint A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO] 2012-08-14 TAO:0005156 TAO ZFIN:curator junctura fibrosa Wikipedia:Fibrous_joint Fibrous joint in which the articulating bones or cartilages of the vertebral column and the limbs as well as articulating ossicles, are connected by skeletal ligaments or membranes. Examples: Intervertebral syndesmosis, inferior tibiofibular joint.[FMA]. EMAPA:37465 FMA:7494 MA:0001500 SCTID:89358004 Wikipedia:Syndesmosis uberon UBERON:0002210 syndesmosis Fibrous joint in which the articulating bones or cartilages of the vertebral column and the limbs as well as articulating ossicles, are connected by skeletal ligaments or membranes. Examples: Intervertebral syndesmosis, inferior tibiofibular joint.[FMA]. FMA:FMA Wikipedia:Syndesmosis EMAPA:37465 MA:th Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]. EMAPA:36581 FMA:7496 MA:0000320 SCTID:58442004 TAO:0005155 Wikipedia:Cartilaginous_joint ZFA:0005155 articulatio cartilaginea uberon junctura cartilaginea UBERON:0002213 cartilaginous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]. FMA:FMA Wikipedia:Cartilaginous_joint junctura cartilaginea Wikipedia:Cartilaginous_joint Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA]. WP considers epiphyseal plates as subtypes of this consider adding link to hyaline cartilage EMAPA:35846 FMA:7497 MA:0001501 SCTID:42903008 Wikipedia:Synchondrosis cartilago epiphysialis primary cartilaginous joint uberon epiphysial cartilage UBERON:0002215 synchondrosis http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA]. FMA:FMA Wikipedia:Synchondrosis cartilago epiphysialis FMA:7497 FMA:TA primary cartilaginous joint FMA:7497 epiphysial cartilage FMA:7497 Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA]. consider adding fibrocartilage class EMAPA:37758 FMA:7498 MA:0001504 SCTID:1584001 Wikipedia:Symphysis secondary cartilaginous joint uberon UBERON:0002216 symphysis http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png MA FMA Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA]. FMA:FMA Wikipedia:Symphysis EMAPA:37758 MA:th secondary cartilaginous joint FMA:7498 Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 SCTID:113234001 TAO:0005153 Wikipedia:Synovial_joint ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint uberon diarthrodial joints UBERON:0002217 synovial joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]. FMA:7501 Wikipedia:Synovial_joint Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] 2012-08-14 TAO:0005153 TAO ZFIN:Curator diarthroses ZFA:0005153 diarthrodial joints ZFA:0005153 Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP]. Anatomical structure that is a membranous gap between bones of the skull.[TAO] FMA:75438 MA:0001465 NCIT:C32621 SCTID:272681004 TAO:0001738 UMLS:C0224548 Wikipedia:Fontanelle ZFA:0005536 fontanel fontanelles fontanels uberon fonticuli cranii UBERON:0002221 fontanelle https://github.com/obophenotype/uberon/issues/1795 http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray197.png MA ZFA Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP]. Wikipedia:Fontanelle https://orcid.org/0000-0002-2825-0621 Anatomical structure that is a membranous gap between bones of the skull.[TAO] 2012-08-14 TAO:0001738 TAO TAO:wd UMLS:C0224548 ncithesaurus:Fontanelle fontanelles TAO:0001738 fontanels TAO:0001738 fonticuli cranii Wikipedia:Fontanelle The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 MA:0000032 MESH:D035423 NCIT:C12905 SCTID:243949006 UMLS:C0230139 Wikipedia:Thoracic_cavity cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon UBERON:0002224 thoracic cavity http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:cjm Wikipedia:Thoracic_cavity UMLS:C0230139 ncithesaurus:Thoracic_Cavity cavitas thoracis Wikipedia:Thoracic_cavity space of thoracic compartment FMA:7565 An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses. Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO] Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO] costal In most vertebrates, ribs surround the chest. In some species, especially snakes, ribs may provide support and protection for the entire body They protect and support internal organs and enable lungs to expand by expanding the chest. AAO:0000545 CALOHA:TS-2209 EFO:0003066 EMAPA:18010 FMA:7574 GAID:245 MA:0000315 MESH:D012272 NCIT:C12782 SCTID:302523002 TAO:0000538 UMLS:C0035561 VHOG:0001154 VO:0012403 Wikipedia:Rib ZFA:0000538 galen:Rib uberon dorsal rib pleural rib ribs UBERON:0002228 rib definitional An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses. Wikipedia:Rib ZFIN:curator Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO] 2012-08-14 TAO:0000538 TAO ZFIN:curator Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO] 2012-06-20 AAO:0000545 AAO AAO:Pugener_2002 UMLS:C0035561 ncithesaurus:Rib VO:0012403 https://github.com/biopragmatics/biomappings ribs TAO:0000538 A proximal phalanx that is part of a finger [Automatically generated definition]. EMAPA:37307 FMA:75816 MA:0001395 NCIT:C52786 SCTID:181986000 SCTID:361325003 UMLS:C0730117 hand proximal phalanx phalanx proximalis manus proximal manual phalanx proximal phalanx of finger proximal phalanx of fore digit proximal phalanx of hand proximal phalanx of manual digit uberon UBERON:0002234 proximal phalanx of manus A proximal phalanx that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37307 MA:th UMLS:C0730117 ncithesaurus:Proximal_Phalanx_of_Hand hand proximal phalanx MA:0001395 phalanx proximalis manus FMA:75816 FMA:TA proximal phalanx of finger FMA:75816 A rib that is ventrally connected to the sternum. EMAPA:37774 FMA:7592 MA:0001419 SCTID:368044009 Wikipedia:True_ribs costa vera uberon costae verae UBERON:0002237 true rib http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png A rib that is ventrally connected to the sternum. ISBN:0073040584 Wikipedia:True_ribs EMAPA:37774 MA:th costae verae Wikipedia:True_ribs Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal BIRNLEX:1709 BM:SpC BTO:0001279 CALOHA:TS-0953 DHBA:12890 DMBA:17651 EFO:0000110 EHDAA2:0001255 EHDAA:2863 EMAPA:17577 EV:0100316 FMA:7647 GAID:695 MA:0000216 MAT:0000183 MESH:D013116 MIAA:0000183 NCIT:C12464 SCTID:180959008 TAO:0000075 UMLS:C0037925 VHOG:0000601 Wikipedia:Spinal_cord XAO:0000020 ZFA:0000075 neuronames:22 uberon SpC cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris medulla spinalis spinal cord structure spinal medulla UBERON:0002240 spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb ZFA definitional definitional Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). BIRNLEX:1709 ZFA https://github.com/obophenotype/uberon/issues/378 pending Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] 2012-06-20 AAO:0010151 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000601 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 http://bgee.unil.ch/ UMLS:C0037925 BIRNLEX:1709 ncithesaurus:Spinal_Cord neuronames:22 BIRNLEX:1709 SpC cerebro-cerebellar fissure NeuroNames:22 cerebrocerebellar fissure NeuroNames:22 fissura cerebro-cerebellaris NeuroNames:22 fissura cerebrocerebellaris NeuroNames:22 medulla spinalis BTO:0001279 Wikipedia:Spinal_cord spinal cord structure ZFA:0000075 spinal medulla BTO:0001279 Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal) Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] chondrocranial covers the brain dorsally in chondrichthyans AAO:0010169 EHDAA2:0000243 EMAPA:17681 TAO:0001424 VHOG:0000288 Wikipedia:Chondrocranium ZFA:0001424 uberon calvarium neurocranium UBERON:0002241 chondrocranium Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. Wikipedia:Chondrocranium http://medical-dictionary.thefreedictionary.com/chondrocranium Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] 2012-06-20 AAO:0010169 AAO AAO:BJB Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] 2012-08-14 TAO:0001424 TAO ZFIN:curator calvarium MA:0000317 neurocranium MA:0000317 The jelly-like substance in the middle of the spinal disc which is a remnant of the notochord. The nucleus pulposus consists of chondrocytes, collagen fibrils, and proteoglycan aggrecans that have hyaluronic long chains which attract water. Attached to each hyaluronic chain are side chains of chondroitin sulfate and keratan sulfate[Wikipedia:Nucleus_pulposus] we group two FMA classes together BTO:0003626 EMAPA:18008 FMA:13550 FMA:76703 MA:0000112 MESH:D000070614 SCTID:316586000 Wikipedia:Nucleus_pulposus nucleus pulposus (diskus intervertebralis) pulpy nucleus uberon nucleus propulsus nucleus propulsus of intervertebral disk nucleus pulposus of intervertebral disk UBERON:0002242 Function noyes: It functions to distribute hydraulic pressure in all directions within each disc under compressive loads. nucleus pulposus http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png mah ISBN:0073040584 Wikipedia The jelly-like substance in the middle of the spinal disc which is a remnant of the notochord. MGI:llw2 MP:0006392 we group two FMA classes together FMA MESH:D000070614 https://github.com/biopragmatics/biomappings nucleus pulposus (diskus intervertebralis) FMA:13550 nucleus propulsus Wikipedia:Nucleus_pulposus nucleus propulsus of intervertebral disk Wikipedia:Nucleus_pulposus nucleus pulposus of intervertebral disk FMA:13550 An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint AAO:0010180 BTO:0001772 FBbt:00005158 FMA:77659 VHOG:0000287 XAO:0000273 olfactory organ olfactory sense organ olfactory sensory organ main olfactory organ primary olfactory organ uberon olfactory neuroepithelium organ olfactus organum olfactorium UBERON:0002268 olfactory organ An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. UBERON:cjm FBbt:00005158 olfactory organ BTO:0001772 olfactory sensory organ FBbt:00005158 olfactory neuroepithelium BTO:0001772 organ olfactus BTO:0001772 organum olfactorium BTO:0001772 A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure BAMS:RET EMAPA:35188 FMA:77719 MA:0003185 MESH:D012154 NLX:143558 SCTID:361552007 Wikipedia:Reticular_formation neuronames:1223 brain stem reticular formation brainstem reticular formation reticular formation (classical) reticular formation of the brainstem uberon UBERON:0002275 reticular formation http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). NeuroNames:1223 FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure FMA brain stem reticular formation NeuroNames:1223 brainstem reticular formation MA:0003185 NeuroNames:1223 reticular formation (classical) NeuroNames:1223 reticular formation of the brainstem NeuroNames:1223 A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere. The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] BAMS:LV BAMS:Tel-V BIRNLEX:1263 BM:Tel-LV BTO:0000879 CALOHA:TS-1230 DHBA:10596 DMBA:126651562 EFO:0001961 EHDAA2:0001984 EHDAA:3502 EHDAA:6576 EV:0100307 FMA:78448 GAID:611 HBA:9419 MA:0000192 MBA:81 MESH:D020547 NCIT:C12834 SCTID:180930008 TAO:0000696 UMLS:C0152279 VHOG:0000643 Wikipedia:Lateral_ventricle ZFA:0000696 neuronames:209 lateral ventricle lateral ventricles telencephalic ventricle telencephalon lateral ventricle uberon forebrain ventricle lateral ventricle of brain tectal ventricle telencephalic ventricles telencephalic vesicle UBERON:0002285 modeled as space in EHDAA2 telencephalic ventricle http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png material to immaterial EHDAA2 A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere. Wikipedia:Lateral_ventricle https://orcid.org/0000-0002-6601-2165 The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. Wikipedia:Lateral_ventricle The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. GO:0021670 The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000643 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ UMLS:C0152279 BIRNLEX:1263 ncithesaurus:Lateral_Ventricle lateral ventricle MA:0000192 lateral ventricles telencephalic ventricle VHOG:0000643 ZFA:0000696 telencephalon lateral ventricle EHDAA2:0001984 lateral ventricle of brain BTO:0000879 telencephalic ventricles BAMS:Tel-V telencephalic vesicle ZFA:0000696 Choroid plexus of the fourth ventricle. BAMS:chp4 BAMS:cp4v DHBA:12808 EMAPA:32742 FMA:78492 HBA:9710 MA:0000983 NCIT:C32308 NLX:27388 SCTID:42214001 TAO:0001446 UMLS:C0152293 VHOG:0001375 ZFA:0001446 neuronames:638 chorioid plexus of cerebral hemisphere of fourth ventricle chorioid plexus of fourth ventricle choroid plexus fourth ventricle fourth ventricle chorioid plexus of cerebral hemisphere fourth ventricle choroid plexus uberon 4th ventricle choroid plexus UBERON:0002290 choroid plexus of fourth ventricle Choroid plexus of the fourth ventricle. NLX:27388 UMLS:C0152293 ncithesaurus:Choroid_Plexus_of_the_Fourth_Ventricle chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic choroid plexus fourth ventricle ZFA:0001446 fourth ventricle chorioid plexus of cerebral hemisphere OBOL:automatic Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). FMA:79646 GAID:279 MA:0001273 MESH:D001659 NCIT:C12678 SCTID:361354009 Wikipedia:Biliary_system biliary apparatus uberon biliary tract UBERON:0002294 biliary system http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). Wikipedia:Biliary_system biliary apparatus FMA:79646 biliary tract FMA:79646 MA:0001273 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO] EHDAA2:0004560 EHDAA:3019 EHDAA:3033 EHDAA:3921 EHDAA:3934 EHDAA:3957 EHDAA:3971 FMA:79795 SCTID:308823000 TAO:0005130 Wikipedia:Mesentery#Development ZFA:0005130 uberon dorsal mesogastrium mesenterium dorsale commune UBERON:0002296 dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png EHDAA2 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. Wikipedia:Dorsal_mesentery Wikipedia:Mesentery#Development ZFIN:curator The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO] 2012-08-14 TAO:0005130 TAO ZFIN:curator dorsal mesogastrium Wikipedia:Dorsal_mesentery mesenterium dorsale commune Wikipedia:Dorsal_mesentery Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BIRNLEX:1565 BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 NCIT:C12441 SCTID:180925009 TAO:0002156 UMLS:C0006121 VHOG:0001457 Wikipedia:Brainstem ZFA:0001707 neuronames:236 brain stem truncus encephali uberon accessory medullary lamina of pallidum lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta truncus encephalicus UBERON:0002298 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). brainstem http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. ISBN:0471888893 MP:0005277 Wikipedia:Brainstem ZFA:0001707 we apply a strict definition ZFA ABA https://github.com/obophenotype/uberon/issues/378 pending we apply a strict definition Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] 2012-08-14 TAO:0002156 TAO ISBN:3764351209 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. ZFA:0001707 the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] MP:0005277 UMLS:C0006121 BIRNLEX:1565 ncithesaurus:Brain_Stem neuronames:236 BIRNLEX:1565 brain stem ABA:BS truncus encephali Wikipedia:Brainstem accessory medullary lamina of pallidum NeuroNames:236 lamella pallidi incompleta NeuroNames:236 lamina medullaris accessoria NeuroNames:236 lamina medullaris incompleta pallidi NeuroNames:236 lamina pallidi incompleta NeuroNames:236 truncus encephalicus BTO:0000146 One of the layers of the neocortex. These layers are defined by distinctive populations of cells based on somata size, shape, or density, that are aligned into sheets. cortical layer ABA:CTX1-6b EMAPA:35588 FMA:83138 MA:0000186 layer of neocortex neocortex layer uberon cerebral cortex layer lamina of neocortex UBERON:0002301 layer of neocortex One of the layers of the neocortex. These layers are defined by distinctive populations of cells based on somata size, shape, or density, that are aligned into sheets. ISBN-10:0-87893-742-0 PMID:29081739 http://orcid.org/0000-0002-6601-2165 layer of neocortex FMA:83138 neocortex layer MA:0000186 cerebral cortex layer MA:0000186 lamina of neocortex FMA:83138 The atrial part of middle layer of the heart, comprised of involuntary muscle. As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003087 EMAPA:32746 FMA:83509 MA:0000081 SCTID:191910002 TAO:0001374 VHOG:0000602 ZFA:0001374 atrial myocardium atrium myocardium uberon atrium cardiac muscle UBERON:0002302 myocardium of atrium The atrial part of middle layer of the heart, comprised of involuntary muscle. ISBN:0-683-40008-8 MP:0010493 As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000602 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ atrial myocardium ZFA:0001374 atrium cardiac muscle VHOG:0000602 Mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa. protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons BTO:0003603 CALOHA:TS-0658 EMAPA:36552 FMA:83688 MA:0002535 NCIT:C52551 UMLS:C0225392 Wikipedia:Nasal_mucus#Respiratory_system uberon respiratory mucus UBERON:0002306 EDITOR_NOTE TODO - split nasal vs respiratory tract? nasal mucus Mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa. http://orcid.org/0000-0002-6601-2165 UMLS:C0225392 ncithesaurus:Nasal_Mucus respiratory mucus BTO:0003603 Part of choroid plexus contained in the lateral ventricle. BAMS:cplv DHBA:10601 EHDAA2:0004449 EMAPA:17769 FMA:83711 HBA:9708 MA:0000961 NCIT:C32309 NLX:32548 SCTID:70064002 TAO:0001447 UMLS:C0152289 VHOG:0001376 ZFA:0001447 neuronames:218 chorioid plexus of cerebral hemisphere of lateral ventricle chorioid plexus of lateral ventricle choroid plexus telencephalic ventricle lateral ventricle chorioid plexus of cerebral hemisphere lateral ventricle choroid plexus uberon UBERON:0002307 choroid plexus of lateral ventricle Part of choroid plexus contained in the lateral ventricle. NLX:32548 UMLS:C0152289 ncithesaurus:Choroid_Plexus_of_the_Lateral_Ventricle chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic choroid plexus telencephalic ventricle ZFA:0001447 lateral ventricle chorioid plexus of cerebral hemisphere OBOL:automatic A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 NCIT:C49346 SCTID:426465002 UMLS:C1706993 ZFA:0005575 brain nucleus uberon brain nuclei UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. http://orcid.org/0000-0002-6601-2165 UMLS:C1706993 ncithesaurus:Brain_Nucleus brain nuclei ZFA:0005575 The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. BAMS:Scgrey DHBA:146035048 EMAPA:35792 FMA:256580 MA:0000002 NCIT:C32696 NLXANAT:100204 SCTID:279441003 UMLS:C0475853 neuronames:2619 gray matter of spinal cord gray substance of spinal cord grey matter of spinal cord grey substance of spinal cord spinal cord gray matter spinal cord grey matter spinal cord grey substance substantia grisea medullae spinalis uberon UBERON:0002315 gray matter of spinal cord The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. MP:0008503 UMLS:C0475853 ncithesaurus:Gray_Matter_of_the_Spinal_Cord gray matter of spinal cord OBOL:automatic gray substance of spinal cord FMA:256580 spinal cord gray matter OBOL:automatic spinal cord grey substance OBOL:automatic substantia grisea medullae spinalis FMA:256580 FMA:TA The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 SCTID:361348008 TAO:0001438 UMLS:C0333343 ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen main body cavity space of body compartment ventral body cavity uberon celom coelom coelome hemocoel UBERON:0002323 EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen definitional The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. 2012-09-12 ZFA:0001438 ZFA ZFIN:curator The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. 2012-09-12 BTO:0001707 BTO BTO body cavity BTO:0001707 FBbt:00005060 UMLS:C0333343 ncithesaurus:Cavity coelomic cavity EHDAA2:0000267 coelomic cavity lumen EHDAA2:0000267 space of body compartment FMA:85006 ventral body cavity NCBITaxon:7742 celom BTO:0001707 coelome BTO:0001707 hemocoel FBbt:00005060 Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 FMA:85216 MA:0000496 back muscle back muscle organ muscle organ of back uberon UBERON:0002324 muscle of back prolog Any muscle organ that is part of a back [Automatically generated definition]. OBOL:automatic back muscle organ OBOL:automatic muscle organ of back OBOL:automatic The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. EMAPA:31518 FMA:85275 MA:0001686 NCIT:C49309 UMLS:C1710584 epithelial tissue of urethra urethra epithelial tissue urethra epithelium uberon urethral epithelium urethral plate urethral seam UBERON:0002325 epithelium of urethra GO The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. GO:0061071 UMLS:C1710584 ncithesaurus:Urethra_Epithelium epithelial tissue of urethra OBOL:automatic urethra epithelial tissue OBOL:automatic urethral plate EMAPA:31518 urethral seam EMAPA:31518 A lamina propria that is part of a urethra [Automatically generated definition]. EMAPA:37785 FMA:85276 MA:0001689 lamina propria mucosa of urethra lamina propria mucosae of urethra urethra lamina propria urethra lamina propria mucosa urethra lamina propria mucosae uberon urethral lamina propria UBERON:0002326 lamina propria of urethra A lamina propria that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37785 MA:th lamina propria mucosa of urethra OBOL:automatic lamina propria mucosae of urethra OBOL:automatic urethra lamina propria mucosa OBOL:automatic urethra lamina propria mucosae OBOL:automatic EMAPA:18227 EMAPA:37720 FMA:85315 MA:0001176 intercostal nerve trunk intercostal neural trunk uberon UBERON:0002327 trunk of intercostal nerve EMAPA:37720 MA:th A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] notochordal In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 MAT:0000281 MESH:D009672 NCIT:C12463 SCTID:308820002 TAO:0000135 UMLS:C0028439 VHOG:0000199 VSAO:0000032 Wikipedia:Notochord XAO:0000055 ZFA:0000135 http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg embryonic notocord notocord uberon notochorda UBERON:0002328 The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png PMID:15890825 VSAO http://tolweb.org/Chordata/2499 ZFA EHDAA2 A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. ISBN:0815318960 Wikipedia:Notochord http://tolweb.org/Chordata/2499 https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] 2012-08-14 VSAO:0000032 VSAO PSPUB:0000170 Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000135 TAO ZFIN:curator Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] 2012-06-20 AAO:0000327 AAO AAO:LAP relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] 2012-06-20 AAO:0000327 AAO (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000199 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ UMLS:C0028439 ncithesaurus:Notochord notocord ZFA:0000135 notochorda Wikipedia:Notochord Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] somitic mesodermal cluster AAO:0010569 AEO:0001015 BTO:0001558 EHDAA2:0003436 EHDAA:366 EHDAA:699 EMAPA:31169 FMA:85522 GAID:1306 MAT:0000068 MESH:D019170 MIAA:0000068 NCIT:C34302 TAO:0000155 UMLS:C0376449 VHOG:0000191 Wikipedia:Somite XAO:0000058 ZFA:0000155 uberon epimere epimere mesoderm epithelial somite somites somitic mesoderm somitus UBERON:0002329 When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 GOTAX:0000352 ZFA Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. DOI:10.1111/j.1439-0426.2012.01987.x Wikipedia:Somite PMID:17237766 Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] 2012-06-20 AAO:0010569 AAO AAO:EJS Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000155 TAO ZFIN:curator relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] 2012-06-20 AAO:0010569 AAO (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000191 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) http://bgee.unil.ch/ mesodermal cluster GO:0001756 UMLS:C0376449 ncithesaurus:Somite epimere ISBN:0073040584 epithelial somite https://github.com/obophenotype/uberon/wiki/The-neural-crest somites somitus Wikipedia:Somite Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 NCIT:C12957 UMLS:C1516995 Wikipedia:Exocrine_gland WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. Wikipedia:Exocrine_gland UMLS:C1516995 ncithesaurus:Exocrine_System exocrine glandular system EHDAA2:0002225 The connecting cord from the developing embryo to the placenta. The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]. umbilical BTO:0001415 CALOHA:TS-1078 EFO:0001415 EHDAA2:0000312 EHDAA:158 EMAPA:26115 EV:0100127 FMA:85541 GAID:517 MAT:0000280 MESH:D014470 MIAA:0000280 NCIT:C34320 SCTID:280644003 UMLS:C0041633 Wikipedia:Umbilical_cord chorda umbilicalis funiculus umbilicalis uberon birth cord connecting stalk funiculus umbilicalis yolk stalk UBERON:0002331 See notes for connecting stalk umbilical cord http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb The connecting cord from the developing embryo to the placenta. ISBN:0-683-40008-8 MP:0001725 PMID:9144284 Wikipedia:Umbilical_cord The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]. Wikipedia:Umbilical_cord UMLS:C0041633 ncithesaurus:Umbilical_Cord chorda umbilicalis MP:0012134 funiculus umbilicalis MP:0012134 birth cord Wikipedia:Umbilical_cord funiculus umbilicalis Wikipedia:Umbilical_cord yolk stalk BTO:0001415 An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] EHDAA2:0001576 EHDAA:9831 EMAPA:17015 FMA:8612 MA:0002033 NCIT:C116918 VHOG:0001134 galen:PulmonaryTrunk pulmonary artery (trunk) trunk of pulmonary arterial tree uberon main pulmonary artery UBERON:0002333 pulmonary trunk https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png MA An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. http://orcid.org/0000-0002-6601-2165 An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] 2012-09-17 VHOG:0001134 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+trunk As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] 2012-09-17 VHOG:0001134 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ main pulmonary artery Wikipedia:Pulmonary_artery The duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue. FMA also has 'main submandibular duct' (FMA:59899) BTO:0004556 EMAPA:35833 FMA:86266 MA:0002698 NCIT:C33649 SCTID:181237009 UMLS:C0227472 Wikipedia:Submandibular_duct uberon Wharton's duct ductus submandibularis ductus submaxillaris submandibular salivary duct submaxillar gland duct submaxillary duct UBERON:0002334 submandibular duct http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray1024.png The duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue. ISBN:0-683-40008-8 MP:0009525 FMA also has 'main submandibular duct' (FMA:59899) FMA UMLS:C0227472 ncithesaurus:Submandibular_Duct Wharton's duct FMA:59899 Wikipedia:Submandibular_duct ductus submandibularis BTO:0004556 ductus submaxillaris Wikipedia:Submandibular_duct submaxillar gland duct BTO:0004556 The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle. CALOHA:TS-1266 EMAPA:35310 FMA:86487 MA:0002734 NCIT:C32516 SCTID:254115004 UMLS:C0227849 endometrium stroma stroma of endometrium uberon UBERON:0002337 endometrial stroma The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle. ncithesaurus:Endometrial_Stroma UMLS:C0227849 ncithesaurus:Endometrial_Stroma A lamina propria that is part of a bronchus [Automatically generated definition]. EMAPA:35194 FMA:86619 MA:0001836 NCIT:C49212 UMLS:C1707054 bronchi lamina propria bronchi lamina propria mucosa bronchi lamina propria mucosae bronchial trunk lamina propria bronchial trunk lamina propria mucosa bronchial trunk lamina propria mucosae bronchus lamina propria bronchus lamina propria mucosa bronchus lamina propria mucosae lamina propria mucosa of bronchi lamina propria mucosa of bronchial trunk lamina propria mucosa of bronchus lamina propria mucosae of bronchi lamina propria mucosae of bronchial trunk lamina propria mucosae of bronchus lamina propria of bronchi lamina propria of bronchial trunk uberon bronchial lamina propria UBERON:0002338 lamina propria of bronchus true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707054 ncithesaurus:Bronchus_Lamina_Propria bronchi lamina propria OBOL:automatic bronchi lamina propria mucosa OBOL:automatic bronchi lamina propria mucosae OBOL:automatic bronchial trunk lamina propria OBOL:automatic bronchial trunk lamina propria mucosa OBOL:automatic bronchial trunk lamina propria mucosae OBOL:automatic bronchus lamina propria mucosa OBOL:automatic bronchus lamina propria mucosae OBOL:automatic lamina propria mucosa of bronchi OBOL:automatic lamina propria mucosa of bronchial trunk OBOL:automatic lamina propria mucosa of bronchus OBOL:automatic lamina propria mucosae of bronchi OBOL:automatic lamina propria mucosae of bronchial trunk OBOL:automatic lamina propria mucosae of bronchus OBOL:automatic lamina propria of bronchi OBOL:automatic lamina propria of bronchial trunk OBOL:automatic bronchial lamina propria EMAPA:35194 A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 MAT:0000066 MESH:D009432 MIAA:0000066 NCIT:C34222 SCTID:361462002 TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest XAO:0000048 ZFA:0000045 neuronames:1366 NC uberon crista neuralis neural crest material UBERON:0002342 Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. neural crest http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 BTO PMID:11523831 pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest PMID:11523831 A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 ISBN:0073040584 PMID:17377535 A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000045 TAO ZFIN:curator Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] 2012-06-20 AAO:0010578 AAO AAO:EJS A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] PMID:11523831 We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] 2012-09-17 VHOG:0000057 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) http://bgee.unil.ch/ UMLS:C0027789 ncithesaurus:Neural_Crest NC XAO:0000048 crista neuralis Wikipedia:Neural_crest neural crest material VHOG:0000057 Set of all muscles in abdomen. distinction between abdomen muscle and abdomen musculature FMA:71294 FMA:86917 TAO:0001327 ZFA:0001327 abdominal musculature muscle group of abdomen muscles of abdomen musculature of abdomen musculature of abdominal wall set of muscles of abdomen uberon UBERON:0002343 abdomen musculature Set of all muscles in abdomen. OBOL:automatic muscle group of abdomen FMA:71294 muscles of abdomen FMA:71294 musculature of abdominal wall FMA:86917 set of muscles of abdomen FMA:71294 The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. EFO:0002527 EMAPA:18605 FMA:87217 MA:0002572 SCTID:181301002 uberon UBERON:0002345 descending thoracic aorta The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest. MP:0009868 Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 NCIT:C34228 TAO:0001120 UMLS:C1518271 VHOG:0000150 Wikipedia:Neuroectoderm XAO:0000042 ZFA:0001120 neural ectoderm neuroectoderm uberon epithelium tubi neuralis; neuroectoderma neuaral ectoderm presumptive central nervous system ventral neurogenic region UBERON:0002346 neurectoderm Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] 2012-09-17 VHOG:0000150 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ FBbt:00001057 UMLS:C1518271 ncithesaurus:Neuroectoderm epithelium tubi neuralis; neuroectoderma Wikipedia:Neuroectoderm ventral neurogenic region VHOG:0000150 A thoracic vertebra endochondral element that is composed primarily of a bone tissue. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs EMAPA:18011 FMA:9139 GAID:244 MA:0000314 MESH:D013904 NCIT:C12798 SCTID:181821009 UMLS:C0039987 Wikipedia:Thoracic_vertebrae dorsal vertebra thorax vertebra vertebra of thorax vertebra thoracica uberon UBERON:0002347 thoracic vertebra http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png A thoracic vertebra endochondral element that is composed primarily of a bone tissue. OBOL:automatic UMLS:C0039987 ncithesaurus:Thoracic_Vertebra thorax vertebra OBOL:automatic vertebra of thorax OBOL:automatic A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. External layer of the heart.[TAO] The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium] AAO:0010409 EHDAA2:0002202 FMA:9461 NCIT:C13164 TAO:0005057 UMLS:C0225968 VHOG:0000119 Wikipedia:Epicardium XAO:0000316 ZFA:0005057 galen:Epicardium heart epicardium visceral serous pericardium of heart visceral serous pericardium proper uberon pericardium visceral mesothelium UBERON:0002348 EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. epicardium multiple FMA-inferred FMA A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. http://orcid.org/0000-0002-6601-2165 External layer of the heart.[TAO] 2012-08-14 TAO:0005057 TAO ZFIN:curator The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] 2012-06-20 AAO:0010409 AAO AAO:BJB UMLS:C0225968 ncithesaurus:Epicardium visceral serous pericardium of heart FMA:9461 visceral serous pericardium proper FMA:9461 pericardium visceral mesothelium EMAPA:16589 The middle layer of the heart, comprised mainly of striated cardiac muscle fibers. Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The middle layer of the heart, consisting of cardiac muscle.[AAO] myocardial AAO:0010410 BSA:0000089 BTO:0000901 CALOHA:TS-0440 EFO:0000819 EHDAA2:0004150 EMAPA:32688 EV:0100022 FMA:9462 GAID:173 MA:0000164 MAT:0000453 MESH:D009206 NCIT:C12371 RETIRED_EHDAA2:0001220 SCTID:362012001 TAO:0001319 UMLS:C0027061 VHOG:0000083 Wikipedia:Myocardium XAO:0000065 ZFA:0001319 galen:Myocardium heart myocardium muscle of heart uberon cardiac muscle heart muscle UBERON:0002349 EDITOR_NOTE TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium myocardium http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg The middle layer of the heart, comprised mainly of striated cardiac muscle fibers. ISBN:0-683-40008-8 MP:0005329 Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000083 VHOG http://bgee.unil.ch/ The middle layer of the heart, consisting of cardiac muscle.[AAO] 2012-06-20 AAO:0010410 AAO AAO:BJB UMLS:C0027061 ncithesaurus:Myocardium muscle of heart FMA:9462 cardiac muscle ZFA:0001319 heart muscle FMA:9462 ZFA:0001319 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]. EHDAA2 divides the system from the tissue The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] EFO:0003909 EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 SCTID:281489000 TAO:0005063 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon central conduction system UBERON:0002350 conducting system of heart FMA FMA FMA FMA FMA FMA The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]. GO:0003161 The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] 2012-09-17 VHOG:0001271 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) http://bgee.unil.ch/ cardiac conducting system VHOG:0001271 cardiac impulse conducting system GO:0003161 complexus stimulans cordis FMA:9476 FMA:TA heart conduction system GO:0003161 impulse conducting system MA:0000094 systema conducente cordis FMA:9476 FMA:TA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. BTO:0004358 EHDAA2:0004184 EMAPA:35772 FMA:9477 GAID:561 MA:0000097 MESH:D012849 NCIT:C33555 SCTID:277687007 TAO:0005069 UMLS:C0037189 Wikipedia:Sinoatrial_node ZFA:0005069 Koch's node SA nodal muscle tissue SA node cardiac pacemaker node of Keith-Flack nodus sinuatrialis sinoatrial node sinu-atrial node sinuatrial nodal muscle tissue sinuatrial node sinus node sinus node of Keith and Flack uberon nodus sinuatrialis UBERON:0002351 WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. sinoatrial node http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg cjm ZFA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. GO:0003163 Wikipedia:Sinoatrial_node UMLS:C0037189 ncithesaurus:Sinoatrial_Node Koch's node FMA:9477 SA nodal muscle tissue FMA:9477 SA node FMA:9477 cardiac pacemaker FMA:9477 node of Keith-Flack FMA:9477 nodus sinuatrialis FMA:9477 FMA:TA sinoatrial node FMA:9477 sinu-atrial node FMA:9477 sinuatrial nodal muscle tissue FMA:9477 sinuatrial node FMA:9477 sinus node FMA:9477 sinus node of Keith and Flack FMA:9477 nodus sinuatrialis Wikipedia:Sinoatrial_node An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] BTO:0005689 EFO:0000276 EHDAA2:0004183 EMAPA:35153 FMA:9478 GAID:558 MA:0000095 MAT:0000498 MESH:D001283 NCIT:C32161 SCTID:277688002 TAO:0005070 UMLS:C0004247 VHOG:0001474 Wikipedia:Atrioventricular_node ZFA:0005070 AV nodal muscle tissue AV node Aschoff-Tawara node atrioventricular nodal muscle tissue node of Tawara nodus atrioventricularis uberon A-V node atrio-ventricular node atriovetricular node downstream pacemaker nodus atrioventricularis UBERON:0002352 atrioventricular node http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png cjm An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. UBERON:cjm Wikipedia:Atrioventricular_node Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] 2012-09-17 VHOG:0001474 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) http://bgee.unil.ch/ UMLS:C0004247 ncithesaurus:Atrioventricular_Node AV nodal muscle tissue FMA:9478 AV node FMA:9478 MA:0000095 Aschoff-Tawara node FMA:9478 atrioventricular nodal muscle tissue FMA:9478 node of Tawara FMA:9478 nodus atrioventricularis FMA:TA A-V node EMAPA:35153 atrio-ventricular node EMAPA:35153 atriovetricular node TAO:0005070 downstream pacemaker ZFA:0005070 nodus atrioventricularis Wikipedia:Atrioventricular_node The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. pelvic MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA:0000030 MESH:D010388 NCIT:C12767 SCTID:229765004 UMLS:C0030797 Wikipedia:Pelvis galen:Pelvis lesser pelvis pelvic region pelvis pelvis region true pelvis uberon UBERON:0002355 pelvic region of trunk The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. Wikipedia:Pelvis http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/720 MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA UMLS:C0030797 ncithesaurus:Pelvis lesser pelvis FMA:9578 pelvis FMA:9578 MA:0000030 true pelvis FMA:9578 Serous membrane which is divided into parietal and visceral serous pericardium. EMAPA:19030 FMA:9582 MA:0002739 SCTID:243954002 Wikipedia:Serous_pericardium serous portion of pericardium uberon pericardium serosum UBERON:0002357 serous pericardium FMA FMA Serous membrane which is divided into parietal and visceral serous pericardium. Wikipedia:Serous_pericardium http://orcid.org/0000-0002-6601-2165 serous portion of pericardium FMA:9582 pericardium serosum Wikipedia:Serous_pericardium A serous membrane that lines the peritoneal cavity[VHOG,modified]. TODO - in ZFA is_a epithelium An epithelium that lines the peritoneal cavity.[TAO] Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] peritoneal todo: check MA/EMAPA. AAO:0010814 BTO:0001472 CALOHA:TS-2072 EV:0100087 FMA:9584 GAID:18 MA:0000449 MESH:D010537 NCIT:C12770 TAO:0005120 UMLS:C0031153 VHOG:0001257 Wikipedia:Peritoneum XAO:0000139 ZFA:0005120 galen:Peritoneum uberon peritonaeum UBERON:0002358 peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png MP A serous membrane that lines the peritoneal cavity[VHOG,modified]. VHOG:0001257 An epithelium that lines the peritoneal cavity.[TAO] 2012-08-14 TAO:0005120 TAO ZFIN:curator Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] 2012-06-20 AAO:0010814 AAO AAO:JMG todo: check MA/EMAPA. MA UMLS:C0031153 ncithesaurus:Peritoneum peritonaeum VHOG:0001257 Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]. most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] EMAPA:19029 FMA:9586 MA:0002738 SCTID:243953008 Wikipedia:Fibrous_pericardium fibrous portion of pericardium uberon pericardium fibrosum UBERON:0002359 fibrous pericardium FMA FMA WP Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]. FMA:9586 pericardium fibrosum Wikipedia:Fibrous_pericardium Membrane organ that surrounds the brain and the spinal cord. Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] meningeal Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx). Not consider part of the CNS/neuraxis in FMA BTO:0000144 CALOHA:TS-1177 EFO:0000867 EMAPA:32660 EV:0100312 FMA:9589 GAID:687 MA:0001113 MAT:0000113 MESH:D008578 NCIT:C12348 NLXANAT:090204 TAO:0001355 UMLS:C0025285 VHOG:0001295 Wikipedia:Meninx ZFA:0001355 layer of meninges meningeal layer meninx primitiva uberon UBERON:0002360 meninx https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg FMA Bgee:AN Membrane organ that surrounds the brain and the spinal cord. FMA:9589 Wikipedia:Meninx http://www.shsu.edu/~bio_mlt/Chap15.html Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] 2012-09-17 VHOG:0001295 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/meninges In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0001295 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ Not consider part of the CNS/neuraxis in FMA FMA https://github.com/obophenotype/uberon/issues/1261 UMLS:C0025285 ncithesaurus:Meninges meninx primitiva VHOG:0001295 The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]. BTO:0001635 EHDAA2:0004318 EHDAA:1367 EHDAA:1961 EHDAA:2001 EHDAA:2099 EHDAA:2685 EHDAA:2833 EHDAA:2867 EHDAA:3692 EHDAA:3710 EHDAA:6566 EHDAA:6583 EMAPA:32663 EV:0100315 FMA:9590 GAID:693 MA:0001116 MESH:D010841 NCIT:C33321 NLXANAT:090209 RETIRED_EHDAA2:0001464 SCTID:362305004 UMLS:C0031869 Wikipedia:Pia_mater neuronames:1463 pia mater of neuraxis pial membrane uberon pia UBERON:0002361 pia mater http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png check-aves ISBN:0073040584 The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. NLXANAT:090209 delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]. Wikipedia:Pia_mater UMLS:C0031869 ncithesaurus:Pia_Mater pial membrane NLXANAT:090209 pia NLXANAT:090209 A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space. BTO:0001636 CALOHA:TS-0052 EMAPA:32659 EV:0100314 FMA:9591 GAID:688 MA:0001114 MESH:D001099 NCIT:C32136 NLXANAT:090208 SCTID:362304000 UMLS:C1510935 Wikipedia:Arachnoid_mater neuronames:1464 arachnoid arachnoid mater of neuraxis arachnoid membrane uberon arachnoidea mater UBERON:0002362 arachnoid mater http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png ISBN:0073040584 A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space. ISBN:0471888893 Wikipedia:Arachnoid_mater ISBN:0471888893 UMLS:C1510935 ncithesaurus:Arachnoid_Membrane arachnoid membrane NLXANAT:090208 arachnoidea mater BTO:0001636 Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]. capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288 some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261] BTO:0001637 CALOHA:TS-2008 EMAPA:32664 EV:0100313 FMA:9592 GAID:691 MA:0001115 MESH:D004388 NCIT:C32488 NLXANAT:090206 SCTID:362301008 UMLS:C0013313 Wikipedia:Dura_mater neuronames:1462 dura mater of neuraxis pachymeninges uberon dura UBERON:0002363 dura mater http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg PMID:16496288 definitional Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. NLXANAT:090206 ISBN:0073040584 the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]. Wikipedia:Dura_mater UMLS:C0013313 ncithesaurus:Dura_Mater pachymeninges NLXANAT:090206 dura BTO:0001637 A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted]. The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG] The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint. EMAPA:19062 FMA:9595 GAID:870 MA:0000257 MESH:D014432 NCIT:C12502 SCTID:181180005 UMLS:C0041445 VHOG:0001146 Wikipedia:Tympanic_membrane XAO:0000212 Rivinus' membrane ear drum eardrum lateral wall of tympanic cavity membranous wall of tympanic cavity myrinx paries membranaceus cavi tympani uberon tympanum UBERON:0002364 tympanic membrane FMA MA cjm Wikipedia cjm A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted]. PMID:11237469 Wikipedia:Tympanic_membrane Wikipedia The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001146 VHOG http://bgee.unil.ch/ In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG] 2012-09-17 VHOG:0001146 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418 http://bgee.unil.ch/ most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint. PMID:11237469 UMLS:C0041445 ncithesaurus:Tympanic_Membrane paries membranaceus cavi tympani FMA:9595 FMA:TA tympanum Wikipedia:Tympanic_membrane A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas. Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 SCTID:115976003 UMLS:C0015282 Wikipedia:Exocrine_gland ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas. Wikipedia:Exocrine_gland UMLS:C0015282 ncithesaurus:Exocrine_Gland ducted gland AEO:0000097 glandula exocrina Wikipedia:Exocrine_gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. TODO - FMA treats the gland as part of the prostate - see also FMA:74119. prostatic BTO:0001129 CALOHA:TS-0828 EFO:0000858 EMAPA:19287 EV:0100104 FMA:9600 GAID:392 MA:0000404 MAT:0000078 MESH:D011467 MIAA:0000078 NCIT:C12410 SCTID:181422007 UMLS:C0033572 VHOG:0001261 Wikipedia:Prostate galen:ProstateGland male prostate prostate uberon prostata UBERON:0002367 prostate gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb Wikipedia The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. GO:0030850 Wikipedia:Prostate UMLS:C0033572 ncithesaurus:Prostate_Gland male prostate PMID:10668204 prostata Wikipedia:Prostate Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 SCTID:40818001 UMLS:C0014133 Wikipedia:Endocrine_gland ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine gland http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. Wikipedia:Endocrine_gland UMLS:C0014133 ncithesaurus:Endocrine_Gland ductless gland AEO:0000098 ductless gland Wikipedia:Ductless_gland glandulae endocrinae Wikipedia:Endocrine_gland Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. AAO:0010551 BTO:0000047 CALOHA:TS-0016 EFO:0000238 EMAPA:18426 EV:0100135 FMA:9604 GAID:446 MA:0000116 MAT:0000071 MESH:D000311 MIAA:0000071 NCIT:C12666 SCTID:181127006 UMLS:C0001625 VHOG:0001141 Wikipedia:Adrenal_gland XAO:0000164 galen:AdrenalGland glandula adrenalis glandula suprarenalis uberon adrenal adrenal capsule adrenal medulla cell atrabiliary capsule epinephric gland epinephros glandula suprarenalis interrenal gland suprarenal capsule suprarenal gland UBERON:0002369 adrenal gland http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg FMA-abduced-lr Wikipedia Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. BTO:0000047 Wikipedia:Adrenal_gland Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] 2012-06-20 AAO:0010551 AAO AAO:BJB All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 http://bgee.unil.ch/ UMLS:C0001625 ncithesaurus:Adrenal_Gland glandula adrenalis Wikipedia:Adrenal_gland glandula suprarenalis Wikipedia:Adrenal_gland adrenal BTO:0000047 adrenal capsule BTO:0000047 atrabiliary capsule BTO:0000047 epinephric gland Wikipedia:Adrenal_gland epinephros BTO:0000047 glandula suprarenalis BTO:0000047 interrenal gland GO:0030325 suprarenal capsule BTO:0000047 suprarenal gland Wikipedia:Adrenal_gland Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland. Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO] A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG] thymic AAO:0010548 BTO:0001374 CALOHA:TS-1043 EFO:0000860 EHDAA2:0002017 EHDAA:9119 EMAPA:18768 EV:0100138 FMA:9607 GAID:464 MA:0000142 MAT:0000080 MESH:D013950 MIAA:0000080 NCIT:C12433 SCTID:118507000 TAO:0001078 UMLS:C0040113 VHOG:0000253 Wikipedia:Thymus XAO:0000163 ZFA:0001078 thymus gland thymus organ uberon UBERON:0002370 thymus https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Thymus.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb https://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg EHDAA2 multiple sources - true thymus appears in jawed vertebrates ZFA Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. NLM:thymus Wikipedia:Thymus Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO] 2012-06-20 AAO:0010548 AAO AAO:BJB A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG] 2012-09-17 VHOG:0000253 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558 http://bgee.unil.ch/ UMLS:C0040113 ncithesaurus:Thymus_Gland The soft tissue that fills the cavities of bones. TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 NCIT:C12431 SCTID:421320006 UMLS:C0005953 VHOG:0001218 Wikipedia:Bone_marrow XAO:0000123 galen:BoneMarrow medulla ossea medulla ossium uberon medulla of bone medullary bone UBERON:0002371 bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg FMA MA The soft tissue that fills the cavities of bones. MGI:cwg MP:0002397 The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] 2012-09-17 VHOG:0001218 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) http://bgee.unil.ch/ UMLS:C0005953 ncithesaurus:Bone_Marrow medulla ossea BTO:0000141 FMA:9608 medulla ossium BTO:0000141 Wikipedia:Bone_marrow medulla of bone BTO:0000141 Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx. the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region BTO:0001387 CALOHA:TS-1053 EFO:0001401 EMAPA:35871 EV:0100052 FMA:9609 GAID:341 MA:0000143 MESH:D014066 NCIT:C12802 UMLS:C0836921 UMLS:C1519547 UMLS:C1519548 VHOG:0001139 Wikipedia:Tonsil neuronames:671 uberon Mandel UBERON:0002372 tonsil cjm Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx. MGI:cwg MP:0002380 UMLS:C0836921 ncithesaurus:Tonsil UMLS:C1519547 ncithesaurus:Tonsilar_Tissue UMLS:C1519548 ncithesaurus:Tonsillar_Lymphoid_Tissue Mandel BTO:0001387 Tonsils on the left and right sides at the back of the throat. one of the mucosa-associated lymphoid tissues (MALT), located at the entrance to the upper respiratory and gastrointestinal tracts to protect the body from the entry of exogenous material through mucosal sites[WP]. tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches tonsil BTO:0004714 EFO:0001977 EMAPA:35644 EV:0100393 FMA:9610 MA:0000775 MAT:0000291 MESH:D014066 MIAA:0000291 NCIT:C33250 SCTID:265787001 UMLS:C0040421 VHOG:0001140 Wikipedia:Palatine_tonsil faucial tonsil uberon tonsilla palatina UBERON:0002373 palatine tonsil https://upload.wikimedia.org/wikipedia/commons/f/f6/Illu_mouth.jpg the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract ISBN:1607950324 MP:anna PMID:20144910 Wikipedia Tonsils on the left and right sides at the back of the throat. one of the mucosa-associated lymphoid tissues (MALT), located at the entrance to the upper respiratory and gastrointestinal tracts to protect the body from the entry of exogenous material through mucosal sites[WP]. Wikipedia:Palatine_tonsil PMID:20144910 tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches ISBN:1607950324 MESH:D014066 https://github.com/biopragmatics/biomappings UMLS:C0040421 ncithesaurus:Palatine_Tonsil tonsilla palatina Wikipedia:Palatine_tonsil A bone that is part of the metacarpal skeleton. EFO:0003886 EMAPA:36158 FMA:9612 MA:0000302 NCIT:C12751 SCTID:181977005 SCTID:425761003 UMLS:C0025526 Wikipedia:Metacarpal_bone galen:Metacarpal metacarpal uberon UBERON:0002374 metacarpal bone https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg true A bone that is part of the metacarpal skeleton. Wikipedia:Metacarpal_bone https://orcid.org/0000-0002-6601-2165 UMLS:C0025526 ncithesaurus:Metacarpal_Bone Any skeletal muscle that is part of the head region. UBERON:0003899 AAO:0000107 BTO:0000021 EFO:0003524 EHDAA2:0000322 EMAPA:18172 FMA:9616 MA:0000578 SCTID:244718003 ZFA:0001652 cephalic muscle cephalic musculature head muscle head muscle organ muscle of head muscle organ of adult head muscle organ of head musculus caput adult head muscle organ uberon cranial muscle head muscles UBERON:0002376 defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships EHDAA2-abduced Any skeletal muscle that is part of the head region. http://orcid.org/0000-0002-6601-2165 cephalic muscle ZFA:0001652 head muscle MA:0000578 head muscle organ OBOL:automatic muscle of head FMA:9616 muscle organ of adult head OBOL:automatic muscle organ of head OBOL:automatic adult head muscle organ OBOL:automatic cranial muscle ZFA:0001652 Any muscle that is part of the cervical (neck) region. EMAPA:36050 FMA:9617 GAID:149 MA:0000587 MESH:D009334 NCIT:C33163 UMLS:C0027532 muscle organ of neck muscle organ of neck (volume) neck (volume) muscle organ neck muscle neck muscle organ uberon UBERON:0002377 muscle of neck prolog Any muscle that is part of the cervical (neck) region. http://orcid.org/0000-0002-6601-2165 UMLS:C0027532 ncithesaurus:Neck_Muscle muscle organ of neck OBOL:automatic muscle organ of neck (volume) OBOL:automatic neck (volume) muscle organ OBOL:automatic neck muscle organ OBOL:automatic Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. BTO:0001261 EMAPA:35103 FMA:9620 GAID:89 MA:0000520 MESH:D000009 NCIT:C32040 SCTID:361352008 UMLS:C0000739 Wikipedia:Abdominal_muscle abdomen muscle abdomen muscle organ abdominal muscle abdominal wall muscle muscle organ of abdomen uberon abdominal wall musculature UBERON:0002378 muscle of abdomen prolog Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. Wikipedia:Abdominal_muscle UMLS:C0000739 ncithesaurus:Abdominal_Muscle abdomen muscle organ OBOL:automatic muscle organ of abdomen OBOL:automatic abdominal wall musculature EMAPA:35103 A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted]. The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG] EMAPA:18183 FMA:9626 MA:0002398 NCIT:C33809 SCTID:181740005 UMLS:C0224361 VHOG:0000834 Wikipedia:Trapezius_muscle trapezius uberon musculus trapezius spinotrapezius UBERON:0002380 trapezius muscle http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12 dbpedia external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12 dbpedia posterior border of the lateral third of the clavicle acromion process and spine of scapula dbpedia posterior border of the lateral third of the clavicle acromion process and spine of scapula dbpedia dbpedia dbpedia A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted]. Wikipedia:Trapezius_muscle The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG] 2012-09-17 VHOG:0000834 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345 http://bgee.unil.ch/ UMLS:C0224361 ncithesaurus:Trapezius_Muscle musculus trapezius Wikipedia:Trapezius_muscle spinotrapezius Wikipedia:Trapezius_muscle Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 NCIT:C12374 SCTID:361919005 TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon Bindegewebe UBERON:0002384 connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. GO_REF:0000034 PSPUB:0000170 VSAO:0000017 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] 2012-06-20 AAO:0000098 AAO AAO:LAP Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] 2012-08-14 TAO:0001641 TAO TAO:wd Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] 2012-08-14 VSAO:0000017 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 MA also has set of connective tissues MA UMLS:C0009780 ncithesaurus:Connective_Tissue portion of connective tissue FMA:9640 Bindegewebe BTO:0000421 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 NCIT:C12435 SCTID:91727004 UMLS:C2328219 Wikipedia:Muscle_tissue galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon UBERON:0002385 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. GO:0060537 Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] 2012-06-20 AAO:0000306 AAO AAO:LAP UMLS:C2328219 ncithesaurus:Muscle_Tissue muscular tissue portion of muscle tissue FMA:9641 The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here BTO:0001447 CALOHA:TS-2205 EFO:0003053 EHDAA2:0000553 EHDAA:4172 EHDAA:6218 EMAPA:17417 FMA:9663 GAID:55 MA:0000034 MESH:D005542 NCIT:C32628 SCTID:362741001 UMLS:C0016536 VHOG:0000341 VSAO:0005058 Wikipedia:Forearm galen:Forearm antebrachial region antebrachium antibrachium arm middle limb segment arm zeugopod brachial region middle limb segment brachial region zeugopod forearm forelimb epipodium forelimb zeugopodium forelimb zygopod intermediate segment of free upper limb lower arm lower segment of arm middle limb segment of arm middle limb segment of brachial region middle limb segment of forelimb middle limb segment of proximal segment of free upper limb regio antebrachialis zeugopod of arm zeugopod of brachial region zeugopod of forelimb zeugopod of proximal segment of free upper limb wing zeugopod uberon antebrachium fore epipodium UBERON:0002386 forelimb zeugopod http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg https://upload.wikimedia.org/wikipedia/commons/5/50/Forearm_labeled.png MA The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. PHENOSCAPE:curators The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0000341 VHOG http://bgee.unil.ch/ Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000341 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ UMLS:C0016536 ncithesaurus:Forearm antebrachium VSAO:0005058 Wikipedia:Forearm arm middle limb segment OBOL:automatic arm zeugopod OBOL:automatic brachial region middle limb segment OBOL:automatic brachial region zeugopod OBOL:automatic lower arm MA:0000034 middle limb segment of arm OBOL:automatic middle limb segment of brachial region OBOL:automatic middle limb segment of forelimb https://orcid.org/0000-0002-6601-2165 middle limb segment of proximal segment of free upper limb OBOL:automatic regio antebrachialis FMA:9663 FMA:TA zeugopod of brachial region OBOL:automatic zeugopod of proximal segment of free upper limb OBOL:automatic wing zeugopod NCBITaxon:8782 OBOL:automatic antebrachium Wikipedia:Forearm Distal portion of the hind limb, including tarsal region, metatarsal region and digits. pedal BTO:0000476 CALOHA:TS-0377 EFO:0003065 EHDAA2:0000546 EMAPA:17459 FMA:9664 GAID:40 MA:0000044 MESH:D005528 NCIT:C32622 SCTID:302545001 UMLS:C0016504 VHOG:0000350 Wikipedia:Pes_(anatomy) galen:Foot foot hindlimb autopod hindlimb autopodium hindlimb distal free limb segment pes terminal segment of free lower limb hind foot hind paw hind-paw hindfeet hindfoot hindfoot of quadruped hindpaw uberon hind limb autopodium UBERON:0002387 pes http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg Distal portion of the hind limb, including tarsal region, metatarsal region and digits. Wikipedia:Foot Wikipedia:Pes_(anatomy) UMLS:C0016504 ncithesaurus:Foot foot MA:0000044 hindlimb autopod OBOL:automatic hindlimb autopodium OBOL:automatic hindlimb distal free limb segment OBOL:automatic pes https://orcid.org/0000-0002-6601-2165 hind paw EMAPA:17428 OBOL:automatic hind-paw EMAPA:17428 hindfeet hindpaw MA:0000044 hind limb autopodium VHOG:0000350 A digit that is part of a manus (hand). One of the fingers of the manus.[AAO] UBERON:0000028 AAO:0000857 BTO:0004669 EHDAA2:0000404 EMAPA:32642 FMA:9666 GAID:57 MA:0000041 MESH:D005385 NCIT:C32608 NLXANAT:20090602 SCTID:283992002 UMLS:C0016129 Wikipedia:Finger XAO:0003036 galen:Finger digit of hand digit of manus digitus manus finger fore digit forelimb digit hand digit manual digit (phalangeal portion) plus soft tissue uberon UBERON:0002389 manual digit PHENOSCAPE:ni A digit that is part of a manus (hand). http://orcid.org/0000-0002-6601-2165 One of the fingers of the manus.[AAO] 2012-06-20 AAO:0000857 AAO AAO:LAP UMLS:C0016129 ncithesaurus:Finger digit of hand FMA:9666 finger FMA:9666 fore digit AAO:0000857 XAO:0003036 hand digit MA:0000041 manual digit (phalangeal portion) plus soft tissue http://orcid.org/0000-0002-6601-2165 Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 SCTID:362587009 TAO:0005023 UMLS:C0018957 VHOG:0001624 Wikipedia:Haematopoiesis XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 hematopoietic system FMA definitional Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis Anatomical system that consists of the blood and blood forming tissues.[AAO] 2012-06-20 AAO:0011002 AAO AAO:EJS Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] 2012-09-17 VHOG:0001624 VHOG DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) http://bgee.unil.ch/ In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes WP UMLS:C0018957 ncithesaurus:Hematopoietic_System Blutbildungssystem BTO:0000570 Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. BTO:0000855 CALOHA:TS-0580 EFO:0000871 ENVO:02000041 EV:0100049 FMA:9671 GAID:1186 MA:0002520 MAT:0000055 MESH:D008196 MIAA:0000055 NCIT:C13252 UMLS:C0024202 VHOG:0001590 Wikipedia:Lymph ZFA:0005658 galen:Lymph uberon lympha UBERON:0002391 lymph http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. Wikipedia:Lymph UMLS:C0024202 ncithesaurus:Lymph lympha Wikipedia:Lymph The paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity. The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG] the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue nasolacrimal duct - posterior naris AAO:0000643 EHDAA2:0001237 EHDAA:7849 EHDAA:9094 EMAPA:17853 FMA:9703 GAID:902 MA:0001299 MESH:D009301 NCIT:C33161 SCTID:280643009 UMLS:C0027437 VHOG:0000664 Wikipedia:Nasolacrimal_duct uberon d. nasolacrimalis lacrimal duct tear duct UBERON:0002392 nasolacrimal duct http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png The paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity. ISBN:0-683-40008-8 MP:0008969 The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG] 2012-09-17 VHOG:0000664 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256 http://bgee.unil.ch/ nasolacrimal duct - posterior naris VHOG:0000664 UMLS:C0027437 ncithesaurus:Nasolacrimal_Duct d. nasolacrimalis Wikipedia:Nasolacrimal_duct lacrimal duct PMID:30285382 tear duct Wikipedia:Nasolacrimal_duct Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. A duct that carries bile from the liver to the intestine. Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA AAO:0011019 BTO:0000122 CALOHA:TS-0075 EHDAA2:0000741 EMAPA:35171 EV:0100091 FMA:9706 GAID:280 MA:0000354 MESH:D001652 NCIT:C12376 SCTID:276157007 TAO:0001100 UMLS:C0005400 VHOG:0000212 Wikipedia:Bile_duct XAO:0000134 ZFA:0001100 uberon bile tube biliary duct gall duct hepatic duct UBERON:0002394 bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png EMAPA MA XAO Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. Wikipedia:Bile_duct http://orcid.org/0000-0002-6601-2165 A duct that carries bile from the liver to the intestine. ZFA:0001100, ZFA:curator Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] 2012-09-17 VHOG:0000212 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/bile+duct (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] 2012-09-17 VHOG:0000212 VHOG DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) http://bgee.unil.ch/ we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA ZFA UMLS:C0005400 ncithesaurus:Bile_Duct biliary duct FMA:9706 gall duct BTO:0000122 hepatic duct ZFA:0001100 The triangular flat bone of the nasal septum. Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO] Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO] relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO] relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO] In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP] The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO] AAO:0000633 FMA:9710 MA:0001496 MESH:D055172 NCIT:C33888 SCTID:272678009 TAO:0000308 UMLS:C0242403 Wikipedia:Vomer ZFA:0000308 vomer bone uberon prevomer UBERON:0002396 vomer http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg FMA The triangular flat bone of the nasal septum. ISBN:0-683-40008-8 MP:0000098 Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO] 2012-08-14 TAO:0000308 TAO ZFIN:curator Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO] 2012-06-20 AAO:0000633 AAO AAO:LAP relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO] 2012-08-14 TAO:0000308 TAO relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO] 2012-08-14 TAO:0000308 TAO In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP] Wikipedia:Vomer#In_other_animals The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO] 2012-09-06 TAO:0000308 TAO Curator MESH:D055172 https://github.com/biopragmatics/biomappings UMLS:C0242403 ncithesaurus:Vomer prevomer TAO:0000308 Distal segment of the fore limb, including carpal region, metacarpal region and digits. like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton manual AAO:0010803 BTO:0004668 CALOHA:TS-2213 EHDAA2:0000728 EMAPA:17428 FMA:9712 GAID:56 MA:0000037 MESH:D006225 NCIT:C32712 NLXANAT:20090603 SCTID:302539009 UMLS:C0018563 VHOG:0000344 Wikipedia:Manus_(anatomy) galen:Hand forelimb autopod forelimb autopodium hand hand region terminal segment of free upper limb fore foot fore paw fore-paw forefeet forefoot forefoot of quadruped forepaw uberon UBERON:0002398 manus http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg Distal segment of the fore limb, including carpal region, metacarpal region and digits. Wikipedia:Hand Wikipedia:Manus_(anatomy) UMLS:C0018563 ncithesaurus:Hand forelimb autopod OBOL:automatic forelimb autopodium OBOL:automatic hand MA:0000037 hand region EHDAA2:0000728 fore foot fore paw EMAPA:17428 OBOL:automatic fore-paw EMAPA:17428 forefeet forefoot forepaw MA:0000037 The outer serous membrane of the pulmonary pleural. EMAPA:16776 FMA:9733 MA:0002488 NCIT:C33273 SCTID:361998003 UMLS:C0225777 VHOG:0001495 Wikipedia:Parietal_pleura uberon pleura parietalis UBERON:0002400 the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax parietal pleura The outer serous membrane of the pulmonary pleural. UBERON:cjm Wikipedia:Pulmonary_pleurae UMLS:C0225777 ncithesaurus:Parietal_Pleura pleura parietalis Wikipedia:Parietal_pleura The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. FMA treats this as part of the lungs EHDAA2:0002205 EMAPA:16777 FMA:9734 MA:0002489 NCIT:C33881 SCTID:361997008 UMLS:C0225776 VHOG:0001496 pleura pulmonalis pleura visceralis pleura visceralis (pulmonalis) pulmonary visceral pleura uberon lung mesothelium lung pleura pulmonary pleura UBERON:0002401 visceral pleura FMA The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. UBERON:cjm Wikipedia:Pulmonary_pleurae Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. Wikipedia:Visceral_pleura FMA treats this as part of the lungs FMA UMLS:C0225776 ncithesaurus:Visceral_Pleura pleura pulmonalis FMA:9734 FMA:TA pleura visceralis Wikipedia:Visceral_pleura lung mesothelium EHDAA2:0002205 pulmonary pleura FMA:9734 The fluid-filled cavity that lies between the visceral and parietal pleurae. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 BTO:0004422 EHDAA2:0001475 EMAPA:16773 EMAPA:16774 FMA:9740 GAID:95 MA:0000055 MESH:D035422 NCIT:C12840 SCTID:361999006 UMLS:C0178802 VHOG:0000581 Wikipedia:Pleural_cavity cavitas pleuralis uberon cavitum pleuralae cavitum pleurale UBERON:0002402 pleural cavity http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png Wikipedia The fluid-filled cavity that lies between the visceral and parietal pleurae. Wikipedia:Pleural_cavity https://github.com/obophenotype/uberon/issues/86 In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000581 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 EHDAA2 UMLS:C0178802 ncithesaurus:Pleural_Cavity cavitas pleuralis Wikipedia:Pleural_cavity cavitum pleuralae Wikipedia:Pleural_cavity cavitum pleurale Wikipedia:Pleural_cavity Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 FMA:9825 GAID:328 MA:0002711 MESH:D007107 NCIT:C12735 SCTID:362590003 TAO:0001159 UMLS:C0020962 VHOG:0001247 Wikipedia:Immune_system XAO:0003152 ZFA:0001159 uberon UBERON:0002405 immune system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] 2012-09-17 VHOG:0001247 VHOG PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) http://bgee.unil.ch/ UMLS:C0020962 ncithesaurus:Immune_System A double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 SCTID:361326002 TAO:0000054 uberon pericardium UBERON:0002406 pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png FMA A double-walled sac containing the heart and the roots of the great vessels. Wikipedia:Pericardium https://github.com/obophenotype/uberon/issues/86 The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Peritoneum that surrounds the heart.[AAO] pericardial In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium AAO:0010817 BSA:0000090 BTO:0000717 CALOHA:TS-0761 EFO:0000820 EHDAA:5376 EMAPA:16133 EV:0100023 FMA:9869 GAID:569 MA:0000099 MAT:0000454 MESH:D010496 NCIT:C13005 RETIRED_EHDAA2:0001443 SCTID:181295003 TAO:0000054 UMLS:C0031050 VHOG:0001280 Wikipedia:Pericardium XAO:0004182 ZFA:0000054 galen:Pericardium uberon UBERON:0002407 pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png MA The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Wikipedia:Pericardium http://orcid.org/0000-0002-6601-2165 Peritoneum that surrounds the heart.[AAO] 2012-06-20 AAO:0010817 AAO AAO:JMG In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity FMA this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) ZFA we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium FMA UMLS:C0031050 ncithesaurus:Pericardium Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. EHDAA:3422 EHDAA:5378 EMAPA:19031 FMA:9870 MA:0000483 NCIT:C94500 SCTID:243956000 UMLS:C0225969 VHOG:0000537 Wikipedia:Parietal_pericardium lamina parietalis (pericardii serosum) lamina parietalis pericardii parietal layer of serous pericardium parietal pericardium uberon pericardial sac UBERON:0002408 parietal serous pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. http://orcid.org/0000-0002-6601-2165 UMLS:C0225969 ncithesaurus:Parietal_Pericardium lamina parietalis pericardii FMA:9870 FMA:TA parietal pericardium VHOG:0000537 pericardial sac DOI:10.5962/bhl.title.1013 Transudate contained in the pericardial cavity.[FMA]. BTO:0001016 FMA:9887 MA:0002530 MESH:D000069236 Wikipedia:Pericardial_fluid uberon UBERON:0002409 pericardial fluid FMA Transudate contained in the pericardial cavity.[FMA]. FMA:9887 Wikipedia:Pericardial_fluid MESH:D000069236 https://github.com/biopragmatics/biomappings The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib AAO:0000033 BIRNLEX:1123 BTO:0002507 CALOHA:TS-2001 EHDA:10095 EHDAA2:0000158 EHDAA:3767 EMAPA:16984 FMA:65553 GAID:706 IDOMAL:0002126 MA:0000219 MESH:D001341 NCIT:C12673 SCTID:362481007 TAO:0001574 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 Wikipedia:Autonomic_nervous_system ZFA:0001574 neuronames:2054 autonomic division of peripheral nervous system autonomic part of peripheral nervous system divisio autonomica systematis nervosi peripherici pars autonomica systematis nervosi peripherici peripheral autonomic nervous system visceral nervous system uberon ANS divisio autonomica systematis nervosi peripherici UBERON:0002410 autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm EMAPA MA NIFSTD ZFA-modified-from-isa The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. GO:0048483 Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000396 VHOG http://bgee.unil.ch/ Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] 2012-06-20 AAO:0000033 AAO AAO:BJB From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] 2012-09-17 VHOG:0000396 VHOG DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000) http://bgee.unil.ch/ FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA IDOMAL:0002126 https://github.com/biopragmatics/biomappings UMLS:C0004388 BIRNLEX:1123 ncithesaurus:Autonomic_Nervous_System UMLS:C1305381 BIRNLEX:1123 autonomic division of peripheral nervous system FMA:65553 autonomic part of peripheral nervous system FMA:65553 divisio autonomica systematis nervosi peripherici FMA:TA pars autonomica systematis nervosi peripherici FMA:TA peripheral autonomic nervous system FMA:65553 ANS divisio autonomica systematis nervosi peripherici Wikipedia:Autonomic_nervous_system The small, erectile body located at the anterior end of the vulva. clitoral BTO:0002020 EHDAA2:0000255 EHDAA:9360 EMAPA:30819 FMA:9909 GAID:385 MA:0000382 MESH:D002987 NCIT:C12308 SCTID:181442003 UMLS:C0008984 VHOG:0000700 Wikipedia:Clitoris galen:Clitoris uberon UBERON:0002411 clitoris http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg Wikipedia MA Wikipedia EHDAA2 Wikipedia The small, erectile body located at the anterior end of the vulva. ISBN:0-683-40008-8 MP:0003127 UMLS:C0008984 ncithesaurus:Clitoris The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. Consider changing name to make distinction from inferred superclass 'vertebral element' clear we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] AAO:0000691 BTO:0006196 CALOHA:TS-2352 EFO:0001371 EMAPA:32740 FMA:9914 MA:0000309 NCIT:C12933 SCTID:181817002 TAO:0001189 UMLS:C0549207 Wikipedia:Vertebra XAO:0004019 ZFA:0001189 galen:Vertebra vertebra bone vertebrae uberon UBERON:0002412 vertebra FMA The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 Wikipedia Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] 2012-08-14 TAO:0001189 TAO ZFIN:curator Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] 2012-06-20 AAO:0000691 AAO AAO:Pugener_and_Maglia_2008 BTO:0006196 https://github.com/biopragmatics/biomappings UMLS:C0549207 ncithesaurus:Vertebra vertebrae PHENOSCAPE:ad A vertebra that is located in the cervical region of the vertebral column. In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery. EMAPA:17674 FMA:9915 GAID:235 MA:0000311 MESH:D002574 NCIT:C12693 SCTID:181820005 Wikipedia:Cervical_vertebrae XAO:0003076 galen:CervicalVertebra cervical vertebrae uberon vertebrae cervicales UBERON:0002413 cervical vertebra http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg true A vertebra that is located in the cervical region of the vertebral column. http://orcid.org/0000-0002-6601-2165 cervical vertebrae vertebrae cervicales Wikipedia:Cervical_vertebrae Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body. Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J CALOHA:TS-2364 EMAPA:18007 FMA:9921 GAID:240 MA:0000312 MESH:D008159 NCIT:C12744 SCTID:181822002 UMLS:C0024091 Wikipedia:Lumbar_vertebrae galen:LumbarVertebra uberon UBERON:0002414 lumbar vertebra http://upload.wikimedia.org/wikipedia/commons/c/c8/Gray93.png Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body. Wikipedia:Lumbar_vertebrae Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J PMCID:PMC2700063 UMLS:C0024091 ncithesaurus:Lumbar_Vertebra An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin AEO:0000109 BILA:0000117 BTO:0001348 EFO:0000963 EHDAA:9198 GAID:1245 MAT:0000094 MESH:D013623 MIAA:0000094 WBbt:0005741 Wikipedia:Tail caudal subdivision uberon UBERON:0002415 tail An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. AEO:0000109 Wikipedia:Tail caudal subdivision https://orcid.org/0000-0002-6601-2165 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 SCTID:361692004 TADS:0000108 UMLS:C0037267 VHOG:0000403 Wikipedia:Integumentary_system XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. CARO:0002001 http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/29 (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] 2012-09-17 VHOG:0000403 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) http://bgee.unil.ch/ FBbt:00004969 UMLS:C0037267 ncithesaurus:Integumentary_System integumentary system FMA:72979 dermal system MIAA:0000033 integumentum commune Wikipedia:Integumentary_system organism surface EHDAA2:0003154 surface BILA:0000118 The abdominal segment of the torso. EMAPA:35104 FMA:259211 MA:0000021 SCTID:362875007 Wikipedia:Lumbar uberon abdomen/pelvis/perineum lower body lower trunk lumbar region UBERON:0002417 abdominal segment of trunk FMA The abdominal segment of the torso. Wikipedia:Lumbar abdomen/pelvis/perineum MA:0000021 lower body MA:0000021 lower trunk FMA:259211 lumbar region https://orcid.org/0000-0002-6601-2165 Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] AAO:0000060 AEO:0000087 BTO:0000206 EFO:0000949 EHDAA2:0003087 EMAPA:32730 EV:0100141 FMA:37377 GAID:99 MA:0000104 MAT:0000189 MESH:D002356 MIAA:0000189 NCIT:C12373 NCIT:C32268 SCTID:309312004 TAO:0001501 UMLS:C0007301 VHOG:0001207 VSAO:0000040 Wikipedia:Cartilage XAO:0000170 ZFA:0005622 galen:Cartilage cartilage tissue cartilaginous tissue chondrogenic tissue uberon cartilage cartilages portion of cartilage tissue UBERON:0002418 Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] cartilage tissue http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg https://github.com/obophenotype/uberon/issues/117 Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000040 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/37 https://sourceforge.net/p/obo/vertebrate-skeletal-anatomy-vsao-term-requests/5 A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] 2012-06-20 AAO:0000060 AAO AAO:LAP Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] 2012-08-14 TAO:0001501 TAO ZFIN:curator Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] 2012-08-14 VSAO:0000040 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000060 AAO Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] 2012-09-17 VHOG:0001207 VHOG DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012) http://bgee.unil.ch/ UMLS:C0007301 ncithesaurus:Cartilage cartilage tissue FMA:37377 chondrogenic tissue VSAO:0000040 cartilages VHOG:0001207 portion of cartilage tissue FMA:37377 A gland that is part of a skin of body [Automatically generated definition]. check FMA, use plural for now as general class not there EMAPA:35774 FMA:71878 MA:0000146 SCTID:110485007 glandulae cutis uberon set of skin glands skin glands skin glands set UBERON:0002419 skin gland A gland that is part of a skin of body [Automatically generated definition]. OBOL:automatic glandulae cutis FMA:71878 FMA:TA set of skin glands FMA:71878 skin glands skin glands set Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures. Fluid-filled brain cavity. Kimmel et al, 1995.[TAO] Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO] The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]. The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] AAO:0011043 BAMS:4V BAMS:V4 BIRNLEX:1256 BM:Pons-4V BTO:0003426 CALOHA:TS-2015 DHBA:10669 DHBA:12805 DMBA:126651782 EHDAA2:0000100 EHDAA:896 EMAPA:16917 EV:0100310 FMA:78469 GAID:610 HBA:9421 MA:0000196 MBA:145 MESH:D020546 NCIT:C12828 SCTID:180932000 TAO:0000110 UMLS:C0149556 VHOG:0000006 Wikipedia:Fourth_ventricle XAO:0003099 ZFA:0000110 neuronames:621 ventricle IV rhombencephalic vesicle uberon 4th ventricle IVth ventricle fourth ventricle proper hindbrain ventricle rhombencephalic ventricle ventricle of hindbrain ventricle of rhombencephalon ventriculus quartus UBERON:0002422 fourth ventricle http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb EHDAA2 Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures. BIRNLEX:1256 Fluid-filled brain cavity. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000110 TAO ZFIN:curator Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO] 2012-06-20 AAO:0011043 AAO UBERON:0002422 The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]. GO:0021592 The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000006 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ UMLS:C0149556 ncithesaurus:Fourth_Ventricle_of_the_Brain ventricle IV ZFA:0000110 rhombencephalic vesicle ZFA:0000110 4th ventricle MA:0000196 IVth ventricle VHOG:0000006 fourth ventricle proper BAMS:V4 hindbrain ventricle VHOG:0000006 rhombencephalic ventricle VHOG:0000006 ventricle of hindbrain BTO:0003426 ventricle of rhombencephalon BTO:0003426 ventriculus quartus Wikipedia:Fourth_ventricle The part of the digestive system that contains the liver and the biliary system. System responsible for the production and movement of bile[ZFIN:curator]. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008] AAO:0011056 CALOHA:TS-1308 EFO:0000800 EHDAA2:0000998 EHDAA:2189 EMAPA:16840 EV:0100088 MA:0000324 MAT:0000024 MIAA:0000024 NCIT:C43612 TAO:0000036 UMLS:C1711359 VHOG:0000294 Wikipedia:Hepatobiliary_system XAO:0000132 ZFA:0000036 hepaticobiliary system liver and biliary system uberon liver/biliary system UBERON:0002423 hepatobiliary system The part of the digestive system that contains the liver and the biliary system. http://orcid.org/0000-0002-6601-2165 System responsible for the production and movement of bile[ZFIN:curator]. ZFIN:curator UMLS:C1711359 ncithesaurus:Hepatobiliary_System hepaticobiliary system GO:0061008 An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme AAO:0010357 BTO:0001775 CALOHA:TS-0715 EHDAA2:0001325 EHDAA:2187 EMAPA:16839 EMAPA:26942 FMA:265152 MA:0000344 NCIT:C49595 TAO:0000816 UMLS:C1709332 VHOG:0000187 XAO:0003201 ZFA:0000816 epithelium of mucosa of mouth epithelium of oral mucosa uberon UBERON:0002424 oral epithelium AAO-modified An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues. https://orcid.org/0000-0002-6601-2165 The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. ZFA:0000816 the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme PMID:16488870 UMLS:C1709332 ncithesaurus:Oral_Cavity_Epithelium epithelium of mucosa of mouth FMA:265152 epithelium of oral mucosa FMA:265152 Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. EMAPA:16589 EMAPA:19032 FMA:84882 MA:0000484 SCTID:243955001 VHOG:0000538 Wikipedia:Visceral_pericardium lamina visceralis pericardii serosi serous visceral pericardium visceral lamina of serous pericardium visceral layer of serous pericardium visceral pericardium uberon epicardium pericardium visceral mesothelium UBERON:0002425 visceral serous pericardium cjm FMA Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. Wikipedia:Visceral_pericardium lamina visceralis pericardii serosi Wikipedia:Epicardium visceral pericardium VHOG:0000538 epicardium MA:0000484 pericardium visceral mesothelium EMAPA:16589 Any muscle organ that is part of a chest [Automatically generated definition]. BTO:0000508 CALOHA:TS-1037 EMAPA:17747 EMAPA:17748 FMA:9619 MA:0000548 anterior thoracic region muscle organ anterolateral part of thorax muscle organ chest muscle organ front of thorax muscle organ muscle of thorax muscle organ of anterior thoracic region muscle organ of anterolateral part of thorax muscle organ of chest muscle organ of front of thorax musculus thoracicus thoracic muscle uberon UBERON:0002426 chest muscle Any muscle organ that is part of a chest [Automatically generated definition]. OBOL:automatic anterior thoracic region muscle organ OBOL:automatic anterolateral part of thorax muscle organ OBOL:automatic chest muscle organ OBOL:automatic front of thorax muscle organ OBOL:automatic muscle of thorax FMA:9619 muscle organ of anterior thoracic region OBOL:automatic muscle organ of anterolateral part of thorax OBOL:automatic muscle organ of chest OBOL:automatic muscle organ of front of thorax OBOL:automatic A zone of skin that is part of an arm [Automatically generated definition]. EMAPA:37350 MA:0000596 NCIT:C52754 UMLS:C0222204 skin of arm uberon brachial region skin UBERON:0002427 arm skin A zone of skin that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37350 MA:th UMLS:C0222204 ncithesaurus:Arm_Skin skin of arm OBOL:automatic brachial region skin OBOL:automatic A bone that is part of a limb [Automatically generated definition]. the formal definition is very inclusive, and includes sesamoids NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle EFO:0000945 MAT:0000151 MIAA:0000151 NCIT:C32223 SCTID:304149004 UMLS:C0582791 bone of extremity bone of limb free limb bone uberon UBERON:0002428 limb bone A bone that is part of a limb [Automatically generated definition]. OBOL:automatic NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle NCIT UMLS:C0582791 ncithesaurus:Bone_of_the_Extremity bone of limb OBOL:automatic free limb bone UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. FMA:61213 MA:0000736 NCIT:C32298 SCTID:181757009 UMLS:C0588054 Wikipedia:Cervical_lymph_nodes lymph node of neck uberon UBERON:0002429 cervical lymph node http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. Wikipedia:Cervical_lymph_node UMLS:C0588054 ncithesaurus:Cervical_Lymph_Node EMAPA:37719 FMA:65265 MA:0001175 right axillary neural trunk trunk of right axillary nerve uberon circumflex nerve trunk UBERON:0002442 axillary nerve trunk EMAPA:37719 MA:th trunk of right axillary nerve FMA:65265 circumflex nerve trunk MA:0001175 A blood vessel that is part of a choroid [Automatically generated definition]. EMAPA:17828 FMA:76550 MA:0001237 blood vessel of choroid blood vessel of choroid coat blood vessel of choroidea blood vessel of posterior uvea choroid blood vessel choroid blood vessels choroid blood vessels set choroid coat blood vessel choroidea blood vessel posterior uvea blood vessel vasa sanguinea choroideae uberon set of choroid blood vessels UBERON:0002443 cannot find singular in FMA, using Set class choroidal blood vessel A blood vessel that is part of a choroid [Automatically generated definition]. OBOL:automatic blood vessel of choroid OBOL:automatic blood vessel of choroid coat OBOL:automatic blood vessel of choroidea OBOL:automatic blood vessel of posterior uvea OBOL:automatic choroid blood vessel OBOL:automatic choroid coat blood vessel OBOL:automatic choroidea blood vessel OBOL:automatic posterior uvea blood vessel OBOL:automatic vasa sanguinea choroideae FMA:76550 FMA:TA set of choroid blood vessels FMA:76550 A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad]. patellar EMAPA:35668 FMA:24485 GAID:203 MA:0001374 MESH:D010329 NCIT:C33282 SCTID:182083008 UMLS:C0030647 Wikipedia:Patella galen:Patella uberon knee bone knee cap patella UBERON:0002446 The patella, also known as the knee cap or kneepan, is the largest sesamoid bone in the human body. The primary functional role of the patella is knee extension. The patella has convergently evolved in placental mammals and birds; marsupials have only rudimentary, non-ossified patellae. In more primitive tetrapods, including living amphibians and reptiles, the muscle tendons from the upper leg are attached directly to the tibia, and the patella is not present. See also: fabella. patella https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg FMA A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad]. PHENOSCAPE:ad https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=3470151&group_id=76834 UMLS:C0030647 ncithesaurus:Patella knee bone FMA:24485 knee cap Wikipedia:Patella patella Wikipedia:Patella The maternal uterine-derived portion of the placenta. TODO - check mp syn formed under the influence of progesterone and forms highly-characteristic cells. [Wikipedia:Decidua] BTO:0001360 CALOHA:TS-0193 EMAPA:35269 FMA:85538 GAID:378 MA:0001722 MAT:0000290 MESH:D003656 MIAA:0000290 NCIT:C32425 SCTID:362842004 UMLS:C0011106 Wikipedia:Decidua decidous membrane uberon decidua basalis endometrium extraembryonic part of placenta extraembryonic placenta maternal decidual layer maternal part of placenta maternal placenta placenta maternal decidual layer uterine decidua UBERON:0002450 decidua http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png FMA maternal MA The maternal uterine-derived portion of the placenta. MP:0004256 PMID:11433360 UMLS:C0011106 ncithesaurus:Decidua decidous membrane FMA:85538 extraembryonic part of placenta http://orcid.org/0000-0002-6601-2165 extraembryonic placenta http://orcid.org/0000-0002-6601-2165 maternal decidual layer MP:0004256 maternal part of placenta http://orcid.org/0000-0002-6601-2165 maternal placenta EMAPA:35269 GOC:dph uterine decidua BTO:0001360 The mucous secreting gland associated with the mucuous membrane lining the uterus. simple or branched tubular BTO:0003433 BTO:0004518 EMAPA:29919 MA:0001726 NCIT:C33842 SCTID:361377009 UMLS:C1183035 Wikipedia:Uterine_glands endometrial gland endometrial mucuous gland endometrium gland glandulae uterinae uterine gland uberon glandulae uterinae UBERON:0002451 endometrial gland http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png MP Wikipedia:Tubular_gland The mucous secreting gland associated with the mucuous membrane lining the uterus. Wikipedia:Uterine_glands UMLS:C1183035 ncithesaurus:Uterine_Gland endometrial gland BTO:0003433 glandulae uterinae FMA:71647 FMA:TA glandulae uterinae Wikipedia:Uterine_glands An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]. MA has both mammary and thoracic EHDAA2:0000880 EHDAA:8585 EMAPA:18617 FMA:3960 MA:0001982 MA:0001984 NCIT:C52941 SCTID:244239009 UMLS:C0226276 Wikipedia:Internal_thoracic_artery internal mammary artery internal thoracic mammary artery uberon arteria mammaria interna arteria thoracica interna mammary artery UBERON:0002456 internal thoracic artery http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]. Wikipedia:Internal_thoracic_artery MA has both mammary and thoracic MA UMLS:C0226276 ncithesaurus:Internal_Mammary_Artery internal mammary artery MA:0001982 arteria mammaria interna Wikipedia:Internal_thoracic_artery arteria thoracica interna Wikipedia:Internal_thoracic_artery mammary artery EMAPA:18617 The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries. Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]. Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG] UBERON:0006001 EHDAA2:0000882 EHDAA:4340 EMAPA:17616 MA:0001985 SCTID:360401001 TAO:0001061 VHOG:0000225 XAO:0004165 ZFA:0001061 intersegmental artery uberon intersegmental arteries UBERON:0002457 intersomitic artery The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries. MP:0010662 Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]. ZFA:0001061 Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG] 2012-09-17 VHOG:0000225 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612 http://bgee.unil.ch/ intersegmental artery ZFA:0001061 intersegmental arteries ZFA:0001061 Arteries that supply the spinal cord. EHDAA2:0001890 EHDAA:4355 EMAPA:18241 MA:0002043 NCIT:C33587 SCTID:244228006 TAO:0000682 UMLS:C0447043 Wikipedia:Spinal_artery ZFA:0000682 spinal arteries uberon UBERON:0002458 spinal artery Arteries that supply the spinal cord. Wikipedia:Spinal_artery https://orcid.org/0000-0002-6601-2165 UMLS:C0447043 ncithesaurus:Spinal_Artery spinal arteries ZFA:0000682 A tributary of the iliac vein that drains the urinary bladder. EMAPA:37205 MA:0002263 SCTID:12683000 Wikipedia:Vesical_veins venae vesicales vesical veins vesical veins set uberon UBERON:0002460 vesical vein http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png A tributary of the iliac vein that drains the urinary bladder. UBERON:cjm Wikipedia:Vesical_veins EMAPA:37205 MA:th venae vesicales FMA:70911 FMA:TA vesical veins Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913]. UBERON:0001147 BTO:0000927 EHDAA:4675 EMAPA:16986 FMA:14383 FMA:5913 MA:0000229 MA:0002408 SCTID:281248001 peripheral nerve trunk trunk of nerve trunk of peripheral nerve uberon UBERON:0002464 nerve trunk Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913]. FMA:5913 peripheral nerve trunk EMAPA:16986 The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] lymphoid The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013] The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013] We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. UBERON:0002096 EHDAA2:0001043 EHDAA:8677 EMAPA:37664 FMA:74594 GAID:931 MA:0002435 MAT:0000197 MIAA:0000197 NCIT:C12746 SCTID:362589007 TAO:0000385 UMLS:C0024235 VHOG:0000842 Wikipedia:Lymphoid_system XAO:0003199 ZFA:0000385 lymphatic system uberon lymphatic circulatory system lymphatic drainage system systema lymphoideum UBERON:0002465 lymphoid system http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg FMA The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Wikipedia:Lymphoid_system Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] 2012-06-20 AAO:0010522 AAO AAO:BJB Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] 2012-09-17 VHOG:0000842 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627 http://bgee.unil.ch/ We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. https://github.com/obophenotype/mouse-anatomy-ontology/issues/51 EMAPA:37664 MA:th UMLS:C0024235 ncithesaurus:Lymphatic_System lymphatic system ZFA:0000385 lymphatic circulatory system https://orcid.org/0000-0002-6601-2165 lymphatic drainage system https://orcid.org/0000-0002-6601-2165 systema lymphoideum Wikipedia:Lymphoid_system Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. BTO:0000644 FMA:62974 GAID:1162 MA:0002515 MESH:D007419 NCIT:C32875 UMLS:C0021849 Wikipedia:Succus_entericus intestinal secretion succus entericus uberon intestinal juice UBERON:0002466 intestine secretion Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. Wikipedia:Succus_entericus UMLS:C0021849 ncithesaurus:Intestinal_Secretion intestinal secretion FMA:62974 succus entericus Wikipedia:Succus_entericus intestinal juice BTO:0000644 A mucosa that is part of a esophagus [Automatically generated definition]. UBERON:0003345 BTO:0002859 EMAPA:26981 FMA:62996 MA:0002680 MESH:D000071041 NCIT:C32538 SCTID:362127004 UMLS:C0227176 esophageal mucosa esophageal mucous membrane esophagus mucosa esophagus mucous membrane lamina muscularis mucosae oesophageae mucosa of esophagus mucosa of oesophagus mucous membrane of esophagus mucous membrane of oesophagus oesophageal mucosa oesophagus mucosa oesophagus mucous membrane tunica mucosa esophagi tunica mucosa oesophageae tunica mucosa oesophagi uberon muscularis mucosae of oesophagus tunica mucosa oesophagi UBERON:0002469 esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic MESH:D000071041 https://github.com/biopragmatics/biomappings UMLS:C0227176 ncithesaurus:Esophageal_Mucosa esophagus mucosa FMA:62996 esophagus mucous membrane OBOL:automatic lamina muscularis mucosae oesophageae FMA:62996 FMA:TA mucosa of esophagus OBOL:automatic mucosa of oesophagus OBOL:automatic mucous membrane of oesophagus FMA:62996 oesophageal mucosa FMA:62996 oesophagus mucous membrane OBOL:automatic tunica mucosa oesophageae FMA:62996 FMA:TA muscularis mucosae of oesophagus FMA:62996 tunica mucosa oesophagi BTO:0002859 Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot. Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton. autopod BTO:0004359 EFO:0000877 EMAPA:32722 FMA:83015 MA:0002714 MAT:0000091 MIAA:0000091 NCIT:C77660 SCTID:95936004 UMLS:C0687080 autopodial limb segment autopodial segment autopodium autopodium region distal free limb segment distal segment of free limb uberon autopodial element distal segment of limb manus/pes paw paw/hand/foot/hoof pod UBERON:0002470 autopod region definitional Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot. https://github.com/obophenotype/uberon/issues/303 https://orcid.org/0000-0002-6601-2165 autopod MA:0002714 UMLS:C0687080 ncithesaurus:Paw autopodial limb segment MA:th distal free limb segment FMA:83015 distal segment of free limb FMA:83015 distal segment of limb EMAPA:32722 The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus). zeugopodial middle part of limb EFO:0000878 FMA:83016 MA:0002716 MAT:0000092 MIAA:0000092 epipodium middle free limb segment middle limb segment zeugopod limb segment zeugopodial limb segment zeugopodium zygopod zygopodium uberon middle segment of free limb UBERON:0002471 There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators] zeugopod The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus). PHENOSCAPE:curators https://github.com/obophenotype/uberon/issues/101 epipodium MA:th middle free limb segment FMA:83016 zeugopod limb segment MA:th zeugopodial limb segment MA:th middle segment of free limb FMA:83016 The proximal free limb segment. Includes as parts the stylopod skeleton. stylopodial Naming conventions for pod terms under discussion within phenoscape group proximal part of limb EFO:0000879 FMA:83014 MA:0002717 MAT:0000093 MIAA:0000093 propodium proximal free limb segment stylopodial limb segment stylopodium uberon proximal segment of free limb UBERON:0002472 stylopod The proximal free limb segment. Includes as parts the stylopod skeleton. http://orcid.org/0000-0002-6601-2165 propodium MA:th proximal free limb segment FMA:83014 stylopodial limb segment MA:th proximal segment of free limb FMA:83014 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 NCIT:C13076 UMLS:C0391978 VSAO:0000047 Wikipedia:Bone_tissue XAO:0004040 ZFA:0005621 galen:BoneTissue calcium tissue osseous tissue osteogenic tissue mineralized bone tissue uberon bone portion of bone tissue UBERON:0002481 bone tissue VSAO Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] 2012-08-14 VSAO:0000047 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 UMLS:C0391978 ncithesaurus:Bone_Tissue osteogenic tissue VSAO:curator mineralized bone tissue XAO:0004040 bone MESH:A02.835.232 portion of bone tissue FMA:224804 The minute canals that pass the prostatic secretions to the urethra. EMAPA:36568 FMA:19580 MA:0002785 NCIT:C13102 SCTID:362276000 UMLS:C0227965 Wikipedia:Prostatic_ducts duct of prostate duct of prostate gland prostate duct prostate gland duct prostatic duct uberon UBERON:0002485 prostate duct https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb PMID:18977204 The minute canals that pass the prostatic secretions to the urethra. MP:0009734 UMLS:C0227965 ncithesaurus:Prostatic_Duct 2 A suture that connects the two frontal bones of the skull. in humans, the frontal suture is a dense connective tissue structure that divides the two halves of the frontal bone of the skull in infants and children. It usually disappears by the age of six, with the two halves of the frontal bone being fused together. If it does not disappear it may be called a 'metopic suture' or 'sutura frontalis persistens. ' If the suture is not present at birth (craniosynostosis) it will cause a keel-shaped deformity of the skull called 'trigonocephaly. ' It is present in a fetal skull so that the skull can bend and is very elastic at the time of birth. The baby's head literally bends when coming out of the mother's womb. The space is filled as the child grows older. [WP,unvetted] EMAPA:19226 EMAPA:35358 FMA:52989 MA:0002796 SCTID:136854008 Wikipedia:Frontal_suture frontal suture of skull median frontal suture sutura frontalis sutura metopica uberon metopic suture sutura frontalis UBERON:0002490 frontal suture http://upload.wikimedia.org/wikipedia/commons/1/17/Gray134.png https://upload.wikimedia.org/wikipedia/commons/d/d1/Frontal_suture.png two halves of the frontal bone A suture that connects the two frontal bones of the skull. http://orcid.org/0000-0002-6601-2165 sutura frontalis Wikipedia:Frontal_suture sutura metopica FMA:52989 FMA:TA metopic suture MA:0002796 sutura frontalis Wikipedia:Frontal_suture A long bone is a bone that has a shaft and 2 ends and is longer than it is wide. Long bones have a thick outside layer of compact bone and an inner medullary cavity containing bone marrow. The ends of a long bone contain spongy bone and an epiphyseal plate or line depending on the stage of development. The epiphyseal plate is a hyaline cartilage, where new bone growth takes place, lengthening the bone prior to adulthood. Bone lengthening ceases when this cartilage is lost, leaving a remnant referred to as an epiphyseal line. BTO:0004256 EMAPA:35503 FMA:7474 MA:0002802 NCIT:C33003 SCTID:332709000 UMLS:C0222647 Wikipedia:Long_bone galen:LongBone uberon os longum UBERON:0002495 Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251] long bone A long bone is a bone that has a shaft and 2 ends and is longer than it is wide. Long bones have a thick outside layer of compact bone and an inner medullary cavity containing bone marrow. The ends of a long bone contain spongy bone and an epiphyseal plate or line depending on the stage of development. The epiphyseal plate is a hyaline cartilage, where new bone growth takes place, lengthening the bone prior to adulthood. Bone lengthening ceases when this cartilage is lost, leaving a remnant referred to as an epiphyseal line. Wikipedia:Long_bone https://medlineplus.gov/ency/imagepages/9582.htm https://github.com/obophenotype/uberon/issues/2010 https://github.com/obophenotype/uberon/issues/32 UMLS:C0222647 ncithesaurus:Long_Bone os longum BTO:0004256 Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa. Anterior rounded projection of the pars acromialis of the scapula.[AAO] relationship loss: part_of pars acromialis (AAO:0000752)[AAO] AAO:0000826 EMAPA:25119 FMA:23260 GAID:187 MA:0002805 MESH:D000174 NCIT:C32048 SCTID:181911000 UMLS:C0001209 VSAO:0005067 Wikipedia:Acromion acromion process scapular acromion uberon acromion of scapula acromion of the scapula UBERON:0002497 acromion http://upload.wikimedia.org/wikipedia/commons/7/79/Gray206.png Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa. VSAO:0005067 Anterior rounded projection of the pars acromialis of the scapula.[AAO] 2012-06-20 AAO:0000826 AAO AAO:LAP relationship loss: part_of pars acromialis (AAO:0000752)[AAO] 2012-06-20 AAO:0000826 AAO UMLS:C0001209 ncithesaurus:Acromion acromion process VSAO:0005067 scapular acromion VSAO:0005067 acromion of scapula Wikipedia:Acromion acromion of the scapula Wikipedia:Acromion A rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches. In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad] AAO:0000736 EMAPA:25052 FMA:23418 MA:0002808 Wikipedia:Deltoid_tuberosity crista ventralis deltoid crest deltoid eminence deltoid impression deltoid tuberosity deltoid tuberosity of humerus tuberositas deltoidea tuberositas deltoidea (corpus humeri) tuberositas deltoidea humeri uberon crista ventralis humeri deltoid process pectoral process UBERON:0002498 deltopectoral crest http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png A rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches. ISBN:0-683-40008-8 MP:0004353 crista ventralis AAO:0000736 deltoid crest AAO:0000736 MP:0004353 deltoid eminence MP:0004353 deltoid impression MP:0004353 deltoid tuberosity FMA:23418 deltoid tuberosity of humerus FMA:23418 tuberositas deltoidea FMA:23418 FMA:TA tuberositas deltoidea humeri Wikipedia:Deltoid_tuberosity crista ventralis humeri AAO:0000736 deltoid process MP:0004353 An epithelium that is part of a iris [Automatically generated definition]. EMAPA:35447 FMA:58517 MA:0002826 epithelial tissue of iris epithelium of iris epithelium pigmentosum (iris) epithelium pigmentosum iridis iris epithelial tissue iris epithelium pigmented epithelium of iris uberon iris pigmented epithelium UBERON:0002506 iris epithelium FMA MA MP An epithelium that is part of a iris [Automatically generated definition]. OBOL:automatic epithelial tissue of iris OBOL:automatic epithelium of iris OBOL:automatic epithelium pigmentosum (iris) FMA:58517 epithelium pigmentosum iridis FMA:58517 FMA:TA iris epithelial tissue OBOL:automatic iris epithelium FMA:58517 pigmented epithelium of iris FMA:58517 iris pigmented epithelium MA:0002826 A lymph node that is part of an abdomen [Automatically generated definition]. EMAPA:35992 FMA:12787 MA:0002827 SCTID:245342005 abdomen lymph node lymph node of abdomen uberon parietal abdominal lymph node UBERON:0002507 abdominal lymph node A lymph node that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen lymph node OBOL:automatic parietal abdominal lymph node FMA:12787 The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. BTO:0000767 EMAPA:35561 FMA:12795 MA:0002829 NCIT:C77641 UMLS:C0229792 Wikipedia:Mesenteric_lymph_nodes mesenteric node uberon nodi lymphoidei mesenterici UBERON:0002509 mesenteric lymph node https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb FMA The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. MP:0005232 UMLS:C0229792 ncithesaurus:Mesenteric_Lymph_Node nodi lymphoidei mesenterici BTO:0000767 Replacement bone that forms within cartilage. placement in this class to be inferred Replacement bone that forms within cartilage.[VSAO] some structures, e.g. in ZFA are both intramembrane and endochondral AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 TAO:0001591 VSAO:0000145 XAO:0004018 ZFA:0001591 ossified chondrogenic bone uberon cartilaginous bone endochondral bones UBERON:0002513 endochondral bone https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg VSAO VSAO Replacement bone that forms within cartilage. GO:0001958 GO_REF:0000034 VSAO:0000145 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/54 Replacement bone that forms within cartilage.[VSAO] 2012-08-14 VSAO:0000145 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 some structures, e.g. in ZFA are both intramembrane and endochondral ZFA ossified chondrogenic bone VSAO:0000145 cartilaginous bone BTO:0002157 endochondral bones ZFA:0001591 Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] EMAPA:36615 TAO:0001644 Wikipedia:Intramembranous_ossification ZFA:0001635 uberon intramembranous bones membrane bone UBERON:0002514 intramembranous bone VSAO Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. GO:0001957 Wikipedia:Intramembranous_ossification https://github.com/obophenotype/uberon/issues/267 Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] 2012-08-14 TAO:0001644 TAO TAO:wd [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] 2012-09-06 TAO:0001644 TAO Curator intramembranous bones ZFA:0001635 membrane bone AEO:0000085 The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. basicranial FMA:52801 MA:0002840 MESH:D019291 MFMO:0000044 NCIT:C12493 SCTID:181890004 UMLS:C0149543 Wikipedia:Base_of_skull base of cranium base of skull basis cranii cranial base uberon UBERON:0002517 The skull base is formed from a series of cartilages either side of, and rostral to, the notochord, whose tip lies just caudal to the pituitary gland. It is closely associated with the sensory capsules, which partially or completely sur- round the olfactory epithelium, the eye, and the inner ear[PMID:11523816] basicranium http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. Wikipedia:Base_of_skull UMLS:C0149543 ncithesaurus:Base_of_the_Skull base of skull FMA:52801 basis cranii FMA:52801 FMA:TA Wikipedia:Base_of_skull cranial base FMA:52801 MA:0002840 Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 NCIT:C32495 SCTID:27197004 Wikipedia:Elastic_fiber elastic connective tissue textus connectivus elasticus elastic fiber uberon UBERON:0002521 elastic tissue http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png Connective tissue composed of elastic fibers. http://orcid.org/0000-0002-6601-2165 textus connectivus elasticus The middle layer of an artery or vein. [WP,unvetted]. BTO:0002011 EMAPA:36298 FMA:55590 GAID:170 MA:0002855 MESH:D017540 NCIT:C33821 SCTID:61695000 UMLS:C0162867 Wikipedia:Tunica_media uberon tunica media vasorum UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg MA cjm cjm The middle layer of an artery or vein. [WP,unvetted]. Wikipedia:Tunica_media UMLS:C0162867 ncithesaurus:Tunica_Media tunica media vasorum BTO:0002011 Wikipedia:Tunica_media The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] BTO:0002012 EMAPA:36297 FMA:55589 GAID:523 MA:0002861 MESH:D017539 NCIT:C33820 SCTID:8361002 SCTID:87483006 UMLS:C0162864 Wikipedia:Tunica_intima uberon Bichat's tunic intima tunica intima vasorum UBERON:0002523 tunica intima https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg FMA check for exceptions, e.g. capillaries ISBN:0073040584 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. ISBN:0073040584 NCIT:C33820 Wikipedia:Tunica_intima The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] Wikipedia Wikipedia:Tunica_intima UMLS:C0162864 ncithesaurus:Tunica_Intima Bichat's tunic BTO:0002012 intima BTO:0002012 tunica intima vasorum BTO:0002012 A lymph node that is part of a pancreas [Automatically generated definition]. FMA:16626 MA:0002881 NCIT:C77642 SCTID:276170003 UMLS:C0229783 lymph node of pancreas pancreas lymph node pancreatic node uberon aJCC level 19 node pyloric lymph node UBERON:0002527 pancreatic lymph node A lymph node that is part of a pancreas [Automatically generated definition]. OBOL:automatic UMLS:C0229783 ncithesaurus:Pancreatic_Lymph_Node lymph node of pancreas OBOL:automatic pancreas lymph node OBOL:automatic aJCC level 19 node FMA:16626 pyloric lymph node MA:0002881 A lymph node located in the sacral region. FMA:16655 MA:0002883 NCIT:C77647 SCTID:279797001 UMLS:C0229827 Wikipedia:Sacral_lymph_nodes sacral node uberon UBERON:0002528 sacral lymph node A lymph node located in the sacral region. ncithesaurus:Sacral_Lymph_Node UMLS:C0229827 ncithesaurus:Sacral_Lymph_Node A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA:241863 MA:0002889 NCIT:C38630 UMLS:C1268195 free limb segment segment of limb subdivision of limb uberon extremity part limb region region of limb UBERON:0002529 limb segment A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. https://orcid.org/0000-0002-6601-2165 FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA UMLS:C1268195 ncithesaurus:Extremity_Part free limb segment FMA:241863 An organ that functions as a secretory or excretory organ. glandular AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 SCTID:134358001 UMLS:C1285092 Wikipedia:Gland WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png An organ that functions as a secretory or excretory organ. MGI:csmith MP:0002163 FBbt:00100317 UMLS:C1285092 ncithesaurus:Gland glandular organ http://orcid.org/0000-0002-6601-2165 Druese BTO:0000522 glandula BTO:0000522 Wikipedia:Gland In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 MIAA:0000067 VHOG:0000243 Wikipedia:Epiblast epiblast uberon blastocyst ectoblast epiblastus primitive ectoderm UBERON:0002532 epiblast (generic) http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. Wikipedia:Epiblast ZFIN:curator In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] 2012-09-17 VHOG:0000243 VHOG DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) http://bgee.unil.ch/ epiblast VHOG:0000243 ectoblast MP:0003886 epiblastus Wikipedia:Epiblast primitive ectoderm VHOG:0000243 The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] AAO:0011104 BTO:0001445 EFO:0002748 EHDAA2:0001976 EHDAA:1595 EMAPA:16580 MAT:0000070 MIAA:0000070 TAO:0000077 VHOG:0000201 XAO:0000107 ZFA:0000077 tail bud tailbud uberon end bud tail bud mesenchyme UBERON:0002533 post-anal tail bud The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. BTO:0001445 Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] 2012-06-20 AAO:0011104 AAO ISBN:0815318960 OMD:tail+bud (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] 2012-09-17 VHOG:0000201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ tail bud ZFA:0000077 end bud BTO:0001445 tail bud mesenchyme ZFA:0000077 A gonad with both testicular and ovarian aspects[WP]. BTO:0000981 EFO:0000971 MAT:0000165 MIAA:0000165 WBbt:0005178 Wikipedia:Ovotestis hermaphrodite genitalia glandula hermaphroditica hermaphrodite gland uberon ovotestis UBERON:0002537 hermaphrodite gonad A gonad with both testicular and ovarian aspects[WP]. Wikipedia:Ovotestis hermaphrodite genitalia GO:0040035 glandula hermaphroditica Wikipedia:Ovotestis#In_gastropods hermaphrodite gland Wikipedia:Ovotestis#In_gastropods ovotestis BTO:0000981 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:D001934 MIAA:0000242 NCIT:C34249 SCTID:308766004 TAO:0001306 UMLS:C0080322 VHOG:0000155 Wikipedia:Pharyngeal_arch XAO:0000096 ZFA:0001306 pharyngeal arches branchial arch uberon arcus pharyngei visceral arch UBERON:0002539 pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png EHDAA2 PMID:16313389 http://tolweb.org/Chordata/2499 PMID:16313389 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. PMID:16313389 ZFA:yb http://orcid.org/0000-0002-6601-2165 One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010359 AAO NLM:branchial+arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] 2012-09-17 VHOG:0000155 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ UMLS:C0080322 ncithesaurus:Pharyngeal_Arch pharyngeal arches branchial arch BTO:0001785 MP:0002884 arcus pharyngei Wikipedia:Pharyngeal_arch A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] digital AAO:0011126 EFO:0000881 EMAPA:32725 FMA:85518 MA:0000690 MAT:0000285 MIAA:0000285 NCIT:C40186 SCTID:361367007 UMLS:C0582802 VHOG:0000944 Wikipedia:Digit_(anatomy) XAO:0003032 galen:Digit acropodial unit digit (phalangeal portion) plus soft tissue limb digit uberon UBERON:0002544 digit A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/420 Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] 2012-09-17 VHOG:0000944 VHOG DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008) http://bgee.unil.ch/ FMA:85518 GAT UMLS:C0582802 ncithesaurus:Digit digit (phalangeal portion) plus soft tissue http://orcid.org/0000-0002-6601-2165 limb digit MA:0000690 Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 ectodermal cranial placode uberon cranial placodes UBERON:0002546 cranial placode cjm PMID:11523831 PMID:22512454 Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. http://www.ncbi.nlm.nih.gov/books/NBK53175/ https://github.com/obophenotype/uberon/issues/135 https://github.com/seger/aao/issues/4 https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/ Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons PMID:11523831 ectodermal placode FMA:293966 PMID:22512454 placode Wikipedia:Placode ectodermal cranial placode UBERON:cjm cranial placodes XAO:0000305 Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity BIRNLEX:1011 EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity uberon UBERON:0002553 anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 EMAPA:37442 MA:th BIRNLEX:1019 FMA:12237 SCTID:362606005 cavity of organ uberon UBERON:0002558 organ cavity cavity of organ FMA:12237 The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube. BIRNLEX:1029 FMA:75007 cavity of neuraxis cavity of ventricular system of neuraxis neuraxis cavity neuraxis lumen uberon UBERON:0002561 lumen of central nervous system The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube. https://orcid.org/0000-0002-6601-2165 DOI:10.1186/s12983-014-0089-2 cavity of neuraxis FMA:75007 cavity of ventricular system of neuraxis FMA:75007 neuraxis cavity FMA:75007 Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 FMA:55676 NCIT:C13031 SCTID:384763002 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon UBERON:0002616 regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 UMLS:C0445620 ncithesaurus:Brain_Part anatomical structure of brain OBOL:automatic biological structure of brain OBOL:automatic brain anatomical structure OBOL:automatic brain biological structure OBOL:automatic neuraxis segment FMA:55676 segment of brain BIRNLEX:1167 A spinal cord segment that adjacent_to a cervical region. BIRNLEX:1499 FMA:71166 MA:0003081 MESH:D066193 NCIT:C12892 SCTID:180960003 UMLS:C0581619 UMLS:C1278837 neuronames:1654 cervical segment of spinal cord cervical segments of spinal cord [1-8] cervical spinal cord pars cervicalis medullae spinalis segmenta cervicalia medullae spinalis [1-8 uberon UBERON:0002726 cervical spinal cord A spinal cord segment that adjacent_to a cervical region. OBOL:automatic MESH:D066193 https://github.com/biopragmatics/biomappings UMLS:C0581619 BIRNLEX:1499 ncithesaurus:Cervical_Spinal_Cord UMLS:C1278837 BIRNLEX:1499 cervical segment of spinal cord FMA:71166 cervical segments of spinal cord [1-8] FMA:71166 cervical spinal cord FMA:71166 pars cervicalis medullae spinalis FMA:71166 FMA:TA segmenta cervicalia medullae spinalis [1-8 FMA:71166 FMA:TA A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]. BIRNLEX:1571 FMA:76924 cerebellar cortical segment segment of cerebellar cortex uberon UBERON:0002749 regional part of cerebellar cortex A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]. OBOL:automatic cerebellar cortical segment FMA:76924 segment of cerebellar cortex BIRNLEX:1571 BIRNLEX:1704 FMA:71168 MA:0003083 NCIT:C12895 SCTID:180962006 UMLS:C0581620 UMLS:C0581621 UMLS:C1278838 Wikipedia:Lumbar_spinal_cord neuronames:1677 lumbar segment of spinal cord lumbar segments of spinal cord [1-5] lumbar spinal cord pars lumbalis medullae spinalis segmenta lumbalia medullae spinalis [1-5] spinal cord lumbar segment uberon UBERON:0002792 lumbar spinal cord UMLS:C0581620 BIRNLEX:1704 UMLS:C0581621 ncithesaurus:Lumbar_Spinal_Cord UMLS:C1278838 BIRNLEX:1704 lumbar segment of spinal cord FMA:71168 lumbar segments of spinal cord [1-5] FMA:71168 lumbar spinal cord FMA:71168 pars lumbalis medullae spinalis FMA:71168 FMA:TA segmenta lumbalia medullae spinalis [1-5] FMA:71168 FMA:TA spinal cord lumbar segment MA:0003083 Parietal lobe of the left hemisphere of the brain. BIRNLEX:1728 FMA:72974 SCTID:314147009 UMLS:C1281960 uberon UBERON:0002802 left parietal lobe Parietal lobe of the left hemisphere of the brain. BIRNLEX:1728 UMLS:C1281960 BIRNLEX:1728 Parietal lobe of the right hemisphere of the brain. BIRNLEX:1729 FMA:72973 SCTID:314146000 UMLS:C1281959 uberon UBERON:0002803 right parietal lobe Parietal lobe of the right hemisphere of the brain. BIRNLEX:1729 UMLS:C1281959 BIRNLEX:1729 A temporal lobe that is part of a left cerebral hemisphere. BIRNLEX:1784 FMA:72972 SCTID:314158000 UMLS:C1281971 uberon UBERON:0002808 left temporal lobe A temporal lobe that is part of a left cerebral hemisphere. OBOL:automatic UMLS:C1281971 BIRNLEX:1784 A temporal lobe that is part of a right cerebral hemisphere. BIRNLEX:1785 FMA:72971 SCTID:314157005 UMLS:C1281970 uberon UBERON:0002809 right temporal lobe A temporal lobe that is part of a right cerebral hemisphere. OBOL:automatic UMLS:C1281970 BIRNLEX:1785 A frontal cortex that is part of a right cerebral hemisphere. BIRNLEX:1786 FMA:72969 SCTID:314141005 UMLS:C1281954 uberon UBERON:0002810 right frontal lobe A frontal cortex that is part of a right cerebral hemisphere. OBOL:automatic UMLS:C1281954 BIRNLEX:1786 A frontal cortex that is part of a left cerebral hemisphere. BIRNLEX:1787 FMA:72970 SCTID:314142003 UMLS:C1281955 uberon UBERON:0002811 left frontal lobe A frontal cortex that is part of a left cerebral hemisphere. OBOL:automatic UMLS:C1281955 BIRNLEX:1787 A cerebral hemisphere that is in the left side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1795 FMA:61819 NCIT:C32955 SCTID:362323007 UMLS:C0228176 left hemisphere uberon UBERON:0002812 left cerebral hemisphere https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb A cerebral hemisphere that is in the left side of a brain. OBOL:automatic UMLS:C0228176 ncithesaurus:Left_Cerebral_Hemisphere left hemisphere BIRNLEX:1795 A cerebral hemisphere that is in the right side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1797 FMA:67292 NCIT:C33472 SCTID:362322002 UMLS:C0228175 right hemisphere uberon UBERON:0002813 right cerebral hemisphere https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb A cerebral hemisphere that is in the right side of a brain. OBOL:automatic UMLS:C0228175 ncithesaurus:Right_Cerebral_Hemisphere right hemisphere BIRNLEX:1797 Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453). BAMS:12 BAMS:12N BAMS:XII BIRNLEX:2644 BM:XII DHBA:12545 EHDAA2:0004635 EMAPA:35416 EV:0100286 FMA:54505 HBA:9557 MA:0001039 MBA:773 NCIT:C12899 SCTID:47361005 UMLS:C0228802 VHOG:0001358 Wikipedia:Hypoglossal_nucleus ncithesaurus:Nucleus_of_the_Hypoglossal_Nerve neuronames:757 hypoglossal XII nucleus hypoglossal nerve nucleus hypoglossal nucleus nucleus nervi hypoglossi nucleus of hypoglossal nerve twelfth cranial nerve nucleus uberon nucleus hypoglossalis nucleus nervi hypoglossi UBERON:0002871 hypoglossal nucleus http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453). BIRNLEX:2644 ABA ABA ABA ABA ABA ABA ABA ABA ABA UMLS:C0228802 BIRNLEX:2644 ncithesaurus:Hypoglossal_Nucleus neuronames:757 BIRNLEX:2644 hypoglossal XII nucleus MA:0001039 hypoglossal nerve nucleus FMA:54505 hypoglossal nucleus FMA:54505 nucleus nervi hypoglossi FMA:54505 FMA:TA nucleus of hypoglossal nerve FMA:54505 twelfth cranial nerve nucleus FMA:54505 nucleus hypoglossalis NeuroNames:757 nucleus nervi hypoglossi Wikipedia:Hypoglossal_nucleus The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]. LF BAMS:lf BAMS:lfh BIRNLEX:4041 DHBA:10622 FMA:83727 HBA:9401 NCIT:C33005 SCTID:369225004 UMLS:C0228186 Wikipedia:Medial_longitudinal_fissure neuronames:35 fissura interhemispherica fissura longitudinalis cerebrales fissura longitudinalis cerebri fissura longitudinalis magna hemispheric sulcus interhemispheric fissure longitudinal cerebral fissure longitudinal fissure of hemisphere longitudinal fissure of the cerebrum longitudinal sulcus medial longitudinal fissure sagittal fissure uberon UBERON:0002921 longitudinal fissure http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png FMA The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]. Wikipedia:Medial_longitudinal_fissure LF BIRNLEX:4041 NIFSTD:NeuroNames_abbrevSource UMLS:C0228186 BIRNLEX:4041 ncithesaurus:Longitudinal_Fissure neuronames:35 BIRNLEX:4041 fissura interhemispherica BIRNLEX:4041 fissura longitudinalis cerebrales BIRNLEX:4041 fissura longitudinalis cerebri BIRNLEX:4041 fissura longitudinalis magna BIRNLEX:4041 hemispheric sulcus FMA:83727 interhemispheric fissure FMA:83727 longitudinal cerebral fissure FMA:83727 longitudinal fissure of hemisphere BIRNLEX:4041 longitudinal fissure of the cerebrum BIRNLEX:4041 longitudinal sulcus FMA:83727 medial longitudinal fissure FMA:83727 sagittal fissure FMA:83727 A nucleus of brain that is part of a trigeminal nuclear complex. massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. BM:V BTO:0001074 CALOHA:TS-2077 EMAPA:35883 EV:0100271 FMA:71247 GAID:604 MA:0001028 MESH:D014278 NCIT:C12807 SCTID:280164007 UMLS:C0040999 VHOG:0001353 http://uri.neuinfo.org/nif/nifstd/nifext_11 nucleus of trigeminal nuclear complex trigeminal V nucleus trigeminal nuclear complex nucleus trigeminal nucleus uberon nucleus mesencephalicus nervi trigemini nucleus mesencephalicus trigeminalis nucleus tractus mesencephali nervi trigeminalis UBERON:0002925 trigeminal nucleus A nucleus of brain that is part of a trigeminal nuclear complex. OBOL:automatic massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. GO https://github.com/obophenotype/mouse-anatomy-ontology/issues/58 UMLS:C0040999 ncithesaurus:Trigeminal_Nucleus nucleus of trigeminal nuclear complex FMA:71247 trigeminal V nucleus MA:0001028 trigeminal nuclear complex nucleus FMA:71247 trigeminal nucleus FMA:71248 nucleus mesencephalicus nervi trigemini BTO:0001074 nucleus mesencephalicus trigeminalis BTO:0001074 nucleus tractus mesencephali nervi trigeminalis BTO:0001074 A sensory epithelium that is part of a gustatory system. FMA:62412 http://uri.neuinfo.org/nif/nifstd/nifext_12 uberon UBERON:0002926 gustatory epithelium NIFSTD A sensory epithelium that is part of a gustatory system. OBOL:automatic Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] BAMS:PTg BIRNLEX:923 DHBA:12416 FMA:71108 HBA:9135 MESH:D065821 SCTID:362401009 UMLS:C0228426 Wikipedia:Pontine_tegmentum neuronames:557 dorsal pons dorsal portion of pons tegmental portion of pons tegmentum of pons tegmentum pontis uberon pars dorsalis pontis pars posterior pontis tegmentum pontis UBERON:0003023 pontine tegmentum https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). BIRNLEX:923 MESH:D065821 https://github.com/biopragmatics/biomappings UMLS:C0228426 BIRNLEX:923 neuronames:557 BIRNLEX:923 dorsal portion of pons FMA:71108 tegmental portion of pons FMA:71108 tegmentum of pons FMA:71108 tegmentum pontis FMA:71108 FMA:TA pars dorsalis pontis NeuroNames:557 pars posterior pontis NeuroNames:557 tegmentum pontis Wikipedia:Pontine_tegmentum A wall, dividing a cavity or structure into smaller ones[WP]. septal AAO:0011127 FMA:86461 Wikipedia:Septum septa uberon UBERON:0003037 general anatomical term in FMA septum A wall, dividing a cavity or structure into smaller ones[WP]. Wikipedia:Septum septa The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. BIRNLEX:966 FMA:71167 MA:0003082 NCIT:C12894 SCTID:278750009 UMLS:C0581620 Wikipedia:Thoracic_spinal_cord neuronames:1718 pars thoracica medullae spinalis segmenta thoracica medullae spinalis [1-12] thoracic region of spinal cord thoracic segment of spinal cord thoracic segments of spinal cord [1-12] thoracic spinal cord uberon UBERON:0003038 thoracic spinal cord http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. Wikipedia:Thoracic_spinal_cord UMLS:C0581620 BIRNLEX:966 ncithesaurus:Thoracic_Spinal_Cord pars thoracica medullae spinalis FMA:71167 FMA:TA segmenta thoracica medullae spinalis [1-12] FMA:71167 FMA:TA thoracic region of spinal cord FMA:71167 thoracic segment of spinal cord FMA:71167 thoracic segments of spinal cord [1-12] FMA:71167 thoracic spinal cord FMA:71167 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] AAO:0011076 BTO:0006222 EFO:0003420 EHDAA2:0001232 EHDAA:1504 EMAPA:16543 FMA:293971 TAO:0000048 VHOG:0000186 Wikipedia:Nasal_placode XAO:0000005 ZFA:0000048 olfactory placodes placoda nasalis placoda olfactoria uberon nasal I placode nasal placode UBERON:0003050 Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic olfactory placode NCBIBook:NBK53171 ZFA EHDAA2 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. Wikipedia:Nasal_placode XAO:0000005 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000186 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ BTO:0006222 https://github.com/biopragmatics/biomappings olfactory placodes placoda nasalis placoda olfactoria An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]. Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 UBERON:0004373 AAO:0011080 BTO:0002661 EHDAA2:0001342 EMAPA:16669 FMA:302920 NCIT:C34240 SCTID:308792006 TAO:0000051 UMLS:C1518678 VHOG:0001148 Wikipedia:Otic_vesicle XAO:0000006 ZFA:0000051 otic vesicle uberon OV acoustic vesicle auditory vesicle otocyst UBERON:0003051 ear vesicle http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]. MP:0009806 Wikipedia:Otic_vesicle Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000051 TAO ZFIN:curator One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] 2012-09-17 VHOG:0001148 VHOG http://bgee.unil.ch/ The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] 2012-09-17 VHOG:0001148 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413 http://bgee.unil.ch/ MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 MP UMLS:C1518678 ncithesaurus:Otic_Vesicle otic vesicle MP:0004311 acoustic vesicle VHOG:0001148 auditory vesicle BTO:0002661 otocyst MP:0004311 The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 NCIT:C93172 TAO:0000042 VHOG:0000649 XAO:0000016 ZFA:0000042 neuronames:2076 MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB UBERON:0003052 midbrain-hindbrain boundary ZFA https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/ ZFA ZFA The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000649 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ isthmic organizer territory XAO:0000016 isthmo-cerebellar region VHOG:0000649 isthmus/MHB Geisha:syn NCBITaxon:8782 A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) BTO:0003377 EHDAA2:0001846 EHDAA:6538 FMA:295662 NCIT:C34247 TAO:0001185 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 skin periderm uberon EVL epidermis epithelial layer epidermis outer layer epitrichium periderm UBERON:0003055 periderm EHDAA2 EHDAA2 ZFA A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. ISBN:9780878932504 The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001185 TAO ZFIN:curator relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] 2012-08-14 TAO:0001185 TAO BTO:0003377 https://github.com/biopragmatics/biomappings UMLS:C1518973 ncithesaurus:Periderm skin periderm EHDAA2:0001846 EVL ZFA:0001185 epitrichium MP:0013530 The portion of neural plate anterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 XAO:0000045 ZFA:0007016 uberon anterior neural plate UBERON:0003056 pre-chordal neural plate The portion of neural plate anterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001200 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The portion of neural plate posterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 ZFA:0007017 uberon posterior neural plate UBERON:0003057 chordal neural plate The portion of neural plate posterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 TAO:0000279 VHOG:0000559 XAO:0000057 ZFA:0000279 segmental plate unsegmented paraxial mesoderm uberon PSM presumptive somite mesoderm somitogenic mesoderm somitomeric mesoderm unsegmented mesenchyme UBERON:0003059 presomitic mesoderm Bgee:AN Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000279 TAO ZFIN:curator It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] 2012-09-17 VHOG:0000559 VHOG DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) http://bgee.unil.ch/ unsegmented paraxial mesoderm https://orcid.org/0000-0002-6601-2165 somitomeric mesoderm GO:0002075 unsegmented mesenchyme VHOG:0000559 In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 BTO:0005991 NCIT:C34279 SCTID:361406002 TAO:0000150 UMLS:C1283945 VHOG:0000082 Wikipedia:Pronephric_duct XAO:0000063 ZFA:0000150 uberon archinephric duct ductus pronephricus pronephric ducts UBERON:0003060 The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct GO Wikipedia XAO In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Wikipedia:Pronephric_duct Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000150 TAO ZFIN:curator The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG http://bgee.unil.ch/ (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 http://bgee.unil.ch/ BTO:0005991 https://github.com/biopragmatics/biomappings UMLS:C1283945 ncithesaurus:Pronephric_Duct archinephric duct VHOG:0000082 ductus pronephricus Wikipedia:Pronephric_duct pronephric ducts ZFA:0000150 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 EHDAA:207 NCIT:C34113 TAO:0000094 TE:E5.11.2.0.0.0.4 UMLS:C1511224 VHOG:0000085 Wikipedia:Blood_island_of_umbilical_vesicle XAO:0000067 ZFA:0000094 blood islands uberon VBI caudal hematopoietic tissue posterior ICM posterior blood island ventral blood island UBERON:0003061 blood island Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000094 TAO ZFIN:curator Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] 2012-06-20 AAO:0011006 AAO AAO:EJS relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] 2012-08-14 TAO:0000094 TAO Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000085 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) http://bgee.unil.ch/ EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA2 UMLS:C1511224 ncithesaurus:Blood_Island blood islands A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue. TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] UBERON:0004881 head mesenchyme head mesoderm AAO:0011085 EHDAA2:0001493 EHDAA:181 FMA:295532 TAO:0000060 VHOG:0000086 Wikipedia:Prechordal_plate XAO:0000079 ZFA:0000060 uberon UBERON:0003063 prechordal plate ZFA PMID:16313393 A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue. ISBN:0838580343 MP:0004387 Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000060 TAO ZFIN:curator Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] 2012-09-17 VHOG:0000086 VHOG http://bgee.unil.ch/ There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] 2012-09-17 VHOG:0000086 VHOG DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008) http://bgee.unil.ch/ head mesenchyme XAO:0000079 head mesoderm XAO:0000079 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 NCIT:C34193 SCTID:361476001 TAO:0001206 UMLS:C1284010 VHOG:0000087 Wikipedia:Intermediate_mesoderm XAO:0000085 ZFA:0001206 uberon IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium UBERON:0003064 intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png AAO EMAPA XAO The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. GOC:curators Wikipedia:Intermediate_mesoderm Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] 2012-06-20 AAO:0010575 AAO AAO:EJS (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] 2012-09-17 VHOG:0000087 VHOG Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 http://bgee.unil.ch/ all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). ZFA UMLS:C1284010 ncithesaurus:Intermediate_Mesoderm intermediate mesenchyme https://github.com/obophenotype/uberon/wiki/The-neural-crest intermediate plate EMAPA:16178 intermediate plate mesoderm https://orcid.org/0000-0002-6601-2165 mesenchyma intermedium Wikipedia:Intermediate_mesoderm The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, develops from visceral pouch 2 2 AAO:0010363 EHDAA2:0000050 EHDAA:611 EMAPA:16272 FMA:293017 NCIT:C34288 SCTID:308768003 TAO:0001596 VHOG:0000297 Wikipedia:Second_pharyngeal_arch XAO:0000098 ZFA:0001611 2nd pharyngeal arch arcus pharyngeus secundus branchial arch 2 hyoid arch pharyngeal arch 2 second branchial arch second pharyngeal arch second visceral arch visceral arch 2 uberon 2nd arch 2nd visceral arch hyoid bars pharyngeal arches 2 UBERON:0003066 pharyngeal arch 2 http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. PMID:12784288 ZFIN:yb https://github.com/obophenotype/uberon/issues/258 The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010363 AAO XAO:EJS A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000297 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, develops from visceral pouch 2 XAO arcus pharyngeus secundus Wikipedia:Second_pharyngeal_arch branchial arch 2 hyoid arch XAO:0000098 second branchial arch second visceral arch visceral arch 2 2nd arch EHDAA2:0000050 2nd visceral arch VHOG:0000297 pharyngeal arches 2 VHOG:0000297 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] TAO:0001310 VHOG:0000103 XAO:0000187 ZFA:0001310 dorsolateral placodes uberon UBERON:0003067 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode NCBIBook:NBK53175 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. ZFIN:curator In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000103 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ dorsolateral placodes ZFA:0001310 The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 VHOG:0000107 Wikipedia:Chordamesoderm XAO:0000205 ZFA:0001204 uberon chordamesoderm UBERON:0003068 axial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GO:0048318 Wikipedia:Chordamesoderm The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000107 VHOG http://bgee.unil.ch/ chordamesoderm Wikipedia:Chordamesoderm A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]. Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). AAO:0011079 EFO:0003429 EHDAA2:0001339 EHDAA:506 EMAPA:16195 FMA:293973 NCIT:C34239 TAO:0000138 UMLS:C1518677 VHOG:0000235 Wikipedia:Otic_placode XAO:0000223 ZFA:0000138 placoda otica uberon auditory placode ear placode ear/otic placode octaval VIII placode octaval placode UBERON:0003069 otic placode invaginates NCBIBook:NBK53175 A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]. NCBIBook:NBK53175 Wikipedia:Otic_placode Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000138 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000235 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). NCBIBook:NBK53175 UMLS:C1518677 ncithesaurus:Otic_Placodes placoda otica octaval VIII placode ISBN:0471888893 octaval placode ISBN:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...' EFO:0003433 EHDAA2:0004209 TAO:0000162 VHOG:0000109 XAO:0000225 ZFA:0000162 trigeminal V placode trigeminal placode uberon profundus V placode profundus placode trigeminal placodes UBERON:0003070 trigeminal placode complex ISBN:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. PMID:22512454 http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/693 The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] XAO The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000162 TAO ZFIN:curator The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000109 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ trigeminal placode EHDAA2:0004209 VHOG:0000109 XAO:0000225 ZFA:0000162 profundus V placode ISBN:0471888893 profundus placode ISBN:0471888893 trigeminal placodes ZFA:0000162 Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 TAO:0000570 XAO:0000227 XAO:0004090 ZFA:0000570 eye placode occular primordium ocular primordium optic placode optic placode of camera-type eye optic primordium uberon eye anlage eye field optic field optic placodes UBERON:0003071 eye primordium EHDAA2 PMID:16496288 XAO Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. GO:0046619 ZFA:0000570 TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. GO eye placode OBOL:automatic optic placode GO:0046619 optic placode of camera-type eye GO:0046619 https://orcid.org/0000-0002-6601-2165 eye anlage XAO:0000227 optic placodes Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 EMAPA:16674 NCIT:C34233 SCTID:308789007 TAO:0001202 UMLS:C0231109 VHOG:0000167 ZFA:0001202 uberon eye cup eyecup ocular cup ophtalmic cup UBERON:0003072 optic cup ZFA ZFA Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. MP:0004269 Wikipedia:Optic_cup_(embryology) ZFA:0001202 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] 2012-09-17 VHOG:0000167 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C0231109 ncithesaurus:Optic_Cup eyecup BTO:0005351 ocular cup VHOG:0000167 ophtalmic cup BTO:0005351 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 FMA:296767 NCIT:C34202 TAO:0000122 UMLS:C1517770 VHOG:0000166 Wikipedia:Lens_placode XAO:0000240 ZFA:0000122 uberon lens placodes placoda lentis UBERON:0003073 lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png NCBIBook:NBK53175 ZFA A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Wikipedia:Lens_placode ZFIN:curator Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000122 TAO ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000166 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) NCBIBook:NBK53175 UMLS:C1517770 ncithesaurus:Lens_Placodes lens placodes ZFA:0000122 placoda lentis Wikipedia:Lens_placode Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. AAO:0000637 BTO:0005990 EHDAA2:0001243 EHDAA:1590 EMAPA:16577 GAID:1315 MESH:D014928 NCIT:C26469 SCTID:308800003 TAO:0000546 UMLS:C0043204 VHOG:0000082 Wikipedia:Mesonephric_duct XAO:0000242 ZFA:0000546 Wolffian duct uberon Leydig's duct archinephric duct ductus mesonephricus; ductus Wolffi renal duct UBERON:0003074 mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png GO EHDAA2 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Wikipedia:Mesonephric_duct ZFIN:curator https://github.com/obophenotype/uberon/issues/28 Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] 2012-06-20 AAO:0000637 AAO AAO:BJB The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG http://bgee.unil.ch/ (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 http://bgee.unil.ch/ BTO:0005990 https://github.com/biopragmatics/biomappings UMLS:C0043204 ncithesaurus:Mesonephric_Duct Wolffian duct GOC:yaf Wikipedia:Wolffian_duct ZFA:0000546 Leydig's duct Wikipedia:Wolffian_duct archinephric duct VHOG:0000082 Wikipedia:Wolffian_duct ductus mesonephricus; ductus Wolffi Wikipedia:Mesonephric_duct A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 Wikipedia:Neural_plate XAO:0000249 ZFA:0000132 neuronames:1362 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png GOTAX:0000352 Wikipedia Bgee:AN A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. ISBN:0815318960 OMD:neural+plate Wikipedia:Neural_plate ZFIN:curator The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000132 TAO ZFIN:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000068 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ MESH:D054258 https://github.com/biopragmatics/biomappings UMLS:C0920623 ncithesaurus:Neural_Plate lamina neuralis Wikipedia:Neural_plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon UBERON:0003076 posterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001383 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 NCIT:C34244 SCTID:361475002 TAO:0000255 UMLS:C1284009 VHOG:0000114 Wikipedia:Paraxial_mesoderm XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 Bgee:AN The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. GO:0048339 https://github.com/obophenotype/uberon/issues/30 Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] 2012-06-20 AAO:0010568 AAO AAO:EJS Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] 2012-09-17 VHOG:0000114 VHOG DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) http://bgee.unil.ch/ note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) ZFA UMLS:C1284009 ncithesaurus:Paraxial_Mesoderm paraxial mesenchyme ZFA:0000255 https://github.com/obophenotype/uberon/issues/30 https://github.com/obophenotype/uberon/wiki/The-neural-crest somitic mesoderm ISBN:9780878932504 mesoderma paraxiale Wikipedia:Paraxial_mesoderm Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group AAO:0011036 EFO:0003455 FMA:293968 TAO:0001294 VHOG:0000117 XAO:0000284 ZFA:0001294 epibranchial placodes uberon ventrolateral placode UBERON:0003078 epibranchial placode NCBIBook:NBK53175 ZFA ZFA EHDAA2-abduced Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. VHOG:0000117 Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] 2012-09-17 VHOG:0000117 VHOG http://bgee.unil.ch/ These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000117 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively NCBIBook:NBK53175 in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group XAO epibranchial placodes ZFA:0001294 ventrolateral placode ISBN:0471888893 TODO - add grouping class for the anterior end of the neural tube at all stages (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon UBERON:0003080 anterior neural tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001384 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 NCIT:C34199 SCTID:361477005 TAO:0000121 UMLS:C1517749 VHOG:0000118 Wikipedia:Lateral_plate_mesoderm XAO:0000311 ZFA:0000121 LPM lateral mesoderm uberon lateral plate lateral plate mesenchyme mesoderma laminae lateralis UBERON:0003081 lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 EHDAA2 VHOG Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. MP:0010117 Wikipedia:Lateral_plate_mesoderm Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] 2012-06-20 AAO:0010574 AAO AAO:EJS The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000118 VHOG http://bgee.unil.ch/ A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] 2012-09-17 VHOG:0000118 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ subclass of mesoderm in ZFA. ZFA UMLS:C1517749 ncithesaurus:Lateral_Mesoderm LPM ZFA:0000121 lateral mesoderm GO:0048368 lateral plate mesenchyme EHDAA2:0000919 mesoderma laminae lateralis Wikipedia:Lateral_plate_mesoderm A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 NCIT:C34214 SCTID:344535001 TAO:0001056 UMLS:C1513802 VHOG:0001244 Wikipedia:Myotome XAO:0000315 ZFA:0001056 myomeres uberon muscle plate myomere myotome region myotomes myotomus UBERON:0003082 myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001056 TAO ZFIN:curator In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] 2012-09-17 VHOG:0001244 VHOG DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) http://bgee.unil.ch/ UMLS:C1513802 ncithesaurus:Myotome_Region myomeres TAO:0001056 myotomus Wikipedia:Myotome Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010582 EFO:0003605 EHDAA2:0001901 TAO:0001024 VHOG:0000062 Wikipedia:Trunk_neural_crest XAO:0000319 ZFA:0001024 TNC uberon trunk crest UBERON:0003083 trunk neural crest ZFA Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. ISBN:0815318960 Wikipedia:Trunk_neural_crest Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] 2012-06-20 AAO:0010582 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000062 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ TNC XAO:0000319 Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 TAO:0000028 UMLS:C1514450 XAO:0000336 ZFA:0000028 uberon cardiac field fused heart primordium UBERON:0003084 heart primordium Obol ZFA ZFA XAO Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] 2012-08-14 TAO:0000028 TAO ZFIN:curator The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] 2012-06-20 AAO:0011044 AAO XAO:curator relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] 2012-08-14 TAO:0000028 TAO UMLS:C1514450 ncithesaurus:Primordium_of_the_Heart cardiac field ZFA:0000028 Extension of the dorsal aorta in the tail. Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] AAO:0011023 EFO:0003472 TAO:0000011 VHOG:0000123 Wikipedia:Caudal_artery XAO:0000364 ZFA:0000011 uberon CA UBERON:0003086 caudal artery Extension of the dorsal aorta in the tail. Wikipedia:Caudal_artery ZFIN:curator Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000011 TAO ZFIN:curator The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] 2012-06-20 AAO:0011023 AAO ISBN:0-226-55763-4 Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] part_of somite in XAO AAO:0010571 AEO:0000212 BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 NCIT:C34287 TAO:0001080 UMLS:C0183176 VHOG:0000680 Wikipedia:Sclerotome XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png EHDAA2 EHDAA2 VHOG:0000680 ZFA Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Wikipedia:Sclerotome XB:curator https://github.com/obophenotype/uberon/issues/316 Skeletogenic portion of somites.[AAO] 2012-06-20 AAO:0010571 AAO AAO:EJS The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] 2012-09-17 VHOG:0000680 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ part_of somite in XAO XAO BTO:0006255 https://github.com/biopragmatics/biomappings UMLS:C0183176 ncithesaurus:Sclerotome sclerotomes TAO:0001080 sclerotomus Wikipedia:Sclerotome The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm AAO:0011106 BTO:0004709 EHDAA2:0002033 EHDAA:952 EMAPA:16361 NCIT:C34312 TAO:0001081 UMLS:C1519512 XAO:0000444 ZFA:0001081 uberon thyroid primordia UBERON:0003091 thyroid primordium ZFA ZFA VHOG ISBN:0073040584 PMID:16313389 The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. http://emedicine.medscape.com/article/845125-overview Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. ZFIN:curator In all vertebrates the thyroid arises from the ventral aspect of the second pouch PMID:16313389 Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm EHDAA2 UMLS:C1519512 ncithesaurus:Thyroid_Primordium thyroid primordia ZFA:0001081 Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] Neural crest that is part of the head.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 EMAPA:16091 TAO:0001194 VHOG:0000063 Wikipedia:Cranial_neural_crest XAO:0001001 ZFA:0001194 CNC cephalic neural crest cranial NCC population head NCC population uberon crista neuralis cranialis head crest head neural crest UBERON:0003099 cranial neural crest Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] 2012-06-20 AAO:0010580 AAO AAO:EJS Neural crest that is part of the head.[TAO] 2012-08-14 TAO:0001194 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000063 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ CNC XAO:0001001 cephalic neural crest EMAPA:16091 crista neuralis cranialis Wikipedia:Cranial_neural_crest Gonochoristic organism that can produce female gametes. AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 HAO:0000028 SCTID:362608006 TAO:0000303 TGMA:0001839 XAO:0003005 ZFA:0000303 female human body uberon female UBERON:0003100 female organism Gonochoristic organism that can produce female gametes. CARO:0000028 FBbt:00007011 female human body FMA:67812 female TAO:0000303 Gonochoristic organism that can produce male gametes. AAO:0010033 BILA:0000027 CARO:0000027 FBbt:00007004 FMA:67811 HAO:0000027 SCTID:362609003 TAO:0000242 TGMA:0001838 WBbt:0007850 XAO:0003006 ZFA:0000242 male human body uberon male UBERON:0003101 male organism Gonochoristic organism that can produce male gametes. CARO:0000027 FBbt:00007004 male human body FMA:67811 male TAO:0000242 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. consider obsoleting. See issue/1305 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 Wikipedia:Surface_structure XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature uberon surface feature surface region surface structures UBERON:0003102 surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/24 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] 2012-08-14 TAO:0000292 TAO ZFIN:curator anatomical surface feature EHDAA2:0003010 surface structures ZFA:0000292 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 uberon organ UBERON:0003103 compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. CARO:0000024 Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 NCIT:C13301 TAO:0000393 UMLS:C0162415 VHOG:0000170 Wikipedia:Mesenchyme XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000393 TAO ZFIN:curator Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] 2012-06-20 AAO:0010427 AAO AAO:EJS UMLS:C0162415 ncithesaurus:Mesenchyme mesenchyma Wikipedia:Mesenchyme Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ. Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO] Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO] AAO:0010206 EFO:0003525 NCIT:C98765 TAO:0000351 XAO:0003172 ZFA:0000351 uberon ethmoid region UBERON:0003112 olfactory region Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ. TAO:0000351 Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO] 2012-08-14 TAO:0000351 TAO TAO:MAH Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO] 2012-06-20 AAO:0010206 AAO AAO:EJS ethmoid region ZFA:0000351 Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] AAO:0010154 TAO:0000863 VHOG:0001665 Wikipedia:Skull_roof XAO:0003169 ZFA:0000863 dendrocranium exocranium dermal skull roof dermatocranial cover roof of skull skull roof uberon dermal bone cranium dermal part of skull dermal skull bones roofing bones of the skull skull exoskeleton UBERON:0003113 dermatocranium Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. Wikipedia:Skull_roof ZFA:0000863 ISBN:0073040584 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] 2012-08-14 TAO:0000863 TAO ZFIN:curator Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] 2012-06-20 AAO:0010154 AAO AAO:BJB dendrocranium TAO:0000863 exocranium UBERONREF:0000007 dermal skull roof PMID:11523816 Wikipedia:Skull_roof roof of skull Wikipedia:Skull_roof skull roof PMID:11523816 Wikipedia:Skull_roof dermal bone cranium ZFA:0000863 roofing bones of the skull Wikipedia:Skull_roof The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 1 and df VP3 3 AAO:0010365 EHDAA2:0000069 EHDAA:1080 EMAPA:16399 FMA:293029 SCTID:308769006 TAO:0001598 VHOG:0000298 XAO:0000447 ZFA:0001606 3rd pharyngeal arch first gill arch gill arch 1 third pharyngeal arch third visceral arch visceral arch 3 uberon 3rd arch 3rd visceral arch branchial arch 1 first branchial arch UBERON:0003114 pharyngeal arch 3 The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. MP:0006339 The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] 2012-06-20 AAO:0010365 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000298 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, called branchial arch 1 and df VP3 XAO first gill arch ZFA:0001606 gill arch 1 ZFA:0001606 3rd arch EHDAA2:0000069 3rd visceral arch VHOG:0000298 branchial arch 1 AAO:0010365 ZFA:0001606 first branchial arch ZFA:0001606 Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus. The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 2 and df VP4 4 AAO:0010366 EHDAA2:0000086 EHDAA:1663 EMAPA:16760 FMA:293035 SCTID:308770007 TAO:0001599 VHOG:0000299 XAO:0000449 ZFA:0001607 4th branchial arch 4th pharyngeal arch 4th visceral arch fourth pharyngeal arch gill arch 2 second gill arch visceral arch 4 uberon 4th arch branchial arch 2 fourth visceral arch second branchial arch UBERON:0003115 pharyngeal arch 4 Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus. MP:0006340 The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] 2012-06-20 AAO:0010366 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000299 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, called branchial arch 2 and df VP4 XAO 4th branchial arch gill arch 2 ZFA:0001607 second gill arch ZFA:0001607 4th arch EHDAA2:0000086 branchial arch 2 AAO:0010366 ZFA:0001607 fourth visceral arch VHOG:0000299 second branchial arch ZFA:0001607 The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] A fifth arch never establishes itself in amniotes in XAO, called branchial arch 3 and df VP5 5 AAO:0010367 FMA:293045 SCTID:308771006 TAO:0001600 VHOG:0001204 XAO:0000451 ZFA:0001608 fifth visceral arch gill arch 3 visceral arch 5 uberon 5th pharyngeal arch 5th visceral arch branchial arch 3 fifth pharyngeal arch third branchial arch UBERON:0003116 pharyngeal arch 5 The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] 2012-06-20 AAO:0010367 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001204 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, called branchial arch 3 and df VP5 XAO fifth visceral arch XAO:0000451 gill arch 3 ZFA:0001608 visceral arch 5 ZFA:0001608 5th pharyngeal arch VHOG:0001204 5th visceral arch VHOG:0001204 branchial arch 3 AAO:0010367 XAO:0000451 ZFA:0001608 fifth pharyngeal arch VHOG:0001204 third branchial arch XAO:0000451 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles. The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 6 UBERON:0004349 AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 SCTID:308772004 TAO:0001601 VHOG:0001205 XAO:0000453 ZFA:0001609 6th arch gill arch 4 sixth branchial arch visceral arch 6 uberon 6th pharyngeal arch 6th visceral arch branchial arch 4 fourth branchial arch sixth pharyngeal arch sixth visceral arch UBERON:0003117 pharyngeal arch 6 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles. MP:0006347 The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] 2012-06-20 AAO:0010368 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001205 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ 6th arch EHDAA2:0004075 gill arch 4 ZFA:0001609 visceral arch 6 ZFA:0001609 6th pharyngeal arch VHOG:0001205 6th visceral arch VHOG:0001205 branchial arch 4 AAO:0010368 ZFA:0001609 fourth branchial arch sixth pharyngeal arch VHOG:0001205 sixth visceral arch XAO:0000453 The vessels formed within the first pair of branchial arches in embryogenesis. Disappears early in development in tetrapods ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas UBERON:0004371 AAO:0010415 EHDAA2:0000007 EMAPA:16202 EMAPA:16685 SCTID:308774003 TAO:0005005 VHOG:0000149 XAO:0000342 ZFA:0005005 1st arch artery AA1 aortic arch 1 first aortic arch first branchial arch artery mandibular aortic arch uberon 1st aortic arch artery 1st branchial arch artery 1st pharyngeal arch artery first arch artery UBERON:0003118 pharyngeal arch artery 1 The vessels formed within the first pair of branchial arches in embryogenesis. MP:0010355 ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas ZFA 1st arch artery EMAPA:16685 AA1 ZFA:0005005 aortic arch 1 ZFA:0005005 first aortic arch XAO:0000342 mandibular aortic arch ZFA:0005005 1st aortic arch artery EMAPA:16685 1st branchial arch artery EMAPA:16685 1st pharyngeal arch artery EMAPA:16685 first arch artery EMAPA:16685 The vessels formed within the second pair of branchial arches in embryogenesis. The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] UBERON:0004372 AAO:0010418 EHDAA2:0000051 EMAPA:16203 EMAPA:16686 SCTID:308775002 TAO:0005006 VHOG:0000148 Wikipedia:Aortic_arches#Arches_1_and_2 XAO:0000343 ZFA:0005006 2nd arch artery AA2 aortic arch 2 hyoid aortic arch second aortic arch second branchial arch artery uberon 2nd aortic arch artery 2nd branchial arch artery 2nd pharyngeal arch artery UBERON:0003119 pharyngeal arch artery 2 The vessels formed within the second pair of branchial arches in embryogenesis. MP:0010356 The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. Wikipedia:Aortic_arches#Arches_1_and_2 The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] 2012-06-20 AAO:0010418 AAO ISBN:0-02-377110-0 2nd arch artery EHDAA2:0000051 AA2 ZFA:0005006 aortic arch 2 ZFA:0005006 hyoid aortic arch ZFA:0005006 second aortic arch XAO:0000343 2nd aortic arch artery EMAPA:16686 2nd branchial arch artery EMAPA:16686 2nd pharyngeal arch artery EMAPA:16686 The vessels formed within the third pair of branchial arches in embryogenesis. Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] UBERON:0004352 AAO:0010419 EHDAA2:0000070 EMAPA:16687 SCTID:308776001 TAO:0005007 VHOG:0000147 Wikipedia:Aortic_arches#Arch_3 XAO:0000344 ZFA:0005007 3rd arch artery AA3 aortic arch 3 carotid arch third aortic arch third branchial arch artery uberon 3rd aortic arch artery 3rd branchial arch artery 3rd pharyngeal arch artery UBERON:0003120 pharyngeal arch artery 3 The vessels formed within the third pair of branchial arches in embryogenesis. MP:0006356 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005007 TAO ZFIN:curator The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. Wikipedia:Aortic_arches#Arch_3 The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010419 AAO ISBN:0-02-377110-0 3rd arch artery EHDAA2:0000070 AA3 ZFA:0005007 aortic arch 3 ZFA:0005007 carotid arch Wikipedia:Aortic_arches#Arch_3 third aortic arch XAO:0000344 3rd aortic arch artery EMAPA:16687 3rd branchial arch artery EMAPA:16687 3rd pharyngeal arch artery EMAPA:16687 The vessels formed within the fourth pair of branchial arches in embryogenesis. Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta UBERON:0004350 AAO:0010420 EHDAA2:0000087 EMAPA:17004 SCTID:308777005 TAO:0005008 Wikipedia:Aortic_arches#Arch_4 XAO:0000355 ZFA:0005008 4th arch artery AA4 aortic arch 4 fourth aortic arch fourth branchial arch artery uberon 4th aortic arch artery 4th branchial arch artery 4th pharyngeal arch artery systemic arch UBERON:0003121 proximal right subclavian pharyngeal arch artery 4 The vessels formed within the fourth pair of branchial arches in embryogenesis. MP:0006354 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005008 TAO ZFIN:curator The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010420 AAO ISBN:0-02-377110-0 The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Wikipedia:Aortic_arches#Arch_4 4th arch artery EHDAA2:0000087 AA4 ZFA:0005008 aortic arch 4 ZFA:0005008 fourth aortic arch XAO:0000355 4th aortic arch artery EMAPA:17004 4th branchial arch artery EMAPA:17004 4th pharyngeal arch artery EMAPA:17004 systemic arch ISBN:0073040584 XAO:0000355 The vessels formed within the fifth pair of pharyngeal arches in embryogenesis. The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5]. The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO] In humans the 5th arch disappears on both sides AAO:0010421 SCTID:308778000 TAO:0005009 VHOG:0000145 Wikipedia:Aortic_arches#Arch_5 XAO:0000352 ZFA:0005009 AA5 aortic arch 5 fifth aortic arch uberon UBERON:0003122 pharyngeal arch artery 5 The vessels formed within the fifth pair of pharyngeal arches in embryogenesis. http://orcid.org/0000-0002-6601-2165 The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005009 TAO ZFIN:curator The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5]. Wikipedia:Aortic_arches#Arch_5 The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO] 2012-06-20 AAO:0010421 AAO ISBN:0-02-377110-0 AA5 ZFA:0005009 aortic arch 5 ZFA:0005009 fifth aortic arch XAO:0000352 The vessels formed within the sixth pair of branchial arches in embryogenesis. The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries UBERON:0004351 AAO:0010422 EHDAA2:0000102 EMAPA:17005 SCTID:308779008 TAO:0005016 VHOG:0000144 Wikipedia:Aortic_arches#Arch_6 XAO:0000353 ZFA:0005016 6th arch artery AA6 aortic arch 6 sixth aortic arch sixth branchial arch artery uberon 6th aortic arch artery 6th branchial arch artery 6th pharyngeal arch artery pulmonary arch UBERON:0003123 pharyngeal arch artery 6 The vessels formed within the sixth pair of branchial arches in embryogenesis. MP:0006355 The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005016 TAO ZFIN:curator The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] 2012-06-20 AAO:0010422 AAO ISBN:0-02-377110-0 The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. Wikipedia:Aortic_arches#Arch_6 the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries http://emedicine.medscape.com/article/899609-overview 6th arch artery EMAPA:17005 AA6 ZFA:0005016 aortic arch 6 ZFA:0005016 sixth aortic arch XAO:0000353 6th aortic arch artery EMAPA:17005 6th branchial arch artery EMAPA:17005 6th pharyngeal arch artery EMAPA:17005 pulmonary arch ISBN:0073040584 The outermost extraembryonic membrane of amniotes. The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG] The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]. Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] chorionic The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584] Extra-embryonic ectoderm BTO:0000252 CALOHA:TS-0144 EFO:0002780 EHDAA2:0000245 EHDAA:150 EMAPA:16112 EV:0100121 FMA:80224 GAID:1299 MESH:D002823 NCIT:C34122 NCIT:C34124 UMLS:C0008503 UMLS:C1516505 VHOG:0000200 Wikipedia:Chorion chorion chorion (vertebrates) embryonic chorion fetal chorion uterine chorion uberon chorion frondosum chorionic sac UBERON:0003124 This term refers to the amniote structure. It is distinct from the concept of chorion in insects chorion membrane http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png Hymans ISBN:0073040584 The outermost extraembryonic membrane of amniotes. MESH:A10.615.284.473 MP:0002836 http://orcid.org/0000-0002-6601-2165 https://github.com/geneontology/go-ontology/issues/22603 The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG] 2012-09-17 VHOG:0000200 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/chorion The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]. BTO:0000252 Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000200 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 http://bgee.unil.ch/ Extra-embryonic ectoderm PMID:19829370 UMLS:C0008503 ncithesaurus:Chorion UMLS:C1516505 ncithesaurus:Chorionic_Sac uterine chorion ZFIN:curator http://orcid.org/0000-0002-6601-2165 chorion frondosum Wikipedia:Chorion chorionic sac Wikipedia:Chorion The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. An elongated tube which carries air to and from the lungs.[AAO] The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] tracheal In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. in mouse 15-18 C-rings, 15-20 in human. AAO:0010140 BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 NCIT:C12428 SCTID:181213009 UMLS:C0040578 VHOG:0000371 Wikipedia:Vertebrate_trachea XAO:0000118 cartilaginous trachea vertebrate trachea windpipe uberon tracheal tubule UBERON:0003126 trachea http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb EHDAA2 The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. GO:0060438 Wikipedia:Vertebrate_trachea An elongated tube which carries air to and from the lungs.[AAO] 2012-06-20 AAO:0010140 AAO AAO:BJB The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000371 VHOG http://bgee.unil.ch/ In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] 2012-09-17 VHOG:0000371 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409 http://bgee.unil.ch/ in mouse 15-18 C-rings, 15-20 in human. ISBN:0123813611 UMLS:C0040578 ncithesaurus:Trachea vertebrate trachea tracheal tubule BTO:0001388 Upper portion of the skull that excludes the mandible (when present in the organism). cranial the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton BTO:0001328 EFO:0000831 EHDAA:6029 EMAPA:17680 FMA:71325 MA:0000316 MAT:0000340 MESH:D012886 MIAA:0000340 SCTID:181889008 VHOG:0000334 Wikipedia:Cranium_(anatomy) bones of cranium ossa cranii set of bones of cranium skull minus mandible upper part of skull uberon calvarium epicranial plate skeletal system of head UBERON:0003128 cranium FMA-inferred Upper portion of the skull that excludes the mandible (when present in the organism). Wikipedia:Cranium_(anatomy) http://orcid.org/0000-0002-6601-2165 the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium FMA The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton WP MESH:D012886 https://github.com/biopragmatics/biomappings bones of cranium FMA:71325 ossa cranii FMA:71325 FMA:TA set of bones of cranium FMA:71325 calvarium BTO:0001328 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 NCIT:C12789 SCTID:110530005 UMLS:C0037303 Wikipedia:Skull WikipediaCategory:Skull galen:Skull uberon cranial skeleton skeletal system of head UBERON:0003129 skull FMA Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. PMID:11523816 Wikipedia:Skull http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376 in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. FMA A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates WP UMLS:C0037303 ncithesaurus:Skull An organ involved in reproduction. GO uses genitalia for the singular organ EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 SCTID:128181006 TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ uberon genitalia UBERON:0003133 reproductive organ An organ involved in reproduction. UBERON:xp GO uses genitalia for the singular organ GO EMAPA:37731 MA:th UMLS:C0017420 ncithesaurus:Genitalia genitalia A female organ involved in reproduction. EMAPA:28540 MA:0000544 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon UBERON:0003134 female reproductive organ A female organ involved in reproduction. UBERON:xp female organism reproductive organ OBOL:automatic female organism reproductive structure OBOL:automatic female organism reproductive system organ OBOL:automatic female organism sex organ OBOL:automatic female reproductive gland/organ MA:0000544 reproductive organ of female organism OBOL:automatic reproductive structure of female organism OBOL:automatic reproductive system organ of female organism OBOL:automatic sex organ of female organism OBOL:automatic A male organ involved in reproduction. MA:0000545 WBbt:0008423 male organism reproductive organ male organism reproductive structure male organism reproductive system organ male organism sex organ male reproductive gland/organ male reproductive system organ male sex organ reproductive organ of male organism reproductive structure of male organism reproductive system organ of male organism sex organ of male organism uberon male genital UBERON:0003135 male reproductive organ A male organ involved in reproduction. UBERON:xp male organism reproductive organ OBOL:automatic male organism reproductive structure OBOL:automatic male organism reproductive system organ OBOL:automatic male organism sex organ OBOL:automatic male reproductive gland/organ MA:0000545 reproductive organ of male organism OBOL:automatic reproductive structure of male organism OBOL:automatic reproductive system organ of male organism OBOL:automatic sex organ of male organism OBOL:automatic male genital WBbt:0008423 Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBbt:00005159 FMA:77853 gustatory organ system organ gustatory system organ organ of gustatory organ system organ of gustatory system organ of taste system taste organ taste system organ uberon UBERON:0003212 gustatory organ Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBC:auto_generated_definition FBbt:00005159 gustatory organ system organ OBOL:automatic gustatory system organ OBOL:automatic organ of gustatory organ system OBOL:automatic organ of gustatory system OBOL:automatic organ of taste system OBOL:automatic taste system organ OBOL:automatic Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. uberon UBERON:0003218 ovary septum Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. GO:0080126 One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]. A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 EHDAA:5915 EMAPA:17375 SCTID:361529008 VHOG:0000540 Wikipedia:Metanephric_blastema metanephric blastema metanephric mesoderm metanephrogenic mesenchyme metanephros associated mesenchyme uberon UBERON:0003220 Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme ISBN:9780878932504 One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]. GO:0072075 Wikipedia:Metanephric_blastema A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] 2012-09-17 VHOG:0000540 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] 2012-09-17 VHOG:0000540 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 http://bgee.unil.ch/ metanephric blastema Wikipedia:Metanephric_blastema metanephric mesoderm Wikipedia:Metanephric_blastema metanephrogenic mesenchyme EHDAA:5021 metanephros associated mesenchyme RETIRED_EHDAA2:0001139 Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits. phalangeal In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three CALOHA:TS-2211 EMAPA:32614 FMA:321661 MA:0000304 NCIT:C33317 SCTID:290029003 UMLS:C0222682 VSAO:0000199 Wikipedia:Phalanx_bones galen:Phalanx digit long bone long bone of digit phalange phalanges phalanx bone uberon UBERON:0003221 phalanx Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits. VSAO:0000199 Wikipedia:Phalanx_bones In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three WP UMLS:C0222682 ncithesaurus:Phalanx digit long bone OBOL:automatic long bone of digit OBOL:automatic phalanges phalanx bone Wikipedia:Phalanx_bones An extraembryonic structure that develops_from a syncytiotrophoblast and is part of a chorion. TODO - check EHDAA2:0001973 EHDAA:156 uberon UBERON:0003224 chorion syncytiotrophoblast EHDAA2 polar trophectoderm syncytiotrophoblast EHDAA2 An extraembryonic structure that develops_from a syncytiotrophoblast and is part of a chorion. OBOL:automatic An epithelium that is part of a elbow [Automatically generated definition]. EHDAA2:0000430 EHDAA:4168 EHDAA:6214 EMAPA:17415 VHOG:0001044 cubital region epithelial tissue cubital region epithelium elbow epithelial tissue elbow epithelium epithelial tissue of cubital region epithelial tissue of elbow epithelium of cubital region uberon UBERON:0003229 epithelium of elbow EHDAA2 An epithelium that is part of a elbow [Automatically generated definition]. OBOL:automatic cubital region epithelial tissue OBOL:automatic cubital region epithelium OBOL:automatic elbow epithelial tissue OBOL:automatic elbow epithelium OBOL:automatic epithelial tissue of cubital region OBOL:automatic epithelial tissue of elbow OBOL:automatic epithelium of cubital region OBOL:automatic An epithelium that is part of a wrist [Automatically generated definition]. EHDAA2:0000219 EHDAA:5198 carpal region epithelial tissue carpal region epithelium epithelial tissue of carpal region epithelial tissue of wrist epithelium of wrist wrist epithelial tissue wrist epithelium uberon UBERON:0003230 epithelium of carpal region EHDAA2 EHDAA2 An epithelium that is part of a wrist [Automatically generated definition]. OBOL:automatic carpal region epithelial tissue OBOL:automatic carpal region epithelium OBOL:automatic epithelial tissue of carpal region OBOL:automatic epithelial tissue of wrist OBOL:automatic epithelium of wrist OBOL:automatic wrist epithelial tissue OBOL:automatic wrist epithelium OBOL:automatic An epithelium that is part of a hip [Automatically generated definition]. EHDAA2:0000784 EHDAA:5155 EHDAA:6180 EMAPA:17491 VHOG:0000779 epithelial tissue of hip epithelial tissue of hip region epithelial tissue of regio coxae epithelium of hip region epithelium of regio coxae hip epithelial tissue hip epithelium hip region epithelial tissue hip region epithelium regio coxae epithelial tissue regio coxae epithelium uberon UBERON:0003231 epithelium of hip EHDAA2 An epithelium that is part of a hip [Automatically generated definition]. OBOL:automatic epithelial tissue of hip OBOL:automatic epithelial tissue of hip region OBOL:automatic epithelial tissue of regio coxae OBOL:automatic epithelium of hip region OBOL:automatic epithelium of regio coxae OBOL:automatic hip epithelial tissue OBOL:automatic hip epithelium OBOL:automatic hip region epithelial tissue OBOL:automatic hip region epithelium OBOL:automatic regio coxae epithelial tissue OBOL:automatic regio coxae epithelium OBOL:automatic An epithelium that is part of a knee [Automatically generated definition]. EHDAA2:0000896 EHDAA:5161 EHDAA:6186 EMAPA:17494 VHOG:0000810 epithelial tissue of knee knee epithelial tissue knee epithelium uberon UBERON:0003232 epithelium of knee EHDAA2 An epithelium that is part of a knee [Automatically generated definition]. OBOL:automatic epithelial tissue of knee OBOL:automatic knee epithelial tissue OBOL:automatic knee epithelium OBOL:automatic An epithelium that is part of a shoulder [Automatically generated definition]. EHDAA2:0001835 EHDAA:4182 EHDAA:6230 EMAPA:17422 VHOG:0000761 epithelial tissue of shoulder shoulder epithelial tissue shoulder epithelium uberon UBERON:0003233 epithelium of shoulder EHDAA2 An epithelium that is part of a shoulder [Automatically generated definition]. OBOL:automatic epithelial tissue of shoulder OBOL:automatic shoulder epithelial tissue OBOL:automatic shoulder epithelium OBOL:automatic An epithelium that is part of a upper jaw [Automatically generated definition]. EHDAA2:0002119 EHDAA:8027 EMAPA:17943 EMAPA:18971 epithelial tissue of palatoquadrate arch epithelial tissue of upper jaw epithelium of palatoquadrate arch palatoquadrate arch epithelial tissue palatoquadrate arch epithelium upper jaw epithelial tissue upper jaw epithelium uberon UBERON:0003235 epithelium of upper jaw An epithelium that is part of a upper jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of palatoquadrate arch OBOL:automatic epithelial tissue of upper jaw OBOL:automatic epithelium of palatoquadrate arch OBOL:automatic palatoquadrate arch epithelial tissue OBOL:automatic palatoquadrate arch epithelium OBOL:automatic upper jaw epithelial tissue OBOL:automatic upper jaw epithelium OBOL:automatic An epithelium that is part of a lower jaw [Automatically generated definition]. EHDAA2:0001019 EHDAA:7999 EMAPA:35516 VHOG:0000802 epithelial tissue of lower jaw epithelial tissue of ventral mandibular arch epithelium of ventral mandibular arch lower jaw epithelial tissue lower jaw epithelium ventral mandibular arch epithelial tissue ventral mandibular arch epithelium uberon UBERON:0003236 epithelium of lower jaw An epithelium that is part of a lower jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of lower jaw OBOL:automatic epithelial tissue of ventral mandibular arch OBOL:automatic epithelium of ventral mandibular arch OBOL:automatic lower jaw epithelial tissue OBOL:automatic lower jaw epithelium OBOL:automatic ventral mandibular arch epithelial tissue OBOL:automatic ventral mandibular arch epithelium OBOL:automatic The epithelial layer of the luminal surfaces of the mammary gland. BTO:0001430 CALOHA:TS-0593 EHDAA2:0001057 EHDAA:6526 EMAPA:17760 FMA:74445 MA:0000792 NCIT:C12937 UMLS:C0596882 VHOG:0001088 epithelium of lactiferous gland lactiferous gland epithelium mammary epithelium mammary gland epithelial tissue mammary gland epithelium uberon UBERON:0003244 epithelium of mammary gland EHDAA2 Wikipathways:WP2062 The epithelial layer of the luminal surfaces of the mammary gland. MGI:csmith MP:0009504 UMLS:C0596882 ncithesaurus:Mammary_Epithelium epithelium of lactiferous gland FMA:74445 lactiferous gland epithelium FMA:74445 mammary epithelium BTO:0001430 mammary gland epithelial tissue OBOL:automatic mammary gland epithelium OBOL:automatic An epithelium that is part of a lower arm [Automatically generated definition]. EHDAA2:0000554 EHDAA:4174 EHDAA:6220 EMAPA:17418 VHOG:0001096 forearm epithelium uberon UBERON:0003247 epithelium of forearm EHDAA2 An epithelium that is part of a lower arm [Automatically generated definition]. OBOL:automatic An epithelium that is part of a footplate. EHDAA2:0000548 EHDAA:5145 EHDAA:6144 EMAPA:32655 foot plate epithelium footplate epithelium uberon UBERON:0003248 epithelium of footplate EHDAA2 EHDAA2 An epithelium that is part of a footplate. OBOL:automatic footplate epithelium EHDAA2:0000548 An epithelium that is part of a otic placode [Automatically generated definition]. check ZFA, placemeant, appears to refer to both adult structures and primordium EHDAA2:0001341 EHDAA:510 EMAPA:16197 VHOG:0000636 ZFA:0007068 epithelial tissue of otic placode otic epithelium otic placode epithelial tissue otic placode epithelium uberon UBERON:0003249 epithelium of otic placode An epithelium that is part of a otic placode [Automatically generated definition]. OBOL:automatic epithelial tissue of otic placode OBOL:automatic otic epithelium https://orcid.org/0000-0002-6601-2165 otic placode epithelial tissue OBOL:automatic otic placode epithelium OBOL:automatic Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case. Anatomical cluster that consists of more than one rib in an individual.[TAO] FMA:7480 SCTID:361741004 Wikipedia:Human_rib_cage Wikipedia:Rib_cage galen:RibCage cavea thoracis rib cage thoracic cage uberon cavea thoracis UBERON:0003252 thoracic rib cage http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case. https://orcid.org/0000-0002-6601-2165 Anatomical cluster that consists of more than one rib in an individual.[TAO] 2012-08-14 TAO:0002100 TAO TAO:wd cavea thoracis FMA:7480 FMA:TA rib cage FMA:7480 thoracic cage FMA:7480 cavea thoracis Wikipedia:Human_rib_cage The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs. EMAPA:37826 FMA:7576 SCTID:263359009 Wikipedia:Neck_of_rib collum costae rib neck uberon collum costae UBERON:0003253 neck of rib http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png PMID:15906248 The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs. Wikipedia:Neck_of_rib EMAPA:37826 MA:th collum costae Wikipedia:Neck_of_rib rib neck FMA:7576 collum costae Wikipedia:Neck_of_rib we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion. UBERON:0008359 BTO:0000897 EHDAA2:0000117 EHDAA:138 EMAPA:16110 VHOG:0000621 amnion ectoderm amnionic ectoderm uberon amnion epithelium UBERON:0003254 amniotic ectoderm EHDAA2 EHDAA2 EHDAA2 EHDAA2-via-amnioblasts ISBN:9780878932504 amnion ectoderm EHDAA2:0000117 OBOL:automatic amnionic ectoderm ISBN:9780878932504 http://placentation.ucsd.edu/glossfs.html amnion epithelium BTO:0000897 The portion of the yolk sac that is derived from endoderm and lines the yolk sac. EHDAA2:0002215 EHDAA:166 EMAPA:16086 VHOG:0000626 uberon UBERON:0003257 yolk sac endoderm EHDAA2 The portion of the yolk sac that is derived from endoderm and lines the yolk sac. UBERON:cjm An endoderm that is part of a foregut [Automatically generated definition]. TODO - check EHDAA2:0004568 EHDAA:524 foregut endoderm uberon UBERON:0003258 endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut endoderm OBOL:automatic An endoderm that is part of a midgut [Automatically generated definition]. TODO - check EHDAA:987 EMAPA:16257 RETIRED_EHDAA2:0001194 VHOG:0001080 midgut endoderm uberon UBERON:0003259 endoderm of midgut An endoderm that is part of a midgut [Automatically generated definition]. OBOL:automatic midgut endoderm OBOL:automatic An endoderm that is part of a hindgut [Automatically generated definition]. TODO - check EHDAA:979 RETIRED_EHDAA2:0000781 hindgut endoderm uberon UBERON:0003260 endoderm of hindgut An endoderm that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut endoderm OBOL:automatic An endoderm that is part of a thyroid primordium. UBERON:0005235 EHDAA:956 EMAPA:25357 RETIRED_EHDAA2:0002035 VHOG:0001089 endoderm of thyroid primordium uberon UBERON:0003261 thyroid primordium endoderm ZFA-propagated An endoderm that is part of a thyroid primordium. OBOL:automatic endoderm of thyroid primordium OBOL:automatic A mesenchyme that is part of a amnion. we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion. UBERON:0003411 EHDAA2:0000118 EHDAA:140 EMAPA:16111 EMAPA:16265 VHOG:0000622 amnion mesenchyme amnion mesoderm amnionic mesoderm mesenchyme of amnion uberon amnionic mesenchyme amnionic mesoderm UBERON:0003262 amniotic mesoderm EHDAA2 EHDAA2 A mesenchyme that is part of a amnion. OBOL:automatic amnion mesenchyme EHDAA2:0000118 amnion mesoderm OBOL:automatic amnionic mesoderm http://placentation.ucsd.edu/glossfs.html mesenchyme of amnion EMAPA:16265 amnionic mesenchyme EMAPA:16265 amnionic mesoderm EMAPA:16111 A mesenchyme that is part of a chorion. TODO - check UBERON:0003423 EHDAA2:0003245 EHDAA:154 EMAPA:16114 EMAPA:16266 RETIRED_EHDAA2:0000247 VHOG:0000620 chorion mesenchyme chorion mesoderm chorionic mesenchyme mesenchyme of chorion mesenchyme of chorion (vertebrates) uberon UBERON:0003265 chorionic mesenchyme EHDAA2 EHDAA2 ISBN:0073040584 A mesenchyme that is part of a chorion. OBOL:automatic chorion mesenchyme OBOL:automatic chorion mesoderm RETIRED_EHDAA2:0000247 chorionic mesenchyme EHDAA2:0003245 mesenchyme of chorion (vertebrates) OBOL:automatic A calcareous tooth that is part of the upper jaw region. In mammals, the upper jaw teeth are attached to the maxilla. Note that we follow EHDAA2 and consider teeth part of the jaw skeleton EHDAA:8045 EMAPA:17938 MA:0001909 NCIT:C49792 SCTID:422279005 UMLS:C1710581 upper jaw tooth maxillary tooth uberon UBERON:0003267 tooth of upper jaw A calcareous tooth that is part of the upper jaw region. In mammals, the upper jaw teeth are attached to the maxilla. http://orcid.org/0000-0002-6601-2165 UMLS:C1710581 ncithesaurus:Upper_Jaw_Tooth upper jaw tooth MA:0001909 maxillary tooth NCBITaxon:40674 A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary). EHDAA2:0001029 EHDAA:8009 EMAPA:17917 FMA:321647 MA:0001907 NCIT:C49582 SCTID:422032003 UMLS:C1708757 calcareous tooth of lower jaw lower jaw calcareous tooth lower jaw dentine containing tooth lower jaw tooth lower jaw vertebrate tooth mandibular tooth uberon UBERON:0003268 tooth of lower jaw A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary). http://orcid.org/0000-0002-6601-2165 UMLS:C1708757 ncithesaurus:Lower_Jaw_Tooth calcareous tooth of lower jaw OBOL:automatic lower jaw calcareous tooth OBOL:automatic lower jaw dentine containing tooth OBOL:automatic lower jaw tooth OBOL:automatic lower jaw vertebrate tooth OBOL:automatic mandibular tooth NCBITaxon:40674 A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. EHDAA2:0000486 EHDAA:2923 EMAPA:17844 eye skeletal muscle eye skeletal muscle tissue skeletal muscle tissue of eye uberon eye skeletal muscle group UBERON:0003269 skeletal muscle tissue of eye A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. OBOL:automatic eye skeletal muscle OBOL:automatic eye skeletal muscle tissue OBOL:automatic skeletal muscle tissue of eye OBOL:automatic eye skeletal muscle group EHDAA2:0000486 A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones. The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 upper jaw AAO:0000622 EHDAA2:0002128 EHDAA:8041 EMAPA:17927 FMA:54397 MA:0001908 VHOG:0000429 XAO:0003087 upper jaw skeleton uberon UBERON:0003277 skeleton of upper jaw A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones. http://orcid.org/0000-0002-6601-2165 The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000429 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 http://bgee.unil.ch/ EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 EMAPA upper jaw MA:0001908 A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 lower jaw mandible AAO:0000274 EHDAA2:0004606 EHDAA:8005 EMAPA:17906 EMAPA:17910 FMA:54398 MA:0001906 TAO:0001273 VHOG:0000428 XAO:0003084 ZFA:0001273 lower jaw skeleton uberon mandibles mandibular series UBERON:0003278 skeleton of lower jaw EHDAA2 VHOG-modified A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. http://orcid.org/0000-0002-6601-2165 The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] 2012-08-14 TAO:0001273 TAO ZFIN:curator The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000428 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 http://bgee.unil.ch/ Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 FMA lower jaw MA:0001906 ZFA:0001273 mandible ZFA:0001273 lower jaw skeleton AAO:0000274 mandibles TAO:0001273 mandibular series ZFA:0001273 An endothelium that is part of a trachea. EHDAA:3082 RETIRED_EHDAA2:0002068 endothelium of windpipe trachea endothelium windpipe endothelium uberon UBERON:0003279 endothelium of trachea An endothelium that is part of a trachea. OBOL:automatic endothelium of windpipe OBOL:automatic trachea endothelium OBOL:automatic windpipe endothelium OBOL:automatic The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. TODO - check primitive vs developed The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG] EHDAA2:0001922 EHDAA:2999 EMAPA:17024 MA:0001617 SCTID:261623000 VHOG:0000358 mesentery of ventriculus mesogaster mesogastium mesogastrium stomach mesentery ventriculus mesentery uberon UBERON:0003281 mesentery of stomach MA MA The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. http://medical-dictionary.thefreedictionary.com/mesogastrium The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG] 2012-09-17 VHOG:0000358 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mesogastrium mesentery of ventriculus OBOL:automatic mesogaster http://medical-dictionary.thefreedictionary.com/mesogastrium mesogastium MA:0001617 mesogastrium http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/peritoneum.html stomach mesentery Obol:obol ventriculus mesentery OBOL:automatic A mesentery that surrounds the heart. EHDAA:432 EMAPA:16212 RETIRED_EHDAA2:0000739 VHOG:0000353 heart mesentery uberon cardiac mesentery mesocardium UBERON:0003282 mesentery of heart A mesentery that surrounds the heart. MA:th heart mesentery OBOL:automatic cardiac mesentery EMAPA:16212 mesocardium MA:0000098 A mesentery that is part of a esophagus [Automatically generated definition]. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0001288 EHDAA:2943 EMAPA:16836 MA:0001569 VHOG:0000415 esophagus mesentery gullet mesentery mesentery of esophagus mesentery of gullet meso-esophagus oesophagus mesentery uberon UBERON:0003283 mesentery of oesophagus A mesentery that is part of a esophagus [Automatically generated definition]. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000415 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ esophagus mesentery MA:0001569 gullet mesentery OBOL:automatic mesentery of esophagus OBOL:automatic mesentery of gullet OBOL:automatic oesophagus mesentery VHOG:0000415 A mesentery that is part of a midgut [Automatically generated definition]. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0001202 EHDAA:3031 EMAPA:16721 EMAPA:17039 EMAPA:17197 VHOG:0000413 midgut mesentery uberon UBERON:0003284 mesentery of midgut A mesentery that is part of a midgut [Automatically generated definition]. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000413 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ midgut mesentery OBOL:automatic A meninx that is part of a midbrain [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001174 EHDAA:3708 EMAPA:17791 MA:0001058 RETIRED_EHDAA2:0001109 VHOG:0000012 meninges of midbrain midbrain meninges midbrain meninx uberon mesencephalon meninges UBERON:0003288 meninx of midbrain A meninx that is part of a midbrain [Automatically generated definition]. OBOL:automatic Meninges that are part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000012 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000012 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ meninges of midbrain OBOL:automatic midbrain meninges OBOL:automatic midbrain meninx OBOL:automatic mesencephalon meninges VHOG:0000012 A meninx that is part of a telencephalon [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the telencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001990 EHDAA:5476 EMAPA:17774 MA:0000979 VHOG:0000010 meninges of telencephalon telencephalon meninges telencephalon meninx uberon UBERON:0003289 meninx of telencephalon A meninx that is part of a telencephalon [Automatically generated definition]. OBOL:automatic Meninges that are part of the telencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000010 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000010 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ meninges of telencephalon OBOL:automatic telencephalon meninges OBOL:automatic telencephalon meninx OBOL:automatic A meninx that is part of a diencephalon [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000399 EHDAA:5458 EMAPA:17764 MA:0000826 VHOG:0000009 between brain meninges between brain meninx diencephalon meninges diencephalon meninx interbrain meninges interbrain meninx mature diencephalon meninges mature diencephalon meninx meninges of between brain meninges of diencephalon meninges of interbrain meninges of mature diencephalon meninx of between brain meninx of interbrain meninx of mature diencephalon uberon UBERON:0003290 meninx of diencephalon A meninx that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Meninges that are part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000009 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000009 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ between brain meninges OBOL:automatic between brain meninx OBOL:automatic diencephalon meninges OBOL:automatic diencephalon meninx OBOL:automatic interbrain meninges OBOL:automatic interbrain meninx OBOL:automatic mature diencephalon meninges OBOL:automatic mature diencephalon meninx OBOL:automatic meninges of between brain OBOL:automatic meninges of diencephalon OBOL:automatic meninges of interbrain OBOL:automatic meninges of mature diencephalon OBOL:automatic meninx of between brain OBOL:automatic meninx of interbrain OBOL:automatic meninx of mature diencephalon OBOL:automatic A meninx that is part of a hindbrain [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000770 EHDAA:3688 EMAPA:17783 MA:0000987 VHOG:0000011 hindbrain meninges hindbrain meninx meninges of hindbrain uberon rhomencephalon meninges UBERON:0003291 meninx of hindbrain definitional A meninx that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Meninges that are part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000011 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000011 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ hindbrain meninges OBOL:automatic hindbrain meninx OBOL:automatic meninges of hindbrain OBOL:automatic rhomencephalon meninges VHOG:0000011 A meninx that is part of a spinal cord [Automatically generated definition]. Meninges that are part of the spinal cord. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] CALOHA:TS-2148 EHDAA2:0001895 EHDAA:2865 EMAPA:17804 MA:0001130 NCIT:C12350 SCTID:181097002 UMLS:C0037938 VHOG:0000443 menines of spinal cord meninges of spinal cord spinal cord meninges spinal cord meninx spinal meninges spinal meninx uberon UBERON:0003292 meninx of spinal cord A meninx that is part of a spinal cord [Automatically generated definition]. OBOL:automatic Meninges that are part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000443 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000443 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ UMLS:C0037938 ncithesaurus:Spinal_Meninges menines of spinal cord meninges of spinal cord OBOL:automatic spinal cord meninges OBOL:automatic spinal cord meninx OBOL:automatic spinal meninges A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 VHOG:0000650 foregut gland uberon UBERON:0003294 gland of foregut A gland that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut gland OBOL:automatic Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 EHDAA:2967 FMA:55075 pharynx gland uberon glandulae pharyngeae UBERON:0003295 pharyngeal gland BTO Racemose mucous glands beneath the mucous membrane of the pharynx. http://www.biology-online.org/dictionary/ pharynx gland EHDAA2:0001461 glandulae pharyngeae BTO:0004849 Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. EHDAA2:0000395 EHDAA:4475 EMAPA:16897 VHOG:0000653 diencephalon gland interbrain gland uberon UBERON:0003296 gland of diencephalon Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. http://orcid.org/0000-0002-6601-2165 diencephalon gland OBOL:automatic interbrain gland OBOL:automatic A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. OBOL:automatic integumental gland http://orcid.org/0000-0002-6601-2165 integumental system gland http://orcid.org/0000-0002-6601-2165 integumentary gland http://orcid.org/0000-0002-6601-2165 A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 EHDAA2:0003241 EHDAA:170 EMAPA:16115 mesoderm blood islands uberon mesenchyme blood island UBERON:0003304 mesoderm blood island EHDAA2 EHDAA2 A blood island that is part of a mesoderm. OBOL:automatic in EHDAA2, gives rise to blood and dorsal aorta EHDAA2 mesoderm blood islands EHDAA2:0003241 mesenchyme blood island OBOL:automatic Mesenchyme that is part of a developing testis [Automatically generated definition]. EHDAA2:0002010 EHDAA:8150 EMAPA:35858 VHOG:0001442 testis mesenchyme uberon UBERON:0003312 mesenchyme of testis Mesenchyme that is part of a developing testis [Automatically generated definition]. OBOL:automatic testis mesenchyme OBOL:automatic Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 EHDAA:2910 EMAPA:16673 VHOG:0001084 mesenchyme of eye uberon UBERON:0003314 eye mesenchyme EHDAA2 Mesenchyme that is part of a developing camera-type eye. OBOL:automatic mesenchyme of eye OBOL:automatic Mesenchyme that is part of a developing ovary [Automatically generated definition]. EHDAA2:0001362 EHDAA:8128 VHOG:0001441 female reproductive system gonad mesenchyme female reproductive system gonada mesenchyme gonad of female reproductive system mesenchyme gonada of female reproductive system mesenchyme mesenchyme of female reproductive system gonad mesenchyme of female reproductive system gonada mesenchyme of gonad of female reproductive system mesenchyme of gonada of female reproductive system ovary mesenchyme uberon UBERON:0003315 mesenchyme of ovary Mesenchyme that is part of a developing ovary [Automatically generated definition]. OBOL:automatic female reproductive system gonad mesenchyme OBOL:automatic female reproductive system gonada mesenchyme OBOL:automatic gonad of female reproductive system mesenchyme OBOL:automatic gonada of female reproductive system mesenchyme OBOL:automatic mesenchyme of female reproductive system gonad OBOL:automatic mesenchyme of female reproductive system gonada OBOL:automatic mesenchyme of gonad of female reproductive system OBOL:automatic mesenchyme of gonada of female reproductive system OBOL:automatic ovary mesenchyme OBOL:automatic The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme. UBERON:0003264 EHDAA2:0002216 EHDAA:168 EHDAA:205 EMAPA:16087 EMAPA:16267 VHOG:0000503 VHOG:0000617 yolk sac mesenchyme uberon UBERON:0003316 mesenchyme of yolk sac The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme. UBERON:cjm yolk sac mesenchyme OBOL:automatic Mesenchyme that is part of a developing elbow [Automatically generated definition]. EHDAA2:0000432 EHDAA:4170 EHDAA:6216 EMAPA:17416 VHOG:0001075 cubital region mesenchyme elbow mesenchyme mesenchyme of cubital region uberon UBERON:0003318 mesenchyme of elbow Mesenchyme that is part of a developing elbow [Automatically generated definition]. OBOL:automatic cubital region mesenchyme OBOL:automatic elbow mesenchyme OBOL:automatic mesenchyme of cubital region OBOL:automatic Mesenchyme of the carpal region that contributes to the carpal skeleton. EHDAA2:0000220 EHDAA:5200 EMAPA:19122 carpal region mesenchyme carpus mesenchyme mesenchyme of wrist wrist mesenchyme uberon UBERON:0003319 mesenchyme of carpal region Mesenchyme of the carpal region that contributes to the carpal skeleton. https://orcid.org/0000-0002-6601-2165 carpal region mesenchyme OBOL:automatic carpus mesenchyme OBOL:automatic mesenchyme of wrist OBOL:automatic wrist mesenchyme OBOL:automatic Mesenchyme that is part of a developing hip [Automatically generated definition]. EHDAA2:0000786 EHDAA:5157 EHDAA:6182 EMAPA:17492 VHOG:0001029 hip mesenchyme hip region mesenchyme mesenchyme of hip region mesenchyme of regio coxae regio coxae mesenchyme uberon UBERON:0003320 mesenchyme of hip Mesenchyme that is part of a developing hip [Automatically generated definition]. OBOL:automatic hip mesenchyme OBOL:automatic hip region mesenchyme OBOL:automatic mesenchyme of hip region OBOL:automatic mesenchyme of regio coxae OBOL:automatic regio coxae mesenchyme OBOL:automatic Mesenchyme that is part of a developing knee [Automatically generated definition]. EHDAA2:0000898 EHDAA:5163 EHDAA:6188 EMAPA:17495 VHOG:0001070 knee mesenchyme uberon UBERON:0003321 mesenchyme of knee Mesenchyme that is part of a developing knee [Automatically generated definition]. OBOL:automatic knee mesenchyme OBOL:automatic Mesenchyme that is part of a developing shoulder [Automatically generated definition]. EHDAA2:0001837 EHDAA:4184 EHDAA:6232 EMAPA:17423 VHOG:0001035 shoulder mesenchyme uberon UBERON:0003322 mesenchyme of shoulder Mesenchyme that is part of a developing shoulder [Automatically generated definition]. OBOL:automatic shoulder mesenchyme OBOL:automatic Mesenchyme that is part of a developing upper jaw [Automatically generated definition]. EHDAA2:0002124 EHDAA:8031 EMAPA:17929 VHOG:0001099 mesenchyme of palatoquadrate arch palatoquadrate arch mesenchyme upper jaw mesenchyme uberon UBERON:0003323 mesenchyme of upper jaw EHDAA2 Mesenchyme that is part of a developing upper jaw [Automatically generated definition]. OBOL:automatic mesenchyme of palatoquadrate arch OBOL:automatic palatoquadrate arch mesenchyme OBOL:automatic upper jaw mesenchyme OBOL:automatic Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 EMAPA:17916 VHOG:0001069 lower jaw mesenchyme mesenchyme of ventral mandibular arch ventral mandibular arch mesenchyme uberon UBERON:0003324 mesenchyme of lower jaw EHDAA2 Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. OBOL:automatic lower jaw mesenchyme OBOL:automatic mesenchyme of ventral mandibular arch OBOL:automatic ventral mandibular arch mesenchyme OBOL:automatic Mesenchyme that is part of a developing pinna [Automatically generated definition]. EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation EHDAA2:0001469 EHDAA:8981 EMAPA:17591 VHOG:0000747 auricle mesenchyme auricle of ear mesenchyme auricle of external ear mesenchyme auricula (auris externa) mesenchyme auricula mesenchyme mesenchyme of auricle mesenchyme of auricle of ear mesenchyme of auricle of external ear mesenchyme of auricula mesenchyme of auricula (auris externa) mesenchyme of pinna of ear pinna mesenchyme pinna of ear mesenchyme uberon UBERON:0003325 mesenchyme of pinna Mesenchyme that is part of a developing pinna [Automatically generated definition]. OBOL:automatic EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation EMAPA auricle mesenchyme OBOL:automatic auricle of ear mesenchyme OBOL:automatic auricle of external ear mesenchyme OBOL:automatic auricula (auris externa) mesenchyme OBOL:automatic auricula mesenchyme OBOL:automatic mesenchyme of auricle OBOL:automatic mesenchyme of auricle of ear OBOL:automatic mesenchyme of auricle of external ear OBOL:automatic mesenchyme of auricula OBOL:automatic mesenchyme of auricula (auris externa) OBOL:automatic mesenchyme of pinna of ear OBOL:automatic pinna mesenchyme OBOL:automatic pinna of ear mesenchyme OBOL:automatic Mesenchyme that is part of a developing mammary gland. EHDAA2:0001058 EHDAA:6528 EMAPA:17761 VHOG:0001087 lactiferous gland mesenchyme lobe of breast mesenchyme lobe of mammary gland mesenchyme mammary gland mesenchyme mammary mesenchyme mesenchyme of lactiferous gland mesenchyme of lobe of breast mesenchyme of lobe of mammary gland uberon UBERON:0003326 mesenchyme of mammary gland Mesenchyme that is part of a developing mammary gland. OBOL:automatic lactiferous gland mesenchyme OBOL:automatic lobe of breast mesenchyme OBOL:automatic lobe of mammary gland mesenchyme OBOL:automatic mammary gland mesenchyme OBOL:automatic mesenchyme of lactiferous gland OBOL:automatic mesenchyme of lobe of breast OBOL:automatic mesenchyme of lobe of mammary gland OBOL:automatic Mesenchyme that is part of a developing lower arm [Automatically generated definition]. EHDAA2:0000555 EHDAA:4176 EHDAA:6222 EMAPA:17419 VHOG:0000504 uberon UBERON:0003327 mesenchyme of forearm Mesenchyme that is part of a developing lower arm [Automatically generated definition]. OBOL:automatic Mesenchyme that is part of a footplate. We group two EMAPA classes here but these may need to be separated UBERON:0005260 EHDAA2:0000549 EHDAA:5149 EHDAA:6172 EMAPA:17252 EMAPA:17488 VHOG_RETIRED:0001055 foot plate mesenchyme uberon UBERON:0003328 mesenchyme of footplate EHDAA2 Mesenchyme that is part of a footplate. OBOL:automatic We group two EMAPA classes here but these may need to be separated EMAPA A submucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27217 EMAPA:27227 EMAPA:27535 FMA:85399 SCTID:7892006 anal canal submucosa anal canal viewed anatomically submucosa anal region submucosa anatomical anal canal submucosa submucosa of anal canal viewed anatomically submucosa of anal region submucosa of anatomical anal canal uberon UBERON:0003329 submucosa of anal canal A submucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic anal canal submucosa OBOL:automatic anal canal viewed anatomically submucosa OBOL:automatic anal region submucosa OBOL:automatic anatomical anal canal submucosa OBOL:automatic submucosa of anal canal viewed anatomically OBOL:automatic submucosa of anal region OBOL:automatic submucosa of anatomical anal canal OBOL:automatic The submucous layer of the wall of the rectum. BTO:0002114 EMAPA:27083 FMA:15034 SCTID:71683001 rectal submucosa rectum submucosa tela submucosa recti uberon UBERON:0003330 submucosa of rectum The submucous layer of the wall of the rectum. BTO:0002114 rectal submucosa FMA:15034 rectum submucosa OBOL:automatic tela submucosa recti BTO:0002114 A submucosa that is part of a colon [Automatically generated definition]. EMAPA:27379 FMA:14985 MA:0003200 SCTID:61647009 colon submucosa colonic submucosa large bowel submucosa submucosa of large bowel uberon UBERON:0003331 submucosa of colon A submucosa that is part of a colon [Automatically generated definition]. OBOL:automatic colon submucosa OBOL:automatic colonic submucosa FMA:14985 large bowel submucosa OBOL:automatic submucosa of large bowel OBOL:automatic A submucosa that is part of a duodenum [Automatically generated definition]. EMAPA:27027 EMAPA:27097 EMAPA:27239 FMA:14943 MA:0003213 SCTID:76519004 doudenal submucosa duodenal submucosa duodenum submucosa uberon UBERON:0003332 submucosa of duodenum A submucosa that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal submucosa FMA:14943 duodenal submucosa FMA:14943 duodenum submucosa OBOL:automatic A submucosa that is part of a jejunum [Automatically generated definition]. EMAPA:27111 FMA:14950 SCTID:70192009 jejunal submucosa jejunum submucosa uberon UBERON:0003333 submucosa of jejunum A submucosa that is part of a jejunum [Automatically generated definition]. OBOL:automatic jejunal submucosa FMA:14950 jejunum submucosa OBOL:automatic A serous membrane that is part of a rectum [Automatically generated definition]. EMAPA:27087 FMA:15039 rectal serosa rectum serosa rectum serous membrane serous membrane of rectum visceral peritoneum of rectum uberon UBERON:0003334 serosa of rectum A serous membrane that is part of a rectum [Automatically generated definition]. OBOL:automatic rectal serosa FMA:15039 rectum serosa OBOL:automatic rectum serous membrane OBOL:automatic serous membrane of rectum OBOL:automatic visceral peritoneum of rectum FMA:15039 A serous membrane that is part of a colon [Automatically generated definition]. EMAPA:27387 FMA:14990 MA:0003199 SCTID:90132000 colon serosa colon serous membrane colonic serosa large bowel serosa large bowel serous membrane serosa of large bowel serous membrane of colon serous membrane of large bowel visceral peritoneum of colon uberon UBERON:0003335 serosa of colon A serous membrane that is part of a colon [Automatically generated definition]. OBOL:automatic colon serosa OBOL:automatic colon serous membrane OBOL:automatic colonic serosa FMA:14990 large bowel serosa OBOL:automatic large bowel serous membrane OBOL:automatic serosa of large bowel OBOL:automatic serous membrane of colon OBOL:automatic serous membrane of large bowel OBOL:automatic visceral peritoneum of colon FMA:14990 A serous membrane that is part of a duodenum [Automatically generated definition]. 1st part serosa, 2nd - 4th adventitia EMAPA:27247 FMA:14948 MA:0003212 SCTID:1236009 doudenal serosa duodenal serosa duodenum serosa duodenum serous membrane serous membrane of duodenum visceral peritoneum of duodenum uberon UBERON:0003336 serosa of duodenum A serous membrane that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal serosa FMA:14948 duodenal serosa FMA:14948 duodenum serosa OBOL:automatic duodenum serous membrane OBOL:automatic serous membrane of duodenum OBOL:automatic visceral peritoneum of duodenum FMA:14948 A serous membrane that is part of a jejunum [Automatically generated definition]. EMAPA:27115 FMA:14955 jejunal serosa jejunum serosa jejunum serous membrane serous membrane of jejunum visceral peritoneum of jejunum uberon UBERON:0003337 serosa of jejunum A serous membrane that is part of a jejunum [Automatically generated definition]. OBOL:automatic jejunal serosa FMA:14955 jejunum serosa OBOL:automatic jejunum serous membrane OBOL:automatic serous membrane of jejunum OBOL:automatic visceral peritoneum of jejunum FMA:14955 A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS BIRNLEX:2548 BTO:0001123 EMAPA:32814 MA:0001161 peripheral nervous system ganglion uberon UBERON:0003338 ganglion of peripheral nervous system A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). BIRNLEX:2548 we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS MA peripheral nervous system ganglion OBOL:automatic A ganglion that is part of a central nervous system [Automatically generated definition]. this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia EHDAA2:0000227 EMAPA:16658 FMA:83843 central nervous system ganglion ganglion of neuraxis neuraxis ganglion uberon UBERON:0003339 ganglion of central nervous system A ganglion that is part of a central nervous system [Automatically generated definition]. OBOL:automatic this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia FMA central nervous system ganglion OBOL:automatic ganglion of neuraxis OBOL:automatic neuraxis ganglion OBOL:automatic A mucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27531 FMA:74654 NCIT:C60784 SCTID:362170004 UMLS:C0227414 anal canal mucosa anal canal mucosa of organ anal canal mucous membrane anal canal organ mucosa anal canal viewed anatomically mucosa anal canal viewed anatomically mucosa of organ anal canal viewed anatomically mucous membrane anal canal viewed anatomically organ mucosa anal mucosa anal mucous membrane anal region mucosa anal region mucosa of organ anal region mucous membrane anal region organ mucosa anatomical anal canal mucosa anatomical anal canal mucosa of organ anatomical anal canal mucous membrane anatomical anal canal organ mucosa mucosa of anal canal viewed anatomically mucosa of anal region mucosa of anatomical anal canal mucosa of organ of anal canal mucosa of organ of anal canal viewed anatomically mucosa of organ of anal region mucosa of organ of anatomical anal canal mucous membrane of anal canal mucous membrane of anal canal viewed anatomically mucous membrane of anal region mucous membrane of anatomical anal canal organ mucosa of anal canal organ mucosa of anal canal viewed anatomically organ mucosa of anal region organ mucosa of anatomical anal canal uberon UBERON:0003342 mucosa of anal canal A mucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0227414 ncithesaurus:Anal_Mucosa anal canal mucosa OBOL:automatic anal canal mucosa of organ OBOL:automatic anal canal mucous membrane OBOL:automatic anal canal organ mucosa OBOL:automatic anal canal viewed anatomically mucosa OBOL:automatic anal canal viewed anatomically mucosa of organ OBOL:automatic anal canal viewed anatomically mucous membrane OBOL:automatic anal canal viewed anatomically organ mucosa OBOL:automatic anal mucosa FMA:74654 anal mucous membrane FMA:74654 anal region mucosa OBOL:automatic anal region mucosa of organ OBOL:automatic anal region mucous membrane OBOL:automatic anal region organ mucosa OBOL:automatic anatomical anal canal mucosa OBOL:automatic anatomical anal canal mucosa of organ OBOL:automatic anatomical anal canal mucous membrane OBOL:automatic anatomical anal canal organ mucosa OBOL:automatic mucosa of anal canal viewed anatomically OBOL:automatic mucosa of anal region OBOL:automatic mucosa of anatomical anal canal OBOL:automatic mucosa of organ of anal canal OBOL:automatic mucosa of organ of anal canal viewed anatomically OBOL:automatic mucosa of organ of anal region OBOL:automatic mucosa of organ of anatomical anal canal OBOL:automatic mucous membrane of anal canal OBOL:automatic mucous membrane of anal canal viewed anatomically OBOL:automatic mucous membrane of anal region OBOL:automatic mucous membrane of anatomical anal canal OBOL:automatic organ mucosa of anal canal OBOL:automatic organ mucosa of anal canal viewed anatomically OBOL:automatic organ mucosa of anal region OBOL:automatic organ mucosa of anatomical anal canal OBOL:automatic A mucosa that is part of a oral opening [Automatically generated definition]. EMAPA:26937 SCTID:362083000 mucosa of oral opening mucosa of oral part of face mucosa of organ of oral opening mucosa of organ of oral part of face mucosa of organ of oral region mucosa of organ of subdivision of mouth mucosa of subdivision of mouth mucous membrane of oral opening mucous membrane of oral part of face mucous membrane of oral region mucous membrane of subdivision of mouth oral opening mucosa oral opening mucosa of organ oral opening mucous membrane oral opening organ mucosa oral part of face mucosa oral part of face mucosa of organ oral part of face mucous membrane oral part of face organ mucosa oral region mucosa oral region mucosa of organ oral region mucous membrane oral region organ mucosa organ mucosa of oral opening organ mucosa of oral part of face organ mucosa of oral region organ mucosa of subdivision of mouth subdivision of mouth mucosa subdivision of mouth mucosa of organ subdivision of mouth mucous membrane subdivision of mouth organ mucosa uberon UBERON:0003343 mucosa of oral region A mucosa that is part of a oral opening [Automatically generated definition]. OBOL:automatic mucosa of oral opening OBOL:automatic mucosa of oral part of face OBOL:automatic mucosa of organ of oral opening OBOL:automatic mucosa of organ of oral part of face OBOL:automatic mucosa of organ of oral region OBOL:automatic mucosa of organ of subdivision of mouth OBOL:automatic mucosa of subdivision of mouth OBOL:automatic mucous membrane of oral opening OBOL:automatic mucous membrane of oral part of face OBOL:automatic mucous membrane of oral region OBOL:automatic mucous membrane of subdivision of mouth OBOL:automatic oral opening mucosa OBOL:automatic oral opening mucosa of organ OBOL:automatic oral opening mucous membrane OBOL:automatic oral opening organ mucosa OBOL:automatic oral part of face mucosa OBOL:automatic oral part of face mucosa of organ OBOL:automatic oral part of face mucous membrane OBOL:automatic oral part of face organ mucosa OBOL:automatic oral region mucosa OBOL:automatic oral region mucosa of organ OBOL:automatic oral region mucous membrane OBOL:automatic oral region organ mucosa OBOL:automatic organ mucosa of oral opening OBOL:automatic organ mucosa of oral part of face OBOL:automatic organ mucosa of oral region OBOL:automatic organ mucosa of subdivision of mouth OBOL:automatic subdivision of mouth mucosa OBOL:automatic subdivision of mouth mucosa of organ OBOL:automatic subdivision of mouth mucous membrane OBOL:automatic subdivision of mouth organ mucosa OBOL:automatic A mucosa that is part of a rectum [Automatically generated definition]. CALOHA:TS-2107 EMAPA:27081 FMA:15033 MA:0003218 SCTID:362167003 mucosa of organ of rectum mucous membrane of rectum organ mucosa of rectum rectal mucosa rectal mucous membrane rectum mucosa rectum mucosa of organ rectum mucous membrane rectum organ mucosa uberon UBERON:0003346 mucosa of rectum A mucosa that is part of a rectum [Automatically generated definition]. OBOL:automatic mucosa of organ of rectum OBOL:automatic mucous membrane of rectum OBOL:automatic organ mucosa of rectum OBOL:automatic rectal mucosa FMA:15033 rectal mucous membrane FMA:15033 rectum mucosa OBOL:automatic rectum mucosa of organ OBOL:automatic rectum mucous membrane OBOL:automatic rectum organ mucosa OBOL:automatic A layer of epithelial cells on the surface of the mucosa. BTO:0003752 uberon lamina epithelialis mucosa lamina epithelialis mucosae UBERON:0003350 lies on top of lamina propria epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 lamina epithelialis mucosa BTO:0003752 lamina epithelialis mucosae BTO:0003752 An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 BTO:0005240 EMAPA:16708 MA:0002725 RETIRED_EHDAA2:0001460 TAO:0001174 XAO:0003202 ZFA:0001174 epithelial tissue of pharynx epithelium of pharynx pharynx epithelial tissue pharynx epithelium uberon UBERON:0003351 pharyngeal epithelium ZFA ZFA An epithelium that is part of a pharynx [Automatically generated definition]. OBOL:automatic Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001174 TAO ZFIN:curator epithelial tissue of pharynx OBOL:automatic epithelium of pharynx OBOL:automatic pharynx epithelial tissue OBOL:automatic pharynx epithelium OBOL:automatic An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 EMAPA:16569 MA:0003205 epithelial tissue of midgut midgut epithelial tissue midgut epithelium uberon UBERON:0003352 epithelium of midgut BTO An epithelium that is part of a midgut. OBOL:automatic epithelial tissue of midgut OBOL:automatic midgut epithelial tissue OBOL:automatic midgut epithelium BTO:0005053 OBOL:automatic An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon UBERON:0003353 epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. OBOL:automatic epithelial tissue of hindgut OBOL:automatic hindgut epithelial tissue OBOL:automatic hindgut epithelium OBOL:automatic An epithelium that is part of a rectum [Automatically generated definition]. CALOHA:TS-2066 EHDAA2:0001594 EMAPA:17898 FMA:17510 MA:0003219 VHOG:0001037 epithelial tissue of rectum rectal epithelium rectum epithelial tissue rectum epithelium uberon UBERON:0003354 epithelium of rectum An epithelium that is part of a rectum [Automatically generated definition]. OBOL:automatic epithelial tissue of rectum OBOL:automatic rectal epithelium FMA:17510 rectum epithelial tissue OBOL:automatic rectum epithelium OBOL:automatic An epithelium that is part of a nasal septum [Automatically generated definition]. EMAPA:18442 epithelial tissue of nasal septum nasal septum epithelial tissue nasal septum epithelium uberon UBERON:0003356 epithelium of nasal septum An epithelium that is part of a nasal septum [Automatically generated definition]. OBOL:automatic epithelial tissue of nasal septum OBOL:automatic nasal septum epithelial tissue OBOL:automatic nasal septum epithelium OBOL:automatic An epithelium that is part of a tongue [Automatically generated definition]. BTO:0000992 CALOHA:TS-1051 EHDAA2:0004598 EMAPA:17881 FMA:284658 MA:0001592 NCIT:C49300 UMLS:C1710436 epithelial tissue of tongue tongue epithelial tissue tongue epithelium uberon lingual epithelium UBERON:0003357 examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies. epithelium of tongue An epithelium that is part of a tongue [Automatically generated definition]. OBOL:automatic UMLS:C1710436 ncithesaurus:Tongue_Epithelium epithelial tissue of tongue OBOL:automatic tongue epithelial tissue OBOL:automatic tongue epithelium OBOL:automatic lingual epithelium BTO:0000992 An epithelium that is part of a submandibular gland [Automatically generated definition]. BTO:0004557 EMAPA:18813 VHOG:0000989 epithelial tissue of submandibular gland submandibular gland epithelial tissue submandibular gland epithelium uberon submandibular duct epithelium submandibular gland duct epithelium submaxillary gland epithelium UBERON:0003359 epithelium of submandibular gland An epithelium that is part of a submandibular gland [Automatically generated definition]. OBOL:automatic epithelial tissue of submandibular gland OBOL:automatic submandibular gland epithelial tissue OBOL:automatic submandibular gland epithelium OBOL:automatic submandibular duct epithelium BTO:0004557 submandibular gland duct epithelium BTO:0004557 submaxillary gland epithelium EMAPA:18813 An epithelium that is part of a right lung [Automatically generated definition]. EMAPA:17663 MA:0003132 epithelial tissue of right lung right lung epithelial tissue right lung epithelium uberon UBERON:0003364 epithelium of right lung An epithelium that is part of a right lung [Automatically generated definition]. OBOL:automatic epithelial tissue of right lung OBOL:automatic right lung epithelial tissue OBOL:automatic right lung epithelium OBOL:automatic An epithelium that is part of a left lung [Automatically generated definition]. EMAPA:17655 MA:0003131 epithelial tissue of left lung left lung epithelial tissue left lung epithelium uberon UBERON:0003365 epithelium of left lung An epithelium that is part of a left lung [Automatically generated definition]. OBOL:automatic epithelial tissue of left lung OBOL:automatic left lung epithelial tissue OBOL:automatic left lung epithelium OBOL:automatic An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 EMAPA:16780 VHOG:0001048 hindlimb ectoderm hindlimb bud ectoderm hindlimb ectoderm lower limb bud ectoderm pelvic fin bud ectoderm uberon leg ectoderm UBERON:0003371 pelvic appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pelvic appendage bud. OBOL:automatic hindlimb ectoderm VHOG:0001048 hindlimb bud ectoderm EMAPA:16780 hindlimb ectoderm VHOG:0001048 lower limb bud ectoderm EHDAA2:0001034 pelvic fin bud ectoderm leg ectoderm OBOL:automatic An unilaminar epithelium that surrounds a pectoral appendage bud. UBERON:0005231 UBERON:0005663 EHDAA2:0002134 EMAPA:16407 VHOG:0001047 forelimb bud ectoderm forelimb ectoderm pectoral fin bud ectoderm upper limb bud ectoderm wing ectoderm uberon arm ectoderm UBERON:0003372 pectoral appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pectoral appendage bud. OBOL:automatic forelimb bud ectoderm EMAPA:16407 forelimb ectoderm VHOG:0001047 pectoral fin bud ectoderm upper limb bud ectoderm EHDAA2:0002134 wing ectoderm Geisha:syn NCBITaxon:8782 arm ectoderm OBOL:automatic An ectoderm that is part of a footplate. EMAPA:17250 uberon UBERON:0003373 ectoderm of footplate An ectoderm that is part of a footplate. OBOL:automatic An extraembryonic structure that develops_from a ectoderm and is part of a chorion. BTO:0005145 EMAPA:16113 chorion ectoderm uberon chorion epithelium chorionic epithelium UBERON:0003374 chorionic ectoderm ISBN:0073040584 An extraembryonic structure that develops_from a ectoderm and is part of a chorion. OBOL:automatic chorion ectoderm OBOL:automatic chorionic epithelium BTO:0005145 A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. EHDAA2:0004155 EMAPA:17326 FMA:7282 SCTID:362018002 VHOG:0001227 cardiac muscle of cardiac right atrium cardiac muscle of heart right atrium cardiac muscle tissue of heart right atrium cardiac muscle tissue of right atrium cardiac muscle tissue of right atrium of heart myocardium of right atrium right atrium heart muscle right atrium myocardium textus muscularis of myocardium of right atrium textus muscularis of myocardium of right atrium of heart textus muscularis of myocardium of right cardiac atrium uberon UBERON:0003379 cardiac muscle of right atrium A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. OBOL:automatic cardiac muscle of cardiac right atrium OBOL:automatic cardiac muscle of heart right atrium OBOL:automatic cardiac muscle tissue of heart right atrium OBOL:automatic cardiac muscle tissue of right atrium OBOL:automatic cardiac muscle tissue of right atrium of heart OBOL:automatic right atrium heart muscle EHDAA2:0004155 right atrium myocardium VHOG:0001227 textus muscularis of myocardium of right atrium OBOL:automatic textus muscularis of myocardium of right atrium of heart OBOL:automatic textus muscularis of myocardium of right cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. EHDAA2:0004154 EMAPA:17320 FMA:7285 SCTID:189936008 VHOG:0001225 cardiac left atrium cardiac muscle cardiac left atrium cardiac muscle tissue cardiac muscle of cardiac left atrium cardiac muscle of heart left atrium cardiac muscle of left atrium of heart left atrium heart muscle left atrium myocardium myocardium of left atrium textus muscularis of myocardium of cardiac left atrium textus muscularis of myocardium of heart left atrium textus muscularis of myocardium of left atrium textus muscularis of myocardium of left atrium of heart textus muscularis of myocardium of left cardiac atrium uberon UBERON:0003380 cardiac muscle of left atrium A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. OBOL:automatic cardiac left atrium cardiac muscle OBOL:automatic cardiac left atrium cardiac muscle tissue OBOL:automatic cardiac muscle of cardiac left atrium OBOL:automatic cardiac muscle of heart left atrium OBOL:automatic cardiac muscle of left atrium of heart OBOL:automatic left atrium heart muscle EHDAA2:0004154 left atrium myocardium VHOG:0001225 textus muscularis of myocardium of cardiac left atrium OBOL:automatic textus muscularis of myocardium of heart left atrium OBOL:automatic textus muscularis of myocardium of left atrium OBOL:automatic textus muscularis of myocardium of left atrium of heart OBOL:automatic textus muscularis of myocardium of left cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. EMAPA:17342 FMA:83452 VHOG:0001236 cardiac muscle tissue of right ventricle right ventricular cardiac muscle tissue uberon right ventricle cardiac muscle UBERON:0003381 cardiac muscle of right ventricle A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of right ventricle FMA:83452 right ventricular cardiac muscle tissue GO:0003221 right ventricle cardiac muscle VHOG:0001236 A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. EMAPA:17339 FMA:83453 VHOG:0001234 cardiac muscle tissue of left ventricle left ventricular cardiac muscle tissue uberon left ventricle cardiac muscle UBERON:0003382 cardiac muscle of left ventricle A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of left ventricle FMA:83453 left ventricular cardiac muscle tissue GO:0003220 left ventricle cardiac muscle VHOG:0001234 A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. EHDAA2:0004158 EMAPA:17335 FMA:84084 VHOG:0000999 cardiac muscle of interventricular septum cardiac muscle tissue of interventricular septum interventricular septum cardiac muscle interventricular septum heart muscle interventricular septum myocardium uberon interventricular septum muscle UBERON:0003383 cardiac muscle tissue of interventricular septum A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of interventricular septum FMA:84084 interventricular septum cardiac muscle VHOG:0000999 interventricular septum heart muscle EHDAA2:0004158 interventricular septum myocardium VHOG:0000999 interventricular septum muscle http://orcid.org/0000-0002-6601-2165 A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. EMAPA:18963 pharynx skeletal muscle pharynx skeletal muscle tissue skeletal muscle tissue of pharynx uberon UBERON:0003384 skeletal muscle tissue of pharynx A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. OBOL:automatic pharynx skeletal muscle OBOL:automatic pharynx skeletal muscle tissue OBOL:automatic skeletal muscle tissue of pharynx OBOL:automatic Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi. Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle EMAPA:18807 MA:0001268 ocular smooth muscle uberon UBERON:0003386 smooth muscle of eye Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi. MGI:cwg MP:0005247 ocular smooth muscle MA:0001268 A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. UBERON:0004244 BTO:0001391 EMAPA:19192 FMA:262010 MA:0001863 NCIT:C49306 UMLS:C1710458 trachea smooth muscle tracheal smooth muscle uberon UBERON:0003387 smooth muscle of trachea A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic UMLS:C1710458 ncithesaurus:Trachea_Smooth_Muscle_Tissue trachea smooth muscle MA:0001863 tracheal smooth muscle BTO:0001391 A mesothelium that is part of a pericardium [Automatically generated definition]. RETIRED_EHDAA2:0001436 cavity of pericardial sac meso-epithelium cavity of pericardial sac mesothelium meso-epithelium of cavity of pericardial sac meso-epithelium of pericardial cavity mesothelium of cavity of pericardial sac pericardial cavity meso-epithelium pericardial cavity mesothelium uberon UBERON:0003388 mesothelium of pericardial cavity A mesothelium that is part of a pericardium [Automatically generated definition]. OBOL:automatic cavity of pericardial sac meso-epithelium OBOL:automatic cavity of pericardial sac mesothelium OBOL:automatic meso-epithelium of cavity of pericardial sac OBOL:automatic meso-epithelium of pericardial cavity OBOL:automatic mesothelium of cavity of pericardial sac OBOL:automatic pericardial cavity meso-epithelium OBOL:automatic pericardial cavity mesothelium OBOL:automatic A mesothelium that is part of a diaphragm [Automatically generated definition]. EMAPA:18429 diaphragm meso-epithelium diaphragm mesothelium meso-epithelium of diaphragm meso-epithelium of thoracic diaphragm mesothelium of thoracic diaphragm thoracic diaphragm meso-epithelium thoracic diaphragm mesothelium uberon UBERON:0003389 mesothelium of diaphragm A mesothelium that is part of a diaphragm [Automatically generated definition]. OBOL:automatic diaphragm meso-epithelium OBOL:automatic diaphragm mesothelium OBOL:automatic meso-epithelium of diaphragm OBOL:automatic meso-epithelium of thoracic diaphragm OBOL:automatic mesothelium of thoracic diaphragm OBOL:automatic thoracic diaphragm meso-epithelium OBOL:automatic thoracic diaphragm mesothelium OBOL:automatic A mesothelium that is part of a pleural cavity [Automatically generated definition]. BTO:0003155 EHDAA2:0001476 EMAPA:16775 FMA:18148 meso-epithelium of pleural cavity mesothelium of pleura pleural cavity meso-epithelium pleural cavity mesothelium pleural mesothelium uberon pleura UBERON:0003390 mesothelium of pleural cavity A mesothelium that is part of a pleural cavity [Automatically generated definition]. OBOL:automatic meso-epithelium of pleural cavity OBOL:automatic mesothelium of pleura FMA:18148 pleural cavity meso-epithelium OBOL:automatic pleural cavity mesothelium OBOL:automatic pleural mesothelium EMAPA:16775 pleura EMAPA:16775 A mesentery that is part of a urinary system [Automatically generated definition]. EMAPA:17367 MA:0003233 excretory system mesentery mesentery of excretory system mesentery of renal system mesentery of systema urinaria renal system mesentery systema urinaria mesentery urinary system mesentery uberon UBERON:0003393 mesentery of urinary system A mesentery that is part of a urinary system [Automatically generated definition]. OBOL:automatic excretory system mesentery OBOL:automatic mesentery of excretory system OBOL:automatic mesentery of renal system OBOL:automatic mesentery of systema urinaria OBOL:automatic renal system mesentery OBOL:automatic systema urinaria mesentery OBOL:automatic urinary system mesentery OBOL:automatic A mesentery that is part of a hindgut [Automatically generated definition]. EMAPA:16718 hindgut mesentery uberon UBERON:0003394 mesentery of hindgut A mesentery that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut mesentery OBOL:automatic A mesentery that is part of a rectum [Automatically generated definition]. EMAPA:18664 rectum mesentery uberon UBERON:0003395 mesentery of rectum A mesentery that is part of a rectum [Automatically generated definition]. OBOL:automatic rectum mesentery OBOL:automatic A mesentery that is part of a colon [Automatically generated definition]. EMAPA:18942 FMA:14645 SCTID:245457004 colon mesentery large bowel mesentery large intestinal mesentery mesentery of large bowel mesentery of large intestine mesocolon uberon UBERON:0003396 mesentery of colon FMA A mesentery that is part of a colon [Automatically generated definition]. OBOL:automatic colon mesentery OBOL:automatic large bowel mesentery OBOL:automatic large intestinal mesentery FMA:14645 mesentery of large bowel OBOL:automatic mesentery of large intestine FMA:14645 mesocolon https://github.com/obophenotype/uberon/issues/1473 A mesentery that is part of a duodenum [Automatically generated definition]. EMAPA:19081 duodenum mesentery uberon UBERON:0003397 mesentery of duodenum A mesentery that is part of a duodenum [Automatically generated definition]. OBOL:automatic duodenum mesentery OBOL:automatic A mesentery that is part of a jejunum [Automatically generated definition]. EMAPA:18670 FMA:14651 SCTID:261286003 jejunal mesentery jejunum mesentery mesojejunum uberon UBERON:0003398 mesentery of jejunum A mesentery that is part of a jejunum [Automatically generated definition]. OBOL:automatic mesojejunum http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/peritoneum.html A zone of skin that is part of a lower arm [Automatically generated definition]. EMAPA:18056 FMA:38265 MA:0000602 SCTID:181537008 forearm skin lower arm skin lower segment of arm skin skin of antebrachial region skin of lower arm skin of lower segment of arm skin of zeugopod of arm uberon UBERON:0003403 skin of forearm A zone of skin that is part of a lower arm [Automatically generated definition]. OBOL:automatic forearm skin FMA:38265 lower arm skin OBOL:automatic lower segment of arm skin OBOL:automatic skin of antebrachial region OBOL:automatic skin of lower arm OBOL:automatic skin of lower segment of arm OBOL:automatic skin of zeugopod of arm OBOL:automatic A cartilage element that is part of a respiratory system [Automatically generated definition]. EMAPA:18694 MA:0001818 apparatus respiratorius cartilage cartilage of apparatus respiratorius respiratory system cartilage uberon UBERON:0003406 cartilage of respiratory system A cartilage element that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius cartilage OBOL:automatic cartilage of apparatus respiratorius OBOL:automatic respiratory system cartilage OBOL:automatic A cartilage that is part of a nasal septum [Automatically generated definition]. EMAPA:25091 FMA:59503 MA:0003138 cartilago septal nasi nasal septum cartilage septal nasal cartilage uberon UBERON:0003407 cartilage of nasal septum A cartilage that is part of a nasal septum [Automatically generated definition]. OBOL:automatic cartilago septal nasi FMA:59503 nasal septum cartilage OBOL:automatic septal nasal cartilage FMA:59503 A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract A gland that is part of a digestive tract [Automatically generated definition]. OBOL:automatic digestive tract gland OBOL:automatic gland of digestive tract OBOL:automatic gland of lower gastrointestinal tract OBOL:automatic gut gland MA:0003202 lower gastrointestinal tract gland OBOL:automatic Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue. EMAPA:25097 lingual gland tongue gland uberon UBERON:0003409 gland of tongue Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue. http://www.merriam-webster.com/medical/lingual%20gland lingual gland OBOL:automatic tongue gland OBOL:automatic A gland that is part of a oropharynx [Automatically generated definition]. EMAPA:25095 gland of oral part of pharynx gland of oropharynx oral part of pharynx gland oropharynx gland uberon UBERON:0003410 oropharyngeal gland A gland that is part of a oropharynx [Automatically generated definition]. OBOL:automatic gland of oral part of pharynx OBOL:automatic gland of oropharynx EMAPA:25095 oral part of pharynx gland OBOL:automatic oropharynx gland OBOL:automatic Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] EHDAA2:0001035 EMAPA:16781 TAO:0001386 ZFA:0001386 leg mesenchyme lower limb bud mesenchyme hindlimb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon UBERON:0003412 pelvic appendage bud mesenchyme Mesenchyme that is part of a pelvic appendage bud. OBOL:automatic Mesoderm part of pelvic fin bud.[TAO] 2012-08-14 TAO:0001386 TAO ZFIN:curator leg mesenchyme OBOL:automatic lower limb bud mesenchyme EHDAA2:0001035 hindlimb bud mesenchyme EMAPA:16781 mesoderm pelvic fin bud ZFA:0001386 pelvic fin bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. Mesoderm that is part of the pectoral fin bud.[TAO] UBERON:0005703 EHDAA2:0002135 EHDAA:1703 EMAPA:16408 TAO:0000789 ZFA:0000789 arm mesenchyme forelimb bud mesenchyme mesoderm pectoral fin bud pectoral fin bud mesenchyme upper limb bud mesenchyme wing mesenchyme uberon UBERON:0003413 pectoral appendage bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. OBOL:automatic Mesoderm that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000789 TAO ZFIN:curator arm mesenchyme OBOL:automatic forelimb bud mesenchyme EMAPA:16408 mesoderm pectoral fin bud ZFA:0000789 pectoral fin bud mesenchyme upper limb bud mesenchyme EHDAA2:0002135 wing mesenchyme OBOL:automatic Mesenchyme that is part of a developing nasal septum [Automatically generated definition]. EMAPA:18443 FMA:312700 nasal septum mesenchyme uberon UBERON:0003415 mesenchyme of nasal septum Mesenchyme that is part of a developing nasal septum [Automatically generated definition]. OBOL:automatic nasal septum mesenchyme OBOL:automatic Mesenchyme that is part of a developing tongue [Automatically generated definition]. TODO - develops_from EHDAA2:0004614 EMAPA:17882 tongue mesenchyme uberon UBERON:0003416 mesenchyme of tongue Mesenchyme that is part of a developing tongue [Automatically generated definition]. OBOL:automatic tongue mesenchyme EHDAA2:0004614 Mesenchyme that is part of a developing submandibular gland [Automatically generated definition]. EMAPA:18814 VHOG:0001110 submandibular gland mesenchyme uberon submaxillary gland mesenchyme UBERON:0003418 mesenchyme of submandibular gland Mesenchyme that is part of a developing submandibular gland [Automatically generated definition]. OBOL:automatic submandibular gland mesenchyme OBOL:automatic submaxillary gland mesenchyme EMAPA:18814 A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]. TODO - check EMAPA:26127 EMAPA:35925 SCTID:368069009 Wikipedia:Wharton's_jelly Wharton's jelly umbilical cord mesenchyme uberon UBERON:0003422 mesenchyme of umbilical cord Wikipedia A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]. Wikipedia:Wharton's_jelly Wharton's jelly EMAPA:26127 umbilical cord mesenchyme OBOL:automatic A lymph node that is located in a kidney [Automatically generated definition]. Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland para-renal lymph node pararenal lymph node perirenal lymph node FMA:276799 MA:0002882 NCIT:C77646 UMLS:C2699031 kidney lymph node lymph node of kidney uberon UBERON:0003425 renal lymph node A lymph node that is located in a kidney [Automatically generated definition]. OBOL:automatic Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland PMID:16624319 NCBITaxon:10090 para-renal lymph node PMID:22740822 pararenal lymph node PMID:28346247 perirenal lymph node PMID:35764904 UMLS:C2699031 ncithesaurus:Renal_Lymph_Node kidney lymph node OBOL:automatic lymph node of kidney OBOL:automatic An adipose tissue that is part of a dermis [Automatically generated definition]. MA:0000798 adipose tissue of dermis dermis fat tissue dermis fatty tissue fat tissue of dermis fatty tissue of dermis uberon UBERON:0003426 dermis adipose tissue An adipose tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic adipose tissue of dermis OBOL:automatic dermis fat tissue OBOL:automatic dermis fatty tissue OBOL:automatic fat tissue of dermis OBOL:automatic fatty tissue of dermis OBOL:automatic A nerve that is part of an abdomen [Automatically generated definition]. MA:0000521 nerve of abdomen uberon UBERON:0003429 abdomen nerve A nerve that is part of an abdomen [Automatically generated definition]. OBOL:automatic nerve of abdomen OBOL:automatic A nerve that is part of a neck [Automatically generated definition]. EMAPA:37263 MA:0000588 neck (volume) nerve nerve of neck nerve of neck (volume) uberon UBERON:0003430 neck nerve A nerve that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37263 MA:th neck (volume) nerve OBOL:automatic nerve of neck OBOL:automatic nerve of neck (volume) OBOL:automatic A nerve that is part of a leg [Automatically generated definition]. EMAPA:37343 MA:0000673 nerve of leg uberon UBERON:0003431 leg nerve A nerve that is part of a leg [Automatically generated definition]. OBOL:automatic EMAPA:37343 MA:th nerve of leg OBOL:automatic A nerve that is part of a chest [Automatically generated definition]. EMAPA:37266 MA:0000551 anterior thoracic region nerve anterolateral part of thorax nerve front of thorax nerve nerve of anterior thoracic region nerve of anterolateral part of thorax nerve of chest nerve of front of thorax uberon UBERON:0003432 chest nerve A nerve that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37266 MA:th anterior thoracic region nerve OBOL:automatic anterolateral part of thorax nerve OBOL:automatic front of thorax nerve OBOL:automatic nerve of anterior thoracic region OBOL:automatic nerve of anterolateral part of thorax OBOL:automatic nerve of chest OBOL:automatic nerve of front of thorax OBOL:automatic A nerve that is part of an arm [Automatically generated definition]. EMAPA:37336 MA:0000595 brachial region nerve nerve of arm nerve of brachial region uberon UBERON:0003433 arm nerve A nerve that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37336 MA:th brachial region nerve OBOL:automatic nerve of arm OBOL:automatic nerve of brachial region OBOL:automatic A nerve that is part of a wrist [Automatically generated definition]. EMAPA:37339 MA:0000637 carpal region nerve nerve of carpal region nerve of wrist uberon UBERON:0003434 wrist nerve A nerve that is part of a wrist [Automatically generated definition]. OBOL:automatic EMAPA:37339 MA:th carpal region nerve OBOL:automatic nerve of carpal region OBOL:automatic nerve of wrist OBOL:automatic A nerve that is part of a toe [Automatically generated definition]. EMAPA:37348 MA:0000649 SCTID:300056004 digit of foot nerve digit of terminal segment of free lower limb nerve digitus pedis nerve foot digit nerve hind limb digit nerve nerve of digit of foot nerve of digit of terminal segment of free lower limb nerve of digitus pedis nerve of foot digit nerve of terminal segment of free lower limb digit nerve of toe terminal segment of free lower limb digit nerve toe nerve foot digit nerve uberon UBERON:0003435 pedal digit nerve A nerve that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37348 MA:th digit of foot nerve OBOL:automatic digit of terminal segment of free lower limb nerve OBOL:automatic digitus pedis nerve OBOL:automatic foot digit nerve MA:0000649 hind limb digit nerve OBOL:accepted nerve of digit of foot OBOL:automatic nerve of digit of terminal segment of free lower limb OBOL:automatic nerve of digitus pedis OBOL:automatic nerve of foot digit OBOL:automatic nerve of terminal segment of free lower limb digit OBOL:automatic nerve of toe OBOL:automatic terminal segment of free lower limb digit nerve OBOL:automatic toe nerve OBOL:automatic foot digit nerve NCBITaxon:9606 OBOL:accepted A nerve that is part of a shoulder [Automatically generated definition]. EMAPA:37335 MA:0000634 nerve of shoulder uberon UBERON:0003436 shoulder nerve A nerve that is part of a shoulder [Automatically generated definition]. OBOL:automatic EMAPA:37335 MA:th nerve of shoulder OBOL:automatic Any nerve that innervates the iris. added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea EMAPA:35449 MA:0001291 nerve of iris ciliary nerve uberon UBERON:0003438 iris nerve Any nerve that innervates the iris. UBERON:cjm nerve of iris OBOL:automatic A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:0000515 nerve of torso nerve of trunk torso nerve uberon trunk nerve UBERON:0003439 nerve of trunk region A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). http://orcid.org/0000-0002-6601-2165 EMAPA:37264 MA:th nerve of torso OBOL:automatic nerve of trunk OBOL:automatic torso nerve OBOL:automatic trunk nerve MA:0000515 A nerve that is part of a limb [Automatically generated definition]. EMAPA:37291 MA:0000693 SCTID:359923002 nerve of limb uberon UBERON:0003440 limb nerve A nerve that is part of a limb [Automatically generated definition]. OBOL:automatic EMAPA:37291 MA:th nerve of limb OBOL:automatic A nerve that is part of a forelimb [Automatically generated definition]. EMAPA:37334 MA:0000616 fore limb nerve nerve of fore limb nerve of forelimb nerve of superior member nerve of upper extremity wing nerve uberon UBERON:0003441 forelimb nerve A nerve that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37334 MA:th fore limb nerve OBOL:automatic nerve of fore limb OBOL:automatic nerve of forelimb OBOL:automatic nerve of superior member OBOL:automatic nerve of upper extremity OBOL:automatic wing nerve NCBITaxon:8782 OBOL:automatic A nerve that is part of a hindlimb [Automatically generated definition]. EMAPA:37342 MA:0000664 hind limb nerve nerve of hind limb nerve of hindlimb nerve of inferior member nerve of lower extremity uberon UBERON:0003442 hindlimb nerve A nerve that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37342 MA:th hind limb nerve OBOL:automatic nerve of hind limb OBOL:automatic nerve of hindlimb OBOL:automatic nerve of inferior member OBOL:automatic nerve of lower extremity OBOL:automatic A nerve that is located in a thoracic cavity [Automatically generated definition]. consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve EMAPA:37267 MA:0000556 cavity of chest nerve cavity of thorax nerve chest cavity nerve nerve of cavity of chest nerve of cavity of thorax nerve of chest cavity nerve of pectoral cavity nerve of thoracic cavity pectoral cavity nerve uberon UBERON:0003443 thoracic cavity nerve A nerve that is located in a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37267 MA:th cavity of chest nerve OBOL:automatic cavity of thorax nerve OBOL:automatic chest cavity nerve OBOL:automatic nerve of cavity of chest OBOL:automatic nerve of cavity of thorax OBOL:automatic nerve of chest cavity OBOL:automatic nerve of pectoral cavity OBOL:automatic nerve of thoracic cavity OBOL:automatic pectoral cavity nerve OBOL:automatic A nerve that is part of a pelvis [Automatically generated definition]. EMAPA:37269 MA:0000542 nerve of pelvis uberon UBERON:0003444 pelvis nerve A nerve that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37269 MA:th nerve of pelvis OBOL:automatic A nerve that is part of a foot [Automatically generated definition]. EMAPA:37347 MA:0000653 foot nerve nerve of foot uberon UBERON:0003445 pes nerve A nerve that is part of a foot [Automatically generated definition]. OBOL:automatic EMAPA:37347 MA:th foot nerve MA:0000653 nerve of foot OBOL:automatic A nerve that is part of an ankle [Automatically generated definition]. FMA placement dubious EMAPA:37346 MA:0000640 nerve of ankle tarsal region nerve uberon neural network of ankle UBERON:0003446 ankle nerve A nerve that is part of an ankle [Automatically generated definition]. OBOL:automatic FMA placement dubious FMA EMAPA:37346 MA:th nerve of ankle OBOL:automatic tarsal region nerve https://orcid.org/0000-0002-6601-2165 neural network of ankle FMA:86901 A nerve that is part of a finger [Automatically generated definition]. EMAPA:37341 MA:0000625 SCTID:181015006 digit of hand nerve digit of terminal segment of free upper limb nerve digitus manus nerve finger nerve hand digit nerve nerve of digit of hand nerve of digit of terminal segment of free upper limb nerve of digitus manus nerve of finger nerve of hand digit nerve of terminal segment of free upper limb digit terminal segment of free upper limb digit nerve uberon UBERON:0003447 digit nerve of manus A nerve that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37341 MA:th digit of hand nerve OBOL:automatic digit of terminal segment of free upper limb nerve OBOL:automatic digitus manus nerve OBOL:automatic finger nerve OBOL:automatic hand digit nerve MA:0000625 nerve of digit of hand OBOL:automatic nerve of digit of terminal segment of free upper limb OBOL:automatic nerve of digitus manus OBOL:automatic nerve of finger OBOL:automatic nerve of hand digit OBOL:automatic nerve of terminal segment of free upper limb digit OBOL:automatic terminal segment of free upper limb digit nerve OBOL:automatic A nerve that is part of a manus [Automatically generated definition]. EMAPA:37340 MA:0000629 hand nerve nerve of hand nerve of manus uberon UBERON:0003448 manus nerve A nerve that is part of a manus [Automatically generated definition]. OBOL:automatic EMAPA:37340 MA:th hand nerve MA:0000629 nerve of hand UBERON:cjm nerve of manus OBOL:automatic An intervertebral disk that is part of a tail [Automatically generated definition]. EMAPA:19592 MA:0000698 intervertebral disc of post-ventral region intervertebral disc of tail intervertebral disk of post-ventral region intervertebral disk of tail tail intervertebral disk tail spinal disc uberon UBERON:0003449 tail intervertebral disc An intervertebral disk that is part of a tail [Automatically generated definition]. OBOL:automatic intervertebral disc of post-ventral region UBERON:cjm intervertebral disc of tail OBOL:automatic intervertebral disk of post-ventral region OBOL:automatic intervertebral disk of tail OBOL:automatic tail intervertebral disk OBOL:automatic tail spinal disc OBOL:automatic A lymphatic vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37580 MA:0001824 apparatus respiratorius lymph vessel apparatus respiratorius lymphatic vessel lymph vessel of apparatus respiratorius lymph vessel of respiratory system lymphatic vessel of apparatus respiratorius lymphatic vessel of respiratory system respiratory system lymph vessel uberon UBERON:0003456 respiratory system lymphatic vessel A lymphatic vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37580 MA:th apparatus respiratorius lymph vessel OBOL:automatic apparatus respiratorius lymphatic vessel OBOL:automatic lymph vessel of apparatus respiratorius OBOL:automatic lymph vessel of respiratory system OBOL:automatic lymphatic vessel of apparatus respiratorius OBOL:automatic lymphatic vessel of respiratory system OBOL:automatic respiratory system lymph vessel OBOL:automatic A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 SCTID:118646007 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ uberon craniofacial bone UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone A bone that is part of a head [Automatically generated definition]. OBOL:automatic adult head bone OBOL:automatic adult head bone organ OBOL:automatic bone of adult head OBOL:automatic bone of head OBOL:automatic bone organ of adult head OBOL:automatic bone organ of head OBOL:automatic head bone organ OBOL:automatic craniofacial bone http://orcid.org/0000-0002-6601-2165 A bone that is part of a neck [Automatically generated definition]. EMAPA:37246 MA:0000584 bone of neck bone of neck (volume) bone organ of neck bone organ of neck (volume) neck (volume) bone neck (volume) bone organ neck bone organ uberon UBERON:0003458 neck bone A bone that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37246 MA:th bone of neck OBOL:automatic bone of neck (volume) OBOL:automatic bone organ of neck OBOL:automatic bone organ of neck (volume) OBOL:automatic neck (volume) bone OBOL:automatic neck (volume) bone organ OBOL:automatic neck bone organ OBOL:automatic A bone that is part of a chest [Automatically generated definition]. EMAPA:18025 MA:0000547 anterior thoracic region bone anterior thoracic region bone organ anterolateral part of thorax bone anterolateral part of thorax bone organ bone of anterior thoracic region bone of anterolateral part of thorax bone of chest bone of front of thorax bone organ of anterior thoracic region bone organ of anterolateral part of thorax bone organ of chest bone organ of front of thorax chest bone organ front of thorax bone front of thorax bone organ uberon UBERON:0003459 chest bone A bone that is part of a chest [Automatically generated definition]. OBOL:automatic anterior thoracic region bone OBOL:automatic anterior thoracic region bone organ OBOL:automatic anterolateral part of thorax bone OBOL:automatic anterolateral part of thorax bone organ OBOL:automatic bone of anterior thoracic region OBOL:automatic bone of anterolateral part of thorax OBOL:automatic bone of chest OBOL:automatic bone of front of thorax OBOL:automatic bone organ of anterior thoracic region OBOL:automatic bone organ of anterolateral part of thorax OBOL:automatic bone organ of chest OBOL:automatic bone organ of front of thorax OBOL:automatic chest bone organ OBOL:automatic front of thorax bone OBOL:automatic front of thorax bone organ OBOL:automatic A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. EMAPA:37303 MA:0000592 MESH:D050280 arm bone organ bone of arm bone organ of arm uberon bone of upper extremity UBERON:0003460 arm bone A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. https://orcid.org/0000-0002-6601-2165 EMAPA:37303 MA:th MESH:D050280 https://github.com/biopragmatics/biomappings arm bone organ OBOL:automatic bone of arm OBOL:automatic bone organ of arm OBOL:automatic bone of upper extremity GAID:178 A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods. this is a forelimb bone in MA, but this would lead to part-disjointness violations. MA:0000631 bone of shoulder shoulder-articulating bone uberon UBERON:0003461 shoulder bone UBERONREF:0000003 MA A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods. http://orcid.org/0000-0002-6601-2165 this is a forelimb bone in MA, but this would lead to part-disjointness violations. MA bone of shoulder OBOL:automatic A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 MESH:D005147 NCIT:C63706 SCTID:181799005 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone uberon bone of viscerocranium viscerocranium bone UBERON:0003462 facial bone MA A bone that is part of a facial skeleton [Automatically generated definition]. OBOL:automatic MESH:D005147 https://github.com/biopragmatics/biomappings UMLS:C0015455 ncithesaurus:Facial_Bone bone of facial skeleton OBOL:automatic facial bone EMAPA:19019 facial skeleton bone OBOL:automatic bone of viscerocranium OBOL:automatic viscerocranium bone OBOL:automatic A bone that is part of a trunk [Automatically generated definition]. EMAPA:36583 MA:0000512 SCTID:427358002 bone of torso bone of trunk bone organ of torso bone organ of trunk torso bone torso bone organ trunk bone organ uberon UBERON:0003463 trunk bone A bone that is part of a trunk [Automatically generated definition]. OBOL:automatic bone of torso OBOL:automatic bone of trunk OBOL:automatic bone organ of torso OBOL:automatic bone organ of trunk OBOL:automatic torso bone OBOL:automatic torso bone organ OBOL:automatic trunk bone organ OBOL:automatic A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle). the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc EFO:0003842 GAID:198 NCIT:C12982 SCTID:361370006 UMLS:C0448188 bone of hind limb bone of hindlimb bone of inferior member bone of lower extremity bone organ of hind limb bone organ of hindlimb bone organ of lower extremity hind limb bone hind limb bone organ hindlimb bone organ uberon UBERON:0003464 hindlimb bone A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle). https://orcid.org/0000-0002-6601-2165 the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc MA UMLS:C0448188 ncithesaurus:Bone_of_the_Lower_Extremity bone of hind limb OBOL:automatic bone of hindlimb OBOL:automatic bone of inferior member OBOL:automatic bone of lower extremity OBOL:automatic bone organ of hind limb OBOL:automatic bone organ of hindlimb OBOL:automatic bone organ of lower extremity OBOL:automatic hind limb bone OBOL:automatic hind limb bone organ OBOL:automatic hindlimb bone organ OBOL:automatic A bone that is part of a lower arm [Automatically generated definition]. EMAPA:35347 MA:0000598 antebrachial region bone antebrachial region bone organ arm zeugopod bone arm zeugopod bone organ lower arm bone zeugopod bone, forelimb zeugopod bone, upper wing zeugopod bone uberon UBERON:0003466 forelimb zeugopod bone A bone that is part of a lower arm [Automatically generated definition]. OBOL:automatic antebrachial region bone OBOL:automatic antebrachial region bone organ OBOL:automatic arm zeugopod bone OBOL:automatic arm zeugopod bone organ OBOL:automatic lower arm bone MA:0000598 zeugopod bone, forelimb OBOL:automatic zeugopod bone, upper OBOL:automatic wing zeugopod bone NCBITaxon:8782 OBOL:automatic The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery EMAPA:37676 FMA:70491 MA:0002074 SCTID:65376008 Wikipedia:Ureteral_branches_of_renal_artery uberon UBERON:0003468 ureteric segment of renal artery FMA FMA The ureteral branches of renal artery are small branches which supply the ureter. Wikipedia:Ureteral_branches_of_renal_artery ureteric artery MA:0002074 EMAPA:37676 MA:th An artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37569 MA:0001804 uberon UBERON:0003469 respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37569 MA:th The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose. EMAPA:37430 FMA:49570 MA:0001917 SCTID:145137009 Wikipedia:Superior_labial_artery arteria labialis superior ramus labialis superior arteriae facialis superior labial artery superior labial branch of facial artery uberon UBERON:0003470 artery of upper lip FMA The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose. Wikipedia:Superior_labial_artery EMAPA:37430 MA:th arteria labialis superior Wikipedia:Superior_labial_artery ramus labialis superior arteriae facialis Wikipedia:Superior_labial_artery superior labial artery FMA:49570 superior labial branch of facial artery FMA:49570 The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 FMA:49567 MA:0001916 SCTID:145036002 Wikipedia:Inferior_labial_artery arteria labialis inferior inferior labial artery inferior labial branch of facial artery ramus labialis inferior (arteria facialis) ramus labialis inferior arteriae facialis uberon UBERON:0003471 artery of lower lip FMA The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. Wikipedia:Inferior_labial_artery EMAPA:37429 MA:th arteria labialis inferior Wikipedia:Inferior_labial_artery inferior labial artery FMA:49567 inferior labial branch of facial artery FMA:49567 ramus labialis inferior (arteria facialis) FMA:TA ramus labialis inferior arteriae facialis Wikipedia:Inferior_labial_artery An artery that supplies blood to the cerebellum. EHDAA2:0000228 EHDAA:5290 EMAPA:37074 MA:0001933 NCIT:C52845 SCTID:278102002 UMLS:C0226246 Wikipedia:Cerebellar_artery uberon UBERON:0003472 cerebellar artery http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg An artery that supplies blood to the cerebellum. Wikipedia:Cerebellar_artery EMAPA:37074 MA:th UMLS:C0226246 ncithesaurus:Cerebellar_Artery An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity EMAPA:37241 MA:0001902 MESH:D013895 uberon thoracic artery UBERON:0003473 thoracic cavity artery An artery that is part of a thoracic cavity[cjm]. https://sourceforge.net/tracker/index.php?func=detail&aid=3317815&group_id=76834&atid=1205376 in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity MA EMAPA:37241 MA:th thoracic artery MESH:A07.231.114.891 One of the arteries supplying a meninix[Automatically generated definition]. EMAPA:37104 GAID:499 MA:0002001 MESH:D008576 Wikipedia:Meningeal_arteries uberon UBERON:0003474 meningeal artery One of the arteries supplying a meninix[Automatically generated definition]. Wikipedia:Meningeal_arteries EMAPA:37104 MA:th A vein that is part of a ureter [Automatically generated definition]. EMAPA:37679 MA:0002250 ureter vein vein of ureter uberon UBERON:0003475 ureteric vein A vein that is part of a ureter [Automatically generated definition]. OBOL:automatic EMAPA:37679 MA:th ureter vein OBOL:automatic vein of ureter OBOL:automatic A vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37584 MA:0001809 MA:0001810 apparatus respiratorius vein respiratory system vein vein of apparatus respiratorius vein of respiratory system uberon UBERON:0003476 respiratory system venous blood vessel A vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37584 MA:th apparatus respiratorius vein OBOL:automatic respiratory system vein OBOL:automatic vein of apparatus respiratorius OBOL:automatic vein of respiratory system OBOL:automatic The inferior labial vein is the vein receiving blood from the upper lip. EMAPA:37204 FMA:52538 MA:0002255 SCTID:422755007 Wikipedia:Superior_labial_vein superior labial vein upper lip vein vena labialis superior uberon UBERON:0003477 vein of upper lip The inferior labial vein is the vein receiving blood from the upper lip. Wikipedia:Superior_labial_vein EMAPA:37204 MA:th superior labial vein FMA:52538 upper lip vein OBOL:automatic vena labialis superior The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 FMA:52541 MA:0002253 SCTID:422955002 Wikipedia:Inferior_labial_vein inferior labial vein lower lip vein vena labialis inferior uberon venae labiales inferiores UBERON:0003478 vein of lower lip http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png The inferior labial vein is the vein receiving blood from the lower lip. Wikipedia:Inferior_labial_vein EMAPA:37202 MA:th inferior labial vein FMA:52541 lower lip vein OBOL:automatic vena labialis inferior venae labiales inferiores Wikipedia:Inferior_labial_vein A vein that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37242 MA:0001903 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity uberon UBERON:0003479 thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37242 MA:th cavity of chest vein OBOL:automatic cavity of thorax vein OBOL:automatic chest cavity vein OBOL:automatic pectoral cavity vein OBOL:automatic vein of cavity of chest OBOL:automatic vein of cavity of thorax OBOL:automatic vein of chest cavity OBOL:automatic vein of pectoral cavity OBOL:automatic vein of thoracic cavity OBOL:automatic A vein that is part of a clitoris [Automatically generated definition]. EMAPA:37201 MA:0002252 SCTID:360819004 clitoris vein uberon UBERON:0003480 vein of clitoris A vein that is part of a clitoris [Automatically generated definition]. OBOL:automatic EMAPA:37201 MA:th clitoris vein OBOL:automatic A vein that is part of a tail [Automatically generated definition]. see also caudal vein AAO:0011105 EMAPA:37761 MA:0002233 Wikipedia:Tail_vein XAO:0000393 post-vent region vein vein of post-vent region vein of tail uberon caudal vein UBERON:0003481 tail vein A vein that is part of a tail [Automatically generated definition]. OBOL:automatic Wikipedia:Tail_vein EMAPA:37761 MA:th post-vent region vein OBOL:automatic vein of post-vent region OBOL:automatic vein of tail OBOL:automatic caudal vein Wikipedia:Tail_vein A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]. EMAPA:37766 MA:0002673 MESH:D013950 NCIT:C38515 UMLS:C1515429 lymphoid tissue of thymus lymphoid tissue of thymus gland thymus gland lymphoid tissue uberon UBERON:0003483 thymus lymphoid tissue A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]. OBOL:automatic EMAPA:37766 MA:th UMLS:C1515429 ncithesaurus:Thymic_Lymphoid_Tissue lymphoid tissue of thymus OBOL:automatic lymphoid tissue of thymus gland OBOL:automatic thymus gland lymphoid tissue OBOL:automatic A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland. EMAPA:37531 MA:0002452 camera-type eye sebaceous gland sebaceous gland of camera-type eye sebaceous gland of vertebrate eye vertebrate eye sebaceous gland uberon UBERON:0003484 eye sebaceous gland MA A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland. http://orcid.org/0000-0002-6601-2165 EMAPA:37531 MA:th camera-type eye sebaceous gland OBOL:automatic sebaceous gland of camera-type eye OBOL:automatic sebaceous gland of vertebrate eye OBOL:automatic vertebrate eye sebaceous gland OBOL:automatic A sebaceous gland that is part of a vagina [Automatically generated definition]. EMAPA:37793 MA:0001732 sebaceous gland of vagina uberon UBERON:0003485 vagina sebaceous gland A sebaceous gland that is part of a vagina [Automatically generated definition]. OBOL:automatic EMAPA:37793 MA:th sebaceous gland of vagina OBOL:automatic A holocrine gland of the dermis that secretes sebum into hair follicles. MA:0000149 SCTID:115977007 cutaneous sebaceous gland sebaceous gland of skin uberon UBERON:0003487 skin sebaceous gland A holocrine gland of the dermis that secretes sebum into hair follicles. MP:0009535 sebaceous gland of skin OBOL:automatic A lactiferous gland that is part of the abdominal region [Automatically generated definition]. Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml EMAPA:36507 MA:0000787 SCTID:113191002 SCTID:68037003 abdomen lactiferous gland abdomen lobe of breast abdomen lobe of mammary gland abdomen mammary gland lactiferous gland of abdomen lobe of breast of abdomen lobe of mammary gland of abdomen mammary gland of abdomen uberon UBERON:0003488 abdominal mammary gland A lactiferous gland that is part of the abdominal region [Automatically generated definition]. OBOL:automatic abdomen lactiferous gland OBOL:automatic abdomen lobe of breast OBOL:automatic abdomen lobe of mammary gland OBOL:automatic abdomen mammary gland OBOL:automatic lactiferous gland of abdomen OBOL:automatic lobe of breast of abdomen OBOL:automatic lobe of mammary gland of abdomen OBOL:automatic mammary gland of abdomen OBOL:automatic An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 apparatus respiratorius blood capillary endothelium apparatus respiratorius capillary endothelium apparatus respiratorius capillary vessel endothelium apparatus respiratorius endothelium of blood capillary apparatus respiratorius endothelium of capillary apparatus respiratorius endothelium of capillary vessel blood capillary endothelium of apparatus respiratorius blood capillary endothelium of respiratory system capillary endothelium of apparatus respiratorius capillary endothelium of respiratory system capillary vessel endothelium of apparatus respiratorius capillary vessel endothelium of respiratory system endothelium of blood capillary of apparatus respiratorius endothelium of blood capillary of respiratory system endothelium of capillary of apparatus respiratorius endothelium of capillary of respiratory system endothelium of capillary vessel of apparatus respiratorius endothelium of capillary vessel of respiratory system respiratory system blood capillary endothelium respiratory system capillary vessel endothelium respiratory system endothelium of blood capillary respiratory system endothelium of capillary respiratory system endothelium of capillary vessel uberon UBERON:0003489 respiratory system capillary endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37575 MA:th apparatus respiratorius blood capillary endothelium OBOL:automatic apparatus respiratorius capillary endothelium OBOL:automatic apparatus respiratorius capillary vessel endothelium OBOL:automatic apparatus respiratorius endothelium of blood capillary OBOL:automatic apparatus respiratorius endothelium of capillary OBOL:automatic apparatus respiratorius endothelium of capillary vessel OBOL:automatic blood capillary endothelium of apparatus respiratorius OBOL:automatic blood capillary endothelium of respiratory system OBOL:automatic capillary endothelium of apparatus respiratorius OBOL:automatic capillary endothelium of respiratory system OBOL:automatic capillary vessel endothelium of apparatus respiratorius OBOL:automatic capillary vessel endothelium of respiratory system OBOL:automatic endothelium of blood capillary of apparatus respiratorius OBOL:automatic endothelium of blood capillary of respiratory system OBOL:automatic endothelium of capillary of apparatus respiratorius OBOL:automatic endothelium of capillary of respiratory system OBOL:automatic endothelium of capillary vessel of apparatus respiratorius OBOL:automatic endothelium of capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary endothelium OBOL:automatic respiratory system capillary vessel endothelium OBOL:automatic respiratory system endothelium of blood capillary OBOL:automatic respiratory system endothelium of capillary OBOL:automatic respiratory system endothelium of capillary vessel OBOL:automatic A venule that is part of a respiratory system [Automatically generated definition]. EMAPA:37587 MA:0001813 apparatus respiratorius venule venule of apparatus respiratorius venule of respiratory system uberon UBERON:0003494 respiratory system venule A venule that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37587 MA:th apparatus respiratorius venule OBOL:automatic venule of apparatus respiratorius OBOL:automatic venule of respiratory system OBOL:automatic An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 uberon UBERON:0003495 respiratory system arteriole true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An arteriole that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37568 MA:th A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 SCTID:127865000 adult head blood vessel blood vessel of adult head blood vessel of head uberon UBERON:0003496 head blood vessel true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A blood vessel that is part of a head [Automatically generated definition]. OBOL:automatic adult head blood vessel OBOL:automatic blood vessel of adult head OBOL:automatic blood vessel of head OBOL:automatic A blood vessel that is part of an abdomen [Automatically generated definition]. MA:0000518 blood vessel of abdomen uberon UBERON:0003497 abdomen blood vessel UBERON:0012254 A blood vessel that is part of an abdomen [Automatically generated definition]. OBOL:automatic blood vessel of abdomen OBOL:automatic UBERON:0012254 abdominal aorta artery A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 blood vessel of heart uberon cardiac blood vessel UBERON:0003498 heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. OBOL:automatic blood vessel of heart OBOL:automatic cardiac blood vessel EMAPA:35397 A blood vessel that is part of a brain [Automatically generated definition]. EMAPA:35182 MA:0002769 blood vessel of brain uberon UBERON:0003499 brain blood vessel A blood vessel that is part of a brain [Automatically generated definition]. OBOL:automatic blood vessel of brain OBOL:automatic A blood vessel that is part of a cornea [Automatically generated definition]. follow up on tracker item EMAPA:36611 MA:0001241 blood vessel of cornea cornea blood vessel uberon UBERON:0003500 corneal blood vessel A blood vessel that is part of a cornea [Automatically generated definition]. https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/index.php?func=detail&aid=3564332&group_id=36855&atid=440764 PMID:17051153 blood vessel of cornea OBOL:automatic cornea blood vessel OBOL:automatic A blood vessel that is part of a retina [Automatically generated definition]. EMAPA:36520 GAID:509 MA:0001317 MESH:D012171 SCTID:280692003 XAO:0004153 blood vessel of inner layer of eyeball blood vessel of retina blood vessel of tunica interna of eyeball inner layer of eyeball blood vessel retinal blood vessel tunica interna of eyeball blood vessel uberon UBERON:0003501 retina blood vessel A blood vessel that is part of a retina [Automatically generated definition]. OBOL:automatic blood vessel of inner layer of eyeball OBOL:automatic blood vessel of retina OBOL:automatic blood vessel of tunica interna of eyeball OBOL:automatic inner layer of eyeball blood vessel OBOL:automatic retinal blood vessel OBOL:automatic tunica interna of eyeball blood vessel OBOL:automatic A blood vessel that is part of a neck [Automatically generated definition]. EMAPA:37236 MA:0000583 blood vessel of neck blood vessel of neck (volume) neck (volume) blood vessel uberon UBERON:0003502 neck blood vessel A blood vessel that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37236 MA:th blood vessel of neck OBOL:automatic blood vessel of neck (volume) OBOL:automatic neck (volume) blood vessel OBOL:automatic A blood vessel that is part of a leg [Automatically generated definition]. EMAPA:36500 MA:0000669 blood vessel of leg uberon UBERON:0003503 leg blood vessel A blood vessel that is part of a leg [Automatically generated definition]. OBOL:automatic blood vessel of leg OBOL:automatic A blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:35731 EMAPA:35995 MA:0001799 apparatus respiratorius blood vessel blood vessel of apparatus respiratorius blood vessel of respiratory system uberon UBERON:0003504 respiratory system blood vessel A blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius blood vessel OBOL:automatic blood vessel of apparatus respiratorius OBOL:automatic blood vessel of respiratory system OBOL:automatic A blood vessel that is part of a trachea. UBERON:0003525 EMAPA:35874 MA:0001852 blood vessel of trachea uberon UBERON:0003505 trachea blood vessel A blood vessel that is part of a trachea. OBOL:automatic blood vessel of trachea OBOL:automatic A blood vessel that is part of a chest [Automatically generated definition]. EMAPA:37239 MA:0000549 anterior thoracic region blood vessel anterolateral part of thorax blood vessel blood vessel of anterior thoracic region blood vessel of anterolateral part of thorax blood vessel of chest blood vessel of front of thorax front of thorax blood vessel uberon UBERON:0003506 chest blood vessel A blood vessel that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37239 MA:th anterior thoracic region blood vessel OBOL:automatic anterolateral part of thorax blood vessel OBOL:automatic blood vessel of anterior thoracic region OBOL:automatic blood vessel of anterolateral part of thorax OBOL:automatic blood vessel of chest OBOL:automatic blood vessel of front of thorax OBOL:automatic front of thorax blood vessel OBOL:automatic A blood vessel that is part of an arm [Automatically generated definition]. EMAPA:37293 MA:0000591 blood vessel of arm uberon UBERON:0003507 arm blood vessel A blood vessel that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37293 MA:th blood vessel of arm OBOL:automatic A blood vessel that is part of a toe [Automatically generated definition]. EMAPA:37302 MA:0000645 blood vessel of digit of foot blood vessel of digit of terminal segment of free lower limb blood vessel of digitus pedis blood vessel of foot digit blood vessel of terminal segment of free lower limb digit blood vessel of toe digit of foot blood vessel digit of terminal segment of free lower limb blood vessel digitus pedis blood vessel foot digit blood vessel hind limb digit blood vessel terminal segment of free lower limb digit blood vessel toe blood vessel foot digit blood vessel uberon UBERON:0003508 pedal digit blood vessel A blood vessel that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37302 MA:th blood vessel of digit of foot OBOL:automatic blood vessel of digit of terminal segment of free lower limb OBOL:automatic blood vessel of digitus pedis OBOL:automatic blood vessel of foot digit OBOL:automatic blood vessel of terminal segment of free lower limb digit OBOL:automatic blood vessel of toe OBOL:automatic digit of foot blood vessel OBOL:automatic digit of terminal segment of free lower limb blood vessel OBOL:automatic digitus pedis blood vessel OBOL:automatic foot digit blood vessel MA:0000645 hind limb digit blood vessel OBOL:accepted terminal segment of free lower limb digit blood vessel OBOL:automatic toe blood vessel OBOL:automatic foot digit blood vessel NCBITaxon:9606 OBOL:accepted A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 uberon UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. https://orcid.org/0000-0002-6601-2165 A blood vessel that is part of a iris [Automatically generated definition]. EMAPA:37387 MA:0001290 ZFA:0005568 blood vessel of iris uberon UBERON:0003511 iris blood vessel A blood vessel that is part of a iris [Automatically generated definition]. OBOL:automatic EMAPA:37387 MA:th blood vessel of iris OBOL:automatic A blood vessel that is part of a lung [Automatically generated definition]. EMAPA:32867 MA:0002457 blood vessel of lung uberon pulmonary vascular element UBERON:0003512 lung blood vessel A blood vessel that is part of a lung [Automatically generated definition]. OBOL:automatic blood vessel of lung OBOL:automatic pulmonary vascular element EMAPA:32867 A blood vessel that is part of a trunk [Automatically generated definition]. EMAPA:37237 MA:0000511 blood vessel of torso blood vessel of trunk torso blood vessel uberon UBERON:0003513 trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37237 MA:th blood vessel of torso OBOL:automatic blood vessel of trunk OBOL:automatic torso blood vessel OBOL:automatic A blood vessel that is part of a limb [Automatically generated definition]. EMAPA:36598 MA:0000687 blood vessel of limb uberon UBERON:0003514 limb blood vessel A blood vessel that is part of a limb [Automatically generated definition]. OBOL:automatic blood vessel of limb OBOL:automatic A blood vessel that is part of a forelimb [Automatically generated definition]. EMAPA:37292 MA:0000611 anteriormost limb blood vessel blood vessel of anteriormost limb blood vessel of fore limb blood vessel of forelimb blood vessel of upper extremity fore limb blood vessel wing blood vessel uberon UBERON:0003515 forelimb blood vessel A blood vessel that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37292 MA:th anteriormost limb blood vessel OBOL:automatic blood vessel of anteriormost limb OBOL:automatic blood vessel of fore limb OBOL:automatic blood vessel of forelimb OBOL:automatic blood vessel of upper extremity OBOL:automatic fore limb blood vessel OBOL:automatic wing blood vessel NCBITaxon:8782 OBOL:automatic A blood vessel that is part of a hindlimb [Automatically generated definition]. EMAPA:37298 MA:0000659 blood vessel of hind limb blood vessel of hindlimb blood vessel of lower extremity hind limb blood vessel uberon UBERON:0003516 hindlimb blood vessel A blood vessel that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37298 MA:th blood vessel of hind limb OBOL:automatic blood vessel of hindlimb OBOL:automatic blood vessel of lower extremity OBOL:automatic hind limb blood vessel OBOL:automatic A blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:28457 MA:0001682 TAO:0005306 ZFA:0005306 blood vessel of kidney renal blood vessel uberon UBERON:0003517 kidney blood vessel A blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic blood vessel of kidney OBOL:automatic renal blood vessel OBOL:automatic A blood vessel that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37240 MA:0000554 blood vessel of cavity of chest blood vessel of cavity of thorax blood vessel of chest cavity blood vessel of pectoral cavity blood vessel of thoracic cavity cavity of chest blood vessel cavity of thorax blood vessel chest cavity blood vessel pectoral cavity blood vessel uberon UBERON:0003519 thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37240 MA:th blood vessel of cavity of chest OBOL:automatic blood vessel of cavity of thorax OBOL:automatic blood vessel of chest cavity OBOL:automatic blood vessel of pectoral cavity OBOL:automatic blood vessel of thoracic cavity OBOL:automatic cavity of chest blood vessel OBOL:automatic cavity of thorax blood vessel OBOL:automatic chest cavity blood vessel OBOL:automatic pectoral cavity blood vessel OBOL:automatic A blood vessel that is part of a pelvis [Automatically generated definition]. EMAPA:37244 MA:0000531 blood vessel of pelvis uberon UBERON:0003520 pelvis blood vessel A blood vessel that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37244 MA:th blood vessel of pelvis OBOL:automatic A blood vessel that is part of a foot [Automatically generated definition]. EMAPA:37301 MA:0000642 blood vessel of foot foot blood vessel uberon UBERON:0003521 pes blood vessel A blood vessel that is part of a foot [Automatically generated definition]. OBOL:automatic EMAPA:37301 MA:th blood vessel of foot OBOL:automatic foot blood vessel MA:0000642 A blood vessel that is part of a finger [Automatically generated definition]. EMAPA:37297 MA:0000621 blood vessel of digit of terminal segment of free upper limb blood vessel of terminal segment of free upper limb digit digit of terminal segment of free upper limb blood vessel finger blood vessel hand digit blood vessel terminal segment of free upper limb digit blood vessel hand digit blood vessel uberon UBERON:0003522 manual digit blood vessel A blood vessel that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37297 MA:th blood vessel of digit of terminal segment of free upper limb OBOL:automatic blood vessel of terminal segment of free upper limb digit OBOL:automatic digit of terminal segment of free upper limb blood vessel OBOL:automatic finger blood vessel OBOL:automatic hand digit blood vessel MA:0000621 terminal segment of free upper limb digit blood vessel OBOL:automatic hand digit blood vessel NCBITaxon:9606 OBOL:accepted A blood vessel that is part of a manus [Automatically generated definition]. EMAPA:37296 MA:0000618 blood vessel of hand blood vessel of manus hand blood vessel uberon UBERON:0003523 manus blood vessel A blood vessel that is part of a manus [Automatically generated definition]. OBOL:automatic EMAPA:37296 MA:th blood vessel of hand OBOL:automatic blood vessel of manus OBOL:automatic hand blood vessel MA:0000618 A blood vessel that is part of a tail [Automatically generated definition]. EMAPA:35848 MA:0000695 blood vessel of post-vent region blood vessel of tail post-vent region blood vessel uberon UBERON:0003524 tail blood vessel A blood vessel that is part of a tail [Automatically generated definition]. OBOL:automatic blood vessel of post-vent region OBOL:automatic blood vessel of tail OBOL:automatic post-vent region blood vessel OBOL:automatic A capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37574 MA:0001807 apparatus respiratorius blood capillary apparatus respiratorius capillary apparatus respiratorius capillary vessel blood capillary of apparatus respiratorius blood capillary of respiratory system capillary of apparatus respiratorius capillary of respiratory system capillary vessel of apparatus respiratorius capillary vessel of respiratory system respiratory system blood capillary respiratory system capillary vessel uberon UBERON:0003526 respiratory system capillary A capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37574 MA:th apparatus respiratorius blood capillary OBOL:automatic apparatus respiratorius capillary OBOL:automatic apparatus respiratorius capillary vessel OBOL:automatic blood capillary of apparatus respiratorius OBOL:automatic blood capillary of respiratory system OBOL:automatic capillary of apparatus respiratorius OBOL:automatic capillary of respiratory system OBOL:automatic capillary vessel of apparatus respiratorius OBOL:automatic capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary OBOL:automatic respiratory system capillary vessel OBOL:automatic A capillary that is part of a kidney [Automatically generated definition]. EMAPA:31443 MA:0002586 SCTID:275409003 blood capillary of kidney capillary of kidney capillary vessel of kidney kidney blood capillary kidney capillary vessel renal capillary uberon UBERON:0003527 kidney capillary A capillary that is part of a kidney [Automatically generated definition]. OBOL:automatic blood capillary of kidney OBOL:automatic capillary of kidney OBOL:automatic capillary vessel of kidney OBOL:automatic kidney blood capillary OBOL:automatic kidney capillary vessel OBOL:automatic renal capillary OBOL:automatic A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 NCIT:C49333 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon UBERON:0003528 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. OBOL:automatic UMLS:C1707348 ncithesaurus:Cerebral_Gray_Matter brain grey matter MA:0000810 brain grey substance OBOL:automatic gray matter of brain OBOL:automatic grey matter of brain OBOL:automatic grey substance of brain OBOL:automatic An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:37581 MA:0001825 apparatus respiratorius endothelium of lymph vessel apparatus respiratorius lymph vessel endothelium apparatus respiratorius lymphatic vessel endothelium endothelium of lymph vessel of apparatus respiratorius endothelium of lymph vessel of respiratory system lymph vessel endothelium of apparatus respiratorius lymph vessel endothelium of respiratory system lymphatic vessel endothelium of apparatus respiratorius lymphatic vessel endothelium of respiratory system respiratory system endothelium of lymph vessel respiratory system lymph vessel endothelium respiratory system lymphatic vessel endothelium uberon UBERON:0003529 respiratory system lymphatic vessel endothelium An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37581 MA:th apparatus respiratorius endothelium of lymph vessel OBOL:automatic apparatus respiratorius lymph vessel endothelium OBOL:automatic apparatus respiratorius lymphatic vessel endothelium OBOL:automatic endothelium of lymph vessel of apparatus respiratorius OBOL:automatic endothelium of lymph vessel of respiratory system OBOL:automatic lymph vessel endothelium of apparatus respiratorius OBOL:automatic lymph vessel endothelium of respiratory system OBOL:automatic lymphatic vessel endothelium of apparatus respiratorius OBOL:automatic lymphatic vessel endothelium of respiratory system OBOL:automatic respiratory system endothelium of lymph vessel OBOL:automatic respiratory system lymph vessel endothelium OBOL:automatic respiratory system lymphatic vessel endothelium OBOL:automatic A zone of skin that is part of a toe [Automatically generated definition]. EMAPA:32942 FMA:37852 MA:0000650 NCIT:C52719 SCTID:181530005 UMLS:C1708089 digit of foot skin digit of terminal segment of free lower limb skin digitus pedis skin foot digit skin hind limb digit skin skin of digit of foot skin of digit of terminal segment of free lower limb skin of digitus pedis skin of foot digit skin of terminal segment of free lower limb digit skin of toe terminal segment of free lower limb digit skin toe skin foot digit skin uberon UBERON:0003530 pedal digit skin A zone of skin that is part of a toe [Automatically generated definition]. OBOL:automatic UMLS:C1708089 ncithesaurus:Foot_Digit_Skin digit of foot skin OBOL:automatic digit of terminal segment of free lower limb skin OBOL:automatic digitus pedis skin OBOL:automatic foot digit skin MA:0000650 hind limb digit skin OBOL:accepted skin of digit of foot OBOL:automatic skin of digit of terminal segment of free lower limb OBOL:automatic skin of digitus pedis OBOL:automatic skin of foot digit OBOL:automatic skin of terminal segment of free lower limb digit OBOL:automatic skin of toe OBOL:automatic terminal segment of free lower limb digit skin OBOL:automatic toe skin OBOL:automatic foot digit skin NCBITaxon:9606 OBOL:accepted A zone of skin that is part of a forelimb [Automatically generated definition]. TODO - check free limb vs pectoral complex EMAPA:32612 FMA:23101 MA:0000617 NCIT:C12296 SCTID:244130001 UMLS:C0222212 anteriormost limb skin fore limb skin skin of fore limb skin of forelimb skin of upper limb upper limb skin wing skin uberon UBERON:0003531 forelimb skin A zone of skin that is part of a forelimb [Automatically generated definition]. OBOL:automatic UMLS:C0222212 ncithesaurus:Skin_of_the_Upper_Limb_and_Shoulder anteriormost limb skin OBOL:automatic fore limb skin OBOL:automatic skin of fore limb OBOL:automatic skin of forelimb OBOL:automatic skin of upper limb FMA:23101 upper limb skin FMA:23101 wing skin NCBITaxon:8782 OBOL:automatic A zone of skin that is part of a hindlimb [Automatically generated definition]. TODO - check free limb vs pelvic complex EMAPA:32620 FMA:23102 MA:0000665 NCIT:C12297 SCTID:181528008 UMLS:C0222268 hind limb skin lower limb skin skin of hind limb skin of hindlimb skin of lower extremity skin of lower limb uberon UBERON:0003532 hindlimb skin A zone of skin that is part of a hindlimb [Automatically generated definition]. OBOL:automatic UMLS:C0222268 ncithesaurus:Skin_of_the_Lower_Limb_and_Hip hind limb skin OBOL:automatic lower limb skin FMA:23102 lower limb skin https://orcid.org/0000-0002-0819-0473 skin of hind limb OBOL:automatic skin of hindlimb OBOL:automatic skin of lower extremity OBOL:automatic skin of lower limb FMA:23102 A zone of skin that is part of a finger [Automatically generated definition]. EMAPA:32648 FMA:38304 MA:0000626 NCIT:C52720 SCTID:361711001 UMLS:C1708318 digit of hand skin digit of terminal segment of free upper limb skin digitus manus skin finger skin fore limb digit skin hand digit skin skin of digit of hand skin of digit of terminal segment of free upper limb skin of digitus manus skin of finger skin of hand digit skin of terminal segment of free upper limb digit terminal segment of free upper limb digit skin hand digit skin uberon UBERON:0003533 manual digit skin A zone of skin that is part of a finger [Automatically generated definition]. OBOL:automatic UMLS:C1708318 ncithesaurus:Hand_Digit_Skin digit of hand skin OBOL:automatic digit of terminal segment of free upper limb skin OBOL:automatic digitus manus skin OBOL:automatic finger skin OBOL:automatic fore limb digit skin OBOL:accepted hand digit skin MA:0000626 skin of digit of hand OBOL:automatic skin of digit of terminal segment of free upper limb OBOL:automatic skin of digitus manus OBOL:automatic skin of finger OBOL:automatic skin of hand digit OBOL:automatic skin of terminal segment of free upper limb digit OBOL:automatic terminal segment of free upper limb digit skin OBOL:automatic hand digit skin NCBITaxon:9606 OBOL:accepted A zone of skin that is part of a tail [Automatically generated definition]. EMAPA:36502 MA:0000700 SCTID:67214004 post-vent region skin skin of post-vent region skin of tail uberon UBERON:0003534 tail skin A zone of skin that is part of a tail [Automatically generated definition]. OBOL:automatic post-vent region skin OBOL:automatic skin of post-vent region OBOL:automatic skin of tail OBOL:automatic A nerve trunk that is part of a vagus nerve. UBERON:0006308 EHDAA2:0002160 EHDAA:4659 EMAPA:17272 FMA:6221 MA:0001150 SCTID:280308004 VHOG:0000736 trunk of vagal nerve trunk of vagus nerve vagal X nerve trunk vagal nerve trunk vagus nerve trunk vagus neural trunk uberon UBERON:0003535 vagus X nerve trunk A nerve trunk that is part of a vagus nerve. OBOL:automatic trunk of vagus nerve FMA:6221 vagal X nerve trunk EMAPA:17272 vagal nerve trunk EMAPA:17272 vagus neural trunk FMA:6221 A meninx that is part of a brain [Automatically generated definition]. Meninges that are part of the brain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] CALOHA:TS-2147 EMAPA:32662 EV:0100312 MA:0000813 SCTID:180949007 VHOG:0000013 brain meninges meninges of brain meninx of brain uberon UBERON:0003547 brain meninx A meninx that is part of a brain [Automatically generated definition]. OBOL:automatic Meninges that are part of the brain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000013 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000013 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ brain meninges OBOL:automatic meninges of brain OBOL:automatic meninx of brain OBOL:automatic A meninx that is part of a forebrain [Automatically generated definition]. EMAPA:17764 EMAPA:17774 EMAPA:37543 MA:0000883 forebrain meninx meninges of forebrain meninx of forebrain uberon UBERON:0003548 forebrain meninges A meninx that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37543 MA:th forebrain meninx OBOL:automatic meninges of forebrain OBOL:automatic meninx of forebrain OBOL:automatic The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule. The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32667 EV:0100315 MA:0000816 NCIT:C49335 UMLS:C1706994 VHOG:0000470 brain pia mater of neuraxis pia mater of brain pia mater of neuraxis of brain uberon UBERON:0003549 brain pia mater The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule. MP:0009026 The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000470 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pia+mater In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000470 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ UMLS:C1706994 ncithesaurus:Brain_Pia_Mater brain pia mater of neuraxis OBOL:automatic pia mater of brain OBOL:automatic pia mater of neuraxis of brain OBOL:automatic A pia mater that is part of a forebrain [Automatically generated definition]. EMAPA:17767 EMAPA:17777 EMAPA:37546 MA:0000886 forebrain pia mater of neuraxis pia mater of forebrain pia mater of neuraxis of forebrain uberon UBERON:0003550 forebrain pia mater A pia mater that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37546 MA:th forebrain pia mater of neuraxis OBOL:automatic pia mater of forebrain OBOL:automatic pia mater of neuraxis of forebrain OBOL:automatic A pia mater that is part of a midbrain [Automatically generated definition]. Pia mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001175 EMAPA:17794 MA:0001061 RETIRED_EHDAA2:0001110 VHOG:0000467 midbrain pia mater of neuraxis pia mater of midbrain pia mater of neuraxis of midbrain uberon mesencephalon pia mater UBERON:0003551 midbrain pia mater A pia mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Pia mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000467 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000467 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ midbrain pia mater of neuraxis OBOL:automatic pia mater of midbrain OBOL:automatic pia mater of neuraxis of midbrain OBOL:automatic mesencephalon pia mater VHOG:0000467 A pia mater that is part of a telencephalon [Automatically generated definition]. Pia mater that is part of the telencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001992 EMAPA:17777 MA:0000982 VHOG:0000476 pia mater of neuraxis of telencephalon pia mater of telencephalon telencephalon pia mater of neuraxis uberon UBERON:0003552 telencephalon pia mater A pia mater that is part of a telencephalon [Automatically generated definition]. OBOL:automatic Pia mater that is part of the telencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000476 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000476 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ pia mater of neuraxis of telencephalon OBOL:automatic pia mater of telencephalon OBOL:automatic telencephalon pia mater of neuraxis OBOL:automatic A pia mater that is part of a diencephalon [Automatically generated definition]. Pia mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000400 EMAPA:17767 MA:0000829 VHOG:0000475 between brain pia mater between brain pia mater of neuraxis diencephalon pia mater of neuraxis interbrain pia mater interbrain pia mater of neuraxis mature diencephalon pia mater mature diencephalon pia mater of neuraxis pia mater of between brain pia mater of diencephalon pia mater of interbrain pia mater of mature diencephalon pia mater of neuraxis of between brain pia mater of neuraxis of diencephalon pia mater of neuraxis of interbrain pia mater of neuraxis of mature diencephalon uberon UBERON:0003553 diencephalon pia mater A pia mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Pia mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000475 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000475 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ between brain pia mater OBOL:automatic between brain pia mater of neuraxis OBOL:automatic diencephalon pia mater of neuraxis OBOL:automatic interbrain pia mater OBOL:automatic interbrain pia mater of neuraxis OBOL:automatic mature diencephalon pia mater OBOL:automatic mature diencephalon pia mater of neuraxis OBOL:automatic pia mater of between brain OBOL:automatic pia mater of diencephalon OBOL:automatic pia mater of interbrain OBOL:automatic pia mater of mature diencephalon OBOL:automatic pia mater of neuraxis of between brain OBOL:automatic pia mater of neuraxis of diencephalon OBOL:automatic pia mater of neuraxis of interbrain OBOL:automatic pia mater of neuraxis of mature diencephalon OBOL:automatic A pia mater that is part of a hindbrain [Automatically generated definition]. Pia mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000772 EMAPA:17786 MA:0000990 VHOG:0000466 hindbrain pia mater of neuraxis pia mater of hindbrain pia mater of neuraxis of hindbrain uberon rhombencephalon pia mater UBERON:0003554 hindbrain pia mater A pia mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Pia mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000466 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000466 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ hindbrain pia mater of neuraxis OBOL:automatic pia mater of hindbrain OBOL:automatic pia mater of neuraxis of hindbrain OBOL:automatic rhombencephalon pia mater VHOG:0000466 A pia mater that is part of a spinal cord [Automatically generated definition]. The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001896 EMAPA:17807 MA:0001133 NCIT:C49800 UMLS:C1710148 VHOG:0000468 pia mater of neuraxis of spinal cord pia mater of spinal cord spinal cord pia mater of neuraxis uberon UBERON:0003555 spinal cord pia mater A pia mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000468 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pia+mater In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000468 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ UMLS:C1710148 ncithesaurus:Spinal_Cord_Pia_Mater pia mater of neuraxis of spinal cord OBOL:automatic pia mater of spinal cord OBOL:automatic spinal cord pia mater of neuraxis OBOL:automatic An arachnoid mater that is part of a forebrain [Automatically generated definition]. EMAPA:17765 EMAPA:17775 EMAPA:37544 MA:0000884 arachnoid mater of forebrain arachnoid mater of neuraxis of forebrain arachnoid of forebrain forebrain arachnoid forebrain arachnoid mater of neuraxis uberon UBERON:0003556 forebrain arachnoid mater An arachnoid mater that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37544 MA:th arachnoid mater of forebrain OBOL:automatic arachnoid mater of neuraxis of forebrain OBOL:automatic arachnoid of forebrain OBOL:automatic forebrain arachnoid OBOL:automatic forebrain arachnoid mater of neuraxis OBOL:automatic An arachnoid mater that is part of a midbrain [Automatically generated definition]. Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17792 MA:0001059 VHOG:0000233 arachnoid mater of midbrain arachnoid mater of neuraxis of midbrain arachnoid of midbrain midbrain arachnoid midbrain arachnoid mater of neuraxis uberon mesencephalon arachnoid mater UBERON:0003557 midbrain arachnoid mater An arachnoid mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000233 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000233 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ arachnoid mater of midbrain OBOL:automatic arachnoid mater of neuraxis of midbrain OBOL:automatic arachnoid of midbrain OBOL:automatic midbrain arachnoid OBOL:automatic midbrain arachnoid mater of neuraxis OBOL:automatic mesencephalon arachnoid mater VHOG:0000233 An arachnoid mater that is part of a diencephalon [Automatically generated definition]. Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17765 MA:0000827 VHOG:0000231 arachnoid mater of between brain arachnoid mater of diencephalon arachnoid mater of interbrain arachnoid mater of mature diencephalon arachnoid mater of neuraxis of between brain arachnoid mater of neuraxis of diencephalon arachnoid mater of neuraxis of interbrain arachnoid mater of neuraxis of mature diencephalon arachnoid of between brain arachnoid of diencephalon arachnoid of interbrain arachnoid of mature diencephalon between brain arachnoid between brain arachnoid mater between brain arachnoid mater of neuraxis diencephalon arachnoid diencephalon arachnoid mater of neuraxis interbrain arachnoid interbrain arachnoid mater interbrain arachnoid mater of neuraxis mature diencephalon arachnoid mature diencephalon arachnoid mater mature diencephalon arachnoid mater of neuraxis uberon UBERON:0003558 diencephalon arachnoid mater An arachnoid mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000231 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000231 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ arachnoid mater of between brain OBOL:automatic arachnoid mater of diencephalon OBOL:automatic arachnoid mater of interbrain OBOL:automatic arachnoid mater of mature diencephalon OBOL:automatic arachnoid mater of neuraxis of between brain OBOL:automatic arachnoid mater of neuraxis of diencephalon OBOL:automatic arachnoid mater of neuraxis of interbrain OBOL:automatic arachnoid mater of neuraxis of mature diencephalon OBOL:automatic arachnoid of between brain OBOL:automatic arachnoid of diencephalon OBOL:automatic arachnoid of interbrain OBOL:automatic arachnoid of mature diencephalon OBOL:automatic between brain arachnoid OBOL:automatic between brain arachnoid mater OBOL:automatic between brain arachnoid mater of neuraxis OBOL:automatic diencephalon arachnoid OBOL:automatic diencephalon arachnoid mater of neuraxis OBOL:automatic interbrain arachnoid OBOL:automatic interbrain arachnoid mater OBOL:automatic interbrain arachnoid mater of neuraxis OBOL:automatic mature diencephalon arachnoid OBOL:automatic mature diencephalon arachnoid mater OBOL:automatic mature diencephalon arachnoid mater of neuraxis OBOL:automatic An arachnoid mater that is part of a hindbrain [Automatically generated definition]. Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17784 MA:0000988 VHOG:0000236 arachnoid mater of hindbrain arachnoid mater of neuraxis of hindbrain arachnoid of hindbrain hindbrain arachnoid hindbrain arachnoid mater of neuraxis uberon rhombencephalon arachnoid mater UBERON:0003559 hindbrain arachnoid mater An arachnoid mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000236 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000236 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ arachnoid mater of hindbrain OBOL:automatic arachnoid mater of neuraxis of hindbrain OBOL:automatic arachnoid of hindbrain OBOL:automatic hindbrain arachnoid OBOL:automatic hindbrain arachnoid mater of neuraxis OBOL:automatic rhombencephalon arachnoid mater VHOG:0000236 An arachnoid mater that is part of a spinal cord [Automatically generated definition]. The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17805 MA:0001131 VHOG:0000234 arachnoid mater of neuraxis of spinal cord arachnoid mater of spinal cord arachnoid of spinal cord spinal cord arachnoid spinal cord arachnoid mater of neuraxis uberon UBERON:0003560 spinal cord arachnoid mater An arachnoid mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000234 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/arachnoid+mater In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000234 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ arachnoid mater of neuraxis of spinal cord OBOL:automatic arachnoid mater of spinal cord OBOL:automatic arachnoid of spinal cord OBOL:automatic spinal cord arachnoid OBOL:automatic spinal cord arachnoid mater of neuraxis OBOL:automatic A dura mater that is part of a forebrain. EMAPA:17766 EMAPA:37545 MA:0000885 dura mater of forebrain dura mater of neuraxis of forebrain forebrain dura mater of neuraxis uberon UBERON:0003561 forebrain dura mater A dura mater that is part of a forebrain. OBOL:automatic EMAPA:37545 MA:th dura mater of forebrain OBOL:automatic dura mater of neuraxis of forebrain OBOL:automatic forebrain dura mater of neuraxis OBOL:automatic A dura mater that is part of a midbrain [Automatically generated definition]. Dura mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17793 MA:0001060 VHOG:0000410 dura mater of midbrain dura mater of neuraxis of midbrain midbrain dura mater of neuraxis uberon mesencephalon dura mater UBERON:0003562 midbrain dura mater A dura mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Dura mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000410 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000410 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ dura mater of midbrain OBOL:automatic dura mater of neuraxis of midbrain OBOL:automatic midbrain dura mater of neuraxis OBOL:automatic mesencephalon dura mater VHOG:0000410 A dura mater that is part of a telencephalon [Automatically generated definition]. EMAPA:17776 MA:0000981 dura mater of neuraxis of telencephalon dura mater of telencephalon telencephalon dura mater of neuraxis uberon UBERON:0003563 telencephalon dura mater A dura mater that is part of a telencephalon [Automatically generated definition]. OBOL:automatic dura mater of neuraxis of telencephalon OBOL:automatic dura mater of telencephalon OBOL:automatic telencephalon dura mater of neuraxis OBOL:automatic A dura mater that is part of a diencephalon [Automatically generated definition]. Dura mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17766 MA:0000828 VHOG:0000258 between brain dura mater between brain dura mater of neuraxis diencephalon dura mater of neuraxis dura mater of between brain dura mater of diencephalon dura mater of interbrain dura mater of mature diencephalon dura mater of neuraxis of between brain dura mater of neuraxis of diencephalon dura mater of neuraxis of interbrain dura mater of neuraxis of mature diencephalon interbrain dura mater interbrain dura mater of neuraxis mature diencephalon dura mater mature diencephalon dura mater of neuraxis uberon UBERON:0003564 diencephalon dura mater A dura mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Dura mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000258 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000258 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ between brain dura mater OBOL:automatic between brain dura mater of neuraxis OBOL:automatic diencephalon dura mater of neuraxis OBOL:automatic dura mater of between brain OBOL:automatic dura mater of diencephalon OBOL:automatic dura mater of interbrain OBOL:automatic dura mater of mature diencephalon OBOL:automatic dura mater of neuraxis of between brain OBOL:automatic dura mater of neuraxis of diencephalon OBOL:automatic dura mater of neuraxis of interbrain OBOL:automatic dura mater of neuraxis of mature diencephalon OBOL:automatic interbrain dura mater OBOL:automatic interbrain dura mater of neuraxis OBOL:automatic mature diencephalon dura mater OBOL:automatic mature diencephalon dura mater of neuraxis OBOL:automatic A dura mater that is part of a hindbrain [Automatically generated definition]. Dura mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17785 MA:0000989 VHOG:0000409 dura mater of hindbrain dura mater of neuraxis of hindbrain hindbrain dura mater of neuraxis uberon rhombencephalon dura mater UBERON:0003565 hindbrain dura mater A dura mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Dura mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000409 VHOG http://bgee.unil.ch/ In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000409 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ dura mater of hindbrain OBOL:automatic dura mater of neuraxis of hindbrain OBOL:automatic hindbrain dura mater of neuraxis OBOL:automatic rhombencephalon dura mater VHOG:0000409 A portion of connective tissue that is part of a head [Automatically generated definition]. EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue adult head textus connectivus connective tissue of adult head connective tissue of head head portion of connective tissue head textus connectivus portion of connective tissue of adult head portion of connective tissue of head textus connectivus of adult head textus connectivus of head uberon UBERON:0003566 head connective tissue A portion of connective tissue that is part of a head [Automatically generated definition]. OBOL:automatic adult head connective tissue OBOL:automatic adult head portion of connective tissue OBOL:automatic adult head textus connectivus OBOL:automatic connective tissue of adult head OBOL:automatic connective tissue of head OBOL:automatic head portion of connective tissue OBOL:automatic head textus connectivus OBOL:automatic portion of connective tissue of adult head OBOL:automatic portion of connective tissue of head OBOL:automatic textus connectivus of adult head OBOL:automatic textus connectivus of head OBOL:automatic A portion of connective tissue that is part of an abdomen [Automatically generated definition]. MA:0000519 abdomen portion of connective tissue abdomen textus connectivus connective tissue of abdomen portion of connective tissue of abdomen textus connectivus of abdomen uberon UBERON:0003567 abdomen connective tissue A portion of connective tissue that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen portion of connective tissue OBOL:automatic abdomen textus connectivus OBOL:automatic connective tissue of abdomen OBOL:automatic portion of connective tissue of abdomen OBOL:automatic textus connectivus of abdomen OBOL:automatic A portion of connective tissue that is part of a neck [Automatically generated definition]. EMAPA:37250 MA:0000585 connective tissue of neck connective tissue of neck (volume) neck (volume) connective tissue neck (volume) portion of connective tissue neck (volume) textus connectivus neck portion of connective tissue neck textus connectivus portion of connective tissue of neck portion of connective tissue of neck (volume) textus connectivus of neck textus connectivus of neck (volume) uberon UBERON:0003568 neck connective tissue A portion of connective tissue that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37250 MA:th connective tissue of neck OBOL:automatic connective tissue of neck (volume) OBOL:automatic neck (volume) connective tissue OBOL:automatic neck (volume) portion of connective tissue OBOL:automatic neck (volume) textus connectivus OBOL:automatic neck portion of connective tissue OBOL:automatic neck textus connectivus OBOL:automatic portion of connective tissue of neck OBOL:automatic portion of connective tissue of neck (volume) OBOL:automatic textus connectivus of neck OBOL:automatic textus connectivus of neck (volume) OBOL:automatic A portion of connective tissue that is part of a leg [Automatically generated definition]. EMAPA:37324 MA:0000671 connective tissue of leg leg portion of connective tissue leg textus connectivus portion of connective tissue of leg textus connectivus of leg uberon UBERON:0003569 leg connective tissue A portion of connective tissue that is part of a leg [Automatically generated definition]. OBOL:automatic EMAPA:37324 MA:th connective tissue of leg OBOL:automatic leg portion of connective tissue OBOL:automatic leg textus connectivus OBOL:automatic portion of connective tissue of leg OBOL:automatic textus connectivus of leg OBOL:automatic A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:35968 EMAPA:35977 MA:0001814 apparatus respiratorius connective tissue apparatus respiratorius portion of connective tissue apparatus respiratorius textus connectivus connective tissue of apparatus respiratorius connective tissue of respiratory system portion of connective tissue of apparatus respiratorius portion of connective tissue of respiratory system respiratory system portion of connective tissue respiratory system textus connectivus textus connectivus of apparatus respiratorius textus connectivus of respiratory system uberon UBERON:0003570 respiratory system connective tissue A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius connective tissue OBOL:automatic apparatus respiratorius portion of connective tissue OBOL:automatic apparatus respiratorius textus connectivus OBOL:automatic connective tissue of apparatus respiratorius OBOL:automatic connective tissue of respiratory system OBOL:automatic portion of connective tissue of apparatus respiratorius OBOL:automatic portion of connective tissue of respiratory system OBOL:automatic respiratory system portion of connective tissue OBOL:automatic respiratory system textus connectivus OBOL:automatic textus connectivus of apparatus respiratorius OBOL:automatic textus connectivus of respiratory system OBOL:automatic A portion of connective tissue that is part of a trachea. EMAPA:35876 MA:0001853 connective tissue of trachea connective tissue of windpipe uberon UBERON:0003571 trachea connective tissue A portion of connective tissue that is part of a trachea. OBOL:automatic connective tissue of trachea OBOL:automatic connective tissue of windpipe OBOL:automatic A portion of connective tissue that is part of a chest [Automatically generated definition]. EMAPA:37254 MA:0000550 anterior thoracic region connective tissue anterior thoracic region portion of connective tissue anterior thoracic region textus connectivus anterolateral part of thorax connective tissue anterolateral part of thorax portion of connective tissue anterolateral part of thorax textus connectivus chest portion of connective tissue chest textus connectivus connective tissue of anterior thoracic region connective tissue of anterolateral part of thorax connective tissue of chest connective tissue of front of thorax front of thorax connective tissue front of thorax portion of connective tissue front of thorax textus connectivus portion of connective tissue of anterior thoracic region portion of connective tissue of anterolateral part of thorax portion of connective tissue of chest portion of connective tissue of front of thorax textus connectivus of anterior thoracic region textus connectivus of anterolateral part of thorax textus connectivus of chest textus connectivus of front of thorax uberon UBERON:0003572 chest connective tissue A portion of connective tissue that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37254 MA:th anterior thoracic region connective tissue OBOL:automatic anterior thoracic region portion of connective tissue OBOL:automatic anterior thoracic region textus connectivus OBOL:automatic anterolateral part of thorax connective tissue OBOL:automatic anterolateral part of thorax portion of connective tissue OBOL:automatic anterolateral part of thorax textus connectivus OBOL:automatic chest portion of connective tissue OBOL:automatic chest textus connectivus OBOL:automatic connective tissue of anterior thoracic region OBOL:automatic connective tissue of anterolateral part of thorax OBOL:automatic connective tissue of chest OBOL:automatic connective tissue of front of thorax OBOL:automatic front of thorax connective tissue OBOL:automatic front of thorax portion of connective tissue OBOL:automatic front of thorax textus connectivus OBOL:automatic portion of connective tissue of anterior thoracic region OBOL:automatic portion of connective tissue of anterolateral part of thorax OBOL:automatic portion of connective tissue of chest OBOL:automatic portion of connective tissue of front of thorax OBOL:automatic textus connectivus of anterior thoracic region OBOL:automatic textus connectivus of anterolateral part of thorax OBOL:automatic textus connectivus of chest OBOL:automatic textus connectivus of front of thorax OBOL:automatic A portion of connective tissue that is part of an arm [Automatically generated definition]. EMAPA:37316 MA:0000593 uberon UBERON:0003573 arm connective tissue A portion of connective tissue that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37316 MA:th A portion of connective tissue that is part of a elbow [Automatically generated definition]. EMAPA:37318 MA:0000609 connective tissue of cubital region connective tissue of elbow textus connectivus of cubital region uberon UBERON:0003574 elbow connective tissue A portion of connective tissue that is part of a elbow [Automatically generated definition]. OBOL:automatic EMAPA:37318 MA:th connective tissue of cubital region OBOL:automatic connective tissue of elbow OBOL:automatic textus connectivus of cubital region OBOL:automatic A portion of connective tissue that is part of a wrist [Automatically generated definition]. EMAPA:37320 MA:0000636 carpal region connective tissue connective tissue of carpal region connective tissue of wrist uberon UBERON:0003575 wrist connective tissue A portion of connective tissue that is part of a wrist [Automatically generated definition]. OBOL:automatic EMAPA:37320 MA:th carpal region connective tissue OBOL:automatic connective tissue of carpal region OBOL:automatic connective tissue of wrist OBOL:automatic A portion of connective tissue that is part of a hip [Automatically generated definition]. EMAPA:37323 MA:0000656 connective tissue of hip connective tissue of hip region connective tissue of regio coxae uberon UBERON:0003576 hip connective tissue A portion of connective tissue that is part of a hip [Automatically generated definition]. OBOL:automatic EMAPA:37323 MA:th connective tissue of hip OBOL:automatic connective tissue of hip region OBOL:automatic connective tissue of regio coxae OBOL:automatic A portion of connective tissue that is part of a knee [Automatically generated definition]. EMAPA:37326 MA:0000667 connective tissue of knee knee portion of connective tissue uberon UBERON:0003577 knee connective tissue A portion of connective tissue that is part of a knee [Automatically generated definition]. OBOL:automatic EMAPA:37326 MA:th connective tissue of knee OBOL:automatic knee portion of connective tissue OBOL:automatic A portion of connective tissue that is part of a toe [Automatically generated definition]. EMAPA:37330 MA:0000647 connective tissue of digit of foot connective tissue of digitus pedis connective tissue of foot digit connective tissue of toe digitus pedis textus connectivus foot digit connective tissue hind limb digit connective tissue foot digit connective tissue uberon UBERON:0003578 pedal digit connective tissue A portion of connective tissue that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37330 MA:th connective tissue of digit of foot OBOL:automatic connective tissue of digitus pedis OBOL:automatic connective tissue of foot digit OBOL:automatic connective tissue of toe OBOL:automatic digitus pedis textus connectivus OBOL:automatic foot digit connective tissue MA:0000647 hind limb digit connective tissue OBOL:accepted foot digit connective tissue NCBITaxon:9606 OBOL:accepted A portion of connective tissue that is part of a shoulder [Automatically generated definition]. EMAPA:37315 MA:0000632 connective tissue of shoulder portion of connective tissue of shoulder shoulder portion of connective tissue shoulder textus connectivus textus connectivus of shoulder uberon UBERON:0003579 shoulder connective tissue A portion of connective tissue that is part of a shoulder [Automatically generated definition]. OBOL:automatic EMAPA:37315 MA:th connective tissue of shoulder OBOL:automatic portion of connective tissue of shoulder OBOL:automatic shoulder portion of connective tissue OBOL:automatic shoulder textus connectivus OBOL:automatic textus connectivus of shoulder OBOL:automatic A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37548 MA:0002409 connective tissue of lower respiratory tract lower respiratory tract portion of connective tissue lower respiratory tract textus connectivus portion of connective tissue of lower respiratory tract textus connectivus of lower respiratory tract uberon UBERON:0003580 lower respiratory tract connective tissue A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37548 MA:th connective tissue of lower respiratory tract OBOL:automatic lower respiratory tract portion of connective tissue OBOL:automatic lower respiratory tract textus connectivus OBOL:automatic portion of connective tissue of lower respiratory tract OBOL:automatic textus connectivus of lower respiratory tract OBOL:automatic A portion of connective tissue that is part of a nasopharynx [Automatically generated definition]. EMAPA:37682 MA:0001864 connective tissue of nasal part of pharynx connective tissue of nasopharynx connective tissue of rhinopharynx nasal part of pharynx connective tissue nasal part of pharynx portion of connective tissue nasal part of pharynx textus connectivus nasopharynx portion of connective tissue nasopharynx textus connectivus portion of connective tissue of nasal part of pharynx portion of connective tissue of nasopharynx portion of connective tissue of rhinopharynx rhinopharynx connective tissue rhinopharynx portion of connective tissue rhinopharynx textus connectivus textus connectivus of nasal part of pharynx textus connectivus of nasopharynx textus connectivus of rhinopharynx uberon UBERON:0003582 nasopharynx connective tissue A portion of connective tissue that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic EMAPA:37682 MA:th connective tissue of nasal part of pharynx OBOL:automatic connective tissue of nasopharynx OBOL:automatic connective tissue of rhinopharynx OBOL:automatic nasal part of pharynx connective tissue OBOL:automatic nasal part of pharynx portion of connective tissue OBOL:automatic nasal part of pharynx textus connectivus OBOL:automatic nasopharynx portion of connective tissue OBOL:automatic nasopharynx textus connectivus OBOL:automatic portion of connective tissue of nasal part of pharynx OBOL:automatic portion of connective tissue of nasopharynx OBOL:automatic portion of connective tissue of rhinopharynx OBOL:automatic rhinopharynx connective tissue OBOL:automatic rhinopharynx portion of connective tissue OBOL:automatic rhinopharynx textus connectivus OBOL:automatic textus connectivus of nasal part of pharynx OBOL:automatic textus connectivus of nasopharynx OBOL:automatic textus connectivus of rhinopharynx OBOL:automatic A portion of connective tissue that is part of a larynx [Automatically generated definition]. EMAPA:35471 MA:0001754 NCIT:C49245 UMLS:C1708651 connective tissue of larynx larynx portion of connective tissue larynx textus connectivus portion of connective tissue of larynx textus connectivus of larynx uberon laryngeal connective tissue UBERON:0003583 larynx connective tissue A portion of connective tissue that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C1708651 ncithesaurus:Laryngeal_Connective_Tissue connective tissue of larynx OBOL:automatic larynx portion of connective tissue OBOL:automatic larynx textus connectivus OBOL:automatic portion of connective tissue of larynx OBOL:automatic textus connectivus of larynx OBOL:automatic laryngeal connective tissue EMAPA:35471 The fibrous supportive tissue of the mammary gland. EMAPA:35537 FMA:74479 FMA:74483 MA:0002897 connective tissue of lactiferous gland connective tissue of lobe of breast connective tissue of lobe of mammary gland connective tissue of mammary gland lactiferous gland connective tissue lactiferous gland portion of connective tissue lactiferous gland stroma mammary gland stroma mammary stroma stroma of lactiferous gland uberon UBERON:0003584 mammary gland connective tissue The fibrous supportive tissue of the mammary gland. MP:0009507 https://github.com/obophenotype/uberon/issues/1151 connective tissue of lactiferous gland OBOL:automatic connective tissue of lobe of breast OBOL:automatic connective tissue of lobe of mammary gland OBOL:automatic connective tissue of mammary gland OBOL:automatic lactiferous gland connective tissue OBOL:automatic lactiferous gland portion of connective tissue OBOL:automatic lactiferous gland stroma https://github.com/obophenotype/uberon/issues/1151 mammary gland stroma https://github.com/obophenotype/uberon/issues/1151 mammary stroma https://github.com/obophenotype/uberon/issues/1151 stroma of lactiferous gland FMA:74483 A portion of connective tissue that is part of a dermis [Automatically generated definition]. EMAPA:36509 MA:0000799 connective tissue of dermis dermis portion of connective tissue dermis textus connectivus portion of connective tissue of dermis textus connectivus of dermis uberon UBERON:0003585 dermis connective tissue A portion of connective tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic connective tissue of dermis OBOL:automatic dermis portion of connective tissue OBOL:automatic dermis textus connectivus OBOL:automatic portion of connective tissue of dermis OBOL:automatic textus connectivus of dermis OBOL:automatic A portion of connective tissue that is part of a trunk [Automatically generated definition]. EMAPA:37252 MA:0000513 connective tissue of torso connective tissue of trunk portion of connective tissue of torso portion of connective tissue of trunk textus connectivus of torso textus connectivus of trunk torso connective tissue torso portion of connective tissue torso textus connectivus trunk portion of connective tissue trunk textus connectivus uberon UBERON:0003586 trunk connective tissue A portion of connective tissue that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37252 MA:th connective tissue of torso OBOL:automatic connective tissue of trunk OBOL:automatic portion of connective tissue of torso OBOL:automatic portion of connective tissue of trunk OBOL:automatic textus connectivus of torso OBOL:automatic textus connectivus of trunk OBOL:automatic torso connective tissue OBOL:automatic torso portion of connective tissue OBOL:automatic torso textus connectivus OBOL:automatic trunk portion of connective tissue OBOL:automatic trunk textus connectivus OBOL:automatic A portion of connective tissue that is part of a limb [Automatically generated definition]. EMAPA:37313 MA:0000689 connective tissue of limb limb portion of connective tissue limb textus connectivus portion of connective tissue of limb textus connectivus of limb uberon UBERON:0003587 limb connective tissue A portion of connective tissue that is part of a limb [Automatically generated definition]. OBOL:automatic EMAPA:37313 MA:th connective tissue of limb OBOL:automatic limb portion of connective tissue OBOL:automatic limb textus connectivus OBOL:automatic portion of connective tissue of limb OBOL:automatic textus connectivus of limb OBOL:automatic A portion of connective tissue that is part of a forelimb [Automatically generated definition]. EMAPA:37314 MA:0000613 connective tissue of anteriormost limb connective tissue of fore limb connective tissue of forelimb connective tissue of superior member connective tissue of upper extremity wing connective tissue uberon UBERON:0003588 forelimb connective tissue A portion of connective tissue that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37314 MA:th connective tissue of anteriormost limb OBOL:automatic connective tissue of fore limb OBOL:automatic connective tissue of forelimb OBOL:automatic connective tissue of superior member OBOL:automatic connective tissue of upper extremity OBOL:automatic wing connective tissue NCBITaxon:8782 OBOL:automatic A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. EMAPA:37322 MA:0000661 connective tissue of hind limb connective tissue of hindlimb connective tissue of inferior member connective tissue of lower extremity hind limb connective tissue uberon UBERON:0003589 hindlimb connective tissue A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37322 MA:th connective tissue of hind limb OBOL:automatic connective tissue of hindlimb OBOL:automatic connective tissue of inferior member OBOL:automatic connective tissue of lower extremity OBOL:automatic hind limb connective tissue OBOL:automatic A portion of connective tissue that is part of a bronchus [Automatically generated definition]. EMAPA:32690 EMAPA:35193 MA:0001831 NCIT:C49210 UMLS:C1707052 bronchi connective tissue bronchi portion of connective tissue bronchi textus connectivus bronchial trunk connective tissue bronchial trunk portion of connective tissue bronchial trunk textus connectivus bronchus portion of connective tissue bronchus textus connectivus connective tissue of bronchi connective tissue of bronchial trunk connective tissue of bronchus portion of connective tissue of bronchi portion of connective tissue of bronchial trunk portion of connective tissue of bronchus textus connectivus of bronchi textus connectivus of bronchial trunk textus connectivus of bronchus uberon bronchial connective tissue bronchial mesenchyme UBERON:0003592 bronchus connective tissue A portion of connective tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707052 ncithesaurus:Bronchus_Connective_Tissue bronchi connective tissue OBOL:automatic bronchi portion of connective tissue OBOL:automatic bronchi textus connectivus OBOL:automatic bronchial trunk connective tissue OBOL:automatic bronchial trunk portion of connective tissue OBOL:automatic bronchial trunk textus connectivus OBOL:automatic bronchus portion of connective tissue OBOL:automatic bronchus textus connectivus OBOL:automatic connective tissue of bronchi OBOL:automatic connective tissue of bronchial trunk OBOL:automatic connective tissue of bronchus OBOL:automatic portion of connective tissue of bronchi OBOL:automatic portion of connective tissue of bronchial trunk OBOL:automatic portion of connective tissue of bronchus OBOL:automatic textus connectivus of bronchi OBOL:automatic textus connectivus of bronchial trunk OBOL:automatic textus connectivus of bronchus OBOL:automatic bronchial connective tissue EMAPA:35193 bronchial mesenchyme EMAPA:32690 A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37255 MA:0000555 cavity of chest connective tissue cavity of chest portion of connective tissue cavity of chest textus connectivus cavity of thorax connective tissue cavity of thorax portion of connective tissue cavity of thorax textus connectivus chest cavity connective tissue chest cavity portion of connective tissue chest cavity textus connectivus connective tissue of cavity of chest connective tissue of cavity of thorax connective tissue of chest cavity connective tissue of pectoral cavity connective tissue of thoracic cavity pectoral cavity connective tissue pectoral cavity portion of connective tissue pectoral cavity textus connectivus portion of connective tissue of cavity of chest portion of connective tissue of cavity of thorax portion of connective tissue of chest cavity portion of connective tissue of pectoral cavity portion of connective tissue of thoracic cavity textus connectivus of cavity of chest textus connectivus of cavity of thorax textus connectivus of chest cavity textus connectivus of pectoral cavity textus connectivus of thoracic cavity thoracic cavity portion of connective tissue thoracic cavity textus connectivus uberon UBERON:0003593 thoracic cavity connective tissue A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37255 MA:th cavity of chest connective tissue OBOL:automatic cavity of chest portion of connective tissue OBOL:automatic cavity of chest textus connectivus OBOL:automatic cavity of thorax connective tissue OBOL:automatic cavity of thorax portion of connective tissue OBOL:automatic cavity of thorax textus connectivus OBOL:automatic chest cavity connective tissue OBOL:automatic chest cavity portion of connective tissue OBOL:automatic chest cavity textus connectivus OBOL:automatic connective tissue of cavity of chest OBOL:automatic connective tissue of cavity of thorax OBOL:automatic connective tissue of chest cavity OBOL:automatic connective tissue of pectoral cavity OBOL:automatic connective tissue of thoracic cavity OBOL:automatic pectoral cavity connective tissue OBOL:automatic pectoral cavity portion of connective tissue OBOL:automatic pectoral cavity textus connectivus OBOL:automatic portion of connective tissue of cavity of chest OBOL:automatic portion of connective tissue of cavity of thorax OBOL:automatic portion of connective tissue of chest cavity OBOL:automatic portion of connective tissue of pectoral cavity OBOL:automatic portion of connective tissue of thoracic cavity OBOL:automatic textus connectivus of cavity of chest OBOL:automatic textus connectivus of cavity of thorax OBOL:automatic textus connectivus of chest cavity OBOL:automatic textus connectivus of pectoral cavity OBOL:automatic textus connectivus of thoracic cavity OBOL:automatic thoracic cavity portion of connective tissue OBOL:automatic thoracic cavity textus connectivus OBOL:automatic A portion of connective tissue that is part of a pelvis [Automatically generated definition]. EMAPA:37257 MA:0000533 connective tissue of pelvis pelvis portion of connective tissue pelvis textus connectivus portion of connective tissue of pelvis textus connectivus of pelvis uberon UBERON:0003594 pelvis connective tissue A portion of connective tissue that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37257 MA:th connective tissue of pelvis OBOL:automatic pelvis portion of connective tissue OBOL:automatic pelvis textus connectivus OBOL:automatic portion of connective tissue of pelvis OBOL:automatic textus connectivus of pelvis OBOL:automatic A portion of connective tissue that is part of a foot [Automatically generated definition]. EMAPA:37329 MA:0000644 connective tissue of foot connective tissue of terminal segment of free lower limb foot connective tissue textus connectivus of pes uberon UBERON:0003595 pes connective tissue A portion of connective tissue that is part of a foot [Automatically generated definition]. OBOL:automatic EMAPA:37329 MA:th connective tissue of foot OBOL:automatic connective tissue of terminal segment of free lower limb OBOL:automatic foot connective tissue MA:0000644 textus connectivus of pes OBOL:automatic A portion of connective tissue that is part of an ankle [Automatically generated definition]. EMAPA:37328 MA:0000639 connective tissue of ankle tarsal region connective tissue uberon UBERON:0003596 ankle connective tissue A portion of connective tissue that is part of an ankle [Automatically generated definition]. OBOL:automatic EMAPA:37328 MA:th connective tissue of ankle OBOL:automatic tarsal region connective tissue https://orcid.org/0000-0002-6601-2165 A portion of connective tissue that is part of a finger [Automatically generated definition]. EMAPA:37321 MA:0000623 connective tissue of digit of hand connective tissue of digitus manus connective tissue of finger connective tissue of hand digit fore limb digit connective tissue hand digit connective tissue hand digit connective tissue uberon UBERON:0003597 manual digit connective tissue A portion of connective tissue that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37321 MA:th connective tissue of digit of hand OBOL:automatic connective tissue of digitus manus OBOL:automatic connective tissue of finger OBOL:automatic connective tissue of hand digit OBOL:automatic fore limb digit connective tissue OBOL:accepted hand digit connective tissue MA:0000623 hand digit connective tissue NCBITaxon:9606 OBOL:accepted A portion of connective tissue that is part of a hand [Automatically generated definition]. EMAPA:35392 MA:0000620 connective tissue of hand connective tissue of terminal segment of free upper limb hand connective tissue uberon UBERON:0003598 manus connective tissue A portion of connective tissue that is part of a hand [Automatically generated definition]. OBOL:automatic connective tissue of hand OBOL:automatic connective tissue of terminal segment of free upper limb OBOL:automatic hand connective tissue MA:0000620 A portion of connective tissue that is part of a tail [Automatically generated definition]. EMAPA:16749 MA:0000697 connective tissue of post-vent region connective tissue of tail portion of connective tissue of post-vent region portion of connective tissue of tail post-vent region connective tissue post-vent region portion of connective tissue post-vent region textus connectivus tail portion of connective tissue tail textus connectivus textus connectivus of post-vent region textus connectivus of tail uberon UBERON:0003599 tail connective tissue A portion of connective tissue that is part of a tail [Automatically generated definition]. OBOL:automatic connective tissue of post-vent region OBOL:automatic connective tissue of tail OBOL:automatic portion of connective tissue of post-vent region OBOL:automatic portion of connective tissue of tail OBOL:automatic post-vent region connective tissue OBOL:automatic post-vent region portion of connective tissue OBOL:automatic post-vent region textus connectivus OBOL:automatic tail portion of connective tissue OBOL:automatic tail textus connectivus OBOL:automatic textus connectivus of post-vent region OBOL:automatic textus connectivus of tail OBOL:automatic A cartilage that is part of a neck [Automatically generated definition]. EMAPA:37251 MA:0000586 cartilage of neck cartilage of neck (volume) neck (volume) cartilage uberon UBERON:0003601 neck cartilage A cartilage that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37251 MA:th cartilage of neck OBOL:automatic cartilage of neck (volume) OBOL:automatic neck (volume) cartilage OBOL:automatic A cartilage that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37547 MA:0001819 NCIT:C49256 UMLS:C1708759 cartilage of lower respiratory tract uberon UBERON:0003603 lower respiratory tract cartilage A cartilage that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37547 MA:th UMLS:C1708759 ncithesaurus:Lower_Respiratory_Tract_Cartilage cartilage of lower respiratory tract OBOL:automatic The ring-shaped cartilaginous structures that support the trachea. check whether to classify as part of splanchoncranium in mammals the rings are incomplete, in avians the rings are complete. EMAPA:18699 EMAPA:35875 FMA:7434 MA:0001857 NCIT:C49304 SCTID:278979006 UMLS:C1710456 Wikipedia:Tracheal_rings cartilage of trachea cartilage of windpipe cartilaginous ring of trachea cartilaginous trachea cartilage cartilago trachealis tracheal cartilage windpipe cartilage uberon cartilage of the trachea cartilagines tracheales ring of the trachea trachea ring tracheal ring UBERON:0003604 trachea cartilage http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb The ring-shaped cartilaginous structures that support the trachea. J:97123 MGI:smb MP:0003120 http://orcid.org/0000-0002-6601-2165 UMLS:C1710456 ncithesaurus:Trachea_Cartilage cartilage of trachea OBOL:automatic cartilage of windpipe OBOL:automatic cartilaginous ring of trachea EMAPA:18699 cartilaginous trachea cartilage OBOL:automatic cartilago trachealis FMA:7434 tracheal cartilage FMA:7434 windpipe cartilage OBOL:automatic cartilage of the trachea Wikipedia:Tracheal_rings cartilagines tracheales Wikipedia:Tracheal_rings ring of the trachea Wikipedia:Tracheal_rings tracheal ring Wikipedia:Tracheal_rings A skin gland that is part of a camera-type eye [Automatically generated definition]. EMAPA:37530 MA:0002451 camera-type eye skin gland camera-type eye skin glands camera-type eye skin glands set skin gland of camera-type eye skin gland of vertebrate eye skin glands of camera-type eye skin glands of vertebrate eye skin glands set of camera-type eye skin glands set of vertebrate eye vertebrate eye skin gland vertebrate eye skin glands vertebrate eye skin glands set uberon UBERON:0003605 eye skin gland A skin gland that is part of a camera-type eye [Automatically generated definition]. OBOL:automatic EMAPA:37530 MA:th camera-type eye skin gland OBOL:automatic camera-type eye skin glands OBOL:automatic camera-type eye skin glands set OBOL:automatic skin gland of camera-type eye OBOL:automatic skin gland of vertebrate eye OBOL:automatic skin glands of camera-type eye OBOL:automatic skin glands of vertebrate eye OBOL:automatic skin glands set of camera-type eye OBOL:automatic skin glands set of vertebrate eye OBOL:automatic vertebrate eye skin gland OBOL:automatic vertebrate eye skin glands OBOL:automatic vertebrate eye skin glands set OBOL:automatic A long bone that is part of a limb [Automatically generated definition]. EMAPA:35495 MA:0000298 long bone of limb uberon UBERON:0003606 limb long bone A long bone that is part of a limb [Automatically generated definition]. OBOL:automatic long bone of limb OBOL:automatic A long bone that is part of a forelimb [Automatically generated definition]. EMAPA:35350 MA:0000299 anteriormost limb long bone fore limb long bone long bone of anteriormost limb long bone of fore limb long bone of forelimb long bone of superior member long bone of upper extremity superior member long bone upper extremity long bone wing long bone uberon UBERON:0003607 forelimb long bone A long bone that is part of a forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb long bone OBOL:automatic fore limb long bone OBOL:automatic long bone of anteriormost limb OBOL:automatic long bone of fore limb OBOL:automatic long bone of forelimb OBOL:automatic long bone of superior member OBOL:automatic long bone of upper extremity OBOL:automatic superior member long bone OBOL:automatic upper extremity long bone OBOL:automatic wing long bone NCBITaxon:8782 OBOL:automatic A long bone that is part of a hindlimb [Automatically generated definition]. EMAPA:35403 MA:0000300 hind limb long bone inferior member long bone long bone of hind limb long bone of hindlimb long bone of inferior member long bone of lower extremity lower extremity long bone uberon UBERON:0003608 hindlimb long bone A long bone that is part of a hindlimb [Automatically generated definition]. OBOL:automatic hind limb long bone OBOL:automatic inferior member long bone OBOL:automatic long bone of hind limb OBOL:automatic long bone of hindlimb OBOL:automatic long bone of inferior member OBOL:automatic long bone of lower extremity OBOL:automatic lower extremity long bone OBOL:automatic The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MA:0002859 adult aorta elastic connective tissue adult aorta elastic tissue adult aorta textus connectivus elasticus aorta elastic connective tissue aorta elastic lamina aorta elastic laminae aorta textus connectivus elasticus dorsal aorta elastic connective tissue dorsal aorta elastic tissue dorsal aorta textus connectivus elasticus elastic connective tissue of adult aorta elastic connective tissue of aorta elastic connective tissue of dorsal aorta elastic connective tissue of trunk of aortic tree elastic tissue of adult aorta elastic tissue of aorta elastic tissue of dorsal aorta elastic tissue of trunk of aortic tree textus connectivus elasticus of adult aorta textus connectivus elasticus of aorta textus connectivus elasticus of dorsal aorta textus connectivus elasticus of trunk of aortic tree trunk of aortic tree elastic connective tissue trunk of aortic tree elastic tissue trunk of aortic tree textus connectivus elasticus uberon UBERON:0003609 aorta elastic tissue The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MP:0009862 adult aorta elastic connective tissue OBOL:automatic adult aorta elastic tissue OBOL:automatic adult aorta textus connectivus elasticus OBOL:automatic aorta elastic connective tissue OBOL:automatic aorta elastic lamina MP:0009862 aorta elastic laminae MP:0009862 aorta textus connectivus elasticus OBOL:automatic dorsal aorta elastic connective tissue OBOL:automatic dorsal aorta elastic tissue OBOL:automatic dorsal aorta textus connectivus elasticus OBOL:automatic elastic connective tissue of adult aorta OBOL:automatic elastic connective tissue of aorta OBOL:automatic elastic connective tissue of dorsal aorta OBOL:automatic elastic connective tissue of trunk of aortic tree OBOL:automatic elastic tissue of adult aorta OBOL:automatic elastic tissue of aorta OBOL:automatic elastic tissue of dorsal aorta OBOL:automatic elastic tissue of trunk of aortic tree OBOL:automatic textus connectivus elasticus of adult aorta OBOL:automatic textus connectivus elasticus of aorta OBOL:automatic textus connectivus elasticus of dorsal aorta OBOL:automatic textus connectivus elasticus of trunk of aortic tree OBOL:automatic trunk of aortic tree elastic connective tissue OBOL:automatic trunk of aortic tree elastic tissue OBOL:automatic trunk of aortic tree textus connectivus elasticus OBOL:automatic The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MA:0002858 cardiac elastic tissue elastic connective tissue of heart elastic tissue of heart heart elastic connective tissue heart textus connectivus elasticus textus connectivus elasticus of heart uberon UBERON:0003610 heart elastic tissue The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MP:0009863 cardiac elastic tissue MP:0009863 elastic connective tissue of heart OBOL:automatic elastic tissue of heart OBOL:automatic heart elastic connective tissue OBOL:automatic heart textus connectivus elasticus OBOL:automatic textus connectivus elasticus of heart OBOL:automatic An elastic tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37579 MA:0001820 apparatus respiratorius elastic connective tissue apparatus respiratorius elastic tissue apparatus respiratorius textus connectivus elasticus elastic connective tissue of apparatus respiratorius elastic connective tissue of respiratory system elastic tissue of apparatus respiratorius elastic tissue of respiratory system respiratory system elastic connective tissue respiratory system textus connectivus elasticus textus connectivus elasticus of apparatus respiratorius textus connectivus elasticus of respiratory system uberon UBERON:0003611 respiratory system elastic tissue An elastic tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37579 MA:th apparatus respiratorius elastic connective tissue OBOL:automatic apparatus respiratorius elastic tissue OBOL:automatic apparatus respiratorius textus connectivus elasticus OBOL:automatic elastic connective tissue of apparatus respiratorius OBOL:automatic elastic connective tissue of respiratory system OBOL:automatic elastic tissue of apparatus respiratorius OBOL:automatic elastic tissue of respiratory system OBOL:automatic respiratory system elastic connective tissue OBOL:automatic respiratory system textus connectivus elasticus OBOL:automatic textus connectivus elasticus of apparatus respiratorius OBOL:automatic textus connectivus elasticus of respiratory system OBOL:automatic An elastic tissue that is part of a circulatory system [Automatically generated definition]. MA:0002857 cardiovascular system elastic connective tissue cardiovascular system textus connectivus elasticus circulatory system elastic connective tissue circulatory system elastic tissue circulatory system textus connectivus elasticus elastic connective tissue of cardiovascular system elastic connective tissue of circulatory system elastic tissue of cardiovascular system elastic tissue of circulatory system textus connectivus elasticus of cardiovascular system textus connectivus elasticus of circulatory system uberon UBERON:0003613 cardiovascular system elastic tissue An elastic tissue that is part of a circulatory system [Automatically generated definition]. OBOL:automatic cardiovascular system elastic connective tissue OBOL:automatic cardiovascular system textus connectivus elasticus OBOL:automatic circulatory system elastic connective tissue OBOL:automatic circulatory system elastic tissue OBOL:automatic circulatory system textus connectivus elasticus OBOL:automatic elastic connective tissue of cardiovascular system OBOL:automatic elastic connective tissue of circulatory system OBOL:automatic elastic tissue of cardiovascular system OBOL:automatic elastic tissue of circulatory system OBOL:automatic textus connectivus elasticus of cardiovascular system OBOL:automatic textus connectivus elasticus of circulatory system OBOL:automatic Elastic tissue layer that lines a blood vessel layer. elastic lamina elastic laminae EMAPA:36300 MA:0002856 blood vessel elastic connective tissue blood vessel textus connectivus elasticus elastic connective tissue of blood vessel elastic tissue of blood vessel textus connectivus elasticus of blood vessel vascular elastic lamina vascular elastic laminae vascular elastic tissue uberon UBERON:0003614 blood vessel elastic tissue Elastic tissue layer that lines a blood vessel layer. http://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/mammalian-phenotype-requests/2026/ elastic lamina MP:0006083 elastic laminae MP:0006083 blood vessel elastic connective tissue OBOL:automatic blood vessel textus connectivus elasticus OBOL:automatic elastic connective tissue of blood vessel OBOL:automatic elastic tissue of blood vessel OBOL:automatic textus connectivus elasticus of blood vessel OBOL:automatic vascular elastic lamina http://orcid.org/0000-0002-6601-2165 vascular elastic laminae http://orcid.org/0000-0002-6601-2165 vascular elastic tissue MP:0006083 Elastic tissue that is part of a lung [Automatically generated definition]. MA:0002860 elastic connective tissue of lung elastic tissue of lung lung elastic connective tissue lung textus connectivus elasticus textus connectivus elasticus of lung pulmonary elastic fiber uberon UBERON:0003615 lung elastic tissue Elastic tissue that is part of a lung [Automatically generated definition]. OBOL:automatic elastic connective tissue of lung OBOL:automatic elastic tissue of lung OBOL:automatic lung elastic connective tissue OBOL:automatic lung textus connectivus elasticus OBOL:automatic textus connectivus elasticus of lung OBOL:automatic pulmonary elastic fiber http://orcid.org/0000-0002-6601-2165 An elastic tissue that is part of a bronchus [Automatically generated definition]. MA:0001838 NCIT:C49211 UMLS:C1707053 bronchi elastic connective tissue bronchi elastic tissue bronchi textus connectivus elasticus bronchial trunk elastic connective tissue bronchial trunk elastic tissue bronchial trunk textus connectivus elasticus bronchus elastic connective tissue bronchus textus connectivus elasticus elastic connective tissue of bronchi elastic connective tissue of bronchial trunk elastic connective tissue of bronchus elastic tissue of bronchi elastic tissue of bronchial trunk elastic tissue of bronchus textus connectivus elasticus of bronchi textus connectivus elasticus of bronchial trunk textus connectivus elasticus of bronchus uberon UBERON:0003616 bronchus elastic tissue An elastic tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707053 ncithesaurus:Bronchus_Elastic_Tissue bronchi elastic connective tissue OBOL:automatic bronchi elastic tissue OBOL:automatic bronchi textus connectivus elasticus OBOL:automatic bronchial trunk elastic connective tissue OBOL:automatic bronchial trunk elastic tissue OBOL:automatic bronchial trunk textus connectivus elasticus OBOL:automatic bronchus elastic connective tissue OBOL:automatic bronchus textus connectivus elasticus OBOL:automatic elastic connective tissue of bronchi OBOL:automatic elastic connective tissue of bronchial trunk OBOL:automatic elastic connective tissue of bronchus OBOL:automatic elastic tissue of bronchi OBOL:automatic elastic tissue of bronchial trunk OBOL:automatic elastic tissue of bronchus OBOL:automatic textus connectivus elasticus of bronchi OBOL:automatic textus connectivus elasticus of bronchial trunk OBOL:automatic textus connectivus elasticus of bronchus OBOL:automatic An elastic tissue that is part of a trachea [Automatically generated definition]. MA:0001861 cartilaginous trachea elastic connective tissue cartilaginous trachea elastic tissue cartilaginous trachea textus connectivus elasticus elastic connective tissue of cartilaginous trachea elastic connective tissue of vertebrate trachea elastic connective tissue of windpipe elastic tissue of cartilaginous trachea elastic tissue of vertebrate trachea elastic tissue of windpipe textus connectivus elasticus of cartilaginous trachea textus connectivus elasticus of vertebrate trachea textus connectivus elasticus of windpipe vertebrate trachea elastic connective tissue vertebrate trachea elastic tissue vertebrate trachea textus connectivus elasticus windpipe elastic connective tissue windpipe elastic tissue windpipe textus connectivus elasticus uberon UBERON:0003617 trachea elastic tissue An elastic tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic cartilaginous trachea elastic connective tissue OBOL:automatic cartilaginous trachea elastic tissue OBOL:automatic cartilaginous trachea textus connectivus elasticus OBOL:automatic elastic connective tissue of cartilaginous trachea OBOL:automatic elastic connective tissue of vertebrate trachea OBOL:automatic elastic connective tissue of windpipe OBOL:automatic elastic tissue of cartilaginous trachea OBOL:automatic elastic tissue of vertebrate trachea OBOL:automatic elastic tissue of windpipe OBOL:automatic textus connectivus elasticus of cartilaginous trachea OBOL:automatic textus connectivus elasticus of vertebrate trachea OBOL:automatic textus connectivus elasticus of windpipe OBOL:automatic vertebrate trachea elastic connective tissue OBOL:automatic vertebrate trachea elastic tissue OBOL:automatic vertebrate trachea textus connectivus elasticus OBOL:automatic windpipe elastic connective tissue OBOL:automatic windpipe elastic tissue OBOL:automatic windpipe textus connectivus elasticus OBOL:automatic The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. EMAPA:35138 FMA:74433 MA:0002903 SCTID:48467007 adult aorta tunica media dorsal aorta tunica media trunk of aortic tree tunica media tunica media of adult aorta tunica media of aorta tunica media of dorsal aorta tunica media of trunk of aortic tree uberon UBERON:0003618 aorta tunica media The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. MP:0009873 adult aorta tunica media OBOL:automatic dorsal aorta tunica media OBOL:automatic trunk of aortic tree tunica media OBOL:automatic tunica media of adult aorta OBOL:automatic tunica media of aorta OBOL:automatic tunica media of dorsal aorta OBOL:automatic tunica media of trunk of aortic tree OBOL:automatic The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. BTO:0005553 EMAPA:35137 FMA:74419 MA:0002904 SCTID:362031007 adult aorta tunica intima dorsal aorta tunica intima trunk of aortic tree tunica intima tunica intima of adult aorta tunica intima of aorta tunica intima of dorsal aorta tunica intima of trunk of aortic tree uberon UBERON:0003619 aorta tunica intima The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. MP:0009872 adult aorta tunica intima OBOL:automatic dorsal aorta tunica intima OBOL:automatic trunk of aortic tree tunica intima OBOL:automatic tunica intima of adult aorta OBOL:automatic tunica intima of aorta OBOL:automatic tunica intima of dorsal aorta OBOL:automatic tunica intima of trunk of aortic tree OBOL:automatic A phalanx that is part of a hand digit 1 [Automatically generated definition]. EMAPA:19113 FMA:35477 MA:0001389 NCIT:C52777 SCTID:181975002 UMLS:C1711344 fore limb digit 1 phalanx hand digit 1 phalanx manual digit I phalanx phalanx of hand digit 1 phalanx of thumb thumb phalanx hand digit 1 phalanx uberon UBERON:0003620 manual digit 1 phalanx A phalanx that is part of a hand digit 1 [Automatically generated definition]. OBOL:automatic UMLS:C1711344 ncithesaurus:Hand_Digit_1_Phalanx fore limb digit 1 phalanx OBOL:accepted hand digit 1 phalanx MA:0001389 manual digit I phalanx https://github.com/obophenotype/uberon/issues/458 phalanx of hand digit 1 OBOL:automatic phalanx of thumb OBOL:automatic thumb phalanx OBOL:automatic hand digit 1 phalanx NCBITaxon:9606 OBOL:accepted 5th digit of the manus. AAO:0010643 EHDAA2:0000535 EMAPA:17441 FMA:24949 MA:0000458 NCIT:C52838 SCTID:362773007 UMLS:C0230403 Wikipedia:Little_finger 5th digit of hand 5th finger digit 5 of fore-paw fifth digit of hand fifth finger finger 5 fore digit V fore limb digit 5 hand digit 5 manual digit V hand digit 5 little finger uberon manual digitus V manual digitus minimus manus digiti minimi manus quintus UBERON:0003625 manual digit 5 http://upload.wikimedia.org/wikipedia/commons/e/ed/Pink.jpg 5th digit of the manus. Wikipedia:Little_finger UMLS:C0230403 ncithesaurus:Hand_Digit_5 digit 5 of fore-paw EMAPA:17441 fifth digit of hand FMA:24949 finger 5 EHDAA2:0000535 fore digit V AAO:0010643 fore limb digit 5 OBOL:accepted hand digit 5 MA:0000458 manual digit V https://github.com/obophenotype/uberon/issues/458 hand digit 5 NCBITaxon:9606 OBOL:accepted manual digitus V Wikipedia:Little_finger manual digitus minimus Wikipedia:Little_finger manus quintus Wikipedia:Little_finger 1st digit of the hind autopod. AAO:0010644 BTO:0002349 EHDAA2:0002037 EMAPA:17460 FMA:25047 GAID:45 MA:0000465 MESH:D006214 NCIT:C52839 SCTID:21699005 SCTID:302546000 UMLS:C1708079 VSAO:0000201 Wikipedia:Hallux digit 1 of hind-paw digit 1 of pes digitus primus pedis foot digit 1 great toe hallex hallux hallux; digitus primus [I] hind digit 1 hind digit I hind limb digit 1 pedal digit 1 pedal digit I pes digit I preaxial digit of hindlimb toe 1 big toe foot digit 1 hindlimb dewclaw uberon digitus primus (I) pedis first toe large toe UBERON:0003631 pedal digit 1 http://upload.wikimedia.org/wikipedia/commons/a/ab/RightFootToes.jpg 1st digit of the hind autopod. Wikipedia:Hallux UMLS:C1708079 ncithesaurus:Foot_Digit_1 digit 1 of hind-paw EMAPA:17460 digitus primus pedis foot digit 1 MA:0000465 great toe FMA:25047 hallux FMA:TA hallux; digitus primus [I] FMA:25047 hind digit I AAO:0010644 hind limb digit 1 OBOL:accepted pedal digit I https://github.com/obophenotype/uberon/issues/458 toe 1 EHDAA2:0002037 foot digit 1 NCBITaxon:9606 OBOL:accepted hindlimb dewclaw Wikipedia:Dewclaw digitus primus (I) pedis BTO:0002349 first toe EMAPA:17460 large toe EMAPA:17460 5th digit of the hind autopod. AAO:0010658 BTO:0002353 EHDAA2:0002057 EMAPA:17472 FMA:25053 MA:0000469 NCIT:C52843 SCTID:362830009 UMLS:C1708087 Wikipedia:Fifth_toe 5th toe digit 5 of hind-paw digitus V of pes digitus minimus pedis digitus minimus; digitus quintus [v] digitus quintus [V] digitus quintus [V] pedis digitus quintus of pes digitus quintus pedis fifth digit of foot fifth toe foot digit 5 hind digit 5 hind digit V hind limb digit 5 pedal digit V pedal digitus minimus pes digit V toe 5 foot digit 5 little toe uberon digitus quintus (V) pedis UBERON:0003635 pedal digit 5 http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png 5th digit of the hind autopod. Wikipedia:Fifth_toe https://orcid.org/0000-0002-6601-2165 UMLS:C1708087 ncithesaurus:Foot_Digit_5 digit 5 of hind-paw EMAPA:17472 digitus minimus pedis Wikipedia:Fifth_toe digitus minimus; digitus quintus [v] FMA:25053 digitus quintus [V] FMA:25053 digitus quintus [V] pedis FMA:25053 FMA:TA digitus quintus pedis Wikipedia:Fifth_toe fifth digit of foot FMA:25053 fifth toe FMA:25053 foot digit 5 MA:0000469 hind digit V AAO:0010658 hind limb digit 5 OBOL:accepted pedal digit V https://github.com/obophenotype/uberon/issues/458 toe 5 EHDAA2:0002057 foot digit 5 NCBITaxon:9606 OBOL:accepted digitus quintus (V) pedis BTO:0002353 A phalanx that is part of a hand digit 5 [Automatically generated definition]. EMAPA:19121 FMA:35489 MA:0001393 NCIT:C52773 SCTID:361789008 UMLS:C1708317 5 th digit of hand digit long bone 5 th digit of hand long bone of digit 5 th digit of hand phalanx 5 th finger digit long bone 5 th finger long bone of digit 5 th finger phalanx digit long bone of 5 th digit of hand digit long bone of 5 th finger digit long bone of fifth finger digit long bone of hand digit 5 fifth finger digit long bone fifth finger long bone of digit fifth finger phalanx fore limb digit 5 phalanx hand digit 5 digit long bone hand digit 5 long bone of digit hand digit 5 phalanx little finger phalanx long bone of digit of 5 th digit of hand long bone of digit of 5 th finger long bone of digit of fifth finger long bone of digit of hand digit 5 manual digit V phalanx phalanx of 5 th digit of hand phalanx of 5 th finger phalanx of 5th finger phalanx of fifth digit of hand phalanx of fifth finger phalanx of hand digit 5 phalanx of little finger phalanx of manual digitus minimus hand digit 5 phalanx uberon UBERON:0003639 manual digit 5 phalanx A phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic UMLS:C1708317 ncithesaurus:Hand_Digit_5_Phalanx 5 th digit of hand digit long bone OBOL:automatic 5 th digit of hand long bone of digit OBOL:automatic 5 th digit of hand phalanx OBOL:automatic 5 th finger digit long bone OBOL:automatic 5 th finger long bone of digit OBOL:automatic 5 th finger phalanx OBOL:automatic digit long bone of 5 th digit of hand OBOL:automatic digit long bone of 5 th finger OBOL:automatic digit long bone of fifth finger OBOL:automatic digit long bone of hand digit 5 OBOL:automatic fifth finger digit long bone OBOL:automatic fifth finger long bone of digit OBOL:automatic fifth finger phalanx OBOL:automatic fore limb digit 5 phalanx OBOL:accepted hand digit 5 digit long bone OBOL:automatic hand digit 5 long bone of digit OBOL:automatic hand digit 5 phalanx MA:0001393 little finger phalanx FMA:35489 long bone of digit of 5 th digit of hand OBOL:automatic long bone of digit of 5 th finger OBOL:automatic long bone of digit of fifth finger OBOL:automatic long bone of digit of hand digit 5 OBOL:automatic manual digit V phalanx https://github.com/obophenotype/uberon/issues/458 phalanx of 5 th digit of hand OBOL:automatic phalanx of 5 th finger OBOL:automatic phalanx of fifth digit of hand FMA:35489 phalanx of fifth finger OBOL:automatic phalanx of hand digit 5 OBOL:automatic phalanx of little finger FMA:35489 phalanx of manual digitus minimus OBOL:automatic hand digit 5 phalanx NCBITaxon:9606 OBOL:accepted A phalanx that is part of a foot digit 1 [Automatically generated definition]. EMAPA:19124 FMA:32884 MA:0001381 NCIT:C52778 SCTID:361798006 UMLS:C1708080 big toe phalanx digit long bone of foot digit 1 digit long bone of hallux foot digit 1 digit long bone foot digit 1 long bone of digit foot digit 1 phalanx hallux digit long bone hallux long bone of digit hallux phalanx hind limb digit 1 phalanx long bone of digit of foot digit 1 long bone of digit of hallux pedal digit I phalanx phalanx of big toe phalanx of first digit of foot phalanx of foot digit 1 phalanx of great toe phalanx of hallux foot digit 1 phalanx uberon phalanx of first toe UBERON:0003640 pedal digit 1 phalanx A phalanx that is part of a foot digit 1 [Automatically generated definition]. OBOL:automatic UMLS:C1708080 ncithesaurus:Foot_Digit_1_Phalanx big toe phalanx FMA:32884 digit long bone of foot digit 1 OBOL:automatic digit long bone of hallux OBOL:automatic foot digit 1 digit long bone OBOL:automatic foot digit 1 long bone of digit OBOL:automatic foot digit 1 phalanx MA:0001381 hallux digit long bone OBOL:automatic hallux long bone of digit OBOL:automatic hallux phalanx OBOL:automatic hind limb digit 1 phalanx OBOL:accepted long bone of digit of foot digit 1 OBOL:automatic long bone of digit of hallux OBOL:automatic pedal digit I phalanx https://github.com/obophenotype/uberon/issues/458 phalanx of big toe FMA:32884 phalanx of first digit of foot FMA:32884 phalanx of foot digit 1 OBOL:automatic phalanx of great toe FMA:32884 phalanx of hallux OBOL:automatic foot digit 1 phalanx NCBITaxon:9606 OBOL:accepted phalanx of first toe FMA:32884 An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37565 MA:0001800 uberon UBERON:0003643 respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37565 MA:th An arterial blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:31436 MA:0002578 uberon kidney arterial system UBERON:0003644 kidney arterial blood vessel An arterial blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic kidney arterial system EMAPA:31436 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 1. The first metacarpal bone or the metacarpal bone of the thumb is the first bone of the thumb. It is connected to the trapezium of the carpus at the first carpometacarpal joint and to the proximal thumb phalanx at the first metacarpophalangeal joint[Wikipedia:First_metacarpal_bone]. 1 AAO:0010616 EMAPA:19112 FMA:23899 MA:0001364 NCIT:C52796 SCTID:181973009 UMLS:C1708987 finger 1 metacarpus first digit of hand metacarpal first digit of hand metacarpal bone first metacarpal bone hand digit 1 metacarpal hand digit 1 metacarpal bone manual digit 1 metacarpus metacarpal 1 metacarpal I metacarpal bone digit 1 metacarpal bone of digit I metacarpal bone of first digit of hand metacarpal bone of hand digit 1 metacarpal bone of thumb metacarpal of first digit of hand metacarpal of hand digit 1 metacarpal of thumb thumb metacarpal thumb metacarpal bone uberon forelimb digit 1 metacarpus UBERON:0003645 metacarpal bone of digit 1 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 1. OBOL:automatic The first metacarpal bone or the metacarpal bone of the thumb is the first bone of the thumb. It is connected to the trapezium of the carpus at the first carpometacarpal joint and to the proximal thumb phalanx at the first metacarpophalangeal joint[Wikipedia:First_metacarpal_bone]. Wikipedia:First_metacarpal_bone UMLS:C1708987 ncithesaurus:Metacarpal_Bone_Digit_1 first digit of hand metacarpal OBOL:automatic first digit of hand metacarpal bone OBOL:automatic first metacarpal bone FMA:23899 hand digit 1 metacarpal OBOL:automatic hand digit 1 metacarpal bone OBOL:automatic metacarpal I FMA:23899 metacarpal bone digit 1 MA:0001364 metacarpal bone of digit I https://github.com/obophenotype/uberon/issues/458 metacarpal bone of first digit of hand OBOL:automatic metacarpal bone of hand digit 1 OBOL:automatic metacarpal bone of thumb OBOL:automatic metacarpal of first digit of hand OBOL:automatic metacarpal of hand digit 1 OBOL:automatic metacarpal of thumb OBOL:automatic thumb metacarpal OBOL:automatic thumb metacarpal bone OBOL:automatic forelimb digit 1 metacarpus EMAPA:19112 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 5. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that articulates with carpal 5(4) proximally and with the proximal phalanx of digit V(IV) distally.[AAO] The fifth metacarpal bone (metacarpal bone of the little finger or pinky finger) is the most lateral metacarpal[Wikipedia:Fifth_metacarpal_bone]. FMA also has FMA:36782 ! Bone of fifth metacarpal bone 5 AAO:0000855 EMAPA:19120 FMA:23903 MA:0001368 NCIT:C52792 SCTID:263402008 UMLS:C1711224 5 th digit of hand metacarpal 5 th digit of hand metacarpal bone 5 th finger metacarpal 5 th finger metacarpal bone fifth finger metacarpal fifth finger metacarpal bone fifth metacarpal bone finger 5 metacarpus hand digit 5 metacarpal hand digit 5 metacarpal bone manual digit 5 metacarpus metacarpal 5 metacarpal V metacarpal bone digit 5 metacarpal bone of 5 th digit of hand metacarpal bone of 5 th finger metacarpal bone of digit V metacarpal bone of fifth finger metacarpal bone of hand digit 5 metacarpal of 5 th digit of hand metacarpal of 5 th finger metacarpal of fifth finger metacarpal of hand digit 5 uberon forelimb digit 5 metacarpus UBERON:0003649 metacarpal bone of digit 5 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 5. OBOL:automatic Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that articulates with carpal 5(4) proximally and with the proximal phalanx of digit V(IV) distally.[AAO] 2012-06-20 AAO:0000855 AAO AAO:LAP The fifth metacarpal bone (metacarpal bone of the little finger or pinky finger) is the most lateral metacarpal[Wikipedia:Fifth_metacarpal_bone]. Wikipedia:Fifth_metacarpal_bone FMA also has FMA:36782 ! Bone of fifth metacarpal bone FMA UMLS:C1711224 ncithesaurus:Metacarpal_Bone_Digit_5 5 th digit of hand metacarpal OBOL:automatic 5 th digit of hand metacarpal bone OBOL:automatic 5 th finger metacarpal OBOL:automatic 5 th finger metacarpal bone OBOL:automatic fifth finger metacarpal OBOL:automatic fifth finger metacarpal bone OBOL:automatic fifth metacarpal bone FMA:23903 hand digit 5 metacarpal OBOL:automatic hand digit 5 metacarpal bone OBOL:automatic metacarpal bone digit 5 MA:0001368 metacarpal bone of 5 th digit of hand OBOL:automatic metacarpal bone of 5 th finger OBOL:automatic metacarpal bone of digit V https://github.com/obophenotype/uberon/issues/458 metacarpal bone of fifth finger OBOL:automatic metacarpal bone of hand digit 5 OBOL:automatic metacarpal of 5 th digit of hand OBOL:automatic metacarpal of 5 th finger OBOL:automatic metacarpal of fifth finger OBOL:automatic metacarpal of hand digit 5 OBOL:automatic forelimb digit 5 metacarpus EMAPA:19120 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 1. Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and tarsal 1 proximally and with the proximal phalanx of digit I distally.[AAO] The first metatarsal bone is the bone in the body of the foot just behind the big toe. It is remarkable for its great thickness, and is the shortest of the metatarsal bones. The body is strong, and of well-marked prismoid form. The base presents, as a rule, no articular facets on its sides, but occasionally on the lateral side there is an oval facet, by which it articulates with the second metatarsal. Its proximal articular surface is of large size and kidney-shaped; its circumference is grooved, for the tarsometatarsal ligaments, and medially gives insertion to part of the tendon of the Tibialis anterior; its plantar angle presents a rough oval prominence for the insertion of the tendon of the Peronæus longus. The head is large; on its plantar surface are two grooved facets, on which glide sesamoid bones; the facets are separated by a smooth elevation[Wikipedia:First_metatarsal_bone]. 1 AAO:0000925 EMAPA:19123 FMA:24502 MA:0001369 NCIT:C52791 SCTID:182121005 UMLS:C1708999 first metatarsal bone foot digit 1 metatarsal bone hallux metatarsal bone metatarsal 1 metatarsal I metatarsal bone digit 1 metatarsal bone of digit I metatarsal bone of foot digit 1 metatarsal bone of hallux toe 1 metatarsal toe 1 metatarsus uberon hindlimb digit 1 metatarsus UBERON:0003650 metatarsal bone of digit 1 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 1. OBOL:automatic Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and tarsal 1 proximally and with the proximal phalanx of digit I distally.[AAO] 2012-06-20 AAO:0000925 AAO AAO:LAP The first metatarsal bone is the bone in the body of the foot just behind the big toe. It is remarkable for its great thickness, and is the shortest of the metatarsal bones. The body is strong, and of well-marked prismoid form. The base presents, as a rule, no articular facets on its sides, but occasionally on the lateral side there is an oval facet, by which it articulates with the second metatarsal. Its proximal articular surface is of large size and kidney-shaped; its circumference is grooved, for the tarsometatarsal ligaments, and medially gives insertion to part of the tendon of the Tibialis anterior; its plantar angle presents a rough oval prominence for the insertion of the tendon of the Peronæus longus. The head is large; on its plantar surface are two grooved facets, on which glide sesamoid bones; the facets are separated by a smooth elevation[Wikipedia:First_metatarsal_bone]. Wikipedia:First_metatarsal_bone UMLS:C1708999 ncithesaurus:Metatarsal_Bone_Digit_1 first metatarsal bone FMA:24502 foot digit 1 metatarsal bone OBOL:automatic hallux metatarsal bone OBOL:automatic metatarsal I AAO:0000925 metatarsal bone digit 1 MA:0001369 metatarsal bone of digit I https://github.com/obophenotype/uberon/issues/458 metatarsal bone of foot digit 1 OBOL:automatic metatarsal bone of hallux OBOL:automatic hindlimb digit 1 metatarsus EMAPA:19123 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 5. Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 5 or the distal head of the tibiale-fibulare proximally and with the proximal phalanx of digit V distally.[AAO] The fifth metatarsal bone is recognized by a rough eminence, the tuberosity, on the lateral side of its base. The base articulates behind, by a triangular surface cut obliquely in a transverse direction, with the cuboid; and medially, with the fourth metatarsal. On the medial part of its dorsal surface is inserted the tendon of the Peronæus tertius and on the dorsal surface of the tuberosity that of the Peronæus brevis. A strong band of the plantar aponeurosis connects the projecting part of the tuberosity with the lateral process of the tuberosity of the calcaneus. The plantar surface of the base is grooved for the tendon of the Abductor digiti quinti, and gives origin to the Flexor digiti quinti brevis. The base of the metatarsal is often injured and a particularly notorious fracture is the Jones fracture. When the tuberosity is broken, it is called a pseudo-Jones fracture or a dancer's fracture. This is a common fracture of the fifth metatarsal. Stress fractures are common in the fifth metatarsal among athletes[Wikipedia:Fifth_metatarsal_bone]. 5 AAO:0000929 EMAPA:19131 FMA:24506 MA:0001373 NCIT:C52787 SCTID:182144008 UMLS:C1709003 fifth metatarsal bone foot digit 5 metatarsal bone metatarsal 5 metatarsal V metatarsal bone digit 5 metatarsal bone of digit V metatarsal bone of foot digit 5 toe 5 metatarsal toe 5 metatarsus uberon hindlimb digit 5 metatarsus UBERON:0003654 metatarsal bone of digit 5 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 5. OBOL:automatic Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 5 or the distal head of the tibiale-fibulare proximally and with the proximal phalanx of digit V distally.[AAO] 2012-06-20 AAO:0000929 AAO AAO:LAP The fifth metatarsal bone is recognized by a rough eminence, the tuberosity, on the lateral side of its base. The base articulates behind, by a triangular surface cut obliquely in a transverse direction, with the cuboid; and medially, with the fourth metatarsal. On the medial part of its dorsal surface is inserted the tendon of the Peronæus tertius and on the dorsal surface of the tuberosity that of the Peronæus brevis. A strong band of the plantar aponeurosis connects the projecting part of the tuberosity with the lateral process of the tuberosity of the calcaneus. The plantar surface of the base is grooved for the tendon of the Abductor digiti quinti, and gives origin to the Flexor digiti quinti brevis. The base of the metatarsal is often injured and a particularly notorious fracture is the Jones fracture. When the tuberosity is broken, it is called a pseudo-Jones fracture or a dancer's fracture. This is a common fracture of the fifth metatarsal. Stress fractures are common in the fifth metatarsal among athletes[Wikipedia:Fifth_metatarsal_bone]. Wikipedia:Fifth_metatarsal_bone UMLS:C1709003 ncithesaurus:Metatarsal_Bone_Digit_5 fifth metatarsal bone FMA:24506 foot digit 5 metatarsal bone OBOL:automatic metatarsal V AAO:0000929 metatarsal bone digit 5 MA:0001373 metatarsal bone of digit V https://github.com/obophenotype/uberon/issues/458 metatarsal bone of foot digit 5 OBOL:automatic hindlimb digit 5 metatarsus EMAPA:19131 A bone that is part of a mesopodial skeleton. The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost EMAPA:36579 MA:0000295 Wikipedia:Carpus_and_tarsus_of_land_vertebrates basipodium bone carpal/tarsal bone mesopod bone mesopodial bone uberon UBERON:0003656 mesopodium bone UBERON:cjm https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern A bone that is part of a mesopodial skeleton. https://orcid.org/0000-0002-6601-2165 The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost Wikipedia:Carpus_and_tarsus_of_land_vertebrates basipodium bone MA:th carpal/tarsal bone MA:0000295 Any joint that is part of a (free) limb. EMAPA:36501 FMA:321558 MA:0000691 SCTID:312683002 galen:LimbJoint joint of limb joint of limb skeletal system skeletal limb joint uberon UBERON:0003657 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses limb joint Any joint that is part of a (free) limb. https://orcid.org/0000-0002-6601-2165 joint of limb skeletal system OBOL:automatic skeletal limb joint GO:0036023 Any muscle organ that is part of a hip [Automatically generated definition]. MA:0000657 hip muscle organ hip region muscle organ muscle organ of hip muscle organ of hip region muscle organ of regio coxae regio coxae muscle organ uberon UBERON:0003658 hip muscle prolog Any muscle organ that is part of a hip [Automatically generated definition]. OBOL:automatic hip muscle organ OBOL:automatic hip region muscle organ OBOL:automatic muscle organ of hip OBOL:automatic muscle organ of hip region OBOL:automatic muscle organ of regio coxae OBOL:automatic regio coxae muscle organ OBOL:automatic Any muscle organ that is part of a toe [Automatically generated definition]. EMAPA:37333 MA:0000648 digit of foot muscle organ digit of terminal segment of free lower limb muscle organ digitus pedis muscle organ foot digit muscle foot digit muscle organ hind limb digit muscle muscle organ of digit of foot muscle organ of digit of terminal segment of free lower limb muscle organ of digitus pedis muscle organ of foot digit muscle organ of terminal segment of free lower limb digit muscle organ of toe terminal segment of free lower limb digit muscle organ toe muscle organ foot digit muscle uberon UBERON:0003659 pedal digit muscle Any muscle organ that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37333 MA:th digit of foot muscle organ OBOL:automatic digit of terminal segment of free lower limb muscle organ OBOL:automatic digitus pedis muscle organ OBOL:automatic foot digit muscle MA:0000648 foot digit muscle organ OBOL:automatic hind limb digit muscle OBOL:accepted muscle organ of digit of foot OBOL:automatic muscle organ of digit of terminal segment of free lower limb OBOL:automatic muscle organ of digitus pedis OBOL:automatic muscle organ of foot digit OBOL:automatic muscle organ of terminal segment of free lower limb digit OBOL:automatic muscle organ of toe OBOL:automatic terminal segment of free lower limb digit muscle organ OBOL:automatic toe muscle organ OBOL:automatic foot digit muscle NCBITaxon:9606 OBOL:accepted Any muscle organ that is part of a limb [Automatically generated definition]. EMAPA:32700 MA:0000692 limb muscle organ limb skeletal muscle muscle organ of limb uberon UBERON:0003661 limb muscle prolog Any muscle organ that is part of a limb [Automatically generated definition]. OBOL:automatic limb muscle organ OBOL:accepted limb skeletal muscle OBOL:exploratory muscle organ of limb OBOL:accepted Any muscle organ that is part of a forelimb. FMA and MA class actually refer to muscles of entire pectoral complex UBERON:0005634 AAO:0000204 BTO:0000479 EMAPA:36049 FMA:37348 fore limb muscle organ forelimb muscle organ free upper limb muscle muscle of free upper limb muscle of upper limb upper limb skeletal muscle wing muscle uberon arm muscle system musculature of arm musculature of the arm UBERON:0003662 forelimb muscle prolog Any muscle organ that is part of a forelimb. OBOL:automatic FMA and MA class actually refer to muscles of entire pectoral complex FMA fore limb muscle organ OBOL:automatic forelimb muscle organ OBOL:automatic free upper limb muscle FMA:37348 muscle of free upper limb FMA:37348 muscle of upper limb FMA:9621 upper limb skeletal muscle http://orcid.org/0000-0002-6601-2165 wing muscle Geisha:syn NCBITaxon:8782 OBOL:automatic arm muscle system EHDAA2:0000141 musculature of arm musculature of the arm Any muscle organ that is part of a hindlimb [Automatically generated definition]. AAO:0000222 EFO:0001928 FMA:37368 free lower limb muscle hind limb muscle organ hindlimb muscle organ inferior member muscle organ lower extremity muscle organ lower limb skeletal muscle muscle of free lower limb muscle of posterior limb muscle organ of hind limb muscle organ of hindlimb muscle organ of inferior member muscle organ of lower extremity uberon UBERON:0003663 hindlimb muscle prolog Any muscle organ that is part of a hindlimb [Automatically generated definition]. OBOL:automatic free lower limb muscle FMA:37368 hind limb muscle organ OBOL:automatic hindlimb muscle organ OBOL:automatic inferior member muscle organ OBOL:automatic lower extremity muscle organ OBOL:automatic lower limb skeletal muscle http://orcid.org/0000-0002-6601-2165 muscle of free lower limb FMA:37368 muscle of posterior limb https://orcid.org/0000-0002-6601-2165 muscle organ of hind limb OBOL:automatic muscle organ of hindlimb OBOL:automatic muscle organ of inferior member OBOL:automatic muscle organ of lower extremity OBOL:automatic Any muscle organ that is part of a finger [Automatically generated definition]. EMAPA:37331 MA:0000624 digit of hand muscle organ digit of terminal segment of free upper limb muscle organ digitus manus muscle organ finger muscle organ fore limb digit muscle hand digit muscle hand digit muscle organ muscle organ of digit of hand muscle organ of digit of terminal segment of free upper limb muscle organ of digitus manus muscle organ of finger muscle organ of hand digit muscle organ of terminal segment of free upper limb digit terminal segment of free upper limb digit muscle organ hand digit muscle uberon UBERON:0003664 manual digit muscle Any muscle organ that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37331 MA:th digit of hand muscle organ OBOL:automatic digit of terminal segment of free upper limb muscle organ OBOL:automatic digitus manus muscle organ OBOL:automatic finger muscle organ OBOL:automatic fore limb digit muscle OBOL:accepted hand digit muscle MA:0000624 hand digit muscle organ OBOL:automatic muscle organ of digit of hand OBOL:automatic muscle organ of digit of terminal segment of free upper limb OBOL:automatic muscle organ of digitus manus OBOL:automatic muscle organ of finger OBOL:automatic muscle organ of hand digit OBOL:automatic muscle organ of terminal segment of free upper limb digit OBOL:automatic terminal segment of free upper limb digit muscle organ OBOL:automatic hand digit muscle NCBITaxon:9606 OBOL:accepted A muscle organ that attaches to a tail vertebra [Automatically generated definition]. the BTO class may possibly refer to an invertebrate structure AAO:0000081 BTO:0001905 EMAPA:37759 MA:0000699 SCTID:113230005 caudal muscle muscle organ of post-vent region muscle organ of tail post-vent region muscle organ tail muscle tail muscle organ uberon UBERON:0003665 post-anal tail muscle A muscle organ that attaches to a tail vertebra [Automatically generated definition]. OBOL:automatic the BTO class may possibly refer to an invertebrate structure BTO EMAPA:37759 MA:th muscle organ of post-vent region OBOL:automatic muscle organ of tail OBOL:automatic post-vent region muscle organ OBOL:automatic tail muscle MA:0000699 tail muscle organ OBOL:automatic A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body. bursa FMA:9692 GAID:252 MESH:D002061 NCIT:C33717 SCTID:182483003 UMLS:C0006441 Wikipedia:Synovial_bursa galen:Bursa uberon bursa synovialis UBERON:0003668 synovial bursa http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body. Wikipedia:Synovial_bursa bursa FMA:9692 UMLS:C0006441 ncithesaurus:Synovial_Bursa bursa synovialis Wikipedia:Synovial_bursa A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl. Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO] The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition]) In FMA this is an anatomical set AAO:0000126 FMA:75150 GAID:1249 MESH:D003817 NCIT:C13072 SCTID:245543004 UMLS:C0011443 dentes set of teeth teeth teeth set uberon collection of teeth teeth UBERON:0003672 dentition A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl. http://orcid.org/0000-0002-6601-2165 Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO] 2012-06-20 AAO:0000126 AAO AAO:LAP The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition]) ncithesaurus:Dentition In FMA this is an anatomical set FMA UMLS:C0011443 ncithesaurus:Dentition dentes FMA:75150 FMA:TA set of teeth FMA:75150 teeth FMA:75150 teeth set FMA:75150 The part of a tooth that is implanted in the gum; the root is normally located below the neck of the tooth, covered by cementum rather than enamel, and attached by the periodontal ligament to the alveolar bone. EMAPA:37975 FMA:55624 GAID:1280 MESH:D014092 SCTID:245728004 radix corona root of tooth tooth root uberon UBERON:0003677 tooth root The part of a tooth that is implanted in the gum; the root is normally located below the neck of the tooth, covered by cementum rather than enamel, and attached by the periodontal ligament to the alveolar bone. MP:0011165 EMAPA:37975 MA:th radix corona FMA:55624 root of tooth FMA:55624 tooth root FMA:55624 The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity EFO:0000213 EMAPA:36505 FMA:12266 GAID:17 MA:0003057 MESH:D034841 NCIT:C12664 SCTID:361294009 UMLS:C0230168 Wikipedia:Abdominal_cavity galen:AbdominalCavity cavity of abdominal compartment cavity of compartment of abdomen space of abdominal compartment uberon cavitas abdominis UBERON:0003684 abdominal cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). UBERON:cjm in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity FMA UMLS:C0230168 ncithesaurus:Abdominal_Cavity cavity of abdominal compartment FMA:12266 cavity of compartment of abdomen FMA:12266 space of abdominal compartment FMA:12266 cavitas abdominis GAID:17 Wikipedia:Abdominal_cavity Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture. sutura suture EMAPA:35263 FMA:7493 GAID:211 MA:0001475 MESH:D003393 SCTID:244509003 Wikipedia:Suture_(joint) cranium suture suture joint of skull suture of cranium uberon UBERON:0003685 cranial suture GO Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture. FMA:71385 ISBN:3110148986 Wikipedia:Suture_(joint) suture FMA:71385 cranium suture OBOL:automatic suture of cranium OBOL:automatic In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] AAO:0010826 BTO:0006035 EMAPA:37868 FMA:75306 GAID:228 MESH:D005539 NCIT:C12495 SCTID:244679008 TAO:0002045 UMLS:C0016519 Wikipedia:Foramen_magnum ZFA:0005387 uberon UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Wikipedia:Foramen_magnum Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] 2012-08-14 TAO:0002045 TAO TAO:wd BTO:0006035 https://github.com/biopragmatics/biomappings EMAPA:37868 MA:th UMLS:C0016519 ncithesaurus:Foramen_Magnum A collection of sacral vertebrae in the sacral region that are fused and part of the bony pelvis. sacral the AAO class 'sacrum' is deliberately placed under 'sacral vertebra' rather than here CALOHA:TS-2201 EFO:0003071 FMA:16202 GAID:241 MESH:D012447 NCIT:C33508 SCTID:264186006 Wikipedia:Sacrum galen:Sacrum os sacrum [vertebrae sacrales I - V] sacrum sacrum [sacral vertebrae I - V] sacrum [sacral vertebrae I-V] uberon os sacrum sacral bone UBERON:0003690 fused sacrum http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray95.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb FMA FMA A collection of sacral vertebrae in the sacral region that are fused and part of the bony pelvis. https://orcid.org/0000-0002-6601-2165 the AAO class 'sacrum' is deliberately placed under 'sacral vertebra' rather than here AAO os sacrum [vertebrae sacrales I - V] FMA:16202 FMA:TA sacrum FMA:16202 sacrum [sacral vertebrae I - V] FMA:16202 sacrum [sacral vertebrae I-V] FMA:16202 os sacrum Wikipedia:Sacrum sacral bone FMA:16202 The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater. epidural extradural In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail FMA:71228 GAID:243 MESH:D004824 SCTID:281866004 Wikipedia:Epidural_space cavum epidurale cavum extradurale extradural space spatium epidurale spatium extradurale uberon epidural cavity UBERON:0003691 epidural space The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater. Wikipedia:Epidural_space in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail FMA cavum epidurale Wikipedia:Epidural_space cavum extradurale Wikipedia:Epidural_space extradural space FMA:71228 spatium epidurale Wikipedia:Epidural_space spatium extradurale FMA:71228 FMA:TA epidural cavity Wikipedia:Epidural_space Any joint connecting the acromonion of the scapula and clavicle. The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula. FMA:25898 GAID:249 MESH:D000173 NCIT:C32047 SCTID:182166001 UMLS:C0001208 Wikipedia:Acromioclavicular_joint uberon acromioclavicular articulation articulatio acromioclavicularis scapuloclavicular articulation UBERON:0003692 acromioclavicular joint http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png FMA Any joint connecting the acromonion of the scapula and clavicle. Wikipedia:Acromioclavicular_joint http://orcid.org/0000-0002-6601-2165 The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula. MESH:A02.835.583.032 UMLS:C0001208 ncithesaurus:Acromioclavicular_Joint acromioclavicular articulation Wikipedia:Acromioclavicular_joint articulatio acromioclavicularis Wikipedia:Acromioclavicular_joint scapuloclavicular articulation Wikipedia:Acromioclavicular_joint The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas. FMA:25524 GAID:250 MESH:D001268 NCIT:C32157 SCTID:361832004 UMLS:C0004168 Wikipedia:Atlanto-axial_joint atlanto axial joint atlantoaxial joint uberon articulatio atlantoaxialis articulatio atlantoepistrophica atlantoaxial lateral atlanto-axial joint median atlanto-axial joint UBERON:0003694 atlanto-axial joint http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas. Wikipedia:Atlanto-axial_joint UMLS:C0004168 ncithesaurus:Atlanto-axial_Joint atlanto axial joint GAID:250 atlantoaxial joint GAID:250 articulatio atlantoaxialis Wikipedia:Atlanto-axial_joint articulatio atlantoepistrophica Wikipedia:Atlanto-axial_joint atlantoaxial Wikipedia:Atlanto-axial_joint lateral atlanto-axial joint Wikipedia:Atlanto-axial_joint median atlanto-axial joint Wikipedia:Atlanto-axial_joint The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]. we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part metacarpal joint EMAPA:19302 FMA:35246 GAID:255 MA:0000453 MESH:D008662 NCIT:C33106 SCTID:280995004 SCTID:370651001 UMLS:C0025525 Wikipedia:Metacarpophalangeal_joint galen:MetacarpoPhalangealJoint MP joint knuckle knuckles metacarpo-phalangeal joint carpometacarpophalangeal joint uberon articulationes metacarpophalangeae metacarpal phalangeal joint UBERON:0003695 metacarpophalangeal joint http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]. Wikipedia:Metacarpophalangeal_joint metacarpal joint FMA:35246 UMLS:C0025525 ncithesaurus:Metacarpophalangeal_Joint MP joint FMA:35246 knuckle https://orcid.org/0000-0001-5208-3432 knuckles https://orcid.org/0000-0001-5208-3432 metacarpo-phalangeal joint MA:0000453 carpometacarpophalangeal joint NCBITaxon:8782 articulationes metacarpophalangeae Wikipedia:Metacarpophalangeal_joint metacarpal phalangeal joint HP:0004294 The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral. we follow FMA in making these joints part of digits FMA:35222 GAID:258 MESH:D008683 NCIT:C33108 SCTID:239747005 SCTID:302535003 SCTID:370752004 UMLS:C0025589 Wikipedia:Metatarsophalangeal_articulations galen:MetatarsoPhalangealJoint metatarsal-phalangeal joint uberon articulationes metatarsophalangeae metatarsal joint metatarsalphalangeal joint metatarsophalangeal metatarsophalangeal articulation UBERON:0003696 metatarsophalangeal joint http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral. Wikipedia:Metatarsophalangeal_articulations UMLS:C0025589 ncithesaurus:Metatarsophalangeal_Joint metatarsal-phalangeal joint PHENOSCAPE:ad articulationes metatarsophalangeae Wikipedia:Metatarsophalangeal_articulations metatarsal joint FMA:35222 metatarsalphalangeal joint Wikipedia:Metatarsophalangeal_articulations metatarsophalangeal Wikipedia:Metatarsophalangeal_articulations metatarsophalangeal articulation Wikipedia:Metatarsophalangeal_articulations The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. EMAPA:37064 FMA:10429 FMA:259054 GAID:26 MESH:D034861 NCIT:C77608 SCTID:181613000 UMLS:C0836916 Wikipedia:Abdominal_wall paries abdominalis wall of abdomen wall of abdomen proper uberon abdominal wall proper layers of the abdominal wall paries abdominalis UBERON:0003697 abdominal wall http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. ncithesaurus:Abdominal_Wall EMAPA:37064 MA:th UMLS:C0836916 ncithesaurus:Abdominal_Wall paries abdominalis Wikipedia:Abdominal_wall wall of abdomen FMA:259054 wall of abdomen proper FMA:10429 abdominal wall proper FMA:10429 layers of the abdominal wall Wikipedia:Abdominal_wall paries abdominalis Wikipedia:Abdominal_wall Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct FMA:14678 GAID:281 MA:0002659 MESH:D017734 NCIT:C32573 SCTID:276158002 UMLS:C0206187 uberon bile duct extrahepatic part extrahepatic biliary system UBERON:0003703 extrahepatic bile duct Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. MESH:A03.159.183.079 UMLS:C0206187 ncithesaurus:Extrahepatic_Bile_Duct bile duct extrahepatic part MA:0002659 extrahepatic biliary system GAID:281 Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] FMA:15766 GAID:287 MA:0001630 MESH:D001653 NCIT:C12677 SCTID:362193005 TAO:0005169 UMLS:C0005401 ZFA:0005169 bile duct intrahepatic part uberon intrahepatic biliary system UBERON:0003704 intrahepatic bile duct FMA MA Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. MESH:A03.159.183.158 Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] 2012-08-14 TAO:0005169 TAO ZFIN:curator UMLS:C0005401 ncithesaurus:Intrahepatic_Bile_Duct bile duct intrahepatic part MA:0001630 A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle. In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis arterial circle EHDAA2:0000252 EHDAA:9758 EMAPA:37829 FMA:50454 GAID:486 MESH:D002941 SCTID:362047009 Wikipedia:Circle_of_Willis neuronames:1468 arterial circle of Willis cerebral arterial circle uberon Willis circle circulus arteriosus cerebri UBERON:0003709 circle of Willis http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg FMA-modified FMA-modified A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle. Wikipedia:Circle_of_Willis In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html arterial circle Wikipedia:Circle_of_Willis EMAPA:37829 MA:th cerebral arterial circle GAID:486 Willis circle GAID:486 circulus arteriosus cerebri Wikipedia:Circle_of_Willis The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava. EHDAA2:0000182 EHDAA:9868 FMA:4723 GAID:529 MESH:D016121 NCIT:C32816 SCTID:181371003 UMLS:C0006095 Wikipedia:Brachiocephalic_vein galen:BrachiocephalicVein brachiocephalic venous tree innominate vein uberon innomiate vein innominate trunk innominate vein innominate veins vena brachiocephalica venae anonyma UBERON:0003711 brachiocephalic vein http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava. Wikipedia:Brachiocephalic_vein UMLS:C0006095 ncithesaurus:Innominate_Vein brachiocephalic venous tree FMA:4723 innominate vein FMA:4723 innomiate vein Wikipedia:Brachiocephalic_vein innominate trunk Wikipedia:Brachiocephalic_vein innominate vein GAID:529 Wikipedia:Brachiocephalic_vein innominate veins Wikipedia:Brachiocephalic_vein vena brachiocephalica Wikipedia:Brachiocephalic_vein venae anonyma Wikipedia:Brachiocephalic_vein The cavernous sinus (or lateral sellar compartment), within the human head, is a large collection of thin-walled veins creating a cavity bordered by the temporal bone of the skull and the sphenoid bone, lateral to the sella turcica. An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334]. EMAPA:19059 FMA:50772 GAID:532 MESH:D002426 NCIT:C12690 SCTID:244402005 UMLS:C0007473 Wikipedia:Cavernous_sinus uberon cavernous cavernous sinus syndrome cavernous sinuses cavernus sinus vein parasellar syndrome sinus cavernosus UBERON:0003712 cavernous sinus The cavernous sinus (or lateral sellar compartment), within the human head, is a large collection of thin-walled veins creating a cavity bordered by the temporal bone of the skull and the sphenoid bone, lateral to the sella turcica. Wikipedia:Cavernous_sinus An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334]. MESH:A07.231.908.224.334 UMLS:C0007473 ncithesaurus:Cavernous_Sinus cavernous Wikipedia:Cavernous_sinus cavernous sinus syndrome Wikipedia:Cavernous_sinus cavernous sinuses Wikipedia:Cavernous_sinus cavernus sinus vein Wikipedia:Cavernous_sinus parasellar syndrome Wikipedia:Cavernous_sinus sinus cavernosus Wikipedia:Cavernous_sinus A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. EMAPA:37226 FMA:14331 GAID:541 MA:0002164 MESH:D013162 NCIT:C33608 SCTID:278029005 UMLS:C0038001 Wikipedia:Splenic_vein galen:SplenicVein vena splenica uberon lienal vein vena lienalis UBERON:0003713 splenic vein http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. ncithesaurus:Splenic_Vein EMAPA:37226 MA:th UMLS:C0038001 ncithesaurus:Splenic_Vein vena splenica FMA:14331 FMA:TA lienal vein MA:0002164 Wikipedia:Splenic_vein vena lienalis Wikipedia:Splenic_vein Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA:9642 GAID:609 MESH:D009417 NCIT:C13052 SCTID:91728009 UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon UBERON:0003714 neural tissue Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] 2012-06-20 AAO:0000325 AAO AAO:LAP FMA definition includes vasculature FMA UMLS:C0027757 ncithesaurus:Nervous_Tissue nerve tissue FMA:9642 nervous tissue FMA:9642 portion of neural tissue FMA:9642 The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers BAMS:spn EMAPA:37959 FMA:5883 GAID:800 MESH:D013153 SCTID:264198001 Wikipedia:Splanchnic_nerves uberon splanchnic nerves visceral nerve UBERON:0003715 splanchnic nerve The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. MP:0008318 EMAPA:37959 MA:th splanchnic nerves BAMS:spn visceral nerve Wikipedia:Splanchnic_nerves A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. recurrent nerve AAO:0010754 FMA:6246 GAID:804 MESH:D012009 SCTID:24227007 VHOG:0001347 Wikipedia:Recurrent_laryngeal_nerve nervus laryngeus recurrens recurrent laryngeal nerve from vagus nerve vagus X nerve recurrent laryngeal branch uberon inferior laryngeal nerve ramus recurrens UBERON:0003716 recurrent laryngeal nerve Wikipedia A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Wikipedia:Recurrent_laryngeal_nerve Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. AAO:0010754 recurrent nerve Wikipedia:Recurrent_laryngeal_nerve nervus laryngeus recurrens Wikipedia:Recurrent_laryngeal_nerve vagus X nerve recurrent laryngeal branch VHOG:0001347 inferior laryngeal nerve GAID:804 ramus recurrens AAO:0010754 The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue. BAMS:5lg EMAPA:19168 FMA:53218 GAID:835 MA:0001102 MESH:D008036 SCTID:280260006 Wikipedia:Lingual_nerve lingual branch of trigeminal nerve trigeminal V nerve lingual branch trigeminal nerve lingual branch uberon UBERON:0003721 lingual nerve The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue. Wikipedia:Lingual_nerve trigeminal V nerve lingual branch MA:0001102 The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. FMA:5860 GAID:857 MESH:D013900 SCTID:360498003 Wikipedia:Thoracic_nerves neuronames:1725 nervus thoracis thoracic spinal nerve uberon nervi thoracici pectoral nerve UBERON:0003726 thoracic nerve The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. MESH:A08.800.800.720.800 nervus thoracis FMA:5860 FMA:TA thoracic spinal nerve FMA:5860 nervi thoracici Wikipedia:Thoracic_nerves pectoral nerve GAID:857 The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. EMAPA:18227 FMA:6028 GAID:858 MESH:D007367 NCIT:C32825 SCTID:279568001 UMLS:C1285089 Wikipedia:Intercostal_nerves anterior ramus of thoracic nerve anterior ramus of thoracic spinal nerve ramus anterior, nervus thoracicus thoracic anterior ramus ventral ramus of thoracic spinal nerve uberon nervi intercostales UBERON:0003727 intercostal nerve http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. Wikipedia:Intercostal_nerves UMLS:C1285089 ncithesaurus:Intercostal_Nerve anterior ramus of thoracic nerve FMA:6028 anterior ramus of thoracic spinal nerve FMA:6028 ramus anterior, nervus thoracicus FMA:6028 thoracic anterior ramus FMA:6028 ventral ramus of thoracic spinal nerve FMA:6028 nervi intercostales Wikipedia:Intercostal_nerves The central part of the thoracic cavity enclosed by the left and right pleurae. mediastinal CALOHA:TS-2338 EFO:0003057 EMAPA:36001 FMA:9826 GAID:94 MA:0003075 MESH:D008482 NCIT:C12748 SCTID:181217005 UMLS:C0025066 Wikipedia:Mediastinum mediastinal part of chest uberon UBERON:0003728 mediastinum http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png FMA The central part of the thoracic cavity enclosed by the left and right pleurae. UBERON:cjm Wikipedia:Mediastinum UMLS:C0025066 ncithesaurus:Mediastinum mediastinal part of chest FMA:9826 A mucous membrane that lines the mouth. this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. BTO:0002860 CALOHA:TS-0716 EMAPA:26937 FMA:59660 GAID:951 MA:0002794 MESH:D009061 NCIT:C77637 UMLS:C0026639 Wikipedia:Oral_mucosa mouth mucosa mouth mucous membrane mouth organ mucosa mucosa of mouth mucous membrane of mouth oral mucous membrane oral part of viscerocranial mucosa tunica mucosa oris uberon buccal mucosa mucosal lining of mouth oral mucosa tunica mucosa oris UBERON:0003729 mouth mucosa A mucous membrane that lines the mouth. http://orcid.org/0000-0002-6601-2165 the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. Wikipedia:Oral_mucosa UMLS:C0026639 ncithesaurus:Oral_Mucosa mouth mucosa FMA:59660 mouth mucous membrane OBOL:accepted mouth organ mucosa OBOL:accepted mucosa of mouth OBOL:accepted mucous membrane of mouth FMA:59660 oral part of viscerocranial mucosa FMA:59660 tunica mucosa oris FMA:59660 FMA:TA buccal mucosa GAID:951 mucosal lining of mouth MA:0002794 oral mucosa GAID:951 tunica mucosa oris Wikipedia:Oral_mucosa A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204] EMAPA:36141 prostate ductal progenitor prostatic bud uberon prostate gland bud prostate primordium UBERON:0003820 prostate bud PMID:18977204 A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. GO:0060513 prostate ductal progenitor PMID:18977204 prostate gland bud EMAPA:36141 A bone of the metapodial skeleton. EMAPA:37284 MA:0000301 metacarpal or metatarsal bone metacarpal/metatarsal metacarpal/metatarsal bone metapodi bone metapodial bone metapodium bone uberon UBERON:0003821 metapodium bone https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern A bone of the metapodial skeleton. https://orcid.org/0000-0002-6601-2165 EMAPA:37284 MA:th metacarpal/metatarsal bone MA:0000301 metapodi bone https://orcid.org/0000-0002-6601-2165 metapodial bone https://orcid.org/0000-0002-6601-2165 metapodium bone http://en.wiktionary.org/wiki/metapodial https://orcid.org/0000-0002-6601-2165 The part of the forelimb between pectoral region and the elbow, corresponding to the humerus. Segment of the hindleg corresponding to the humerus.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group. AAO:0000199 EHDAA2:0002112 EHDAA:4186 EHDAA:6234 EMAPA:17424 FMA:24890 MA:0000035 MESH:D001132 NCIT:C32141 SCTID:302538001 UMLS:C0446516 VHOG:0000343 VSAO:0005057 galen:Arm brachial region brachium fore propodium forelimb propodium forelimb stylopodial element forelimb stylopodium proximal segment of free upper limb regio brachialis stylopod of arm stylopod of forelimb upper arm wing stylopod uberon arm UBERON:0003822 forelimb stylopod MA The part of the forelimb between pectoral region and the elbow, corresponding to the humerus. http://orcid.org/0000-0002-6601-2165 Segment of the hindleg corresponding to the humerus.[AAO] 2012-06-20 AAO:0000887 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000343 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ UMLS:C0446516 ncithesaurus:Arm brachium VSAO:0005057 fore propodium AAO:0000199 forelimb stylopodial element MA:th forelimb stylopodium OBOL:automatic regio brachialis FMA:24890 FMA:TA upper arm MA:0000035 wing stylopod NCBITaxon:8782 OBOL:automatic arm FMA:24890 The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] sural FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here EFO:0003051 EHDAA2:0001030 EHDAA:5165 EHDAA:6190 EMAPA:17496 FMA:24979 MA:0000051 MESH:D007866 NCIT:C32974 SCTID:244015008 UMLS:C1140621 VHOG:0000348 VO:0010971 VSAO:0005060 Wikipedia:Forearm galen:Leg crus crus of hindlimb hind limb middle limb segment hind limb zeudopodium hind limb zeugopod hindlimb epipodium hindlimb middle limb segment hindlimb zeudopodium hindlimb zeugopod hindlimb zeugopodium intermediate segment of free lower limb lower extremity middle limb segment lower extremity zeugopod lower leg middle limb segment of hind limb middle limb segment of hindlimb shank zeugopod of hind limb zeugopod of hindlimb uberon hind epipodium leg UBERON:0003823 hindlimb zeugopod MA The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants. PHENOSCAPE:curators Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000348 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion FMA UMLS:C1140621 ncithesaurus:Leg VO:0010971 https://github.com/biopragmatics/biomappings crus VSAO:0005060 hind limb middle limb segment OBOL:automatic hind limb zeudopodium VHOG:0000348 hind limb zeugopod OBOL:automatic hindlimb middle limb segment OBOL:automatic hindlimb zeudopodium VHOG:0000348 hindlimb zeugopod OBOL:automatic hindlimb zeugopodium OBOL:automatic intermediate segment of free lower limb FMA:24979 lower extremity middle limb segment OBOL:automatic lower extremity zeugopod OBOL:automatic lower leg MA:0000051 middle limb segment of hind limb OBOL:automatic middle limb segment of hindlimb https://orcid.org/0000-0002-6601-2165 shank VSAO:0005060 zeugopod of hind limb OBOL:automatic zeugopod of hindlimb OBOL:automatic hind epipodium leg FMA:24979 MESH:A01.378.610.500 A nerve that is part of a thorax [Automatically generated definition]. EMAPA:37265 MA:0000562 MESH:D013900 SCTID:359876006 nerve of thorax thoracic segment nerve thorax nerve uberon upper body nerve UBERON:0003824 nerve of thoracic segment A nerve that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37265 MA:th nerve of thorax OBOL:automatic thoracic segment nerve MA:0000562 thorax nerve OBOL:automatic upper body nerve MA:0000562 A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37061 MA:0000528 abdominal segment nerve uberon UBERON:0003825 nerve of abdominal segment A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37061 MA:th abdominal segment nerve MA:0000528 A bone that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:35893 MA:0000682 uberon femur UBERON:0003826 May be merged into femur. See https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 upper leg bone A bone that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 femur https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 A bone that is part of a thorax [Automatically generated definition]. EMAPA:37247 MA:0000559 SCTID:426649006 bone of thorax bone organ of thorax thorax bone thorax bone organ uberon upper body bone UBERON:0003827 thoracic segment bone A bone that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37247 MA:th bone of thorax OBOL:automatic bone organ of thorax OBOL:automatic thorax bone OBOL:automatic thorax bone organ OBOL:automatic upper body bone MA:0000559 A bone that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37058 MA:0000525 abdominal segment of trunk bone abdominal segment of trunk bone organ bone of abdominal segment of trunk bone organ of abdominal segment of trunk uberon UBERON:0003828 abdominal segment bone A bone that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37058 MA:th abdominal segment of trunk bone OBOL:automatic abdominal segment of trunk bone organ OBOL:automatic bone of abdominal segment of trunk OBOL:automatic bone organ of abdominal segment of trunk OBOL:automatic Any muscle tissue that is part of the urethra. EMAPA:37787 MA:0002649 uberon urethral muscle layer UBERON:0003829 urethra muscle tissue Any muscle tissue that is part of the urethra. UBERON:cjm EMAPA:37787 MA:th urethral muscle layer MA:0002649 Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 muscle organ of thorax thorax muscle organ uberon upper body muscle UBERON:0003830 thoracic segment muscle prolog Any muscle organ that is part of a thorax [Automatically generated definition]. OBOL:automatic muscle organ of thorax OBOL:automatic thorax muscle organ OBOL:automatic upper body muscle MA:0000561 Any muscle organ that is part of a respiratory system [Automatically generated definition]. EMAPA:35733 MA:0001828 apparatus respiratorius muscle organ muscle organ of apparatus respiratorius muscle organ of respiratory system respiratory system muscle organ uberon UBERON:0003831 respiratory system muscle Any muscle organ that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius muscle organ OBOL:automatic muscle organ of apparatus respiratorius OBOL:automatic muscle organ of respiratory system OBOL:automatic respiratory system muscle organ OBOL:automatic Any muscle organ that is part of a esophagus [Automatically generated definition]. merge muscle and muscle layer? EMAPA:26983 MA:0002682 SCTID:360961009 esophageal muscle esophagus muscle organ gullet muscle organ muscle organ of esophagus muscle organ of gullet muscle organ of oesophagus oesophagus muscle organ uberon UBERON:0003832 esophagus muscle MA Any muscle organ that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus muscle organ OBOL:automatic gullet muscle organ OBOL:automatic muscle organ of esophagus OBOL:automatic muscle organ of gullet OBOL:automatic muscle organ of oesophagus OBOL:automatic oesophagus muscle organ OBOL:automatic A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37060 MA:0000527 abdominal segment of trunk muscle organ muscle organ of abdominal segment of trunk uberon UBERON:0003833 abdominal segment muscle A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37060 MA:th abdominal segment of trunk muscle organ OBOL:automatic muscle organ of abdominal segment of trunk OBOL:automatic A blood vessel that is part of a thorax [Automatically generated definition]. EMAPA:37238 MA:0000558 blood vessel of thorax thorax blood vessel uberon upper body blood vessel UBERON:0003834 thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37238 MA:th blood vessel of thorax OBOL:automatic thorax blood vessel OBOL:automatic upper body blood vessel MA:0000558 A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37057 MA:0000524 abdominal segment of trunk blood vessel blood vessel of abdominal segment of trunk uberon UBERON:0003835 abdominal segment blood vessel A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37057 MA:th abdominal segment of trunk blood vessel OBOL:automatic blood vessel of abdominal segment of trunk OBOL:automatic A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37063 FMA:264898 MA:0000530 abdominal segment of trunk skin skin of abdominal segment of trunk uberon UBERON:0003836 abdominal segment skin A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37063 MA:th abdominal segment of trunk skin OBOL:automatic skin of abdominal segment of trunk OBOL:automatic A portion of connective tissue that is part of a thorax [Automatically generated definition]. EMAPA:37253 MA:0000560 connective tissue of thorax portion of connective tissue of thorax textus connectivus of thorax thorax connective tissue thorax portion of connective tissue thorax textus connectivus uberon upper body connective tissue UBERON:0003837 thoracic segment connective tissue A portion of connective tissue that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37253 MA:th connective tissue of thorax OBOL:automatic portion of connective tissue of thorax OBOL:automatic textus connectivus of thorax OBOL:automatic thorax connective tissue OBOL:automatic thorax portion of connective tissue OBOL:automatic thorax textus connectivus OBOL:automatic upper body connective tissue MA:0000560 A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37059 MA:0000526 abdominal segment of trunk connective tissue abdominal segment of trunk portion of connective tissue abdominal segment of trunk textus connectivus connective tissue of abdominal segment of trunk portion of connective tissue of abdominal segment of trunk textus connectivus of abdominal segment of trunk uberon UBERON:0003838 abdominal segment connective tissue A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37059 MA:th abdominal segment of trunk connective tissue OBOL:automatic abdominal segment of trunk portion of connective tissue OBOL:automatic abdominal segment of trunk textus connectivus OBOL:automatic connective tissue of abdominal segment of trunk OBOL:automatic portion of connective tissue of abdominal segment of trunk OBOL:automatic textus connectivus of abdominal segment of trunk OBOL:automatic A limb joint that is part of a forelimb [Automatically generated definition]. EMAPA:19204 MA:0000614 anteriormost limb joint of limb anteriormost limb limb joint fore limb joint of limb fore limb limb joint forelimb joint of limb forelimb limb joint joint of free upper limb joint of limb of anteriormost limb joint of limb of fore limb joint of limb of forelimb joint of limb of superior member joint of limb of upper extremity limb joint of anteriormost limb limb joint of fore limb limb joint of forelimb limb joint of superior member limb joint of upper extremity superior member joint of limb superior member limb joint upper extremity joint of limb upper extremity limb joint wing joint uberon UBERON:0003839 forelimb joint A limb joint that is part of a forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb joint of limb OBOL:automatic anteriormost limb limb joint OBOL:automatic fore limb joint of limb OBOL:automatic fore limb limb joint OBOL:automatic forelimb joint of limb OBOL:automatic forelimb limb joint OBOL:automatic joint of free upper limb http://orcid.org/0000-0002-6601-2165 joint of limb of anteriormost limb OBOL:automatic joint of limb of fore limb OBOL:automatic joint of limb of forelimb OBOL:automatic joint of limb of superior member OBOL:automatic joint of limb of upper extremity OBOL:automatic limb joint of anteriormost limb OBOL:automatic limb joint of fore limb OBOL:automatic limb joint of forelimb OBOL:automatic limb joint of superior member OBOL:automatic limb joint of upper extremity OBOL:automatic superior member joint of limb OBOL:automatic superior member limb joint OBOL:automatic upper extremity joint of limb OBOL:automatic upper extremity limb joint OBOL:automatic wing joint NCBITaxon:8782 OBOL:automatic A limb joint that is part of a hindlimb [Automatically generated definition]. EMAPA:32635 MA:0000662 SCTID:304573000 hind limb joint of limb hind limb limb joint hindlimb joint of limb hindlimb limb joint inferior member joint of limb inferior member limb joint joint of free lower limb joint of limb of hind limb joint of limb of hindlimb joint of limb of inferior member joint of limb of lower extremity joint of lower limb limb joint of hind limb limb joint of hindlimb limb joint of inferior member limb joint of lower extremity lower extremity joint of limb lower extremity limb joint uberon UBERON:0003840 hindlimb joint A limb joint that is part of a hindlimb [Automatically generated definition]. OBOL:automatic hind limb joint of limb OBOL:automatic hind limb limb joint OBOL:automatic hindlimb joint of limb OBOL:automatic hindlimb limb joint OBOL:automatic inferior member joint of limb OBOL:automatic inferior member limb joint OBOL:automatic joint of free lower limb http://orcid.org/0000-0002-6601-2165 joint of limb of hind limb OBOL:automatic joint of limb of hindlimb OBOL:automatic joint of limb of inferior member OBOL:automatic joint of limb of lower extremity OBOL:automatic joint of lower limb https://orcid.org/0000-0002-6601-2165 limb joint of hind limb OBOL:automatic limb joint of hindlimb OBOL:automatic limb joint of inferior member OBOL:automatic limb joint of lower extremity OBOL:automatic lower extremity joint of limb OBOL:automatic lower extremity limb joint OBOL:automatic A limb joint that is part of an autopod [Automatically generated definition]. EMAPA:35160 MA:0002715 autopod joint of limb autopod limb joint distal free limb segment joint of limb distal free limb segment limb joint joint of limb of autopod joint of limb of distal free limb segment limb joint of autopod limb joint of distal free limb segment uberon paw joint UBERON:0003841 autopod joint A limb joint that is part of an autopod [Automatically generated definition]. OBOL:automatic autopod joint of limb OBOL:automatic autopod limb joint OBOL:automatic distal free limb segment joint of limb OBOL:automatic distal free limb segment limb joint OBOL:automatic joint of limb of autopod OBOL:automatic joint of limb of distal free limb segment OBOL:automatic limb joint of autopod OBOL:automatic limb joint of distal free limb segment OBOL:automatic paw joint MA:0002715 An anatomical space that surrounded_by a neural tube. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 VHOG:0001119 XAO:0000252 cavity of neural tube lumen of neural tube neural tube neural lumen prosencoel uberon central lumen neural lumen neurocoel UBERON:0003842 neural tube lumen An anatomical space that surrounded_by a neural tube. OBOL:automatic (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001119 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ cavity of neural tube https://orcid.org/0000-0002-6601-2165 lumen of neural tube https://orcid.org/0000-0002-6601-2165 neural tube neural lumen EHDAA2:0001269 neural lumen EHDAA:2889 neurocoel VHOG:0001119 Epithelium that is part of a developing tooth or dental organ. see comments for dental organ. todo - full developmental relationships In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4) AAO:0011027 BTO:0001723 EMAPA:32903 MA:0003151 NCIT:C54296 TAO:0005134 UMLS:C1709309 VHOG:0001443 XAO:0003203 ZFA:0005134 dental epithelia dental epithelium odontogenic epithelium tooth epithelium uberon reduced enamel epithelium UBERON:0003843 dental epithelium epithelium JB Epithelium that is part of a developing tooth or dental organ. ZFA:0005134 https://github.com/cerivs/zebrafish-anatomical-ontology/issues/107 In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4) PMID:10954731 UMLS:C1709309 ncithesaurus:Odontogenic_Epithelial_Remnants dental epithelia ZFA:0005134 dental epithelium ZFA:0005134 reduced enamel epithelium BTO:0001723 An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. BTO:0001836 CALOHA:TS-1040 EHDAA2:0002019 EMAPA:35864 MA:0000768 NCIT:C45713 UMLS:C1711423 VHOG:0001426 ZFA:0005779 epithelial tissue of thymus epithelial tissue of thymus gland epithelium of thymus epithelium of thymus gland thymic epithelial tissue thymic epithelium thymus epithelial tissue thymus gland epithelial tissue thymus gland epithelium uberon UBERON:0003846 thymus epithelium PMID:21293377 An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. MP:0009544 UMLS:C1711423 ncithesaurus:Thymic_Epithelial_Tissue epithelial tissue of thymus OBOL:automatic epithelial tissue of thymus gland OBOL:automatic epithelium of thymus OBOL:automatic epithelium of thymus gland OBOL:automatic thymic epithelium BTO:0001836 thymus epithelial tissue OBOL:automatic thymus gland epithelial tissue OBOL:automatic thymus gland epithelium OBOL:automatic An artery that supplies a thyroid gland. Part of the external carotid which supplies blood to the thyroid gland.[AAO] relationship loss: part_of external carotid (AAO:0010218)[AAO] AAO:0010490 EHDAA2:0002029 EHDAA:7372 EMAPA:18622 MA:0002066 NCIT:C53020 UMLS:C1711424 VHOG:0001366 uberon UBERON:0003847 thyroid artery An artery that supplies a thyroid gland. OBOL:automatic Part of the external carotid which supplies blood to the thyroid gland.[AAO] 2012-06-20 AAO:0010490 AAO AAO:BJB relationship loss: part_of external carotid (AAO:0010218)[AAO] 2012-06-20 AAO:0010490 AAO UMLS:C1711424 ncithesaurus:Thyroid_Artery In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. EHDAA2:0000719 EHDAA:8703 SCTID:278192008 VHOG:0001340 Wikipedia:Gonadal_vein gonad vein gonada vein vein of gonad vein of gonada uberon UBERON:0003848 gonadal vein http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. Wikipedia:Gonadal_vein gonad vein OBOL:automatic gonada vein OBOL:automatic vein of gonad OBOL:automatic vein of gonada OBOL:automatic A neural crest that has_potential_to_developmentally_contribute_to a midbrain. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 VHOG:0000796 ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon UBERON:0003849 mesencephalic neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000796 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ mesencephalic neural crest ZFA:0000935 neural crest midbrain ZFA:0000935 A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. Cranial neural crest that is part of the telencephalon.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003574 RETIRED_EHDAA2:0001991 TAO:0000812 VHOG:0000799 ZFA:0000812 neural crest telencephalon uberon UBERON:0003850 telencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. OBOL:automatic Cranial neural crest that is part of the telencephalon.[TAO] 2012-08-14 TAO:0000812 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000799 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest telencephalon ZFA:0000812 A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003573 EHDAA2:0000603 EMAPA:16518 TAO:0000811 VHOG:0000798 ZFA:0000811 diencephalic neural crest future diencephalon neural crest neural crest diencephalon neural crest of future diencephalon uberon UBERON:0003851 diencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000798 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ diencephalic neural crest ZFA:0000811 future diencephalon neural crest EHDAA2:0000603 neural crest diencephalon ZFA:0000811 neural crest of future diencephalon EMAPA:16518 A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 VHOG:0001210 ZFA:0007063 neural crest hindbrain rhombencephalic neural crest uberon rhombomere neural crest UBERON:0003852 rhombencephalon neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic Cranial neural crest that is part of the hindbrain.[TAO] 2012-08-14 TAO:0007063 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001210 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest hindbrain ZFA:0007063 rhombencephalic neural crest ZFA:0007063 rhombomere neural crest EMAPA:35747 A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 VHOG:0001006 neural crest spinal cord uberon spinal neural crest UBERON:0003853 spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] 2012-09-17 VHOG:0001006 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest spinal cord VHOG:0001006 spinal neural crest VHOG:0001006 A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] FMA:312957 TAO:0007021 VHOG:0000439 ZFA:0007021 neural plate of spinal cord uberon UBERON:0003854 spinal cord neural plate ZFA A neural plate that develops_from a future spinal cord. OBOL:automatic Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000439 VHOG http://bgee.unil.ch/ (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] 2012-09-17 VHOG:0000439 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ neural plate of spinal cord OBOL:automatic Mesenchyme that is part of a developing gonad [Automatically generated definition]. EHDAA:5012 EMAPA:16858 EMAPA:17385 VHOG:0001090 gonada mesenchyme mesenchyme of gonad mesenchyme of gonada uberon UBERON:0003855 gonad mesenchyme Mesenchyme that is part of a developing gonad [Automatically generated definition]. OBOL:automatic gonada mesenchyme OBOL:automatic mesenchyme of gonad OBOL:automatic mesenchyme of gonada OBOL:automatic Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla. we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme Mesenchyme enclosed by dental organ.[MP] Mesenchyme enclosed by dental organ.[TAO] EMAPA:32891 MA:0003152 TAO:0005139 VHOG_RETIRED:0001444 ZFA:0005139 dental mesenchyme dental organ mesenchyme enamel organ mesenchyme tooth enamel organ mesenchyme tooth mesenchyme uberon UBERON:0003856 uncondensed odontogenic mesenchyme see comments Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla. https://github.com/cerivs/zebrafish-anatomical-ontology/issues/107 https://orcid.org/0000-0002-6601-2165 Mesenchyme enclosed by dental organ.[MP] MP J:153554 Mesenchyme enclosed by dental organ.[TAO] 2012-08-14 TAO:0005139 TAO ZFIN:curator dental mesenchyme ZFA:0005139 dental organ mesenchyme OBOL:automatic enamel organ mesenchyme OBOL:automatic tooth enamel organ mesenchyme OBOL:automatic tooth mesenchyme OBOL:automatic Mesenchyme that is part of a developing forelimb [Automatically generated definition]. EMAPA:32628 VHOG:0001109 anteriormost limb mesenchyme fore limb mesenchyme mesenchyme of anteriormost limb mesenchyme of fore limb mesenchyme of forelimb mesenchyme of superior member mesenchyme of upper extremity superior member mesenchyme upper extremity mesenchyme wing mesenchyme uberon UBERON:0003859 forelimb mesenchyme Mesenchyme that is part of a developing forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb mesenchyme OBOL:automatic fore limb mesenchyme OBOL:automatic mesenchyme of anteriormost limb OBOL:automatic mesenchyme of fore limb OBOL:automatic mesenchyme of forelimb OBOL:automatic mesenchyme of superior member OBOL:automatic mesenchyme of upper extremity OBOL:automatic superior member mesenchyme OBOL:automatic upper extremity mesenchyme OBOL:automatic wing mesenchyme Geisha:syn NCBITaxon:8782 OBOL:automatic Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. EMAPA:32637 VHOG:0001074 hind limb mesenchyme inferior member mesenchyme lower extremity mesenchyme mesenchyme of hind limb mesenchyme of hindlimb mesenchyme of inferior member mesenchyme of lower extremity uberon UBERON:0003860 hindlimb mesenchyme Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. OBOL:automatic hind limb mesenchyme OBOL:automatic inferior member mesenchyme OBOL:automatic lower extremity mesenchyme OBOL:automatic mesenchyme of hind limb OBOL:automatic mesenchyme of hindlimb OBOL:automatic mesenchyme of inferior member OBOL:automatic mesenchyme of lower extremity OBOL:automatic Posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine. A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO] Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO] the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process) relationship loss: develops_from basidorsal (TAO:0001060)[TAO] (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] tiny neural arches present in Hagfish (which lack a true vertebraal column). The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone vertebra neural arch AAO:0000725 EFO:0003618 FMA:11946 MA:0001453 NCIT:C32138 SCTID:317373001 TAO:0001066 UMLS:C0223076 VHOG:0001670 Wikipedia:Vertebral_arch ZFA:0001066 arcus vertebra arcus vertebrae arcus vertebrae (vertebralis) dorsal arcocentrum uberon arcus vertebrae vertebra dorsal arch UBERON:0003861 neural arch http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png Posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine. Wikipedia:Vertebral_arch A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO] 2012-08-14 TAO:0001066 TAO ZFIN:curator Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO] 2012-06-20 AAO:0000725 AAO AAO:Pugener_2002 the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process) MP:0004599:csmith relationship loss: develops_from basidorsal (TAO:0001060)[TAO] 2012-08-14 TAO:0001066 TAO (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] 2012-09-17 VHOG:0001670 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270 http://bgee.unil.ch/ vertebra neural arch MA:0001453 UMLS:C0223076 ncithesaurus:Arch_of_the_Vertebra arcus vertebra Wikipedia:Vertebral_arch arcus vertebrae Wikipedia:Vertebral_arch arcus vertebrae (vertebralis) FMA:11946 dorsal arcocentrum ZFA:0001066 arcus vertebrae Wikipedia:Vertebral_arch vertebra dorsal arch MA:0001453 A phalanx that is part of a foot digit 5 [Automatically generated definition]. EMAPA:19132 FMA:32902 MA:0001385 NCIT:C52782 SCTID:361806005 UMLS:C1708088 digit long bone of foot digit 5 foot digit 5 digit long bone foot digit 5 long bone of digit foot digit 5 phalanx hind limb digit 5 phalanx little toe phalanx long bone of digit of foot digit 5 pedal digit V phalanx phalanx of fifth digit of foot phalanx of fifth toe phalanx of foot digit 5 phalanx of little toe foot digit 5 phalanx uberon UBERON:0003863 pedal digit 5 phalanx A phalanx that is part of a foot digit 5 [Automatically generated definition]. OBOL:automatic UMLS:C1708088 ncithesaurus:Foot_Digit_5_Phalanx digit long bone of foot digit 5 OBOL:automatic foot digit 5 digit long bone OBOL:automatic foot digit 5 long bone of digit OBOL:automatic foot digit 5 phalanx MA:0001385 hind limb digit 5 phalanx OBOL:accepted little toe phalanx FMA:32902 long bone of digit of foot digit 5 OBOL:automatic pedal digit V phalanx https://github.com/obophenotype/uberon/issues/458 phalanx of fifth digit of foot FMA:32902 phalanx of fifth toe FMA:32902 phalanx of foot digit 5 OBOL:automatic phalanx of little toe FMA:32902 foot digit 5 phalanx NCBITaxon:9606 OBOL:accepted A middle phalanx that is part of a finger [Automatically generated definition]. EMAPA:37306 FMA:75817 MA:0001394 NCIT:C12863 SCTID:113223004 SCTID:371230003 UMLS:C0223828 hand middle phalanx middle manual phalanx middle phalanx of finger middle phalanx of hand middle phalanx of manual digit phalanx media manus uberon UBERON:0003864 middle phalanx of manus A middle phalanx that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37306 MA:th UMLS:C0223828 ncithesaurus:Middle_Phalanx_of_the_Hand hand middle phalanx MA:0001394 middle phalanx of finger FMA:75817 middle phalanx of hand MA:0001394 phalanx media manus FMA:75817 FMA:TA A distal phalanx that is part of a finger [Automatically generated definition]. EMAPA:35393 FMA:75818 MA:0001388 NCIT:C52784 SCTID:182001007 SCTID:361782004 UMLS:C1269782 distal manual phalanx distal phalanx of finger distal phalanx of hand distal phalanx of manual digit hand distal phalanx phalanx distalis manus terminal phalanx of hand ungual phalanx of hand uberon UBERON:0003865 This is typically proximally connected to the middle phalanx of manus, except in some cases such as the manual digit 1 (thumb) of many mammals such as humans, where it connects to the proximal phalanx. It always connects to some phalanx, by definition distal phalanx of manus A distal phalanx that is part of a finger [Automatically generated definition]. OBOL:automatic UMLS:C1269782 ncithesaurus:Distal_Phalanx_of_Hand distal phalanx of finger FMA:75818 hand distal phalanx MA:0001388 phalanx distalis manus FMA:75818 FMA:TA terminal phalanx of hand https://orcid.org/0000-0002-6601-2165 ungual phalanx of hand http://www.medilexicon.com/medicaldictionary.php?t=67679 A middle phalanx that is part of a toe [Automatically generated definition]. EMAPA:37311 FMA:75829 MA:0001386 SCTID:83207005 foot middle phalanx middle pedal phalanx middle phalanx of foot middle phalanx of toe phalanx media pedis uberon UBERON:0003866 middle phalanx of pes A middle phalanx that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37311 MA:th foot middle phalanx MA:0001386 middle phalanx of toe FMA:75829 phalanx media pedis FMA:75829 FMA:TA A distal phalanx that is part of a pedal digit [Automatically generated definition]. EMAPA:37310 FMA:75830 MA:0001380 NCIT:C52783 SCTID:361797001 UMLS:C0224026 distal pedal phalanx distal phalanx of foot distal phalanx of toe foot distal phalanx phalanx distalis pedis terminal phalanx of foot terminal phalanx of hindlimb ungual phalanx of foot ungual phalanx of hindlimb uberon UBERON:0003867 This is typically proximally connected to the middle phalanx of pes, except in some cases such as the pedal digit 1 (big toe) in many mammals such as humans, where it connects to the proximal phalanx. It always connects to some phalanx, by definition distal phalanx of pes A distal phalanx that is part of a pedal digit [Automatically generated definition]. OBOL:automatic EMAPA:37310 MA:th UMLS:C0224026 ncithesaurus:Distal_Phalanx_of_Foot distal phalanx of toe FMA:75830 foot distal phalanx MA:0001380 phalanx distalis pedis FMA:75830 FMA:TA terminal phalanx of foot https://orcid.org/0000-0002-6601-2165 terminal phalanx of hindlimb https://orcid.org/0000-0002-6601-2165 ungual phalanx of foot http://www.medilexicon.com/medicaldictionary.php?t=67679 ungual phalanx of hindlimb http://www.medilexicon.com/medicaldictionary.php?t=67679 A proximal phalanx that is part of a pedal digit [Automatically generated definition]. EMAPA:37312 FMA:75828 MA:0001387 NCIT:C52785 SCTID:85533000 UMLS:C0224020 foot proximal phalanx phalanx proximalis pedis proximal pedal phalanx proximal phalanx of foot proximal phalanx of foot digit proximal phalanx of hind digit proximal phalanx of pes proximal phalanx of toe uberon UBERON:0003868 proximal phalanx of pes A proximal phalanx that is part of a pedal digit [Automatically generated definition]. OBOL:automatic EMAPA:37312 MA:th UMLS:C0224020 ncithesaurus:Proximal_Phalanx_of_Foot foot proximal phalanx MA:0001387 phalanx proximalis pedis FMA:75828 FMA:TA proximal phalanx of toe FMA:75828 A presumptive structure that has the potential to develop into a ganglion. uberon UBERON:0003869 presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. OBOL:automatic A mesentery that is part of a uterus [Automatically generated definition]. EMAPA:35562 FMA:19816 MA:0002931 SCTID:250172001 Wikipedia:Mesometrium uberon mesentery of uterus UBERON:0003885 mesometrium A mesentery that is part of a uterus [Automatically generated definition]. OBOL:automatic mesentery of uterus FMA:19816 MA:0002931 http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/peritoneum.html An anatomical cavity that has the potential to develop into a coelemic cavity lumen. future coelomic cavity lumen uberon body cavity precursor UBERON:0003886 future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. OBOL:automatic The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 UMLS:C1512940 VHOG:0000316 Wikipedia:Intraembryonic_coelom somatic coelom uberon UBERON:0003887 intraembryonic coelom Wikipedia The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. MGI:anna MP:0012187 (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] 2012-09-17 VHOG:0000316 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 http://bgee.unil.ch/ UMLS:C1512940 ncithesaurus:Intraembryonic_Coelom somatic coelom Wikipedia:Intraembryonic_coelom Initial section of the oviduct through which the ova pass from the ovary to the uterus. Homologous to appendix testis salpinges salpinx CALOHA:TS-0732 EHDAA2:0000504 EMAPA:18984 EMAPA:35660 EV:0100112 FMA:18245 GAID:365 MA:0000385 MESH:D005187 NCIT:C12403 SCTID:181463001 UMLS:C0015560 Wikipedia:Fallopian_tube galen:FallopianTube mammalian oviduct uterine tube (sensu Mammalia) uberon fallopian tubes female paramesonephric duct paramesonephric duct of female tuba uterina UBERON:0003889 fallopian tube http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg FMA-abduced-lr Initial section of the oviduct through which the ova pass from the ovary to the uterus. MGI:smb MP:0003574 http://orcid.org/0000-0002-6601-2165 Homologous to appendix testis Wikipedia:Talk:Fallopian_tube#Homology salpinges UMLS:C0015560 ncithesaurus:Fallopian_Tube mammalian oviduct https://sourceforge.net/p/geneontology/ontology-requests/8397/ female paramesonephric duct EHDAA2:0000504 paramesonephric duct of female EMAPA:35660 tuba uterina Wikipedia:Fallopian_tube Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct UBERON:0005318 AAO:0010141 EHDAA2:0004048 EMAPA:27665 GAID:1309 MESH:D009095 NCIT:C13260 RETIRED_EHDAA2:0001399 SCTID:308802006 UMLS:C0026732 VHOG:0001199 Wikipedia:Paramesonephric_duct XAO:0000330 Muellerian duct Müllerian duct ductus paramesonephricus paramesonephric duct early paramesonephric duct uberon UBERON:0003890 Mullerian duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png Wikipedia Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. GO:0061205 Wikipedia:Paramesonephric_duct http://www.usm.maine.edu/bio/courses/bio205/bio205_26_sex.html Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] 2012-09-17 VHOG:0001199 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/paramesonephric+duct Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] 2012-06-20 AAO:0010141 AAO AAO:RED In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] 2012-09-17 VHOG:0001199 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559 http://bgee.unil.ch/ UMLS:C0026732 ncithesaurus:Mullerian_Duct paramesonephric duct EMAPA:27665 early paramesonephric duct EHDAA2:0004048 Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. stromal FMA:81494 NCIT:C67387 UMLS:C0927195 uberon stromal connective tissue UBERON:0003891 stroma Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. http://orcid.org/0000-0002-6601-2165 UMLS:C0927195 ncithesaurus:Stroma_Connective_Tissue A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]. capsular EHDAA:4739 EHDAA:9061 FMA:85272 Wikipedia:Capsule_(anatomy) galen:Capsule uberon UBERON:0003893 see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells capsule A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]. Wikipedia:Capsule_(anatomy) A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ AAO:0011058 BTO:0003391 EFO:0002577 EFO:0003428 EHDAA2:0000744 EHDAA:973 EMAPA:16847 NCIT:C34277 TAO:0000124 UMLS:C0734013 UMLS:C1514451 XAO:0003266 ZFA:0000124 embryological hepatic plate primordium of the liver uberon hepatic plate liver bud liver endoderm UBERON:0003894 liver primordium EHDAA2 XAO EHDAA2 ventral foregut endoderm Zaret 1996 A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. ISBN:3211492755 UMLS:C0734013 ncithesaurus:Hepatic_Cord UMLS:C1514451 ncithesaurus:Primordium_of_the_Liver embryological hepatic plate https://orcid.org/0000-0002-6601-2165 primordium of the liver ncithesaurus:Primordium_of_the_Liver hepatic plate EHDAA2:0000744 liver bud XAO:0003266 ZFA:0000124 liver endoderm EFO:0002577 One of the skeletal muscles of the head and neck, spine, and ribs. EHDAA:5982 EMAPA:18167 MA:0003153 RETIRED_EHDAA2:0000160 TAO:0001954 uberon UBERON:0003897 axial muscle One of the skeletal muscles of the head and neck, spine, and ribs. HP:0003327 A portion of skeletal muscle tissue in the trunk. SCTID:244848007 skeletal muscle of torso skeletal muscle tissue of torso skeletal muscle tissue of trunk torso skeletal muscle torso skeletal muscle tissue trunk skeletal muscle trunk skeletal muscle tissue uberon UBERON:0003898 skeletal muscle tissue of trunk https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A portion of skeletal muscle tissue in the trunk. http://orcid.org/0000-0002-6601-2165 skeletal muscle of torso OBOL:automatic skeletal muscle tissue of torso OBOL:automatic skeletal muscle tissue of trunk OBOL:automatic torso skeletal muscle OBOL:automatic torso skeletal muscle tissue OBOL:automatic trunk skeletal muscle OBOL:automatic trunk skeletal muscle tissue OBOL:automatic The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 EHDAA2:0001253 EHDAA:4763 EMAPA:17171 EMAPA:18590 FMA:58628 MA:0000277 NCIT:C33166 TAO:0000046 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neuroretina stratum nervosum (retina) stratum nervosum retinae uberon neural retinal epithelium UBERON:0003902 retinal neural layer Bgee:AN The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000535 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C1518263 ncithesaurus:Neural_Retina neural layer of retina FMA:58628 neural retina XAO:0003216 ZFA:0000046 neuroretina ZFA:0000046 stratum nervosum (retina) FMA:58628 stratum nervosum retinae FMA:58628 FMA:TA neural retinal epithelium MA:000027 Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] sinusoidal some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA:63131 SCTID:340163004 TAO:0005261 Wikipedia:Sinusoid_(blood_vessel) ZFA:0005261 sinusoidal blood vessel sinusoidal blood vessel endothelium uberon endothelium of irregular blood filled space sinusoidal capillary sinusoidal endothelium UBERON:0003909 sinusoid Wikipedia ZFA Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Wikipedia:Sinusoid_(blood_vessel) Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] 2012-08-14 TAO:0005261 TAO ZFIN:curator some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA sinusoidal blood vessel endothelium ZFA:0005261 sinusoidal capillary http://www.medilexicon.com/medicaldictionary.php?t=13986 The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue. The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier BTO:0006008 EMAPA:36608 FMA:242811 MA:0000824 NCIT:C42079 UMLS:C1516506 choroid plexus epithelial tissue epithelial tissue of chorioid plexus of cerebral hemisphere epithelial tissue of choroid plexus epithelium of choroid plexus uberon UBERON:0003911 choroid plexus epithelium The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue. UBERON:cjm Wikipedia:Choroid_plexus BTO:0006008 https://github.com/biopragmatics/biomappings UMLS:C1516506 ncithesaurus:Choroid_Plexus_Epithelium choroid plexus epithelial tissue OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic epithelial tissue of choroid plexus OBOL:automatic epithelium of choroid plexus FMA:242811 Hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. HAO:0001019 tooth-like organ uberon UBERON:0003913 see dermal denticle tooth-like structure Hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. http://orcid.org/0000-0002-6601-2165 tooth-like organ http://orcid.org/0000-0002-6601-2165 Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GO:0060562 PMID:12526790 FBbt:00007474 Any endothelium that has the quality of being cylindrical [Automatically generated definition]. uberon UBERON:0003915 endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. OBOL:automatic Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. check this mesenchyme of kidney uberon UBERON:0003918 kidney mesenchyme Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. GO:0072074 A blood vessel that carries blood from the capillaries toward the heart. EMAPA:35932 FMA:86188 MA:0000066 segment of venous tree organ venous tree organ segment uberon UBERON:0003920 Compare to: vein venous blood vessel A blood vessel that carries blood from the capillaries toward the heart. http://www.thefreedictionary.com/venous+blood+vessel segment of venous tree organ FMA:86188 venous tree organ segment FMA:86188 Embryonic structure that develops into pancreatic bud. in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds revisit after standardizing terms 'primordium', 'anlagen', 'bud' EFO:0002579 EFO:0003434 EHDAA2:0001382 EHDAA:2163 EMAPA:17066 FMA:79792 TAO:0000254 XAO:0001101 ZFA:0000254 pancreatic primordium uberon pancreatic anlage pancreatic endoderm primordial pancreas UBERON:0003921 pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png Wikipedia Embryonic structure that develops into pancreatic bud. Wikipedia:Pancreas#Embryological_development in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds EHDAA2 pancreatic anlage ZFA:0000254 pancreatic endoderm EFO:0002579 primordial pancreas FMA:79792 The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. EFO:0003470 EMAPA:35645 NCIT:C34242 SCTID:360398004 TAO:0001390 UMLS:C1283285 Wikipedia:Pancreatic_bud ZFA:0001390 pancreatic bud pancreatic buds uberon pancreas epithelium pancreatic anlage UBERON:0003922 pancreatic epithelial bud http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 EHDAA2 Wikipedia:Pancreas#Embryological_development zebrafish Wikipedia:Pancreatic_bud EHDAA2-inferred The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. PMID:16417468 Wikipedia:Pancreatic_bud UMLS:C1283285 ncithesaurus:Pancreatic_Bud pancreatic bud ZFA:0001390 pancreatic buds TAO:0001390 pancreas epithelium EMAPA:35645 Pancreatic bud that gives rise to the accessory pancreatic duct. The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] AAO:0011031 EFO:0003465 EHDAA2:0001385 EMAPA:17067 SCTID:361435005 TAO:0001370 VHOG:0001428 Wikipedia:Pancreatic_bud XAO:0000467 ZFA:0001370 pancreas dorsal primordium duct bud pancreas primordium dorsal bud primary pancreatic bud uberon dorsal pancreas anlage dorsal pancreatic anlage posterior pancreatic anlage posterior pancreatic bud UBERON:0003923 dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 XAO Pancreatic bud that gives rise to the accessory pancreatic duct. Wikipedia:Pancreatic_bud The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] 2012-06-20 AAO:0011031 AAO XAO:curator In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001428 VHOG DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000) http://bgee.unil.ch/ pancreas dorsal primordium duct bud EHDAA2:0001385 primary pancreatic bud XAO:0000467 Pancreatic bud that gives rise to the major pancreatic duct. In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. AAO:0011111 EFO:0003464 EHDAA2:0001389 EMAPA:17256 SCTID:361437002 TAO:0001369 VHOG:0001429 Wikipedia:Pancreatic_bud XAO:0001103 ZFA:0001369 pancreas primordium ventral bud pancreas ventral primordium duct bud uberon anterior pancreatic anlage anterior pancreatic bud ventral pancreas anlage ventral pancreatic anlage UBERON:0003924 ventral pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 PMID:16417468 WP Pancreatic bud that gives rise to the major pancreatic duct. Wikipedia:Pancreatic_bud In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001429 VHOG DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000) http://bgee.unil.ch/ pancreas ventral primordium duct bud EHDAA2:0001389 A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon UBERON:0003928 digestive system duct A duct that is part of a digestive system [Automatically generated definition]. OBOL:automatic duct of digestive system OBOL:automatic duct of gastrointestinal system OBOL:automatic gastrointestinal system duct OBOL:automatic An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] BTO:0000956 EHDAA2:0004567 EMAPA:32928 FBbt:00047166 MA:0003201 NCIT:C12963 TAO:0005123 UMLS:C0836205 XAO:0003200 ZFA:0005123 digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium uberon alimentary tract epithelium UBERON:0003929 digestive tract epithelium An epithelium that lines the lumen of the digestive tract. http://orcid.org/0000-0002-6601-2165 Epithelium lining the lumen of the gut.[TAO] 2012-08-14 TAO:0005123 TAO ZFIN:curator FBbt:00047166 UMLS:C0836205 ncithesaurus:Gut_Epithelium digestive tract epithelial tissue OBOL:automatic epithelial tissue of digestive tract OBOL:automatic epithelial tissue of gut OBOL:automatic epithelium of digestive tract OBOL:automatic epithelium of gut OBOL:automatic gastrodermis NCBITaxon:6073 https://orcid.org/0000-0003-3308-6245 gut epithelial tissue OBOL:automatic gut epithelium EHDAA2:0004567 MA:0003201 ZFA:0005123 alimentary tract epithelium OBOL:automatic A cartilage element of chondrocranium. Example: neurocranial trabecula. EFO:0003690 TAO:0001461 ZFA:0001461 cartilage of chondrocranium cartilaginous element of chondrocranium chondrocranium cartilage neurocranium cartilage uberon UBERON:0003932 cartilage element of chondrocranium A cartilage element of chondrocranium. Example: neurocranial trabecula. https://orcid.org/0000-0002-6601-2165 cartilage of chondrocranium OBOL:accepted cartilaginous element of chondrocranium OBOL:accepted chondrocranium cartilage ZFA:0001461 neurocranium cartilage ZFA:0001461 A cartilage element that is part of the cranial skeleton. Cartilage which is part of the cranium.[TAO] TAO:0001458 ZFA:0001458 cartilage of cranium cranium cartilage uberon cranial cartilages UBERON:0003933 cranial cartilage A cartilage element that is part of the cranial skeleton. ZFA:0001458 https://orcid.org/0000-0002-6601-2165 Cartilage which is part of the cranium.[TAO] 2012-08-14 TAO:0001458 TAO ZFIN:curator cartilage of cranium OBOL:automatic cranium cartilage OBOL:automatic cranial cartilages ZFA:0001458 Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. BTO:0006162 MA:0001751 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland sex gland uberon UBERON:0003937 reproductive gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MP:0000653 BTO:0006162 https://github.com/biopragmatics/biomappings genitalia gland OBOL:automatic gland of genitalia MP:0000653 gland of reproductive system OBOL:automatic reproductive gland MA:0001751 reproductive system gland OBOL:automatic sex gland MP:0000653 The sensory system for the sense of touch and pain. The neural tissue involved in the transmission of sensory signals MP defines this in a may more appropriate to somatosensory cortex UBERON:0014511 EMAPA:37954 NLXANAT:090818 Wikipedia:Somatosensory_system neuronames:2887 somatic sensory system system for detection of somatic senses uberon UBERON:0003942 somatosensory system The sensory system for the sense of touch and pain. NLXANAT:090818 The neural tissue involved in the transmission of sensory signals MP:0000959 MP defines this in a may more appropriate to somatosensory cortex MP EMAPA:37954 MA:th The brain ventricles or their associated choroid plexuses. TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted TODO merge into BV uberon UBERON:0003947 brain ventricle/choroid plexus The brain ventricles or their associated choroid plexuses. MP:0002200 The posterior concave interior of the eye, consisting of the retina, the choroid, the posterior segment of the sclera, the optic disk, and blood vessels, visible by an ophthalmoscope. TODO - check relationships EMAPA:37916 GAID:908 MESH:D005654 NCIT:C13378 RETIRED_EHDAA2:0000583 SCTID:362519003 UMLS:C0740422 Wikipedia:Fundus_(eye) galen:FundusOculi eye fundus fundus fundus oculi fundus of eye uberon UBERON:0003951 ocular fundus The posterior concave interior of the eye, consisting of the retina, the choroid, the posterior segment of the sclera, the optic disk, and blood vessels, visible by an ophthalmoscope. MP:0002864 Wikipedia:Fundus_(eye) EMAPA:37916 MA:th UMLS:C0740422 ncithesaurus:Fundus fundus HP:0001098 The anterior segment of the lamellated connective tissue layer of the cornea. anterior stroma EMAPA:37414 cornea anterior stroma uberon UBERON:0003952 anterior stroma of cornea lexical The anterior segment of the lamellated connective tissue layer of the cornea. MP:0003093 anterior stroma MP:0003093 EMAPA:37414 MA:th cornea anterior stroma MP:0003093 The posterior segment of the lamellated connective tissue layer of the cornea. posterior stroma EMAPA:37415 cornea posterior stroma uberon UBERON:0003953 posterior stroma of cornea The posterior segment of the lamellated connective tissue layer of the cornea. MP:0003094 posterior stroma MP:0003094 EMAPA:37415 MA:th cornea posterior stroma MP:0003094 The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins. EMAPA:37427 uberon UBERON:0003956 aqueous drainage system The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins. MP:0005198 EMAPA:37427 MA:th An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]. add more specific classification e.g. anastomosing network - consider FMA:3726 EMAPA:18332 FMA:19834 GAID:399 MA:0003013 MESH:D012152 NCIT:C33467 SCTID:279617009 UMLS:C0035278 Wikipedia:Rete_testis Haller's rete uberon UBERON:0003959 rete testis http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg Wikipedia An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]. MP:0006416 Wikipedia:Rete_testis UMLS:C0035278 ncithesaurus:Rete_Testis Haller's rete FMA:19834 The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity. EMAPA:37841 cutaneous elastic fiber dermal elastic fiber uberon UBERON:0003967 cutaneous elastic tissue The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity. MP:0008418 EMAPA:37841 MA:th cutaneous elastic fiber MP:0008418 dermal elastic fiber MP:0008418 One of the conchae of the ethmoid bone, which occupy the caudal part of the nasal fossae and form the lateral and superior portions of the turbinate bones in mammals[MP]. The ethmoturbinals are associated with the cribiform plate. They are covered with olfactory epithelium. Primarily, they serve to increase the surface area over which olfactory receptor neurons can come in contact with respiratory air. These olfactory receptor nerves then synapse with the mitral cells of the olfactory lobes through the cribiform plate in the manner described above[Palaeos]. FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here EMAPA:37914 FMA:57456 ethmo-turbinate ethmoturbinal ethmoturbinate nasal turbinate of ethmoid bone turbinate of ethmoid bone uberon UBERON:0003973 nasal concha of ethmoid bone ISBN:0073040584 One of the conchae of the ethmoid bone, which occupy the caudal part of the nasal fossae and form the lateral and superior portions of the turbinate bones in mammals[MP]. The ethmoturbinals are associated with the cribiform plate. They are covered with olfactory epithelium. Primarily, they serve to increase the surface area over which olfactory receptor neurons can come in contact with respiratory air. These olfactory receptor nerves then synapse with the mitral cells of the olfactory lobes through the cribiform plate in the manner described above[Palaeos]. MP:0008971 http://palaeos.com/vertebrates/bones/braincase/ethmoid.html FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here FMA EMAPA:37914 MA:th ethmoturbinal http://palaeos.com/vertebrates/bones/braincase/ethmoid.html ethmoturbinate MP:0008971 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. BTO:0003099 FMA:45654 SCTID:303518005 female internal genitalia internal female genital organ internal genitalia of female reproductive system uberon organa genitalia feminina interna UBERON:0003975 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal female genitalia The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. MP:0009209 female internal genitalia FMA:45654 internal female genital organ BTO:0003099 internal genitalia of female reproductive system OBOL:automatic organa genitalia feminina interna BTO:0003099 valvular EHDAA2:0004046 EHDAA:1892 EHDAA:4406 FMA:67611 galen:Valve anatomical valve uberon UBERON:0003978 valve https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb anatomical valve FMA:67611 One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows. BAMS:CBf DHBA:12828 EMAPA:37818 FMA:321547 HBA:9406 SCTID:314163001 neuronames:1213 cerebellar fissure fissurae cerebelli uberon cerebellar fissures cerebellar fissures set cerebellar sulci cerebellar sulcus set of cerebellar fissures sulcus of cerebellum UBERON:0003980 cerebellum fissure One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows. MP:0009267 EMAPA:37818 MA:th fissurae cerebelli FMA:77789 FMA:TA cerebellar fissures BAMS:CBf cerebellar fissures set FMA:77789 cerebellar sulci HBA:9406 set of cerebellar fissures FMA:77789 A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] Kardong says absent in adult tetrapods, check AAO we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally AAO:0010250 Wikipedia:Conus_arteriosus uberon UBERON:0003983 conus arteriosus http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. MP:0009464 Wikipedia:Conus_arteriosus Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] 2012-06-20 AAO:0010250 AAO AAO:BJB we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally ISBN:0073040584 The funnel-like expansion of the abdominal extremity of the uterine tube[MP]. The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct. infundibulum EMAPA:29897 FMA:18307 SCTID:362262001 Wikipedia:Infundibulum_of_uterine_tube infundibulum of oviduct infundibulum of uterine tube infundibulum of fallopian tube uberon infundibulum tubae uterinae UBERON:0003984 uterine tube infundibulum https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg FMA The funnel-like expansion of the abdominal extremity of the uterine tube[MP]. MP:0009466 Wikipedia:Infundibulum_of_uterine_tube The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. Wikipedia:Infundibulum_of_uterine_tube In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct. https://orcid.org/0000-0002-2825-0621 infundibulum infundibulum of oviduct FMA:18307 infundibulum of uterine tube FMA:18307 infundibulum of fallopian tube FMA:18307 infundibulum tubae uterinae Wikipedia:Infundibulum_of_uterine_tube The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells. EMAPA:37974 thymic cortico-medullary boundary thymic corticomedullary boundary thymic corticomedullary junction thymic corticomedullary zone thymus CMZ thymus cortico-medullary boundary thymus corticomedullary junction thymus corticomedullary zone uberon UBERON:0003988 thymus corticomedullary boundary The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells. MP:0009543 EMAPA:37974 MA:th thymic cortico-medullary boundary MP:0009543 thymic corticomedullary boundary MP:0009543 thymic corticomedullary junction MP:0009543 thymic corticomedullary zone MP:0009543 thymus CMZ MP:0009543 thymus cortico-medullary boundary MP:0009543 thymus corticomedullary junction MP:0009543 thymus corticomedullary zone MP:0009543 The connection between the embryo proper and extraembryonic tissues. uberon UBERON:0004015 embryonic-extraembryonic boundary The connection between the embryo proper and extraembryonic tissues. MP:0003890 A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 AEO:0001017 BTO:0006248 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 NCIT:C61572 UMLS:C0180383 Wikipedia:Dermatome_(embryology) XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AEO:0001017 AEO:JB BTO:0006248 https://github.com/biopragmatics/biomappings UMLS:C0180383 ncithesaurus:Dermatome cutis plate Wikipedia:Cutis_plate dermatomal mesenchyme Wikipedia:Cutis_plate mesenchyma dermatomiale Wikipedia:Dermatomal_mesenchyme The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells. As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon UBERON:0004022 germinal neuroepithelium NCBIBook:NBK10047 The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells. MP:0004261 http://www.ncbi.nlm.nih.gov/books/NBK10047 germinal neuroepithelial layer http://orcid.org/0000-0002-6601-2165 germinal neuroepithelium NCBIBook:NBK10047 original neural tube NCBIBook:NBK10047 That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate. BTO:0002879 EMAPA:31872 NCIT:C34123 SCTID:256391000 UMLS:C0230972 uberon UBERON:0004027 chorionic plate https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate. MP:0004560 http://www.medilexicon.com/medicaldictionary.php?t=69523 UMLS:C0230972 ncithesaurus:Chorionic_Plate The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate. The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects SP DHBA:10522 EMAPA:32703 PBA:294021932 VO:0011276 Wikipedia:Subplate https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png/360px-Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png neuronames:3233 cerebral cortex subplate subplate subplate zone uberon UBERON:0004035 cortical subplate The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate. MP:0008440 Wikipedia:Subplate https://github.com/obophenotype/mouse-anatomy-ontology/issues/1 The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects WP SP BRAINSPAN:BRAINSPAN VO:0011276 https://github.com/biopragmatics/biomappings cerebral cortex subplate EMAPA:32833 subplate zone DHBA:10522 The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone. IZ EMAPA:17545 EMAPA:32712 uberon cerebral cortex mantle layer cerebral cortex mantle zone cortical mantle layer UBERON:0004040 cortical intermediate zone Wikipedia The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone. MP:0008457 IZ BRAINSPAN:BRAINSPAN cerebral cortex mantle layer EMAPA:17545 The external masculine genital organs, including the penis and scrotum. BTO:0003097 EMAPA:30977 FMA:45642 SCTID:362264000 galen:MaleExternalGenitalia external male genital organ male external genitalia uberon organa genitalia masculina externa UBERON:0004053 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external male genitalia The external masculine genital organs, including the penis and scrotum. MP:0009199 external male genital organ BTO:0003097 male external genitalia FMA:45642 organa genitalia masculina externa BTO:0003097 The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands. consider splitting genitalia from genital organ BTO:0003096 FMA:45655 SCTID:310536002 internal male genital organ male internal genitalia uberon organa genitalia masculina interna UBERON:0004054 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal male genitalia The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands. MP:0009205 internal male genital organ BTO:0003096 male internal genitalia FMA:45655 organa genitalia masculina interna BTO:0003096 One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]. In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) BTO:0002840 EMAPA:37440 TAO:0005164 ZFA:0005164 bile ductule biliary ductule ductuli biliferi uberon bile capillary biliary ductule cholangiole terminal cholangiole UBERON:0004058 biliary ductule BTO One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]. BTO:0002840 MP:0009494 In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) ZFA EMAPA:37440 MA:th bile ductule BTO:0002840 biliary ductule http://www.mondofacto.com/facts/dictionary?ductuli+biliferi ductuli biliferi http://www.mondofacto.com/facts/dictionary?ductuli+biliferi bile capillary BTO:0002840 biliary ductule BTO:0002840 cholangiole BTO:0002840 terminal cholangiole http://orcid.org/0000-0002-6601-2165 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 neural tube ependymal layer neural tube ventricular germinal zone neural tube ventricular zone neural tube ependymal zone uberon UBERON:0004060 neural tube ventricular layer NCBIBook:NBK10047 NCBIBook:NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. MP:0009689 http://www.ncbi.nlm.nih.gov/books/NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen MP:0009689 ependymal layer NCBIBook:NBK10047 neural tube ependymal layer NCBIBook:NBK10047 neural tube ventricular germinal zone NCBIBook:NBK10047 neural tube ventricular zone MP:0009689 neural tube ependymal zone MP:0009689 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. EMAPA:17148 EMAPA:35360 neuronames:1367 neural tube intermediate zone uberon future brain marginal layer UBERON:0004061 neural tube mantle layer NCBIBook:NBK10047 by division NCBIBook:NBK10047 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. MP:0009690 http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube intermediate zone MP:0009690 http://www.ncbi.nlm.nih.gov/books/NBK10047 future brain marginal layer EMAPA:35360 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter. EMAPA:17151 neuronames:1368 neural tube marginal zone uberon brain marginal zone UBERON:0004062 neural tube marginal layer forms from axons The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter. MP:0009691 http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube marginal zone MP:0009691 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. AAO:0010561 EFO:0001904 NCIT:C34111 UMLS:C1511061 Wikipedia:Basal_plate_(neural_tube) neuronames:1372 basal plate basal plate of neural tube spinal cord basal plate uberon motor part of neural tube ventral part of neural tube UBERON:0004064 neural tube basal plate Shh Swenson The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. MP:0009693 Wikipedia:Basal_plate_(neural_tube) http://www.ncbi.nlm.nih.gov/books/NBK10047 UMLS:C1511061 ncithesaurus:Basal_Plate basal plate of neural tube Wikipedia:Basal_plate_(neural_tube) spinal cord basal plate MP:0009693 The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout. UBERON:0006237 EHDAA2:0000578 EHDAA:4778 EMAPA:16681 FMA:293101 NCIT:C34182 SCTID:361486000 UMLS:C1517321 VHOG:0001319 Wikipedia:Frontonasal_prominence embryonic frontonasal prominence uberon forebrain prominence frontonasal mass frontonasal process prominentia frontonasalis UBERON:0004066 frontonasal prominence http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout. MP:0009901 UMLS:C1517321 ncithesaurus:Frontonasal_Prominence embryonic frontonasal prominence http://orcid.org/0000-0002-6601-2165 forebrain prominence MP:0009901 frontonasal mass MP:0009901 frontonasal process MP:0009901 prominentia frontonasalis Wikipedia:Frontonasal_prominence The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it. EHDAA2:0000916 EHDAA:4786 EMAPA:16805 FMA:295864 SCTID:308880000 Wikipedia:Lateral_nasal_prominence lateral nasal process latero-nasal process uberon lateral nasal swelling prominentia nasalis lateralis UBERON:0004067 lateral nasal prominence http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png EHDAA2 Wikipedia lexical The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it. MP:0009902 Wikipedia:Lateral_nasal_prominence lateral nasal process EHDAA2:0000916 latero-nasal process EMAPA:16805 lateral nasal swelling https://orcid.org/0000-0002-6601-2165 prominentia nasalis lateralis Wikipedia:Lateral_nasal_prominence The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it. Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity. EHDAA2:0001076 EHDAA:4792 EMAPA:16808 FMA:295858 SCTID:308877001 VHOG:0000804 Wikipedia:Medial_nasal_prominence medial nasal process medial-nasal process prominentia nasalis medialis uberon medial nasal swelling nasomedial prominence UBERON:0004068 medial nasal prominence http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png EHDAA2 Wikipedia The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it. MP:0009903 Wikipedia:Medial_nasal_prominence medial nasal process EHDAA2:0001076 medial-nasal process EMAPA:16808 prominentia nasalis medialis Wikipedia:Medial_nasal_prominence medial nasal swelling https://orcid.org/0000-0002-6601-2165 nasomedial prominence https://orcid.org/0000-0002-6601-2165 One of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid. Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]. FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. BIRNLEX:1356 BTO:0001442 EFO:0001914 EMAPA:32674 FMA:78447 HBA:9418 MA:0000818 MESH:D002552 NCIT:C12356 SCTID:180929003 UMLS:C0007799 neuronames:2497 brain ventricles cerebral ventricle region of ventricular system of brain uberon UBERON:0004086 brain ventricle One of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid. https://github.com/obophenotype/uberon/issues/300 Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]. BIRNLEX:1356 FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. FMA UMLS:C0007799 ncithesaurus:Ventricle_Brain brain ventricles cerebral ventricle HP:0002118 region of ventricular system of brain FMA:78447 Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. AAO:0010215 BTO:0001438 EMAPA:18415 FMA:321896 GAID:547 MA:0000068 MESH:D014684 NCIT:C12817 SCTID:244405007 UMLS:C0042460 Wikipedia:Venae_cavae uberon caval vein venae cavae UBERON:0004087 vena cava http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. Wikipedia:Venae_cavae http://orcid.org/0000-0002-6601-2165 UMLS:C0042460 ncithesaurus:Vena_Cava venae cavae Wikipedia:Venae_cavae The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region orbital part of face uberon ocular and peri-ocular region ocular region orbital content orbital part of eye UBERON:0004088 orbital region The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. http://orcid.org/0000-0002-6601-2165 in HP covers eyelid, eyebrow. HP:0000284 content of orbital part of eye FMA:260119 eye region http://orcid.org/0000-0002-6601-2165 orbital part of face http://orcid.org/0000-0002-6601-2165 orbital content FMA:260119 orbital part of eye FMA:72951 The middle of the face including the nose and its associated bony structures[MW]. this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface. midfacial EMAPA:32806 FMA:285406 MA:0001910 uberon lower face midface/lower face snout UBERON:0004089 midface The middle of the face including the nose and its associated bony structures[MW]. HP:0000309 http://www.merriam-webster.com/medical/midface snout MA:0001910 Missing definition for term UBERON:0004092. Please replace it using linked reference. uberon UBERON:0004092 hypothalamus-pituitary axis Missing definition for term UBERON:0004092. Please replace it using linked reference. HP:0000864 Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint. FMA:38911 synovial cavity of elbow joint uberon UBERON:0004099 joint space of elbow Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint. HP:0003943 synovial cavity of elbow joint FMA:38911 The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone. FMA:265239 SCTID:279371005 Wikipedia:Collecting_duct_system collecting duct system kidney collecting duct system uberon tubulus renalis colligens UBERON:0004100 renal collecting system http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone. HP:0004742 Wikipedia:Collecting_duct_system collecting duct system Wikipedia:Collecting_duct_system kidney collecting duct system Wikipedia:Collecting_duct_system tubulus renalis colligens Wikipedia:Collecting_duct_system One of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP]. in BTO, this is part of an embryo BTO:0001383 EMAPA:35118 FMA:313923 GAID:215 MA:0003119 MESH:D000539 NCIT:C89749 SCTID:245790000 UMLS:C0447411 Wikipedia:Alveolar_ridge alveolar body alveolar bone alveolar margin alveolar process margo alveolaris uberon UBERON:0004103 alveolar ridge PMID:19767574 Wikipedia One of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP]. HP:0006477 Wikipedia:Alveolar_ridge in BTO, this is part of an embryo BTO UMLS:C0447411 ncithesaurus:Alveolar_Ridge alveolar body MP:0004189 alveolar bone MP:0004189 margo alveolaris 2 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 SCTID:346902003 Wikipedia:Foramen foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA foramen EHDAA2:0003080 foramina https://orcid.org/0000-0002-6601-2165 ostia A muscle of the tympanic cavity that attaches to an auditory ossicle. attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter UBERON:0004112 EMAPA:37776 FMA:49026 MA:0000256 NCIT:C33148 SCTID:244778009 UMLS:C1513769 Wikipedia:Muscles_of_auditory_ossicles auditory ossicles muscle muscle of auditory ossicles muscle of tympanic cavity ossicular muscle tympanic cavity muscle uberon muscle of middle ear UBERON:0004113 muscle of auditory ossicle FMA A muscle of the tympanic cavity that attaches to an auditory ossicle. http://orcid.org/0000-0002-6601-2165 EMAPA:37776 MA:th UMLS:C1513769 ncithesaurus:Muscle_of_the_Tympanum auditory ossicles muscle FMA:49026 muscle of auditory ossicles FMA:49026 ossicular muscle FMA:49026 tympanic cavity muscle MA:0000256 Small cavity surrounding the bones of the middle ear. BTO:0002098 EHDAA2:0004119 EMAPA:37778 FMA:56461 SCTID:362551002 Wikipedia:Tympanic_cavity anatomical cavity of middle ear cavitas tympani cavity of middle ear middle ear cavity middle-ear cavity uberon cavitas tympanica tympanum UBERON:0004114 tympanic cavity http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png EHDAA2 EHDAA2 Small cavity surrounding the bones of the middle ear. Wikipedia:Tympanic_cavity EMAPA:37778 MA:th anatomical cavity of middle ear OBOL:automatic cavitas tympani Wikipedia:Tympanic_cavity cavity of middle ear OBOL:automatic middle ear cavity OBOL:automatic middle-ear cavity OBOL:automatic cavitas tympanica BTO:0002098 tympanum BTO:0002098 A blood vessel that is part of a tympanic cavity [Automatically generated definition]. EMAPA:37775 MA:0001219 anatomical cavity of middle ear blood vessel blood vessel of anatomical cavity of middle ear blood vessel of cavity of middle ear blood vessel of middle ear anatomical cavity blood vessel of middle ear cavity cavity of middle ear blood vessel middle ear anatomical cavity blood vessel middle ear blood vessel middle ear cavity blood vessel tympanic cavity blood vessel uberon UBERON:0004115 blood vessel of tympanic cavity A blood vessel that is part of a tympanic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37775 MA:th anatomical cavity of middle ear blood vessel OBOL:automatic blood vessel of anatomical cavity of middle ear OBOL:automatic blood vessel of cavity of middle ear OBOL:automatic blood vessel of middle ear anatomical cavity OBOL:automatic blood vessel of middle ear cavity OBOL:automatic cavity of middle ear blood vessel OBOL:automatic middle ear anatomical cavity blood vessel OBOL:automatic middle ear cavity blood vessel OBOL:automatic A nerve that is part of a tympanic cavity [Automatically generated definition]. EMAPA:37777 MA:0001222 anatomical cavity of middle ear nerve cavity of middle ear nerve middle ear anatomical cavity nerve middle ear cavity nerve nerve of anatomical cavity of middle ear nerve of cavity of middle ear nerve of middle ear anatomical cavity nerve of middle ear cavity tympanic cavity nerve tympanic cavity nerves uberon UBERON:0004116 nerve of tympanic cavity A nerve that is part of a tympanic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37777 MA:th anatomical cavity of middle ear nerve OBOL:automatic cavity of middle ear nerve OBOL:automatic middle ear anatomical cavity nerve OBOL:automatic middle ear cavity nerve OBOL:automatic nerve of anatomical cavity of middle ear OBOL:automatic nerve of cavity of middle ear OBOL:automatic nerve of middle ear anatomical cavity OBOL:automatic nerve of middle ear cavity OBOL:automatic tympanic cavity nerves MA:0001222 An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] EMAPA also includes a distinct pouch endoderm AAO:0011113 EFO:0003627 EHDAA:1086 EHDAA:1669 EHDAA:579 EHDAA:617 EMAPA:32752 FMA:293063 NCIT:C34252 SCTID:34674002 TAO:0001106 UMLS:C0231067 VHOG:0001203 Wikipedia:Pharyngeal_pouch_(embryology) XAO:0000282 ZFA:0001106 branchial pouch visceral pouch uberon pharyngeal pouches visceral pouches UBERON:0004117 The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389] pharyngeal pouch http://tolweb.org/Chordata/2499 EHDAA2 ZFA An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. PMID:23020903 ZFA:0001106 http://orcid.org/0000-0002-6601-2165 Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] 2012-08-14 TAO:0001106 TAO ZFIN:curator A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001203 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ EMAPA also includes a distinct pouch endoderm EMAPA UMLS:C0231067 ncithesaurus:Pharyngeal_Pouch branchial pouch Wikipedia:Branchial_pouch visceral pouch pharyngeal pouches VHOG:0001203 visceral pouches VHOG:0001203 A vasculature that is part of a iris [Automatically generated definition]. ZFA:0005568 iris blood vessels iris vascular network iris vasculature vascular network of iris uberon UBERON:0004118 vasculature of iris A vasculature that is part of a iris [Automatically generated definition]. OBOL:automatic iris blood vessels ZFA:0005568 iris vascular network OBOL:automatic vascular network of iris OBOL:automatic An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. https://orcid.org/0000-0002-6601-2165 An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. https://orcid.org/0000-0002-6601-2165 mesodermal derivative FBbt:00025998 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. https://orcid.org/0000-0002-6601-2165 ectodermal deriviative FBbt:00025990 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] genitourinary urogenital AAO:0000624 BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 MESH:D014566 NCIT:C12810 SCTID:278861008 UMLS:C0042066 VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem urogenital system uberon GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract UBERON:0004122 genitourinary system Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] 2012-06-20 AAO:0000624 AAO AAO:EJS relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] 2012-06-20 AAO:0000624 AAO Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] 2012-09-17 VHOG:0000286 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 http://bgee.unil.ch/ UMLS:C0042066 ncithesaurus:Genitourinary_System Urogenitalsystem BTO:0003091 genito-urinary system FMA:280610 urogenital tract BTO:0003091 Any of the layers of the myocardium. Example: compact layer, trabecular layer. EMAPA:37475 MA:0000080 layer of myocardium myocardium layer uberon UBERON:0004123 myocardial layer Any of the layers of the myocardium. Example: compact layer, trabecular layer. http://orcid.org/0000-0002-6601-2165 EMAPA:37475 MA:th The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]. The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO] EFO:0003706 MA:0002866 TAO:0005059 ZFA:0005059 myocardial trabecular layer trabecular layer uberon heart muscle trabecula heart muscle trabeculae myocardial trabeculae carneae trabecula of heart muscle trabeculae UBERON:0004124 myocardium trabecular layer The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]. ZFA:0005059 The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO] 2012-08-14 TAO:0005059 TAO ZFIN:curator trabecular layer ZFA:0005059 heart muscle trabeculae myocardial trabeculae carneae trabeculae TAO:0005059 A myocardium trabecular layer that is part of a cardiac ventricle. TODO - check FMA FMA:83511 TAO:0005060 ZFA:0005060 myocardium of region of ventricle trabecular cardiac ventricle muscle ventricular trabecular myocardium uberon UBERON:0004126 trabecular layer of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A myocardium trabecular layer that is part of a cardiac ventricle. OBOL:automatic myocardium of region of ventricle FMA:83511 trabecular cardiac ventricle muscle GO:0003222 ventricular trabecular myocardium GO:0003222 The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 NCIT:C34236 SCTID:362864008 TAO:0000050 UMLS:C0231106 VHOG:0000165 Wikipedia:Optic_vesicles XAO:0000228 ZFA:0000050 uberon evagination eye vesicle ocular vesicle optic vesicles UBERON:0004128 Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png ZFA GO-def ZFA The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. GO:0003404 Wikipedia:Optic_vesicles (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] 2012-09-17 VHOG:0000165 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C0231106 ncithesaurus:Optic_Vesicle eye vesicle XAO:0000228 ocular vesicle VHOG:0000165 optic vesicles ZFA:0000050 A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo. BIRNLEX:880 EMAPA:35212 FMA:83141 MA:0000201 NCIT:C49137 SCTID:360478008 UMLS:C1707522 cell layer of cerebellar cortex cytoarchitectural part of the cerebellar cortex gray matter layer of cerebellum layer of cerebellar cortex layer of cerebellum uberon UBERON:0004130 cerebellar layer A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo. http://orcid.org/0000-0002-6601-2165 ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum UMLS:C1707522 ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum cytoarchitectural part of the cerebellar cortex BIRNLEX:880 gray matter layer of cerebellum FMA:83141 Missing definition for term UBERON:0004133. Please replace it using linked reference. salivary nucleus uberon UBERON:0004133 salivatory nucleus Missing definition for term UBERON:0004133. Please replace it using linked reference. GO:0021751 salivary nucleus GO:0021751 The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 myocardial plate uberon cardiac crescent cardiogenic crescent heart rudiment UBERON:0004139 cardiogenic plate The first recognizable structure derived from the heart field. GO:0003142 (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] 2012-09-17 VHOG:0000975 VHOG PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) http://bgee.unil.ch/ myocardial plate EHDAA2:0000215 cardiac crescent EMAPA:16106 cardiogenic crescent GO:0003142 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field uberon FHF PHF heart field UBERON:0004140 primary heart field GO:0003128 https://orcid.org/0000-0003-3308-6245 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. GO:0003138 GOC:mtg_heart GOC:rl this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] GO first heart field XAO:0004185 primary heart field PMID:17276708 XAO:0004185 FHF XAO:0004185 PHF XAO:0004185 heart field XAO:0004185 An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 NCIT:C34161 TAO:0000360 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube uberon UBERON:0004141 heart tube ZFA-modified An epithelial tube that will give rise to the mature heart. GO:0003143 GOC:mtg_heart the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. MP:0012700 embryonic heart tube GO:0003143 endocardial heart tube MP:0012700 endocardial tube XAO:0000337 The outflow tract septum is a partition in the outflow tract. XAO:0004141 uberon UBERON:0004142 outflow tract septum The outflow tract septum is a partition in the outflow tract. GO:0003148 The outflow tract is the portion of the heart through which blood flows into the arteries. Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] EHDAA2:0001351 EHDAA:464 EHDAA:798 EMAPA:16346 MA:0000100 VHOG:0000670 XAO:0004139 cardiac outflow tract heart outflow tract uberon arterial (outflow) pole UBERON:0004145 outflow tract The outflow tract is the portion of the heart through which blood flows into the arteries. GO:0003151 cardiac outflow tract PMID:20735616 arterial (outflow) pole PMID:20735616 Vein of heart that drains the myocardium. EHDAA2:0004507 EMAPA:37137 FMA:12846 NCIT:C12878 NCIT:C12882 SCTID:277726009 UMLS:C0226654 UMLS:C0226737 Wikipedia:Coronary_circulation ZFA:0005814 galen:CoronaryVein cardiac vein coronary vein heart vein vein of heart uberon coronary vein UBERON:0004148 cardiac vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA Vein of heart that drains the myocardium. http://orcid.org/0000-0002-6601-2165 EMAPA:37137 MA:th UMLS:C0226654 ncithesaurus:Cardiac_Vein UMLS:C0226737 ncithesaurus:Coronary_Vein cardiac vein FMA:12846 coronary vein ZFA:0005814 heart vein OBOL:automatic vein of heart OBOL:automatic coronary vein Wikipedia:Coronary_circulation A cardiac chamber surrounds an enclosed cavity within the heart. FMA:7095 SCTID:276456008 chamber of heart heart chamber uberon UBERON:0004151 generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart. GO:0003205 An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium. propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] EMAPA:36025 ZFA:0005808 proepicardial cluster proepicardial organ uberon UBERON:0004160 proepicardium todo check other taxa ZFA An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium. GO:0003342 http://en.wiktionary.org/wiki/proepicardium proepicardial cluster ZFA:0005808 proepicardial organ ZFIN:ZDB-PUB-080218-16 A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2:0001829 EHDAA:736 EMAPA:16318 FMA:295593 NCIT:C34296 SCTID:308819008 UMLS:C0231004 VHOG:0000019 Wikipedia:Septum_transversum transverse septum uberon UBERON:0004161 septum transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. VHOG:0000019 Wikipedia:Septum_transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] 2012-09-17 VHOG:0000019 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/transverse+septum In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000019 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2 UMLS:C0231004 ncithesaurus:Septum_Transversum transverse septum https://orcid.org/0000-0002-6601-2165 The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. FMA:45652 internal genitalia internal genitals uberon internal reproductive organ internal sex organ UBERON:0004175 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 internal genitalia The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals. GO:0035260 The external genitalia are the outer sex organs, such as the penis or vulva in mammals. FMA:45643 SCTID:362207005 external genitalia uberon external reproductive organ external sex organ UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia The external genitalia are the outer sex organs, such as the penis or vulva in mammals. GO:0035261 Organ that is part of the hematopoietic system. consider splitting out lymph organ, compare with lymph node the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term BTO:0004605 EMAPA:37665 FMA:7143 MA:0000747 SCTID:361338006 haematological system organ haemopoietic system organ hematopoeitic organ hematopoietic system organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hematopoeitic or lymphoid organ lymph organ lymphoid organ uberon UBERON:0004177 hemopoietic organ Organ that is part of the hematopoietic system. GOC:Obol the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs the FMA class 'lymphoid organ' is a general anatomical term FMA EMAPA:37665 MA:th haematological system organ OBOL:automatic haemopoietic system organ OBOL:automatic hematopoietic system organ OBOL:automatic organ of haematological system OBOL:automatic organ of haemopoietic system OBOL:automatic organ of hematopoietic system OBOL:automatic organ of organa haemopoietica OBOL:automatic organa haemopoietica organ OBOL:automatic lymph organ MA:0000747 lymphoid organ BTO:0004605 FMA:7143 The nonstriated, involuntary muscle tissue located in the wall of the aorta. BTO:0001685 CALOHA:TS-0048 EFO:0002775 EMAPA:35135 MA:0000702 NCIT:C49191 UMLS:C1706825 aorta non-striated muscle aorta smooth muscle aortic smooth muscle uberon UBERON:0004178 aorta smooth muscle tissue The nonstriated, involuntary muscle tissue located in the wall of the aorta. MGI:csmith MP:0009865 UMLS:C1706825 ncithesaurus:Aorta_Smooth_Muscle_Tissue aorta non-striated muscle OBOL:automatic aorta smooth muscle OBOL:automatic aortic smooth muscle BTO:0001685 The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts. EMAPA:35539 MA:0002911 adipose tissue of lactiferous gland adipose tissue of mammary gland fat tissue of lactiferous gland fat tissue of lobe of breast fat tissue of lobe of mammary gland fat tissue of mammary gland fatty tissue of lactiferous gland fatty tissue of lobe of breast fatty tissue of lobe of mammary gland fatty tissue of mammary gland lactiferous gland adipose tissue lactiferous gland fat tissue lactiferous gland fatty tissue lobe of breast adipose tissue lobe of breast fat tissue lobe of breast fatty tissue lobe of mammary gland adipose tissue lobe of mammary gland fat tissue lobe of mammary gland fatty tissue mammary gland adipose tissue mammary gland fat tissue mammary gland fatty tissue uberon UBERON:0004180 mammary gland fat The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts. GO:0060611 adipose tissue of lactiferous gland OBOL:automatic adipose tissue of mammary gland OBOL:automatic fat tissue of lactiferous gland OBOL:automatic fat tissue of lobe of breast OBOL:automatic fat tissue of lobe of mammary gland OBOL:automatic fat tissue of mammary gland OBOL:automatic fatty tissue of lactiferous gland OBOL:automatic fatty tissue of lobe of breast OBOL:automatic fatty tissue of lobe of mammary gland OBOL:automatic fatty tissue of mammary gland OBOL:automatic lactiferous gland adipose tissue OBOL:automatic lactiferous gland fat tissue OBOL:automatic lactiferous gland fatty tissue OBOL:automatic lobe of breast adipose tissue OBOL:automatic lobe of breast fat tissue OBOL:automatic lobe of breast fatty tissue OBOL:automatic lobe of mammary gland adipose tissue OBOL:automatic lobe of mammary gland fat tissue OBOL:automatic lobe of mammary gland fatty tissue OBOL:automatic mammary gland adipose tissue OBOL:automatic mammary gland fat tissue OBOL:automatic mammary gland fatty tissue OBOL:automatic The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis. in female mouse embryos, the primary mammary cord (aka 'mammary sprout') is formed between E15.5 and E16.5; once the primary cord reaches the adipocytes of the fat pad (around E16), it begins to branch in a characteristic dichotomous fashion to form the initial ductal tree lactiferous gland cord mammary cord uberon mammary sprout UBERON:0004182 mammary gland cord The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis. MP:0013725 The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland. TODO - check also FMA Stroma of glandular part of prostate UBERON:0005084 EMAPA:35714 FMA:45719 MA:0002912 NCIT:C13104 UMLS:C1521760 prostate stroma prostatic stroma stroma of prostate stroma of prostate gland stroma of glandular part of prostate uberon UBERON:0004184 prostate gland stroma The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland. GO:0060741 UMLS:C1521760 ncithesaurus:Prostatic_Stroma prostate stroma OBOL:automatic prostatic stroma FMA:45719 stroma of prostate OBOL:automatic stroma of prostate gland OBOL:automatic stroma of glandular part of prostate FMA:74349 OBOL:automatic A portions of the gut that is derived from endoderm. EMAPA:32930 endodermal gut gut endoderm uberon UBERON:0004185 endodermal part of digestive tract A portions of the gut that is derived from endoderm. GO:0061031 gut endoderm EMAPA:32930 The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros. TODO - check - GO says outer, BTO says inner. Make this a superclass BTO:0001515 EMAPA:35458 MA:0002847 epithelium of glomerulus epithelium of kidney glomerulus epithelium of renal glomerulus kidney glomerular epithelium uberon glomerular epithelial cell UBERON:0004188 glomerular epithelium The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros. GO:0072010 kidney glomerular epithelium MA:0002847 glomerular epithelial cell BTO:0001515 The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus. BTO:0004631 endothelium of renal glomerulus renal glomerulus endothelium uberon UBERON:0004189 glomerular endothelium The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus. GO:0072011 endothelium of renal glomerulus OBOL:automatic renal glomerulus endothelium OBOL:automatic The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus. glomerulus vasculature renal glomerulus vascular network renal glomerulus vasculature vascular network of renal glomerulus vasculature of renal glomerulus uberon UBERON:0004190 renal glomerulus vasculature The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus. GO:0072012 glomerulus vasculature OBOL:automatic renal glomerulus vascular network OBOL:automatic renal glomerulus vasculature OBOL:automatic vascular network of renal glomerulus OBOL:automatic vasculature of renal glomerulus OBOL:automatic The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 CSB uberon UBERON:0004198 comma-shaped body cjm ZFA The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. GO:0072049 CSB The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 VO:0010896 ZFA:0005589 SSB stage II nephron uberon UBERON:0004199 S-shaped body cjm GO The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. GO:0072050 VO:0010896 https://github.com/biopragmatics/biomappings SSB stage II nephron http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) UBERON:0002449 UBERON:0005098 pyramid BTO:0003926 FMA:258870 MA:0001654 NCIT:C12886 NCIT:C33436 SCTID:361328001 UMLS:C0227629 UMLS:C1514613 Wikipedia:Renal_pyramids Malpighian pyramid renal pyramid uberon Malphigian pyramid Malpighian pyramid medullary pyramid pyramid of Malphigi pyramid of Malpighi pyramides renales pyramis renalis renal medullary region UBERON:0004200 kidney pyramid https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. GO:0072056 http://anatomy.uams.edu/anatomyhtml/kidney.html not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) FMA pyramid GO:0072056 UMLS:C0227629 ncithesaurus:Renal_Pyramid UMLS:C1514613 ncithesaurus:Pyramid_of_Malpighi Malpighian pyramid Wikipedia:Renal_pyramids renal pyramid Wikipedia:Renal_pyramids Malphigian pyramid BTO:0003926 pyramid of Malphigi ncithesaurus:Pyramid_of_Malpighi pyramid of Malpighi UBERON:cjm pyramides renales Wikipedia:Renal_pyramids pyramis renalis BTO:0003926 renal medullary region FMA:258870 The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex. UBERON:0005267 BTO:0002643 EMAPA:28130 MA:0002600 kidney cortex collecting duct uberon renal cortex collecting duct UBERON:0004203 cortical collecting duct The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex. GO:0072059 kidney cortex collecting duct MA:0002600 renal cortex collecting duct MA:0002600 Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron. mesenchyme of nephron nephron mesenchyme uberon UBERON:0004208 The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] nephrogenic mesenchyme Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron. GO:0072076 mesenchyme of nephron OBOL:automatic nephron mesenchyme OBOL:automatic The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap stage I nephron uberon UBERON:0004209 renal vesicle EHDAA2 The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. GO:0072077 stage I nephron ZFA:0005586 http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html The nephron epithelium is a tissue that covers the surface of a nephron. epithelial tissue of nephron epithelium of nephron nephron epithelial tissue uberon UBERON:0004211 nephron epithelium The nephron epithelium is a tissue that covers the surface of a nephron. GO:0072088 epithelial tissue of nephron OBOL:automatic epithelium of nephron OBOL:automatic nephron epithelial tissue OBOL:automatic The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus. Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] EMAPA:28245 FMA:274259 MA:0002587 NCIT:C32684 SCTID:362049007 TAO:0005284 UMLS:C0226356 ZFA:0005284 blood capillary of renal glomerulus capillary of renal glomerulus capillary vessel of renal glomerulus renal glomerulus blood capillary renal glomerulus capillary renal glomerulus capillary vessel uberon glomerular capillaries glomerular capillary system UBERON:0004212 glomerular capillary https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus. MGI:csmith MP:0011320 Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] 2012-08-14 TAO:0005284 TAO ZFIN:ZDB-PUB-000824-1 ZFIN:curator UMLS:C0226356 ncithesaurus:Glomerular_Capillary blood capillary of renal glomerulus OBOL:automatic capillary of renal glomerulus OBOL:automatic capillary vessel of renal glomerulus OBOL:automatic renal glomerulus blood capillary OBOL:automatic renal glomerulus capillary OBOL:automatic renal glomerulus capillary vessel OBOL:automatic glomerular capillaries glomerular capillary system MA:0002587 A nerve that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:37344 MA:0000685 hind limb stylopod nerve hindlimb stylopod nerve lower extremity stylopod nerve thigh RELATED uberon UBERON:0004214 upper leg nerve A nerve that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37344 MA:th hind limb stylopod nerve OBOL:automatic hindlimb stylopod nerve OBOL:automatic lower extremity stylopod nerve OBOL:automatic thigh RELATED OBOL:automatic A nerve that is part of a back [Automatically generated definition]. EMAPA:37268 MA:0000497 nerve of back uberon UBERON:0004215 back nerve A nerve that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37268 MA:th nerve of back OBOL:automatic A nerve that is part of a lower arm [Automatically generated definition]. EMAPA:37338 MA:0000601 uberon UBERON:0004216 lower arm nerve A nerve that is part of a lower arm [Automatically generated definition]. OBOL:automatic EMAPA:37338 MA:th A nerve that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:37337 MA:0000607 uberon UBERON:0004217 upper arm nerve A nerve that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37337 MA:th A nerve that is part of a lower leg [Automatically generated definition]. EMAPA:37345 MA:0000679 uberon UBERON:0004218 lower leg nerve A nerve that is part of a lower leg [Automatically generated definition]. OBOL:automatic EMAPA:37345 MA:th A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:36630 FMA:76909 MA:0001691 muscle layer of urethra muscular coat of urethra muscular layer of urethra smooth muscle of urethra smooth muscle tissue of urethra tunica muscularis urethrae urethra smooth muscle tissue uberon urethral smooth muscle UBERON:0004219 urethra smooth muscle layer A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic muscle layer of urethra FMA:76909 muscular coat of urethra FMA:76909 muscular layer of urethra FMA:76909 smooth muscle of urethra OBOL:automatic smooth muscle tissue of urethra OBOL:automatic tunica muscularis urethrae FMA:TA urethra smooth muscle tissue OBOL:automatic urethral smooth muscle MA:0001691 A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 MA:0001547 involuntary muscle of large intestine large intestine involuntary muscle large intestine non-striated muscle large intestine smooth muscle tissue non-striated muscle of large intestine smooth muscle of large intestine smooth muscle tissue of large intestine uberon UBERON:0004220 large intestine smooth muscle MA consider merging A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of large intestine OBOL:automatic large intestine involuntary muscle OBOL:automatic large intestine non-striated muscle OBOL:automatic large intestine smooth muscle tissue OBOL:automatic non-striated muscle of large intestine OBOL:automatic smooth muscle of large intestine OBOL:automatic smooth muscle tissue of large intestine OBOL:automatic A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa BTO:0000643 EMAPA:35441 EMAPA:35443 MA:0001539 NCIT:C49243 UMLS:C1708547 bowel involuntary muscle bowel non-striated muscle bowel smooth muscle bowel smooth muscle tissue intestine involuntary muscle intestine non-striated muscle intestine smooth muscle tissue involuntary muscle of bowel involuntary muscle of intestine non-striated muscle of bowel non-striated muscle of intestine smooth muscle of bowel smooth muscle of intestine smooth muscle tissue of bowel smooth muscle tissue of intestine uberon intestinal muscularis intestinal smooth muscle UBERON:0004221 intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA UMLS:C1708547 ncithesaurus:Intestinal_Smooth_Muscle_Tissue bowel involuntary muscle OBOL:automatic bowel non-striated muscle OBOL:automatic bowel smooth muscle OBOL:automatic bowel smooth muscle tissue OBOL:automatic intestine involuntary muscle OBOL:automatic intestine non-striated muscle OBOL:automatic intestine smooth muscle tissue OBOL:automatic involuntary muscle of bowel OBOL:automatic involuntary muscle of intestine OBOL:automatic non-striated muscle of bowel OBOL:automatic non-striated muscle of intestine OBOL:automatic smooth muscle of bowel OBOL:automatic smooth muscle of intestine OBOL:automatic smooth muscle tissue of bowel OBOL:automatic smooth muscle tissue of intestine OBOL:automatic intestinal muscularis EMAPA:35441 intestinal smooth muscle BTO:0000643 A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. BTO:0001818 EMAPA:35823 MA:0001627 involuntary muscle of stomach involuntary muscle of ventriculus non-striated muscle of stomach non-striated muscle of ventriculus smooth muscle of stomach smooth muscle of ventriculus smooth muscle tissue of stomach smooth muscle tissue of ventriculus stomach involuntary muscle stomach non-striated muscle stomach smooth muscle tissue ventriculus involuntary muscle ventriculus non-striated muscle ventriculus smooth muscle ventriculus smooth muscle tissue uberon gastric muscle gastric smooth muscle stomach muscle UBERON:0004222 stomach smooth muscle A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. OBOL:automatic involuntary muscle of stomach OBOL:automatic involuntary muscle of ventriculus OBOL:automatic non-striated muscle of stomach OBOL:automatic non-striated muscle of ventriculus OBOL:automatic smooth muscle of stomach OBOL:automatic smooth muscle of ventriculus OBOL:automatic smooth muscle tissue of stomach OBOL:automatic smooth muscle tissue of ventriculus OBOL:automatic stomach involuntary muscle OBOL:automatic stomach non-striated muscle OBOL:automatic stomach smooth muscle tissue OBOL:automatic ventriculus involuntary muscle OBOL:automatic ventriculus non-striated muscle OBOL:automatic ventriculus smooth muscle OBOL:automatic ventriculus smooth muscle tissue OBOL:automatic gastric muscle BTO:0001818 gastric smooth muscle MA:0001627 stomach muscle BTO:0001818 A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. BTO:0004999 EMAPA:30997 MA:0001733 involuntary muscle of vagina non-striated muscle of vagina smooth muscle of vagina smooth muscle tissue of vagina vagina involuntary muscle vagina non-striated muscle vagina smooth muscle tissue vaginal smooth muscle uberon vagina smooth muscle UBERON:0004223 vagina smooth muscle A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. OBOL:automatic involuntary muscle of vagina OBOL:automatic non-striated muscle of vagina OBOL:automatic smooth muscle of vagina OBOL:automatic smooth muscle tissue of vagina OBOL:automatic vagina involuntary muscle OBOL:automatic vagina non-striated muscle OBOL:automatic vagina smooth muscle tissue OBOL:automatic vaginal smooth muscle BTO:0004999 vagina smooth muscle BTO:0004999 A muscular coat that is part of a vas deferens [Automatically generated definition]. TODO - check MA and FMA classes mean the same thing EMAPA:29270 FMA:19239 MA:0001750 SCTID:299705008 muscle layer of deferent duct muscle layer of ductus deferens muscle layer of vas deferens muscular coat of ductus deferens muscular layer of ductus deferens muscularis of vas deferens tunica muscularis (ductus deferens) tunica muscularis ductus deferentis uberon UBERON:0004224 muscular coat of vas deferens A muscular coat that is part of a vas deferens [Automatically generated definition]. OBOL:automatic muscle layer of deferent duct FMA:19239 muscle layer of ductus deferens FMA:19239 muscle layer of vas deferens FMA:19239 muscular coat of ductus deferens FMA:19239 muscular layer of ductus deferens FMA:19239 muscularis of vas deferens FMA:19239 tunica muscularis (ductus deferens) FMA:19239 tunica muscularis ductus deferentis FMA:19239 FMA:TA A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. BTO:0001660 EMAPA:35734 MA:0001830 respiratory smooth muscle smooth muscle of respiratory system uberon airway smooth muscle airway smooth muscle cell UBERON:0004225 respiratory system smooth muscle A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic respiratory smooth muscle BTO:0001660 smooth muscle of respiratory system OBOL:automatic airway smooth muscle BTO:0001660 airway smooth muscle cell BTO:0001660 A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. EMAPA:35117 MA:0001523 smooth muscle tissue of gastrointestinal system uberon UBERON:0004226 gastrointestinal system smooth muscle A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. OBOL:automatic smooth muscle tissue of gastrointestinal system OBOL:automatic The smooth muscle tissue surrounding the urothelium of the kidney pelvis. EMAPA:28120 FMA:262022 MA:0002631 kidney pelvis smooth muscle renal pelvis smooth muscle smooth muscle tissue of renal pelvis uberon pelvic smooth muscle UBERON:0004227 kidney pelvis smooth muscle The smooth muscle tissue surrounding the urothelium of the kidney pelvis. MGI:csmith MP:0011335 kidney pelvis smooth muscle EMAPA:28120 renal pelvis smooth muscle EMAPA:28120 smooth muscle tissue of renal pelvis FMA:262022 pelvic smooth muscle EMAPA:28120 A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. BTO:0001849 CALOHA:TS-1087 EMAPA:37791 MA:0001697 bladder involuntary muscle bladder non-striated muscle bladder smooth muscle bladder smooth muscle tissue involuntary muscle of bladder involuntary muscle of urinary bladder non-striated muscle of bladder non-striated muscle of urinary bladder smooth muscle of bladder smooth muscle of urinary bladder smooth muscle tissue of bladder smooth muscle tissue of urinary bladder urinary bladder involuntary muscle urinary bladder muscle urinary bladder non-striated muscle urinary bladder smooth muscle tissue uberon smooth muscle layer of bladder UBERON:0004228 urinary bladder smooth muscle A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic EMAPA:37791 MA:th bladder involuntary muscle OBOL:automatic bladder non-striated muscle OBOL:automatic bladder smooth muscle OBOL:automatic bladder smooth muscle tissue OBOL:automatic involuntary muscle of bladder OBOL:automatic involuntary muscle of urinary bladder OBOL:automatic non-striated muscle of bladder OBOL:automatic non-striated muscle of urinary bladder OBOL:automatic smooth muscle of bladder OBOL:automatic smooth muscle of urinary bladder OBOL:automatic smooth muscle tissue of bladder OBOL:automatic smooth muscle tissue of urinary bladder OBOL:automatic urinary bladder involuntary muscle OBOL:automatic urinary bladder muscle MA:0001697 urinary bladder non-striated muscle OBOL:automatic urinary bladder smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:30123 FMA:67990 MA:0001699 bladder neck involuntary muscle bladder neck non-striated muscle bladder neck smooth muscle bladder neck smooth muscle tissue involuntary muscle of bladder neck involuntary muscle of neck of bladder involuntary muscle of neck of urinary bladder involuntary muscle of urinary bladder neck involuntary muscle of vesical neck neck of bladder involuntary muscle neck of bladder non-striated muscle neck of bladder smooth muscle neck of bladder smooth muscle tissue neck of urinary bladder involuntary muscle neck of urinary bladder non-striated muscle neck of urinary bladder smooth muscle neck of urinary bladder smooth muscle tissue non-striated muscle of bladder neck non-striated muscle of neck of bladder non-striated muscle of neck of urinary bladder non-striated muscle of urinary bladder neck non-striated muscle of vesical neck smooth muscle of bladder neck smooth muscle of neck of bladder smooth muscle of neck of urinary bladder smooth muscle of urinary bladder neck smooth muscle of vesical neck smooth muscle tissue of bladder neck smooth muscle tissue of neck of bladder smooth muscle tissue of neck of urinary bladder smooth muscle tissue of urinary bladder neck smooth muscle tissue of vesical neck trigonal muscle trigonal muscle of urinary bladder urinary bladder neck involuntary muscle urinary bladder neck muscle urinary bladder neck non-striated muscle urinary bladder neck smooth muscle tissue vesical neck involuntary muscle vesical neck non-striated muscle vesical neck smooth muscle vesical neck smooth muscle tissue uberon UBERON:0004230 urinary bladder neck smooth muscle https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck involuntary muscle OBOL:automatic bladder neck non-striated muscle OBOL:automatic bladder neck smooth muscle OBOL:automatic bladder neck smooth muscle tissue OBOL:automatic involuntary muscle of bladder neck OBOL:automatic involuntary muscle of neck of bladder OBOL:automatic involuntary muscle of neck of urinary bladder OBOL:automatic involuntary muscle of urinary bladder neck OBOL:automatic involuntary muscle of vesical neck OBOL:automatic neck of bladder involuntary muscle OBOL:automatic neck of bladder non-striated muscle OBOL:automatic neck of bladder smooth muscle OBOL:automatic neck of bladder smooth muscle tissue OBOL:automatic neck of urinary bladder involuntary muscle OBOL:automatic neck of urinary bladder non-striated muscle OBOL:automatic neck of urinary bladder smooth muscle OBOL:automatic neck of urinary bladder smooth muscle tissue OBOL:automatic non-striated muscle of bladder neck OBOL:automatic non-striated muscle of neck of bladder OBOL:automatic non-striated muscle of neck of urinary bladder OBOL:automatic non-striated muscle of urinary bladder neck OBOL:automatic non-striated muscle of vesical neck OBOL:automatic smooth muscle of bladder neck OBOL:automatic smooth muscle of neck of bladder OBOL:automatic smooth muscle of neck of urinary bladder OBOL:automatic smooth muscle of urinary bladder neck OBOL:automatic smooth muscle of vesical neck OBOL:automatic smooth muscle tissue of bladder neck OBOL:automatic smooth muscle tissue of neck of bladder OBOL:automatic smooth muscle tissue of neck of urinary bladder OBOL:automatic smooth muscle tissue of urinary bladder neck OBOL:automatic smooth muscle tissue of vesical neck OBOL:automatic trigonal muscle FMA:67990 trigonal muscle of urinary bladder FMA:67990 urinary bladder neck involuntary muscle OBOL:automatic urinary bladder neck muscle MA:0001699 urinary bladder neck non-striated muscle OBOL:automatic urinary bladder neck smooth muscle tissue OBOL:automatic vesical neck involuntary muscle OBOL:automatic vesical neck non-striated muscle OBOL:automatic vesical neck smooth muscle OBOL:automatic vesical neck smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37394 MA:0001532 anal part of perineum involuntary muscle anal part of perineum non-striated muscle anal part of perineum smooth muscle anal part of perineum smooth muscle tissue anal region involuntary muscle anal region non-striated muscle anal region smooth muscle tissue anal triangle involuntary muscle anal triangle non-striated muscle anal triangle smooth muscle anal triangle smooth muscle tissue involuntary muscle of anal part of perineum involuntary muscle of anal region involuntary muscle of anal triangle non-striated muscle of anal part of perineum non-striated muscle of anal region non-striated muscle of anal triangle smooth muscle of anal part of perineum smooth muscle of anal region smooth muscle of anal triangle smooth muscle tissue of anal part of perineum smooth muscle tissue of anal region smooth muscle tissue of anal triangle uberon UBERON:0004231 anal region smooth muscle A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37394 MA:th anal part of perineum involuntary muscle OBOL:automatic anal part of perineum non-striated muscle OBOL:automatic anal part of perineum smooth muscle OBOL:automatic anal part of perineum smooth muscle tissue OBOL:automatic anal region involuntary muscle OBOL:automatic anal region non-striated muscle OBOL:automatic anal region smooth muscle tissue OBOL:automatic anal triangle involuntary muscle OBOL:automatic anal triangle non-striated muscle OBOL:automatic anal triangle smooth muscle OBOL:automatic anal triangle smooth muscle tissue OBOL:automatic involuntary muscle of anal part of perineum OBOL:automatic involuntary muscle of anal region OBOL:automatic involuntary muscle of anal triangle OBOL:automatic non-striated muscle of anal part of perineum OBOL:automatic non-striated muscle of anal region OBOL:automatic non-striated muscle of anal triangle OBOL:automatic smooth muscle of anal part of perineum OBOL:automatic smooth muscle of anal region OBOL:automatic smooth muscle of anal triangle OBOL:automatic smooth muscle tissue of anal part of perineum OBOL:automatic smooth muscle tissue of anal region OBOL:automatic smooth muscle tissue of anal triangle OBOL:automatic A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition]. EMAPA:36313 FMA:262026 MA:0000751 NCIT:C49260 UMLS:C1708791 involuntary muscle of lymph vessel involuntary muscle of lymphatic vessel lymph vessel involuntary muscle lymph vessel non-striated muscle lymph vessel smooth muscle lymph vessel smooth muscle tissue lymphatic vessel involuntary muscle lymphatic vessel non-striated muscle lymphatic vessel smooth muscle tissue non-striated muscle of lymph vessel non-striated muscle of lymphatic vessel smooth muscle of lymph vessel smooth muscle of lymphatic vessel smooth muscle tissue of lymph vessel smooth muscle tissue of lymphatic vessel uberon UBERON:0004232 lymphatic vessel smooth muscle A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition]. OBOL:automatic UMLS:C1708791 ncithesaurus:Lymphatic_Vessel_Smooth_Muscle_Tissue involuntary muscle of lymph vessel OBOL:automatic involuntary muscle of lymphatic vessel OBOL:automatic lymph vessel involuntary muscle OBOL:automatic lymph vessel non-striated muscle OBOL:automatic lymph vessel smooth muscle OBOL:automatic lymph vessel smooth muscle tissue OBOL:automatic lymphatic vessel involuntary muscle OBOL:automatic lymphatic vessel non-striated muscle OBOL:automatic lymphatic vessel smooth muscle tissue OBOL:automatic non-striated muscle of lymph vessel OBOL:automatic non-striated muscle of lymphatic vessel OBOL:automatic smooth muscle of lymph vessel OBOL:automatic smooth muscle of lymphatic vessel OBOL:automatic smooth muscle tissue of lymph vessel OBOL:automatic smooth muscle tissue of lymphatic vessel OBOL:automatic A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:35520 MA:0002410 involuntary muscle of lower respiratory tract lower respiratory tract involuntary muscle lower respiratory tract non-striated muscle lower respiratory tract smooth muscle tissue non-striated muscle of lower respiratory tract smooth muscle of lower respiratory tract smooth muscle tissue of lower respiratory tract uberon UBERON:0004233 lower respiratory tract smooth muscle A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic involuntary muscle of lower respiratory tract OBOL:automatic lower respiratory tract involuntary muscle OBOL:automatic lower respiratory tract non-striated muscle OBOL:automatic lower respiratory tract smooth muscle tissue OBOL:automatic non-striated muscle of lower respiratory tract OBOL:automatic smooth muscle of lower respiratory tract OBOL:automatic smooth muscle tissue of lower respiratory tract OBOL:automatic A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. see notes for muscle of iris. BTO:0000655 EMAPA:35448 FMA:312338 MA:0001270 involuntary muscle of iris iridial smooth muscle iris involuntary muscle iris non-striated muscle iris smooth muscle tissue non-striated muscle of iris smooth muscle of iris smooth muscle tissue of iris uberon UBERON:0004234 iris smooth muscle MA A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. OBOL:automatic involuntary muscle of iris OBOL:automatic iridial smooth muscle http://orcid.org/0000-0002-6601-2165 iris involuntary muscle OBOL:automatic iris non-striated muscle OBOL:automatic iris smooth muscle tissue OBOL:automatic non-striated muscle of iris OBOL:automatic smooth muscle of iris OBOL:automatic smooth muscle tissue of iris OBOL:automatic A portion of smooth muscle tissue that is part of a mammary gland [Automatically generated definition]. EMAPA:37669 MA:0000795 smooth muscle tissue of mammary gland uberon UBERON:0004235 mammary gland smooth muscle A portion of smooth muscle tissue that is part of a mammary gland [Automatically generated definition]. OBOL:automatic EMAPA:37669 MA:th smooth muscle tissue of mammary gland OBOL:automatic A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. EMAPA:36287 FMA:312251 MA:0000706 uberon UBERON:0004236 arteriole smooth muscle A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. OBOL:automatic Smooth muscle found within, and composing the majority of the wall of blood vessels. Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. UBERON:0010508 BTO:0001431 CALOHA:TS-1107 EMAPA:35177 MA:0000710 MESH:D009131 NCIT:C33853 TAO:0005321 UMLS:C1519956 Wikipedia:Vascular_smooth_muscle ZFA:0005321 blood vessel involuntary muscle blood vessel non-striated muscle blood vessel smooth muscle tissue involuntary muscle of blood vessel non-striated muscle of blood vessel smooth muscle of blood vessel smooth muscle tissue of blood vessel vascular smooth muscle vascular smooth muscle tissue uberon UBERON:0004237 blood vessel smooth muscle Smooth muscle found within, and composing the majority of the wall of blood vessels. Wikipedia:Vascular_smooth_muscle UMLS:C1519956 ncithesaurus:Vascular_Smooth_Muscle_Tissue blood vessel involuntary muscle OBOL:automatic blood vessel non-striated muscle OBOL:automatic blood vessel smooth muscle tissue OBOL:automatic involuntary muscle of blood vessel OBOL:automatic non-striated muscle of blood vessel OBOL:automatic smooth muscle of blood vessel OBOL:automatic smooth muscle tissue of blood vessel OBOL:automatic vascular smooth muscle ZFA:0005321 A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]. EMAPA:35807 MA:0000757 involuntary muscle of spleen non-striated muscle of spleen smooth muscle of spleen smooth muscle tissue of spleen spleen involuntary muscle spleen non-striated muscle spleen smooth muscle tissue uberon UBERON:0004238 spleen smooth muscle A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]. OBOL:automatic involuntary muscle of spleen OBOL:automatic non-striated muscle of spleen OBOL:automatic smooth muscle of spleen OBOL:automatic smooth muscle tissue of spleen OBOL:automatic spleen involuntary muscle OBOL:automatic spleen non-striated muscle OBOL:automatic spleen smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35783 MA:0001559 involuntary muscle of small bowel involuntary muscle of small intestine non-striated muscle of small bowel non-striated muscle of small intestine small bowel involuntary muscle small bowel non-striated muscle small bowel smooth muscle small bowel smooth muscle tissue small intestine involuntary muscle small intestine non-striated muscle small intestine smooth muscle tissue smooth muscle of small bowel smooth muscle of small intestine smooth muscle tissue of small bowel smooth muscle tissue of small intestine uberon UBERON:0004239 small intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of small bowel OBOL:automatic involuntary muscle of small intestine OBOL:automatic non-striated muscle of small bowel OBOL:automatic non-striated muscle of small intestine OBOL:automatic small bowel involuntary muscle OBOL:automatic small bowel non-striated muscle OBOL:automatic small bowel smooth muscle OBOL:automatic small bowel smooth muscle tissue OBOL:automatic small intestine involuntary muscle OBOL:automatic small intestine non-striated muscle OBOL:automatic small intestine smooth muscle tissue OBOL:automatic smooth muscle of small bowel OBOL:automatic smooth muscle of small intestine OBOL:automatic smooth muscle tissue of small bowel OBOL:automatic smooth muscle tissue of small intestine OBOL:automatic A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]. EMAPA:35373 MA:0001635 NCIT:C49483 UMLS:C1708179 gall bladder involuntary muscle gall bladder non-striated muscle gall bladder smooth muscle gall bladder smooth muscle tissue gallbladder involuntary muscle gallbladder non-striated muscle gallbladder smooth muscle tissue involuntary muscle of gall bladder involuntary muscle of gallbladder non-striated muscle of gall bladder non-striated muscle of gallbladder smooth muscle of gall bladder smooth muscle of gallbladder smooth muscle tissue of gall bladder smooth muscle tissue of gallbladder uberon biliary smooth muscle UBERON:0004240 gallbladder smooth muscle A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708179 ncithesaurus:Gallbladder_Smooth_Muscle_Tissue gall bladder involuntary muscle OBOL:automatic gall bladder non-striated muscle OBOL:automatic gall bladder smooth muscle OBOL:automatic gall bladder smooth muscle tissue OBOL:automatic gallbladder involuntary muscle OBOL:automatic gallbladder non-striated muscle OBOL:automatic involuntary muscle of gall bladder OBOL:automatic involuntary muscle of gallbladder OBOL:automatic non-striated muscle of gall bladder OBOL:automatic non-striated muscle of gallbladder OBOL:automatic smooth muscle of gall bladder OBOL:automatic smooth muscle of gallbladder OBOL:automatic smooth muscle tissue of gall bladder OBOL:automatic smooth muscle tissue of gallbladder OBOL:automatic biliary smooth muscle MA:0001635 A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. BTO:0004401 EMAPA:35195 MA:0001840 NCIT:C49213 UMLS:C1707055 bronchi involuntary muscle bronchi non-striated muscle bronchi smooth muscle bronchi smooth muscle tissue bronchial trunk involuntary muscle bronchial trunk non-striated muscle bronchial trunk smooth muscle bronchial trunk smooth muscle tissue bronchus involuntary muscle bronchus non-striated muscle bronchus smooth muscle tissue involuntary muscle of bronchi involuntary muscle of bronchial trunk involuntary muscle of bronchus non-striated muscle of bronchi non-striated muscle of bronchial trunk non-striated muscle of bronchus smooth muscle of bronchi smooth muscle of bronchial trunk smooth muscle of bronchus smooth muscle tissue of bronchi smooth muscle tissue of bronchial trunk smooth muscle tissue of bronchus uberon bronchial smooth muscle UBERON:0004242 bronchus smooth muscle A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707055 ncithesaurus:Bronchus_Smooth_Muscle_Tissue bronchi involuntary muscle OBOL:automatic bronchi non-striated muscle OBOL:automatic bronchi smooth muscle OBOL:automatic bronchi smooth muscle tissue OBOL:automatic bronchial trunk involuntary muscle OBOL:automatic bronchial trunk non-striated muscle OBOL:automatic bronchial trunk smooth muscle OBOL:automatic bronchial trunk smooth muscle tissue OBOL:automatic bronchus involuntary muscle OBOL:automatic bronchus non-striated muscle OBOL:automatic bronchus smooth muscle tissue OBOL:automatic involuntary muscle of bronchi OBOL:automatic involuntary muscle of bronchial trunk OBOL:automatic involuntary muscle of bronchus OBOL:automatic non-striated muscle of bronchi OBOL:automatic non-striated muscle of bronchial trunk OBOL:automatic non-striated muscle of bronchus OBOL:automatic smooth muscle of bronchi OBOL:automatic smooth muscle of bronchial trunk OBOL:automatic smooth muscle of bronchus OBOL:automatic smooth muscle tissue of bronchi OBOL:automatic smooth muscle tissue of bronchial trunk OBOL:automatic smooth muscle tissue of bronchus OBOL:automatic bronchial smooth muscle EMAPA:35195 A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]. BTO:0003159 EMAPA:35713 FMA:74245 MA:0001741 involuntary muscle of prostate involuntary muscle of prostate gland muscular tissue of prostate non-striated muscle of prostate non-striated muscle of prostate gland prostate gland involuntary muscle prostate gland non-striated muscle prostate gland smooth muscle tissue prostate involuntary muscle prostate non-striated muscle prostate smooth muscle prostate smooth muscle tissue smooth muscle of prostate smooth muscle of prostate gland smooth muscle tissue of prostate smooth muscle tissue of prostate gland substantia muscularis prostatae uberon UBERON:0004243 prostate gland smooth muscle FMA A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]. OBOL:automatic involuntary muscle of prostate OBOL:automatic involuntary muscle of prostate gland OBOL:automatic muscular tissue of prostate FMA:74245 non-striated muscle of prostate OBOL:automatic non-striated muscle of prostate gland OBOL:automatic prostate gland involuntary muscle OBOL:automatic prostate gland non-striated muscle OBOL:automatic prostate gland smooth muscle tissue OBOL:automatic prostate involuntary muscle OBOL:automatic prostate non-striated muscle OBOL:automatic prostate smooth muscle OBOL:automatic prostate smooth muscle tissue OBOL:automatic smooth muscle of prostate OBOL:automatic smooth muscle of prostate gland OBOL:automatic smooth muscle tissue of prostate OBOL:automatic smooth muscle tissue of prostate gland OBOL:automatic substantia muscularis prostatae FMA:74245 FMA:TA A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. EMAPA:29046 MA:0001721 fallopian tube involuntary muscle fallopian tube non-striated muscle fallopian tube smooth muscle fallopian tube smooth muscle tissue involuntary muscle of fallopian tube non-striated muscle of fallopian tube smooth muscle of fallopian tube smooth muscle tissue of fallopian tube uberon UBERON:0004245 oviduct smooth muscle A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube involuntary muscle OBOL:automatic fallopian tube non-striated muscle OBOL:automatic fallopian tube smooth muscle OBOL:automatic fallopian tube smooth muscle tissue OBOL:automatic involuntary muscle of fallopian tube OBOL:automatic non-striated muscle of fallopian tube OBOL:automatic smooth muscle of fallopian tube OBOL:automatic smooth muscle tissue of fallopian tube OBOL:automatic A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. EMAPA:37708 MA:0000492 involuntary muscle of outflow tract non-striated muscle of outflow tract outflow tract involuntary muscle outflow tract non-striated muscle outflow tract smooth muscle tissue smooth muscle of outflow tract smooth muscle tissue of outflow tract uberon UBERON:0004246 outflow tract smooth muscle A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37708 MA:th involuntary muscle of outflow tract OBOL:automatic non-striated muscle of outflow tract OBOL:automatic outflow tract involuntary muscle OBOL:automatic outflow tract non-striated muscle OBOL:automatic outflow tract smooth muscle tissue OBOL:automatic smooth muscle of outflow tract OBOL:automatic smooth muscle tissue of outflow tract OBOL:automatic A bone that is part of the dorsal region of an animal. this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37248 MA:0000494 uberon back bone bone of back dorsal region bone UBERON:0004247 bone of dorsum A bone that is part of the dorsal region of an animal. http://orcid.org/0000-0002-6601-2165 EMAPA:37248 MA:th back bone MA:0000494 bone of back OBOL:automatic dorsal region bone http://orcid.org/0000-0002-6601-2165 A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37309 MA:0000646 bone of digit of foot digit of foot bone digital bone of foot digital bone of pes digitus pedis bone digitus pedis bone organ foot digit bone foot digit bone organ hind limb digit bone toe bone toe bone organ foot digit bone uberon UBERON:0004248 pedal digit bone A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids. https://orcid.org/0000-0002-6601-2165 EMAPA:37309 MA:th bone of digit of foot OBOL:automatic digit of foot bone OBOL:automatic digitus pedis bone OBOL:automatic digitus pedis bone organ OBOL:automatic foot digit bone MA:0000646 foot digit bone organ OBOL:automatic hind limb digit bone OBOL:accepted toe bone OBOL:automatic toe bone organ OBOL:automatic foot digit bone NCBITaxon:9606 OBOL:accepted A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37305 MA:0000622 digital bone of hand digital bone of manus finger bone fore limb digit bone hand digit bone hand digit bone uberon UBERON:0004249 manual digit bone A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids. https://orcid.org/0000-0002-6601-2165 EMAPA:37305 MA:th finger bone OBOL:automatic fore limb digit bone OBOL:accepted hand digit bone MA:0000622 hand digit bone NCBITaxon:9606 OBOL:accepted A bone that is part of a forelimb stylopod [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35892 MA:0000604 humerus uberon UBERON:0004250 May be merged into humerus. See: https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 upper arm bone A bone that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 humerus https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 A bone that is part of a lower leg [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35519 MA:0000676 bone of hind limb middle limb segment bone of hind limb zeugopod bone of hindlimb middle limb segment bone of hindlimb zeugopod bone of inferior member middle limb segment bone of inferior member zeugopod bone of intermediate segment of free lower limb bone of lower extremity middle limb segment bone of lower extremity zeugopod bone of lower leg bone of middle limb segment of hind limb bone of middle limb segment of hindlimb bone of middle limb segment of inferior member bone of middle limb segment of lower extremity bone of zeugopod of hind limb bone of zeugopod of hindlimb bone of zeugopod of inferior member bone of zeugopod of leg bone of zeugopod of lower extremity bone organ of hind limb middle limb segment bone organ of hind limb zeugopod bone organ of hindlimb middle limb segment bone organ of hindlimb zeugopod bone organ of inferior member middle limb segment bone organ of inferior member zeugopod bone organ of intermediate segment of free lower limb bone organ of lower extremity middle limb segment bone organ of lower extremity zeugopod bone organ of lower leg bone organ of middle limb segment of hind limb bone organ of middle limb segment of hindlimb bone organ of middle limb segment of inferior member bone organ of middle limb segment of lower extremity bone organ of zeugopod of hind limb bone organ of zeugopod of hindlimb bone organ of zeugopod of inferior member bone organ of zeugopod of leg bone organ of zeugopod of lower extremity hind limb middle limb segment bone hind limb middle limb segment bone organ hind limb zeugopod bone hind limb zeugopod bone organ hindlimb middle limb segment bone hindlimb middle limb segment bone organ hindlimb zeugopod bone hindlimb zeugopod bone organ inferior member middle limb segment bone inferior member middle limb segment bone organ inferior member zeugopod bone inferior member zeugopod bone organ intermediate segment of free lower limb bone intermediate segment of free lower limb bone organ lower extremity middle limb segment bone lower extremity middle limb segment bone organ lower extremity zeugopod bone lower extremity zeugopod bone organ lower leg bone middle limb segment of hind limb bone middle limb segment of hind limb bone organ middle limb segment of hindlimb bone middle limb segment of hindlimb bone organ middle limb segment of inferior member bone middle limb segment of inferior member bone organ middle limb segment of lower extremity bone middle limb segment of lower extremity bone organ zeugopod of hind limb bone zeugopod of hind limb bone organ zeugopod of hindlimb bone zeugopod of hindlimb bone organ zeugopod of inferior member bone zeugopod of inferior member bone organ zeugopod of leg bone zeugopod of leg bone organ zeugopod of lower extremity bone zeugopod of lower extremity bone organ uberon UBERON:0004251 hindlimb zeugopod bone A bone that is part of a lower leg [Automatically generated definition]. OBOL:automatic bone of hind limb middle limb segment OBOL:automatic bone of hind limb zeugopod OBOL:automatic bone of hindlimb middle limb segment OBOL:automatic bone of hindlimb zeugopod OBOL:automatic bone of inferior member middle limb segment OBOL:automatic bone of inferior member zeugopod OBOL:automatic bone of intermediate segment of free lower limb OBOL:automatic bone of lower extremity middle limb segment OBOL:automatic bone of lower extremity zeugopod OBOL:automatic bone of lower leg OBOL:automatic bone of middle limb segment of hind limb OBOL:automatic bone of middle limb segment of hindlimb OBOL:automatic bone of middle limb segment of inferior member OBOL:automatic bone of middle limb segment of lower extremity OBOL:automatic bone of zeugopod of hind limb OBOL:automatic bone of zeugopod of hindlimb OBOL:automatic bone of zeugopod of inferior member OBOL:automatic bone of zeugopod of leg OBOL:automatic bone of zeugopod of lower extremity OBOL:automatic bone organ of hind limb middle limb segment OBOL:automatic bone organ of hind limb zeugopod OBOL:automatic bone organ of hindlimb middle limb segment OBOL:automatic bone organ of hindlimb zeugopod OBOL:automatic bone organ of inferior member middle limb segment OBOL:automatic bone organ of inferior member zeugopod OBOL:automatic bone organ of intermediate segment of free lower limb OBOL:automatic bone organ of lower extremity middle limb segment OBOL:automatic bone organ of lower extremity zeugopod OBOL:automatic bone organ of lower leg OBOL:automatic bone organ of middle limb segment of hind limb OBOL:automatic bone organ of middle limb segment of hindlimb OBOL:automatic bone organ of middle limb segment of inferior member OBOL:automatic bone organ of middle limb segment of lower extremity OBOL:automatic bone organ of zeugopod of hind limb OBOL:automatic bone organ of zeugopod of hindlimb OBOL:automatic bone organ of zeugopod of inferior member OBOL:automatic bone organ of zeugopod of leg OBOL:automatic bone organ of zeugopod of lower extremity OBOL:automatic hind limb middle limb segment bone OBOL:automatic hind limb middle limb segment bone organ OBOL:automatic hind limb zeugopod bone OBOL:automatic hind limb zeugopod bone organ OBOL:automatic hindlimb middle limb segment bone OBOL:automatic hindlimb middle limb segment bone organ OBOL:automatic hindlimb zeugopod bone OBOL:automatic hindlimb zeugopod bone organ OBOL:automatic inferior member middle limb segment bone OBOL:automatic inferior member middle limb segment bone organ OBOL:automatic inferior member zeugopod bone OBOL:automatic inferior member zeugopod bone organ OBOL:automatic intermediate segment of free lower limb bone OBOL:automatic intermediate segment of free lower limb bone organ OBOL:automatic lower extremity middle limb segment bone OBOL:automatic lower extremity middle limb segment bone organ OBOL:automatic lower extremity zeugopod bone OBOL:automatic lower extremity zeugopod bone organ OBOL:automatic lower leg bone MA:0000676 middle limb segment of hind limb bone OBOL:automatic middle limb segment of hind limb bone organ OBOL:automatic middle limb segment of hindlimb bone OBOL:automatic middle limb segment of hindlimb bone organ OBOL:automatic middle limb segment of inferior member bone OBOL:automatic middle limb segment of inferior member bone organ OBOL:automatic middle limb segment of lower extremity bone OBOL:automatic middle limb segment of lower extremity bone organ OBOL:automatic zeugopod of hind limb bone OBOL:automatic zeugopod of hind limb bone organ OBOL:automatic zeugopod of hindlimb bone OBOL:automatic zeugopod of hindlimb bone organ OBOL:automatic zeugopod of inferior member bone OBOL:automatic zeugopod of inferior member bone organ OBOL:automatic zeugopod of leg bone OBOL:automatic zeugopod of leg bone organ OBOL:automatic zeugopod of lower extremity bone OBOL:automatic zeugopod of lower extremity bone organ OBOL:automatic Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]. UBERON:0000374 BTO:0001367 EMAPA:19144 FMA:22470 MA:0000684 SCTID:245013005 muscle of thigh thigh muscle upper leg muscle uberon UBERON:0004252 hindlimb stylopod muscle prolog Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]. OBOL:automatic muscle of thigh FMA:22470 thigh muscle FMA:22470 upper leg muscle MA:0000684 Any muscle organ that is part of a skin of body [Automatically generated definition]. review as part of general integumentary system review - part of skin, or more generally, integumental system in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only UBERON:0015797 EMAPA:18187 EMAPA:35776 MA:0002710 MA:0003139 integumental system muscle muscle of integumental system muscle organ of skin skin muscle organ uberon UBERON:0004253 skin muscle Any muscle organ that is part of a skin of body [Automatically generated definition]. OBOL:automatic in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only MA integumental system muscle MA:0003139 muscle of integumental system EMAPA:18187 muscle organ of skin OBOL:automatic skin muscle organ OBOL:automatic Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition]. EMAPA:32622 FMA:37371 MA:0000600 SCTID:181631004 forearm muscle lower arm muscle muscle of forearm wing zeugopod muscle uberon UBERON:0004254 forelimb zeugopod muscle prolog Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition]. OBOL:automatic forearm muscle FMA:37371 lower arm muscle MA:0000600 muscle of forearm FMA:37371 wing zeugopod muscle NCBITaxon:8782 OBOL:automatic Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]. the FMA class 'muscle of arm' belongs here, do not move See notes on UBERON:0001460 for possible terminological confusion over term 'arm' EMAPA:19107 FMA:37370 MA:0000606 SCTID:244979005 muscle of upper arm upper arm muscle wing stylopod muscle uberon muscle of arm skeletal muscle of upper arm UBERON:0004255 forelimb stylopod muscle prolog Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]. OBOL:automatic muscle of upper arm MA:0000606 upper arm muscle MA:0000606 wing stylopod muscle NCBITaxon:8782 OBOL:automatic muscle of arm FMA:37370 skeletal muscle of upper arm EMAPA:19107 Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. the FMA class 'muscle of leg' belongs here, do not move[cjm] See notes on UBERON:0000978 for possible terminological confusion over term 'leg' EMAPA:19318 FMA:22471 MA:0000678 SCTID:265806001 lower leg muscle uberon calf muscle muscle of leg UBERON:0004256 hindlimb zeugopod muscle prolog Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. OBOL:automatic lower leg muscle MA:0000678 calf muscle OBOL:automatic muscle of leg FMA:22471 A blood vessel that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:37299 MA:0000681 blood vessel of stylopod of hind limb blood vessel of stylopod of hindlimb blood vessel of thigh blood vessel of upper leg hind limb stylopod blood vessel hindlimb stylopod blood vessel thigh blood vessel uberon UBERON:0004257 upper leg blood vessel A blood vessel that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37299 MA:th blood vessel of stylopod of hind limb OBOL:automatic blood vessel of stylopod of hindlimb OBOL:automatic blood vessel of thigh OBOL:automatic blood vessel of upper leg OBOL:automatic hind limb stylopod blood vessel OBOL:automatic hindlimb stylopod blood vessel OBOL:automatic thigh blood vessel OBOL:automatic A blood vessel that is part of a back [Automatically generated definition]. EMAPA:37243 MA:0000493 blood vessel of back uberon UBERON:0004258 back blood vessel A blood vessel that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37243 MA:th blood vessel of back OBOL:automatic A blood vessel that is part of a lower arm [Automatically generated definition]. EMAPA:37295 MA:0000597 forelimb zeugopod blood vessel uberon UBERON:0004259 lower arm blood vessel A blood vessel that is part of a lower arm [Automatically generated definition]. OBOL:automatic EMAPA:37295 MA:th forelimb zeugopod blood vessel https://orcid.org/0000-0002-6601-2165 A blood vessel that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:37294 MA:0000603 forelimb stylopod blood vessel uberon UBERON:0004260 upper arm blood vessel A blood vessel that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37294 MA:th forelimb stylopod blood vessel https://orcid.org/0000-0002-6601-2165 A blood vessel that is part of a lower leg [Automatically generated definition]. EMAPA:37300 MA:0000675 hindlimb zeugopod blood vessel uberon UBERON:0004261 lower leg blood vessel A blood vessel that is part of a lower leg [Automatically generated definition]. OBOL:automatic EMAPA:37300 MA:th hindlimb zeugopod blood vessel https://orcid.org/0000-0002-6601-2165 A zone of skin that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:18159 FMA:37790 MA:0000686 SCTID:181547006 hind limb stylopod skin hindlimb stylopod skin skin of upper leg uberon skin of thigh thigh skin UBERON:0004262 upper leg skin A zone of skin that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic hind limb stylopod skin OBOL:automatic hindlimb stylopod skin OBOL:automatic skin of upper leg OBOL:automatic skin of thigh OBOL:automatic thigh skin OBOL:automatic A zone of skin that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:18062 FMA:37721 MA:0000608 SCTID:181531009 arm stylopod skin skin of arm stylopod skin of upper arm uberon UBERON:0004263 upper arm skin A zone of skin that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic arm stylopod skin OBOL:automatic skin of arm stylopod OBOL:automatic skin of upper arm OBOL:automatic A zone of skin that is part of a lower leg [Automatically generated definition]. EMAPA:18156 MA:0000680 SCTID:244180007 hind limb middle limb segment skin hind limb zeugopod skin uberon UBERON:0004264 lower leg skin A zone of skin that is part of a lower leg [Automatically generated definition]. OBOL:automatic hind limb middle limb segment skin OBOL:automatic hind limb zeugopod skin OBOL:automatic A myocardium that is part of a outflow tract [Automatically generated definition]. (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] EHDAA2:0001358 EMAPA:35623 MA:0000489 VHOG:0000603 cardiac muscle of outflow tract heart muscle of outflow tract heart myocardium of outflow tract muscle of heart of outflow tract myocardium of outflow tract outflow tract cardiac muscle outflow tract heart muscle outflow tract heart myocardium outflow tract muscle of heart uberon UBERON:0004265 outflow tract myocardium A myocardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] 2012-09-17 VHOG:0000603 VHOG PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) http://bgee.unil.ch/ cardiac muscle of outflow tract OBOL:automatic heart muscle of outflow tract OBOL:automatic heart myocardium of outflow tract OBOL:automatic muscle of heart of outflow tract OBOL:automatic myocardium of outflow tract OBOL:automatic outflow tract cardiac muscle OBOL:automatic outflow tract heart muscle OBOL:automatic outflow tract heart myocardium OBOL:automatic outflow tract muscle of heart OBOL:automatic A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:37325 MA:0000683 uberon UBERON:0004266 upper leg connective tissue A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37325 MA:th A portion of connective tissue that is part of a back [Automatically generated definition]. EMAPA:37256 MA:0000495 uberon mesenchyne of back UBERON:0004267 back connective tissue A portion of connective tissue that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37256 MA:th mesenchyne of back OBOL:automatic A portion of connective tissue that is part of a lower arm [Automatically generated definition]. EMAPA:37319 MA:0000599 uberon UBERON:0004268 lower arm connective tissue A portion of connective tissue that is part of a lower arm [Automatically generated definition]. OBOL:automatic EMAPA:37319 MA:th A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:37317 MA:0000605 uberon UBERON:0004269 upper arm connective tissue A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37317 MA:th A portion of connective tissue that is part of a lower leg [Automatically generated definition]. EMAPA:37327 MA:0000677 uberon UBERON:0004270 lower leg connective tissue A portion of connective tissue that is part of a lower leg [Automatically generated definition]. OBOL:automatic EMAPA:37327 MA:th A pericardium that is part of a outflow tract [Automatically generated definition]. EMAPA:37707 MA:0000491 pericardium of outflow tract uberon UBERON:0004271 outflow tract pericardium A pericardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37707 MA:th pericardium of outflow tract OBOL:automatic A cranial suture that is part of a cartilaginous joint [Automatically generated definition]. EMAPA:37463 MA:0001498 articulatio cartilaginea cranial suture articulatio cartilaginea cranial sutures articulatio cartilaginea cranial sutures set articulatio cartilaginea cranium suture articulatio cartilaginea suture of cranium cartilaginous joint cranial suture cartilaginous joint cranial sutures cartilaginous joint cranial sutures set cartilaginous joint cranium suture cartilaginous joint suture of cranium cranial suture of articulatio cartilaginea cranial suture of cartilaginous joint cranial sutures of articulatio cartilaginea cranial sutures of cartilaginous joint cranial sutures set of articulatio cartilaginea cranial sutures set of cartilaginous joint cranium suture of articulatio cartilaginea cranium suture of cartilaginous joint suture of cranium of articulatio cartilaginea suture of cranium of cartilaginous joint uberon UBERON:0004273 cartilaginous joint suture A cranial suture that is part of a cartilaginous joint [Automatically generated definition]. OBOL:automatic EMAPA:37463 MA:th articulatio cartilaginea cranial suture OBOL:automatic articulatio cartilaginea cranial sutures OBOL:automatic articulatio cartilaginea cranial sutures set OBOL:automatic articulatio cartilaginea cranium suture OBOL:automatic articulatio cartilaginea suture of cranium OBOL:automatic cartilaginous joint cranial suture OBOL:automatic cartilaginous joint cranial sutures OBOL:automatic cartilaginous joint cranial sutures set OBOL:automatic cartilaginous joint cranium suture OBOL:automatic cartilaginous joint suture of cranium OBOL:automatic cranial suture of articulatio cartilaginea OBOL:automatic cranial suture of cartilaginous joint OBOL:automatic cranial sutures of articulatio cartilaginea OBOL:automatic cranial sutures of cartilaginous joint OBOL:automatic cranial sutures set of articulatio cartilaginea OBOL:automatic cranial sutures set of cartilaginous joint OBOL:automatic cranium suture of articulatio cartilaginea OBOL:automatic cranium suture of cartilaginous joint OBOL:automatic suture of cranium of articulatio cartilaginea OBOL:automatic suture of cranium of cartilaginous joint OBOL:automatic A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]. EHDAA2:0004450 FMA:242815 MA:0000962 NCIT:C49248 UMLS:C1711323 chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle chorioid plexus of cerebral hemisphere epithelium of lateral ventricle choroid plexus epithelial tissue of lateral ventricle choroid plexus epithelium of lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle epithelial tissue of choroid plexus of lateral ventricle epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle epithelium of choroid plexus of lateral ventricle lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue lateral ventricle chorioid plexus of cerebral hemisphere epithelium lateral ventricle choroid plexus epithelial tissue lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere lateral ventricle epithelial tissue of choroid plexus lateral ventricle epithelium of chorioid plexus of cerebral hemisphere lateral ventricle epithelium of choroid plexus uberon UBERON:0004274 lateral ventricle choroid plexus epithelium A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]. OBOL:automatic UMLS:C1711323 ncithesaurus:Choroid_Plexus_Epithelium_of_the_Lateral_Ventricle chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle OBOL:automatic chorioid plexus of cerebral hemisphere epithelium of lateral ventricle OBOL:automatic choroid plexus epithelial tissue of lateral ventricle OBOL:automatic choroid plexus epithelium of lateral ventricle OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic epithelial tissue of choroid plexus of lateral ventricle OBOL:automatic epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic epithelium of choroid plexus of lateral ventricle OBOL:automatic lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue OBOL:automatic lateral ventricle chorioid plexus of cerebral hemisphere epithelium OBOL:automatic lateral ventricle choroid plexus epithelial tissue OBOL:automatic lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic lateral ventricle epithelial tissue of choroid plexus OBOL:automatic lateral ventricle epithelium of chorioid plexus of cerebral hemisphere OBOL:automatic lateral ventricle epithelium of choroid plexus OBOL:automatic A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]. FMA:242823 MA:0000984 NCIT:C49230 UMLS:C1707392 chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle chorioid plexus of cerebral hemisphere epithelium of fourth ventricle choroid plexus epithelial tissue of fourth ventricle choroid plexus epithelium of fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle epithelial tissue of choroid plexus of fourth ventricle epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle epithelium of choroid plexus of fourth ventricle fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue fourth ventricle chorioid plexus of cerebral hemisphere epithelium fourth ventricle choroid plexus epithelial tissue fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere fourth ventricle epithelial tissue of choroid plexus fourth ventricle epithelium of chorioid plexus of cerebral hemisphere fourth ventricle epithelium of choroid plexus uberon UBERON:0004276 fourth ventricle choroid plexus epithelium A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]. OBOL:automatic UMLS:C1707392 ncithesaurus:Choroid_Plexus_Epithelium_of_the_Fourth_Ventricle chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle OBOL:automatic chorioid plexus of cerebral hemisphere epithelium of fourth ventricle OBOL:automatic choroid plexus epithelial tissue of fourth ventricle OBOL:automatic choroid plexus epithelium of fourth ventricle OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic epithelial tissue of choroid plexus of fourth ventricle OBOL:automatic epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic epithelium of choroid plexus of fourth ventricle OBOL:automatic fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue OBOL:automatic fourth ventricle chorioid plexus of cerebral hemisphere epithelium OBOL:automatic fourth ventricle choroid plexus epithelial tissue OBOL:automatic fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic fourth ventricle epithelial tissue of choroid plexus OBOL:automatic fourth ventricle epithelium of chorioid plexus of cerebral hemisphere OBOL:automatic fourth ventricle epithelium of choroid plexus OBOL:automatic A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 uberon UBERON:0004277 eye muscle MA A muscle that is part of the eye region. OBOL:automatic Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 SCTID:361378004 VSAO:0000026 Wikipedia:Skeleton XAO:0004053 galen:Skeleton set of all bones set of bones of body uberon UBERON:0004288 skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] 2012-08-14 VSAO:0000026 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] Portion of somites that gives rise to dermis and muscles.[AAO] all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 FMA:295654 NCIT:C34140 TAO:0001513 UMLS:C1511786 VHOG:0000676 ZFA:0001513 uberon dermamyotome dermomyotomes UBERON:0004290 dermomyotome AEO AEO EHDAA2 ZFA The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] 2012-08-14 TAO:0001513 TAO ZFIN:curator Portion of somites that gives rise to dermis and muscles.[AAO] 2012-06-20 AAO:0010572 AAO AAO:EJS all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. http://medical-dictionary.thefreedictionary.com/dermomyotome Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] 2012-09-17 VHOG:0000676 VHOG DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) http://bgee.unil.ch/ UMLS:C1511786 ncithesaurus:Dermomyotome dermamyotome VHOG:0000676 dermomyotomes VHOG:0000676 A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone rudimentary heart uberon UBERON:0004291 heart rudiment A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] 2012-08-14 TAO:0000115 TAO ZFIN:curator heart cone GO:0003313 rudimentary heart ZFA:0000115 Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP] EMAPA:36645 FMA:9496 Wikipedia:Cardiac_skeleton cardiac fibrous skeleton fibrous skeleton of heart heart fibrous skeleton skeleton of heart uberon anulus fibrosus dexter cordis anulus fibrosus sinister cordis trigona fibrosa trigonum fibrosum dextrum cordis trigonum fibrosum sinistrum cordis UBERON:0004292 cardiac skeleton http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. GO:0003204 Wikipedia:Cardiac_skeleton cardiac fibrous skeleton EMAPA:36645 heart fibrous skeleton GO:0003204 skeleton of heart FMA:9496 anulus fibrosus dexter cordis Wikipedia:Cardiac_skeleton anulus fibrosus sinister cordis Wikipedia:Cardiac_skeleton trigona fibrosa Wikipedia:Cardiac_skeleton trigonum fibrosum dextrum cordis Wikipedia:Cardiac_skeleton trigonum fibrosum sinistrum cordis Wikipedia:Cardiac_skeleton A nerve that is part of a parasympathetic nervous system [Automatically generated definition]. EHDAA2:0001401 EMAPA:17271 MA:0000224 SCTID:276146002 VHOG:0000641 nerve of parasympathetic nervous system uberon UBERON:0004293 parasympathetic nerve NCBIBook:NBK10065 NCBIBook:NBK10065 A nerve that is part of a parasympathetic nervous system [Automatically generated definition]. OBOL:automatic nerve of parasympathetic nervous system OBOL:automatic An endothelium that is part of a glomerular capillary. MA:0001658 NCIT:C32522 SCTID:243993006 UMLS:C0227647 renal glomerulus capillary endothelium uberon UBERON:0004294 glomerular capillary endothelium An endothelium that is part of a glomerular capillary. OBOL:automatic UMLS:C0227647 ncithesaurus:Endothelium_of_the_Glomerular_Capillary renal glomerulus capillary endothelium OBOL:automatic A nerve trunk that is part of a sympathetic nervous system [Automatically generated definition]. EHDAA2:0001970 EMAPA:35845 MA:0000227 nerve trunk of sympathetic nervous system nerve trunk of sympathetic part of autonomic division of nervous system sympathetic nervous system nerve trunk uberon UBERON:0004295 sympathetic nerve trunk A nerve trunk that is part of a sympathetic nervous system [Automatically generated definition]. OBOL:automatic nerve trunk of sympathetic nervous system OBOL:automatic nerve trunk of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system nerve trunk OBOL:automatic A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37582 MA:0001826 smooth muscle of lymph vessel of respiratory system uberon UBERON:0004296 respiratory system lymphatic vessel smooth muscle A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37582 MA:th smooth muscle of lymph vessel of respiratory system OBOL:automatic A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37573 MA:0001806 smooth muscle tissue of blood vessel of respiratory system uberon UBERON:0004297 respiratory system blood vessel smooth muscle A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37573 MA:th smooth muscle tissue of blood vessel of respiratory system OBOL:automatic Distal-most phalanx within a digit. In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans. AAO:0010676 EMAPA:35287 MA:0002914 SCTID:299711006 Wikipedia:Distal_phalanges phalanx distalis terminal phalanx ungual phalanx uberon phalanx distalis UBERON:0004300 distal phalanx http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg Distal-most phalanx within a digit. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/120 phalanx distalis Wikipedia:Distal_phalanges terminal phalanx AAO:0010676 ungual phalanx http://www.medilexicon.com/medicaldictionary.php?t=67679 phalanx distalis Wikipedia:Distal_phalanges A phalanx located between proximal and distal phalanges. consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin in some groups such as whales, there are multiple intermediate phalanges AAO:0010677 EMAPA:35572 MA:0002915 SCTID:299710007 Wikipedia:Intermediate_phalanges intermediate phalanx uberon medial phalanx penultimate phalanx phalanx 2 phalanx II UBERON:0004301 middle phalanx A phalanx located between proximal and distal phalanges. http://orcid.org/0000-0002-6601-2165 Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin WP penultimate phalanx AAO:0010677 Proximal-most phalanx within a digit. Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone) 1 AAO:0010680 EMAPA:35716 MA:0002916 SCTID:299708005 Wikipedia:Proximal_phalanges phalanx 1 phalanx I proximal-most phalanx uberon UBERON:0004302 proximal phalanx Proximal-most phalanx within a digit. http://orcid.org/0000-0002-6601-2165 Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone) WP proximal-most phalanx AAO:0010680 A distal phalanx that is part of a hand digit 5 [Automatically generated definition]. FMA:23949 SCTID:361790004 5th digit of hand distal phalanx 5th finger distal phalanx distal phalanx of 5th digit of hand distal phalanx of 5th finger distal phalanx of fifth digit of hand distal phalanx of fifth finger distal phalanx of little finger distal phalanx of manual digit V fifth distal phalanx of hand fifth finger distal phalanx hand digit 5 distal phalanx uberon UBERON:0004314 distal phalanx of manual digit 5 A distal phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic 5th digit of hand distal phalanx OBOL:automatic 5th finger distal phalanx OBOL:automatic distal phalanx of 5th digit of hand OBOL:automatic distal phalanx of 5th finger OBOL:automatic distal phalanx of fifth digit of hand FMA:23949 distal phalanx of fifth finger OBOL:automatic distal phalanx of little finger FMA:23949 distal phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 fifth distal phalanx of hand FMA:23949 fifth finger distal phalanx OBOL:automatic hand digit 5 distal phalanx OBOL:automatic A distal phalanx that is part of a foot digit 1 [Automatically generated definition]. FMA:32627 SCTID:361799003 distal phalanx of big toe distal phalanx of first digit of foot distal phalanx of foot digit 1 distal phalanx of great toe distal phalanx of hallux distal phalanx of pedal digit I first distal phalanx of foot foot digit 1 distal phalanx hallux distal phalanx uberon UBERON:0004315 distal phalanx of pedal digit 1 A distal phalanx that is part of a foot digit 1 [Automatically generated definition]. OBOL:automatic distal phalanx of big toe FMA:32627 distal phalanx of first digit of foot FMA:32627 distal phalanx of foot digit 1 OBOL:automatic distal phalanx of great toe FMA:32627 distal phalanx of hallux OBOL:automatic distal phalanx of pedal digit I https://github.com/obophenotype/uberon/issues/458 first distal phalanx of foot FMA:32627 foot digit 1 distal phalanx OBOL:automatic hallux distal phalanx OBOL:automatic A distal phalanx that is part of a foot digit 5 [Automatically generated definition]. FMA:32631 SCTID:10770001 SCTID:244674003 5th toe distal phalanx distal phalanx of 5th toe distal phalanx of fifth digit of foot distal phalanx of fifth toe distal phalanx of foot digit 5 distal phalanx of little toe distal phalanx of pedal digit V distal phalanx of the 5th toe fifth distal phalanx of foot foot digit 5 distal phalanx uberon UBERON:0004319 distal phalanx of pedal digit 5 A distal phalanx that is part of a foot digit 5 [Automatically generated definition]. OBOL:automatic 5th toe distal phalanx OBOL:automatic distal phalanx of 5th toe OBOL:automatic distal phalanx of fifth digit of foot FMA:32631 distal phalanx of fifth toe FMA:32631 distal phalanx of foot digit 5 OBOL:automatic distal phalanx of little toe FMA:32631 distal phalanx of pedal digit V https://github.com/obophenotype/uberon/issues/458 distal phalanx of the 5th toe OBOL:automatic fifth distal phalanx of foot FMA:32631 foot digit 5 distal phalanx OBOL:automatic A middle phalanx that is part of a hand digit 5 [Automatically generated definition]. FMA:23936 SCTID:263410009 5th digit of hand intermediate phalanx 5th digit of hand middle phalanx 5th finger intermediate phalanx 5th finger middle phalanx fifth finger intermediate phalanx fifth finger middle phalanx fifth middle phalanx of hand hand digit 5 intermediate phalanx hand digit 5 middle phalanx intermediate phalanx of 5th digit of hand intermediate phalanx of 5th finger intermediate phalanx of fifth finger intermediate phalanx of hand digit 5 middle phalanx of 5th digit of hand middle phalanx of 5th finger middle phalanx of fifth digit of hand middle phalanx of fifth finger middle phalanx of little finger middle phalanx of manual digit V uberon UBERON:0004323 middle phalanx of manual digit 5 A middle phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic 5th digit of hand intermediate phalanx OBOL:automatic 5th digit of hand middle phalanx OBOL:automatic 5th finger intermediate phalanx OBOL:automatic 5th finger middle phalanx OBOL:automatic fifth finger intermediate phalanx OBOL:automatic fifth finger middle phalanx OBOL:automatic fifth middle phalanx of hand FMA:23936 hand digit 5 intermediate phalanx OBOL:automatic hand digit 5 middle phalanx OBOL:automatic intermediate phalanx of 5th digit of hand OBOL:automatic intermediate phalanx of 5th finger OBOL:automatic intermediate phalanx of fifth finger OBOL:automatic intermediate phalanx of hand digit 5 OBOL:automatic middle phalanx of 5th digit of hand OBOL:automatic middle phalanx of 5th finger OBOL:automatic middle phalanx of fifth digit of hand FMA:23936 middle phalanx of fifth finger OBOL:automatic middle phalanx of little finger OBOL:automatic middle phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 A middle phalanx that is part of a pedal digit 5 [Automatically generated definition]. FMA:230984 SCTID:182158005 SCTID:244673009 5th toe intermediate phalanx 5th toe middle phalanx foot digit 5 intermediate phalanx foot digit 5 middle phalanx intermediate phalanx of 5th toe intermediate phalanx of foot digit 5 middle phalanx of 5th toe middle phalanx of foot digit 5 middle phalanx of little toe middle phalanx of pedal digit V middle phalanx of the 5th toe uberon UBERON:0004327 middle phalanx of pedal digit 5 A middle phalanx that is part of a pedal digit 5 [Automatically generated definition]. OBOL:automatic 5th toe intermediate phalanx OBOL:automatic 5th toe middle phalanx OBOL:automatic foot digit 5 intermediate phalanx OBOL:automatic foot digit 5 middle phalanx OBOL:automatic intermediate phalanx of 5th toe OBOL:automatic intermediate phalanx of foot digit 5 OBOL:automatic middle phalanx of 5th toe OBOL:automatic middle phalanx of foot digit 5 OBOL:automatic middle phalanx of little toe OBOL:automatic middle phalanx of pedal digit V https://github.com/obophenotype/uberon/issues/458 middle phalanx of the 5th toe OBOL:automatic A proximal phalanx that is part of a hand digit 5 [Automatically generated definition]. FMA:23922 SCTID:263406006 5th digit of hand proximal phalanx 5th finger proximal phalanx fifth finger proximal phalanx fifth proximal phalanx of hand hand digit 5 proximal phalanx manual digit 5 proximal phalanx manual phalanx V-1 proximal phalanx of 5th digit of hand proximal phalanx of 5th finger proximal phalanx of fifth digit of hand proximal phalanx of fifth finger proximal phalanx of little finger proximal phalanx of manual digit V uberon UBERON:0004331 proximal phalanx of manual digit 5 A proximal phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic 5th digit of hand proximal phalanx OBOL:automatic 5th finger proximal phalanx OBOL:automatic fifth finger proximal phalanx OBOL:automatic fifth proximal phalanx of hand FMA:23922 hand digit 5 proximal phalanx OBOL:automatic manual digit 5 proximal phalanx PHENOSCAPE:wd manual phalanx V-1 PHENOSCAPE:wd proximal phalanx of 5th digit of hand OBOL:automatic proximal phalanx of 5th finger OBOL:automatic proximal phalanx of fifth digit of hand FMA:23922 proximal phalanx of fifth finger OBOL:automatic proximal phalanx of little finger FMA:23922 proximal phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 A proximal phalanx that is part of a pedal digit 1 [Automatically generated definition]. FMA:43252 SCTID:182150003 foot digit 1 proximal phalanx hallux proximal phalanx pedal phalanx I-1 predal digit 1 proximal phalanx proximal phalanx of big toe proximal phalanx of foot digit 1 proximal phalanx of great toe proximal phalanx of hallux proximal phalanx of pedal digit I proximal phalanx of the 1st toe uberon UBERON:0004332 proximal phalanx of pedal digit 1 A proximal phalanx that is part of a pedal digit 1 [Automatically generated definition]. OBOL:automatic foot digit 1 proximal phalanx OBOL:automatic hallux proximal phalanx OBOL:automatic pedal phalanx I-1 PHENOSCAPE:wd predal digit 1 proximal phalanx PHENOSCAPE:wd proximal phalanx of big toe FMA:43252 proximal phalanx of foot digit 1 OBOL:automatic proximal phalanx of great toe FMA:43252 proximal phalanx of hallux OBOL:automatic proximal phalanx of pedal digit I https://github.com/obophenotype/uberon/issues/458 A proximal phalanx that is part of a pedal digit 5 [Automatically generated definition]. FMA:32621 SCTID:182157000 SCTID:244672004 5th toe proximal phalanx fifth proximal phalanx of foot foot digit 5 proximal phalanx pedal phalanx V-1 predal digit 5 proximal phalanx proximal phalanx of 5th toe proximal phalanx of fifth digit of foot proximal phalanx of fifth toe proximal phalanx of foot digit 5 proximal phalanx of little toe proximal phalanx of pedal digit V proximal phalanx of the 5th toe uberon UBERON:0004336 proximal phalanx of pedal digit 5 A proximal phalanx that is part of a pedal digit 5 [Automatically generated definition]. OBOL:automatic 5th toe proximal phalanx OBOL:automatic fifth proximal phalanx of foot FMA:32621 foot digit 5 proximal phalanx OBOL:automatic pedal phalanx V-1 PHENOSCAPE:wd predal digit 5 proximal phalanx PHENOSCAPE:wd proximal phalanx of 5th toe OBOL:automatic proximal phalanx of fifth digit of foot FMA:32621 proximal phalanx of fifth toe FMA:32621 proximal phalanx of foot digit 5 OBOL:automatic proximal phalanx of little toe OBOL:automatic proximal phalanx of pedal digit V https://github.com/obophenotype/uberon/issues/458 A distal phalanx that is part of a hand digit 1 [Automatically generated definition]. The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects. FMA:23945 SCTID:182007006 PDP distal phalanx of first digit of hand distal phalanx of manual digit I distal phalanx of thumb first distal phalanx of hand manual digit 1 distal phalanx pollical distal phalanx thumb distal phalanx uberon UBERON:0004337 distal phalanx of manual digit 1 A distal phalanx that is part of a hand digit 1 [Automatically generated definition]. OBOL:automatic The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects. WP PDP Wikipedia:Distal_phalanges#Thumb distal phalanx of first digit of hand FMA:23945 distal phalanx of manual digit I https://github.com/obophenotype/uberon/issues/458 distal phalanx of thumb OBOL:automatic first distal phalanx of hand FMA:23945 manual digit 1 distal phalanx PHENOSCAPE:wd pollical distal phalanx Wikipedia:Distal_phalanges#Thumb thumb distal phalanx OBOL:automatic A proximal phalanx that is part of a hand digit 1 [Automatically generated definition]. FMA:23918 SCTID:181992006 first proximal phalanx of hand manual digit 1 proximal phalanx manual phalanx I-1 proximal phalanx of first digit of hand proximal phalanx of manual digit I proximal phalanx of thumb thumb proximal uberon UBERON:0004338 proximal phalanx of manual digit 1 A proximal phalanx that is part of a hand digit 1 [Automatically generated definition]. OBOL:automatic first proximal phalanx of hand FMA:23918 manual digit 1 proximal phalanx PHENOSCAPE:wd manual phalanx I-1 PHENOSCAPE:wd proximal phalanx of first digit of hand FMA:23918 proximal phalanx of manual digit I https://github.com/obophenotype/uberon/issues/458 proximal phalanx of thumb OBOL:automatic thumb proximal OBOL:automatic Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid. We follow http://www.ncbi.nlm.nih.gov/pubmed/11523816 (Morriss-Kay) in definingenumerating the components of the skull vault. Note that there is a conflict with Kardong; e.g. in fig 7.10, Kardong places the squamosal in the temporal series. We cannot place the vault as entirely part of the dermatocranium as it has a small splanchnocranium contribution and a sclerotomal contribution The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium.[well established][VHOG] EHDAA2:0002167 EHDAA:9538 EMAPA:18016 FMA:52800 NCIT:C81188 SCTID:140592008 UMLS:C0205950 VHOG:0000331 Wikipedia:Calvaria_(skull) ZFA:0005606 calva cranial vault skull vault skull roof uberon calvaria calvarium skullcap UBERON:0004339 Terminology notes. we include calvarium as a synonym, but Gray's Anatomy's list includes the Ethmoid and Sphenoid bone in the Calvaria. Some books (and HPO) state that calvaria consists of just the frontal bone, parietal bone, temporal bone, and occipital bone. Note vault may not be precisely equivalent to calvaria vault of skull small pharyngeal arch and sclerotomal contribution Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid. MP:0000076 PMID:11523816 Wikipedia:Calvaria_(skull) The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium.[well established][VHOG] 2012-09-17 VHOG:0000331 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256 http://bgee.unil.ch/ UMLS:C0205950 ncithesaurus:Skullcap calva FMA:52800 cranial vault ZFA:0005606 calvaria ZFA:0005606 skullcap ZFA:0005606 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG] Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] allantoic a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)] part_of embryo in EHDAA2 - note differences in humans BTO:0000474 EHDAA2:0001504 EMAPA:16107 EMAPA_RETIRED:16084 MESH:D000482 NCIT:C34101 RETIRED_EHDAA2:0000114 SCTID:308825007 UMLS:C0002084 VHOG:0000738 Wikipedia:Allantois uberon allantoic bud UBERON:0004340 allantois http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png EHDAA2-modified Hymans Hymans hindgut diverticulum endoderm ISBN:0073040584 ISBN:0073040584 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. VHOG:0000738 Wikipedia:Allantois A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG] 2012-09-17 VHOG:0000738 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/allantois Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000738 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 http://bgee.unil.ch/ part_of embryo in EHDAA2 - note differences in humans EHDAA2 UMLS:C0002084 ncithesaurus:Allantois allantoic bud EMAPA:16107 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]. (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 MESH:D054240 NCIT:C28402 SCTID:361438007 UMLS:C0033153 VHOG:0001202 Wikipedia:Primitive_streak primitive streak - blastopore - germ ring uberon UBERON:0004341 primitive streak http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png EHDAA2 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]. MP:0002231 Wikipedia:Primitive_streak (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001202 VHOG PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 http://bgee.unil.ch/ VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 VHOG MESH:D054240 https://github.com/biopragmatics/biomappings UMLS:C0033153 ncithesaurus:Primitive_Streak primitive streak - blastopore - germ ring VHOG:0001202 Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition. distinction between trophectoderm and trophoblast unclear/inconsistent in many sources The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] trophectodermal BTO has this has part of the trophoblast BTO:0001840 EHDAA2:0002091 EHDAA:56 EMAPA:16046 VHOG:0000979 uberon UBERON:0004345 trophectoderm EHDAA2 EHDAA2 EHDAA2 Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition. MP:0005028 The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0000979 VHOG http://bgee.unil.ch/ (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000979 VHOG ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106 http://bgee.unil.ch/ BTO has this has part of the trophoblast BTO An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. Early outgrowth of presumptive limb.[AAO] AAO:0010375 BTO:0001640 EMAPA:35944 FMA:296780 GAID:1307 MESH:D018878 NCIT:C34203 UMLS:C0282505 Wikipedia:Limb_bud XAO:0003161 limb buds limbbud uberon gemmae membrorum UBERON:0004347 developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm limb bud ISBN:9780878932504 An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 Wikipedia:Limb_bud https://orcid.org/0000-0002-6601-2165 Early outgrowth of presumptive limb.[AAO] 2012-06-20 AAO:0010375 AAO AAO:EJS UMLS:C0282505 ncithesaurus:Limb_Bud limb buds limbbud GO:0060174 gemmae membrorum Wikipedia:Limb_bud The embryonic structure that gives rise to the corneal ectoderm. EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 VHOG:0001296 uberon UBERON:0004348 optic eminence The embryonic structure that gives rise to the corneal ectoderm. MP:0006305 Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] Proliferative region that is part of the developing fin fold or fin.[TAO] relationship loss: subclass proliferative region (TAO:0000098)[TAO] The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop AAO:0010760 EMAPA:32744 NCIT:C34109 TAO:0002146 UMLS:C1516037 Wikipedia:Apical_ectodermal_ridge XAO:0004121 ZFA:0001702 apical epidermal ridge uberon AER crista ectodermalis apicalis UBERON:0004356 apical ectodermal ridge http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. MP:0001676 Wikipedia:Apical_ectodermal_ridge Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] 2012-06-20 AAO:0010760 AAO AAO:EJS Proliferative region that is part of the developing fin fold or fin.[TAO] 2012-08-14 TAO:0002146 TAO ZFIN:curator relationship loss: subclass proliferative region (TAO:0000098)[TAO] 2012-08-14 TAO:0002146 TAO The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold PMID:20574421 UMLS:C1516037 ncithesaurus:Apical_Ectodermal_Ridge apical epidermal ridge XAO:0004121 AER MP:0001676 crista ectodermalis apicalis Wikipedia:Apical_ectodermal_ridge An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon UBERON:0004357 Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 https://orcid.org/0000-0002-6601-2165 The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] 2012-09-17 VHOG:0001258 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) http://bgee.unil.ch/ limb - fin bud VHOG:0001258 paired limb/fin bud VHOG:0001258 The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries. The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 1 AAO:0010364 CALOHA:TS-2089 EHDAA2:0000006 EHDAA:573 EMAPA:16118 FMA:293019 MFMO:0000095 NCIT:C34175 SCTID:308767008 TAO:0001595 UMLS:C1517197 VHOG:0000296 Wikipedia:First_pharyngeal_arch XAO:0000097 ZFA:0001612 1st pharyngeal arch branchial arch 1 first branchial arch first pharyngeal arch first visceral arch mandibular arch visceral arch 1 uberon 1st arch 1st visceral arch arcus pharyngeus primus UBERON:0004362 pharyngeal arch 1 http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries. http://orcid.org/0000-0002-6601-2165 The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010364 AAO XAO:EJS the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery MP:0006337,MGI:smb A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000296 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ UMLS:C1517197 ncithesaurus:First_Pharyngeal_Arch branchial arch 1 first branchial arch first visceral arch visceral arch 1 1st arch EHDAA2:0000006 1st visceral arch VHOG:0000296 arcus pharyngeus primus Wikipedia:First_pharyngeal_arch One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]. add specific artery derivatives Do not confuse with arch of aorta. Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches UBERON:0004342 AAO:0010414 EFO:0003695 EHDAA2:0000186 EHDAA:398 EHDAA:7327 EMAPA:16684 NCIT:C32123 TAO:0005004 UMLS:C0003489 VHOG:0000122 Wikipedia:Aortic_arches XAO:0000341 ZFA:0005004 PAA aortic arch aortic arches branchial aortic arches branchial arch artery embryonic aortic arch artery pharyngeal arch artery uberon a. arcuum pharyngeorum aortic arch artery arteriae arcuum pharyngeorum branchial aortic arches pharyngeal arch arteries pharyngeal arch artery UBERON:0004363 pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png ZFA One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]. MP:0002672 Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] 2012-09-17 VHOG:0000122 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/aortic+arches When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000122 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0003489 ncithesaurus:Aortic_Arch PAA MP:0002672 aortic arch ZFA:0005004 aortic arches ZFA:0005004 branchial aortic arches ZFIN:ZDB-PUB-080512-6 branchial arch artery EMAPA:16684 embryonic aortic arch artery EMAPA:16684 MP:0002672 pharyngeal arch artery MP:0002672 a. arcuum pharyngeorum Wikipedia:Aortic_arches aortic arch artery EMAPA:16684 arteriae arcuum pharyngeorum Wikipedia:Aortic_arches branchial aortic arches ZFA:0005004 ZFIN:ZDB-PUB-080512-6 pharyngeal arch arteries pharyngeal arch artery VHOG:0000122 Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta. derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast. BTO:0001715 EMAPA:16059 epamniotic cone placenta - ectoplacental cone uberon UBERON:0004364 ectoplacental cone Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta. MP:0001717 PMID:19829370 derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast. PMID:19829370 Blood vessel that is connected to the yolk sac. EMAPA:36494 uberon UBERON:0004365 vitelline blood vessel Blood vessel that is connected to the yolk sac. http://orcid.org/0000-0002-6601-2165 A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] EMAPA:18804 FMA:58309 GAID:894 MA:0001246 MESH:D003886 NCIT:C32454 SCTID:281076002 TAO:0002157 UMLS:C0011665 Wikipedia:Descemet%27s_membrane ZFA:0001686 Descemet membrane Descemet's posterior elastic lamina lamina limitans posterior lamina limitans posterior corneae posterior limiting lamina posterior limiting lamina of cornea posterior limiting membrane uberon UBERON:0004367 The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed) Descemet's membrane https://github.com/obophenotype/uberon/issues/15 Cline et al lexical A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. MP:0004285 https://github.com/obophenotype/uberon/issues/15 Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] 2016-05-01 TAO:0002157 ZFIN ZFIN:ZDB-PUB-061010-3 https://orcid.org/0000-0001-9114-8737 UMLS:C0011665 ncithesaurus:Descemet_s_Membrane Descemet's posterior elastic lamina FMA:58309 lamina limitans posterior FMA:58309 lamina limitans posterior corneae FMA:58309 FMA:TA posterior limiting lamina MA:0001246 posterior limiting lamina of cornea FMA:58309 posterior limiting membrane ZFA:0001686 A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 SCTID:281075003 TAO:0002155 UMLS:C0229127 Wikipedia:Bowman%27s_membrane ZFA:0001684 Bowman's anterior elastic lamina Bowman's layer Bowman's membrane anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea lamina limitans anterior (cornea) lamina limitans anterior corneae uberon Reichert's membrane anterior limiting membrane UBERON:0004370 anterior limiting lamina of cornea A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] 2012-08-14 TAO:0002155 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0229127 ncithesaurus:Bowman_s_Membrane Bowman's anterior elastic lamina FMA:58273 Bowman's layer FMA:58273 Bowman's membrane FMA:58273 anterior elastic lamina ZFA:0001684 anterior limiting lamina MA:0001240 anterior limiting lamina of cornea FMA:58273 lamina limitans anterior (cornea) FMA:58273 lamina limitans anterior corneae FMA:58273 FMA:TA Reichert's membrane http://sourceforge.net/tracker/?func=detail&aid=2956371&group_id=76834&atid=974957 anterior limiting membrane ZFA:0001684 Vascular network that is connected to the yolk sac. Wikipedia:Vitelline_circulation uberon omphalomesenteric system vitelline bloos vessel system vitelline system UBERON:0004374 vitelline vasculature Vascular network that is connected to the yolk sac. http://orcid.org/0000-0002-6601-2165 omphalomesenteric system https://orcid.org/0000-0002-6601-2165 vitelline bloos vessel system https://orcid.org/0000-0002-6601-2165 vitelline system https://orcid.org/0000-0002-6601-2165 A bone that is part of an appendage [Automatically generated definition]. appendage bone bone of appendage bone of free segment of appendicular skeleton uberon UBERON:0004375 bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. OBOL:automatic A metaphysis that is in the proximal side of a diaphysis. FMA:32823 proximal diaphyseal end of long bone uberon UBERON:0004378 proximal metaphysis A metaphysis that is in the proximal side of a diaphysis. OBOL:automatic proximal diaphyseal end of long bone FMA:32823 An epiphysis that is on the proximal side of the bone. FMA:32821 SCTID:279998003 proximal end of long bone uberon UBERON:0004380 proximal epiphysis An epiphysis that is on the proximal side of the bone. http://orcid.org/0000-0002-6601-2165 proximal end of long bone FMA:32821 The collection of all skeletal elements in an individual limb. Skeletal subdivision that is part of the limb.[VSAO] EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2:0002221 EMAPA:32702 VSAO:0000300 free limb skeleton limb skeleton set of bones of limb uberon UBERON:0004381 skeleton of limb The collection of all skeletal elements in an individual limb. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the limb.[VSAO] 2012-08-14 VSAO:0000300 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2 free limb skeleton VSAO:0000300 limb skeleton EHDAA2:0002221 An epiphysis that is part of a humerus [Automatically generated definition]. FMA:32825 SCTID:313054009 humeral epiphysis uberon UBERON:0004382 epiphysis of humerus An epiphysis that is part of a humerus [Automatically generated definition]. OBOL:automatic humeral epiphysis OBOL:automatic An epiphysis that is part of a tibia [Automatically generated definition]. EMAPA:37771 FMA:33112 MA:0003113 SCTID:314626006 tibial epiphysis uberon UBERON:0004383 epiphysis of tibia An epiphysis that is part of a tibia [Automatically generated definition]. OBOL:automatic EMAPA:37771 MA:th tibial epiphysis FMA:33112 An epiphysis that is part of a femur [Automatically generated definition]. EMAPA:37539 FMA:32838 MA:0003056 SCTID:314625005 femoral epiphysis uberon UBERON:0004384 epiphysis of femur An epiphysis that is part of a femur [Automatically generated definition]. OBOL:automatic EMAPA:37539 MA:th femoral epiphysis FMA:32838 An epiphysis that is part of a phalanx of a manus [Automatically generated definition]. FMA:240707 SCTID:314620000 epiphysis of phalanx of finger uberon epiphysis of phalanx of hand UBERON:0004387 epiphysis of phalanx of manus An epiphysis that is part of a phalanx of a manus [Automatically generated definition]. OBOL:automatic epiphysis of phalanx of hand FMA:240707 An epiphysis that is part of a fibula [Automatically generated definition]. FMA:33726 fibula epiphysis uberon UBERON:0004388 epiphysis of fibula An epiphysis that is part of a fibula [Automatically generated definition]. OBOL:automatic fibula epiphysis FMA:33726 An epiphysis that is part of a metatarsal bone [Automatically generated definition]. FMA:33814 SCTID:313057002 epiphysis of metatarsal metatarsal bone epiphysis metatarsal epiphysis uberon UBERON:0004389 epiphysis of metatarsal bone An epiphysis that is part of a metatarsal bone [Automatically generated definition]. OBOL:automatic metatarsal bone epiphysis FMA:33814 An epiphysis that is part of a metacarpal bone [Automatically generated definition]. FMA:33792 SCTID:314907001 epiphysis of metacarpal metacarpal bone epiphysis metacarpal epiphysis uberon UBERON:0004390 epiphysis of metacarpal bone An epiphysis that is part of a metacarpal bone [Automatically generated definition]. OBOL:automatic metacarpal bone epiphysis FMA:33792 An epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. FMA:33793 first metacarpal bone epiphysis metacarpal 1 epiphysis uberon UBERON:0004391 epiphysis of first metacarpal bone An epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. OBOL:automatic first metacarpal bone epiphysis FMA:33793 An epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. FMA:33815 first metatarsal bone epiphysis metatarsal 1 epiphysis uberon UBERON:0004395 epiphysis of first metatarsal bone An epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. OBOL:automatic first metatarsal bone epiphysis FMA:33815 An epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. FMA:86315 fifth metatarsal bone epiphysis metatarsal 5 epiphysis uberon UBERON:0004399 epiphysis of fifth metatarsal bone An epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. OBOL:automatic fifth metatarsal bone epiphysis FMA:86315 A portion of bone tissue that is part of a epiphysis [Automatically generated definition]. FMA:241364 uberon UBERON:0004400 bone tissue of epiphysis A portion of bone tissue that is part of a epiphysis [Automatically generated definition]. OBOL:automatic A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition]. FMA:241372 uberon UBERON:0004402 bone tissue of proximal epiphysis A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition]. OBOL:automatic The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles. FMA:23362 SCTID:280028008 Wikipedia:Upper_extremity_of_humerus proximal end of humerus proximal humeral epiphysis upper end of humerus uberon head of the humerus humeral head proximal humerus upper extremity of humerus UBERON:0004411 proximal epiphysis of humerus http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles. Wikipedia:Upper_extremity_of_humerus proximal end of humerus FMA:23362 proximal humeral epiphysis OBOL:automatic https://orcid.org/0000-0002-6601-2165 upper end of humerus FMA:23362 head of the humerus Wikipedia:Upper_extremity_of_humerus humeral head Wikipedia:Upper_extremity_of_humerus proximal humerus Wikipedia:Upper_extremity_of_humerus upper extremity of humerus Wikipedia:Upper_extremity_of_humerus A proximal epiphysis that is part of a femur [Automatically generated definition]. FMA:32841 SCTID:244702009 proximal femoral epiphysis uberon capital femoral epiphysis UBERON:0004412 proximal epiphysis of femur A proximal epiphysis that is part of a femur [Automatically generated definition]. OBOL:automatic proximal femoral epiphysis OBOL:automatic https://orcid.org/0000-0002-6601-2165 capital femoral epiphysis http://orcid.org/0000-0002-6601-2165 A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition]. FMA:226482 SCTID:272704004 basal epiphysis of phalanx of finger base of phalanx of finger basis phalangis manus proximal epiphysis of phalanx of finger uberon proximal epiphysis of phalanx of hand UBERON:0004414 proximal epiphysis of phalanx of manus A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition]. OBOL:automatic basal epiphysis of phalanx of finger FMA:226482 base of phalanx of finger FMA:226482 basis phalangis manus FMA:226482 FMA:TA proximal epiphysis of phalanx of hand FMA:226482 A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition]. FMA:33817 SCTID:119545008 base of metatarsal bone basis ossis metatarsi proximal end of metatarsal bone upper end of metatarsal bone uberon UBERON:0004415 proximal epiphysis of metatarsal bone A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition]. OBOL:automatic base of metatarsal bone FMA:33817 basis ossis metatarsi FMA:33817 FMA:TA proximal end of metatarsal bone FMA:33817 upper end of metatarsal bone FMA:33817 A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition]. FMA:33795 SCTID:272695001 base of metacarpal bone basis ossis metacarpi metacarpal bone base proximal end of metacarpal bone upper end of metacarpal bone uberon UBERON:0004416 proximal epiphysis of metacarpal bone A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition]. OBOL:automatic base of metacarpal bone FMA:33795 basis ossis metacarpi FMA:33795 FMA:TA metacarpal bone base FMA:33795 proximal end of metacarpal bone FMA:33795 upper end of metacarpal bone FMA:33795 A proximal epiphysis that is part of a manual digit 1 phalanx [Automatically generated definition]. FMA:37489 SCTID:272700008 basal epiphysis of phalanx of thumb base of phalanx of first digit of hand base of phalanx of thumb proximal epiphysis of phalanx of manual digit 1 proximal epiphysis of phalanx of manual digit I proximal epiphysis of phalanx of thumb uberon UBERON:0004417 proximal epiphysis of phalanx of manual digit 1 A proximal epiphysis that is part of a manual digit 1 phalanx [Automatically generated definition]. OBOL:automatic basal epiphysis of phalanx of thumb FMA:37489 base of phalanx of first digit of hand FMA:37489 base of phalanx of thumb FMA:37489 proximal epiphysis of phalanx of manual digit I https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of phalanx of thumb FMA:37489 NCBITaxon:9606 A proximal epiphysis that is part of a manual digit 5 phalanx [Automatically generated definition]. FMA:37534 SCTID:368351008 basal epiphysis of phalanx of fifth finger basal epiphysis of phalanx of little finger base of phalanx of fifth digit of hand base of phalanx of fifth finger base of phalanx of little finger proximal epiphysis of phalanx of manual digit 5 proximal epiphysis of phalanx of manual digit V proximal epiphysis of phalanx of little finger uberon UBERON:0004421 proximal epiphysis of phalanx of manual digit 5 A proximal epiphysis that is part of a manual digit 5 phalanx [Automatically generated definition]. OBOL:automatic basal epiphysis of phalanx of fifth finger FMA:37534 basal epiphysis of phalanx of little finger FMA:37534 base of phalanx of fifth digit of hand FMA:37534 base of phalanx of fifth finger FMA:37534 base of phalanx of little finger FMA:37534 proximal epiphysis of phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of phalanx of little finger FMA:37534 NCBITaxon:9606 A proximal epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. FMA:42788 SCTID:181978000 base of first metacarpal bone first metacarpal bone base proximal epiphysis of metacarpal 1 uberon UBERON:0004422 proximal epiphysis of first metacarpal bone A proximal epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. OBOL:automatic base of first metacarpal bone FMA:42788 first metacarpal bone base FMA:42788 A proximal epiphysis that is part of a metacarpal bone of digit 5 [Automatically generated definition]. FMA:42800 SCTID:263473004 base of fifth metacarpal bone fifth metacarpal bone base proximal end of fifth metacarpal bone proximal epiphysis of metacarpal 5 uberon UBERON:0004426 proximal epiphysis of fifth metacarpal bone A proximal epiphysis that is part of a metacarpal bone of digit 5 [Automatically generated definition]. OBOL:automatic base of fifth metacarpal bone FMA:42800 fifth metacarpal bone base FMA:42800 proximal end of fifth metacarpal bone FMA:42800 A proximal epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. FMA:42963 SCTID:182124002 base of first metatarsal bone proximal end of first metatarsal bone proximal epiphysis of metatarsal 1 uberon UBERON:0004427 proximal epiphysis of first metatarsal bone A proximal epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. OBOL:automatic base of first metatarsal bone FMA:42963 proximal end of first metatarsal bone FMA:42963 A proximal epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. FMA:42967 SCTID:182145009 base of fifth metatarsal bone proximal end of fifth metatarsal bone proximal epiphysis of metatarsal 5 uberon UBERON:0004431 proximal epiphysis of fifth metatarsal bone A proximal epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. OBOL:automatic base of fifth metatarsal bone FMA:42967 proximal end of fifth metatarsal bone FMA:42967 A proximal epiphysis that is part of a distal phalanx of manual digit 5 [Automatically generated definition]. FMA:37541 SCTID:263448004 basal epiphysis of distal phalanx of fifth finger basal epiphysis of distal phalanx of little finger base of distal phalanx of fifth digit of hand base of distal phalanx of fifth finger base of distal phalanx of little finger proximal epiphysis of distal phalanx of manual digit V proximal epiphysis of distal phalanx of little finger uberon UBERON:0004435 proximal epiphysis of distal phalanx of manual digit 5 A proximal epiphysis that is part of a distal phalanx of manual digit 5 [Automatically generated definition]. OBOL:automatic basal epiphysis of distal phalanx of fifth finger FMA:37541 basal epiphysis of distal phalanx of little finger FMA:37541 base of distal phalanx of fifth digit of hand FMA:37541 base of distal phalanx of fifth finger FMA:37541 base of distal phalanx of little finger FMA:37541 proximal epiphysis of distal phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of distal phalanx of little finger FMA:37541 NCBITaxon:9606 A proximal epiphysis that is part of a middle phalanx of manual digit 5 [Automatically generated definition]. FMA:37538 SCTID:263431007 basal epiphysis of middle phalanx of fifth finger basal epiphysis of middle phalanx of little finger base of middle phalanx of fifth digit of hand base of middle phalanx of fifth finger base of middle phalanx of little finger proximal epiphysis of middle phalanx of manual digit V proximal epiphysis of middle phalanx of little finger uberon UBERON:0004439 proximal epiphysis of middle phalanx of manual digit 5 A proximal epiphysis that is part of a middle phalanx of manual digit 5 [Automatically generated definition]. OBOL:automatic basal epiphysis of middle phalanx of fifth finger FMA:37538 basal epiphysis of middle phalanx of little finger FMA:37538 base of middle phalanx of fifth digit of hand FMA:37538 base of middle phalanx of fifth finger FMA:37538 base of middle phalanx of little finger FMA:37538 proximal epiphysis of middle phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of middle phalanx of little finger FMA:37538 NCBITaxon:9606 A proximal epiphysis that is part of a proximal phalanx of manual digit 5 [Automatically generated definition]. FMA:37535 SCTID:263415004 basal epiphysis of proximal phalanx of little finger base of proximal phalanx of fifth digit of hand base of proximal phalanx of fifth finger base of proximal phalanx of little finger proximal epiphysis of proximal phalanx of manual digit V proximal epiphysis of proximal phalanx of little finger uberon UBERON:0004443 proximal epiphysis of proximal phalanx of manual digit 5 A proximal epiphysis that is part of a proximal phalanx of manual digit 5 [Automatically generated definition]. OBOL:automatic basal epiphysis of proximal phalanx of little finger FMA:37535 base of proximal phalanx of fifth digit of hand FMA:37535 base of proximal phalanx of fifth finger FMA:37535 base of proximal phalanx of little finger FMA:37535 proximal epiphysis of proximal phalanx of manual digit V https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of proximal phalanx of little finger FMA:37535 NCBITaxon:9606 A proximal epiphysis that is part of a distal phalanx of manual digit 1 [Automatically generated definition]. FMA:37493 SCTID:182008001 base of distal phalanx of thumb proximal epiphysis of distal phalanx of manual digit I proximal epiphysis of distal phalanx of thumb uberon UBERON:0004444 proximal epiphysis of distal phalanx of manual digit 1 A proximal epiphysis that is part of a distal phalanx of manual digit 1 [Automatically generated definition]. OBOL:automatic base of distal phalanx of thumb FMA:37493 proximal epiphysis of distal phalanx of manual digit I https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of distal phalanx of thumb FMA:37493 NCBITaxon:9606 A proximal epiphysis that is part of a proximal phalanx of manual digit 1 [Automatically generated definition]. FMA:37490 SCTID:181993001 basal epiphysis of proximal phalanx of thumb base of proximal phalanx of thumb proximal epiphysis of proximal phalanx of manual digit I proximal epiphysis of proximal phalanx of thumb uberon UBERON:0004445 proximal epiphysis of proximal phalanx of manual digit 1 A proximal epiphysis that is part of a proximal phalanx of manual digit 1 [Automatically generated definition]. OBOL:automatic basal epiphysis of proximal phalanx of thumb FMA:37490 base of proximal phalanx of thumb FMA:37490 proximal epiphysis of proximal phalanx of manual digit I https://github.com/obophenotype/uberon/issues/458 proximal epiphysis of proximal phalanx of thumb FMA:37490 NCBITaxon:9606 An epiphysis that is part of a phalanx [Automatically generated definition]. SCTID:280033007 uberon UBERON:0004446 epiphysis of phalanx An epiphysis that is part of a phalanx [Automatically generated definition]. OBOL:automatic A proximal epiphysis that is part of a phalanx [Automatically generated definition]. uberon UBERON:0004447 proximal epiphysis of phalanx A proximal epiphysis that is part of a phalanx [Automatically generated definition]. OBOL:automatic One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO:0010493 BTO:0005205 CALOHA:TS-0126 EHDAA2:0000233 EHDAA:5294 EMAPA:18613 GAID:484 MA:0002562 MESH:D002536 NCIT:C12691 SCTID:181308008 UMLS:C0007770 Wikipedia:Cerebral_artery XAO:0000367 uberon UBERON:0004449 cerebral artery One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Wikipedia:Cerebral_artery Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] 2012-06-20 AAO:0010493 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010493 AAO in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO UMLS:C0007770 ncithesaurus:Cerebral_Artery A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar) it's not clear if the XAO class belongs here or below EMAPA:37722 MA:0002869 XAO:0003077 uberon presacral vertebra UBERON:0004451 trunk or cervical vertebra A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. UBERONREF:0000006 it's not clear if the XAO class belongs here or below XAO EMAPA:37722 MA:th presacral vertebra MA:0002869 A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted]. UBERON:0001462 EHDAA2:0000218 EHDAA:5196 EMAPA:19122 EMAPA:32784 FMA:24922 GAID:59 MA:0000039 MESH:D014953 NCIT:C111033 SCTID:361289009 Wikipedia:Wrist galen:Wrist carpal limb segment carpal segment fore basipodium fore mesopodium hand mesopodium manus mesopodium regio carpalis wrist wrist region carpus of fore-paw uberon articulatio radiocarpea carpus UBERON:0004452 carpal region https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png https://upload.wikimedia.org/wikipedia/commons/c/cc/Hand_parts.jpg FMA A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted]. Wikipedia:Wrist https://orcid.org/0000-0002-6601-2165 fore basipodium MA:th fore mesopodium MA:th regio carpalis FMA:24922 FMA:TA wrist MA:0000039 carpus of fore-paw EMAPA:19122 articulatio radiocarpea Wikipedia:Wrist carpus A metapodium region that is part of a manus. Note that along with FMA we treat this as a limb segment rather than a purely skeletal element metacarpal Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton CALOHA:TS-2218 EMAPA:32654 FMA:24925 MA:0000042 SCTID:370638006 distal segment of hand proper metacarpal part of hand metacarpal part of manus metacarpal region metacarpus forelimb cannon region forelimb equine cannon region uberon UBERON:0004453 metacarpus region https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg FMA PHENOSCAPE:ni A metapodium region that is part of a manus. OBOL:automatic distal segment of hand proper FMA:24925 metacarpal part of hand FMA:24925 metacarpal region FMA:24925 metacarpus MA:0000042 forelimb cannon region NCBITaxon:9788 http://orcid.org/0000-0002-6601-2165 forelimb equine cannon region NCBITaxon:9788 http://orcid.org/0000-0002-6601-2165 Mesopodial segment of the pes, including the tarsal skeleton and associated tissues. this term refers to the limb segment. See also: tarsal bones and tarsal skeleton MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin). UBERON:0002388 CALOHA:TS-2219 EFO:0001409 EMAPA:32783 FMA:9665 GAID:41 MA:0000043 MESH:D000842 SCTID:361292008 Wikipedia:Ankle galen:Ankle ankle ankle region tarsal limb segment uberon articulatio talocruralis hind basipodium hind mesopodium hock UBERON:0004454 tarsal region https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg Mesopodial segment of the pes, including the tarsal skeleton and associated tissues. Wikipedia:Ankle https://orcid.org/0000-0002-6601-2165 MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin). MA ankle MA:0000043 articulatio talocruralis Wikipedia:Ankle hind basipodium MA:th hind mesopodium MA:th hock Wikipedia:Hock_(anatomy) An embryo at the neurula stage. UBERON:0007013 BILA:0000061 BTO:0001766 NCIT:C34229 UMLS:C1518306 neurula uberon UBERON:0004455 neurula embryo An embryo at the neurula stage. http://orcid.org/0000-0002-6601-2165 UMLS:C1518306 ncithesaurus:Neurula neurula BTO:0001766 Sum of all sensory systems in an organism. note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon UBERON:0004456 entire sense organ system Sum of all sensory systems in an organism. http://orcid.org/0000-0002-6601-2165 sense organ system FMA:78499 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. EMAPA:18171 FMA:71287 head musculature muscle group of head muscles of head musculi capitis set of muscles of head uberon UBERON:0004461 This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376 skeletal musculature of head https://github.com/obophenotype/mouse-anatomy-ontology/issues/4 https://github.com/obophenotype/uberon/issues/1405 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. OBOL:automatic head musculature FMA:71287 muscle group of head FMA:71287 muscles of head FMA:71287 musculi capitis FMA:71287 FMA:TA set of muscles of head FMA:71287 Any collection of muscles that is part of a body wall [Automatically generated definition]. define generically to encompass both vertebrates and invertebrates BSA:0000058 BTO:0001863 EMAPA:37853 FMA:86931 WBbt:0005813 body wall musculature uberon body wall muscles UBERON:0004462 musculature of body wall Any collection of muscles that is part of a body wall [Automatically generated definition]. OBOL:automatic EMAPA:37853 MA:th body wall musculature FMA:86931 Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition]. FMA:50208 muscle group of thigh musculature of thigh set of muscles of thigh thigh musculature uberon UBERON:0004463 musculature of hindlimb stylopod Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition]. OBOL:automatic muscle group of thigh FMA:50208 musculature of thigh FMA:50208 set of muscles of thigh FMA:50208 thigh musculature FMA:50208 Any collection of muscles that is part of a thorax [Automatically generated definition]. BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO:0000508 EMAPA:37260 FMA:71293 muscle group of thorax muscles of thorax musculi thoracis set of muscles of thorax thoracic musculature uberon UBERON:0004464 musculature of thorax Any collection of muscles that is part of a thorax [Automatically generated definition]. OBOL:automatic BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO EMAPA:37260 MA:th muscle group of thorax FMA:71293 muscles of thorax FMA:71293 musculi thoracis FMA:71293 FMA:TA set of muscles of thorax FMA:71293 thoracic musculature FMA:71293 Any collection of muscles that is part of a neck [Automatically generated definition]. AAO:0000091 EMAPA:36050 FMA:71290 MESH:D009334 cervical muscles muscle group of neck muscles of neck musculi cervicis musculi colli neck musculature set of muscles of neck uberon UBERON:0004465 musculature of neck Any collection of muscles that is part of a neck [Automatically generated definition]. OBOL:automatic cervical muscles AAO:0000091 muscle group of neck FMA:71290 muscles of neck FMA:71290 musculi cervicis FMA:71290 FMA:TA musculi colli FMA:71290 FMA:TA neck musculature FMA:71290 set of muscles of neck FMA:71290 Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]. see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class) UBERON:0005632 EHDAA2:0000973 leg muscle system uberon UBERON:0004466 musculature of leg Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]. OBOL:automatic leg muscle system EHDAA2:0000973 The collection of muscles that acts on the pharynx. FMA:264609 TAO:0001307 ZFA:0001307 pharyngeal musculature uberon set of muscles of pharynx UBERON:0004467 See comments for 'pharyngeal muscle' musculature of pharynx The collection of muscles that acts on the pharynx. http://orcid.org/0000-0002-6601-2165 pharyngeal musculature TAO:0001307 set of muscles of pharynx FMA:264609 FMA:33061 muscle group of vertebral column uberon UBERON:0004468 set of muscles of vertebral column muscle group of vertebral column FMA:33061 Any collection of muscles that is part of a back [Automatically generated definition]. FMA:71291 muscle group of back muscles of back musculi dorsi set of muscles of back uberon UBERON:0004469 musculature of back Any collection of muscles that is part of a back [Automatically generated definition]. OBOL:automatic muscle group of back FMA:71291 muscles of back FMA:71291 musculi dorsi FMA:71291 FMA:TA set of muscles of back FMA:71291 Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. we merge two FMA classes here UBERON:0004485 UBERON:0005633 AAO:0000427 EHDAA2:0001429 EMAPA:18184 FMA:50205 FMA:50248 muscle group of pelvic girdle muscle group of pelvis pelvic girdle muscle system pelvic girdle muscles pelvic girdle musculature set of muscles of pelvic girdle uberon muscular system of pelvis set of muscles of pelvis UBERON:0004470 musculature of pelvic girdle Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic we merge two FMA classes here FMA muscle group of pelvic girdle FMA:50205 muscle group of pelvis FMA:50248 pelvic girdle muscle system EHDAA2:0001429 pelvic girdle muscles AAO:0000427 pelvic girdle musculature FMA:50205 set of muscles of pelvic girdle FMA:50205 muscular system of pelvis FMA:50248 set of muscles of pelvis FMA:50248 A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. AAO:0000423 EMAPA:37857 FMA:33519 muscle group of pectoral girdle pectoral girdle muscles pectoral girdle musculature set of muscles of pectoral girdle uberon UBERON:0004471 musculature of pectoral girdle A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. https://orcid.org/0000-0002-6601-2165 EMAPA:37857 MA:th muscle group of pectoral girdle FMA:33519 pectoral girdle muscles AAO:0000423 pectoral girdle musculature FMA:33519 set of muscles of pectoral girdle FMA:33519 Any collection of muscles that is part of a face. originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose FMA:71288 entire facial musculature facial muscles muscle group of face musculi faciei uberon set of facial muscles set of muscles of face UBERON:0004473 musculature of face Any collection of muscles that is part of a face. OBOL:automatic entire facial musculature https://orcid.org/0000-0002-6601-2165 facial muscles FMA:71288 muscle group of face FMA:71288 musculi faciei FMA:71288 FMA:TA set of facial muscles FMA:71288 set of muscles of face FMA:71288 Any collection of muscles that is part of an arm [Automatically generated definition]. EHDAA2:0000141 arm muscle system arm musculature muscle group of arm set of muscles of arm uberon UBERON:0004474 musculature of arm Any collection of muscles that is part of an arm [Automatically generated definition]. OBOL:automatic arm muscle system EHDAA2:0000141 arm musculature FMA:50202 muscle group of arm FMA:50202 set of muscles of arm FMA:50202 The collection of muscles that form attachments to the hip skeleton. FMA:50227 hip musculature muscle group of hip set of muscles of hip uberon UBERON:0004475 musculature of hip The collection of muscles that form attachments to the hip skeleton. http://orcid.org/0000-0002-6601-2165 hip musculature FMA:50227 muscle group of hip FMA:50227 set of muscles of hip FMA:50227 The collection of muscles that form attachments to the shoulder skeleton. FMA:50220 muscle group of shoulder set of muscles of shoulder uberon UBERON:0004476 musculature of shoulder The collection of muscles that form attachments to the shoulder skeleton. http://orcid.org/0000-0002-6601-2165 muscle group of shoulder FMA:50220 set of muscles of shoulder FMA:50220 The collection of muscles that are part of the larynx. currently defined by location rather than attachment FMA:264611 FMA:46616 MESH:D007821 Wikipedia:Muscles_of_larynx laryngeal muscles laryngeal muscles set muscle group of larynx set of laryngeal muscles set of muscles of larynx uberon UBERON:0004478 musculature of larynx The collection of muscles that are part of the larynx. http://orcid.org/0000-0002-6601-2165 laryngeal muscles FMA:46616 laryngeal muscles set FMA:46616 muscle group of larynx FMA:46616 set of laryngeal muscles FMA:46616 set of muscles of larynx FMA:264611 Any collection of muscles that is part of a trunk [Automatically generated definition]. currently defined by location rather than attachment AAO:0011572 EFO:0003531 FMA:50187 muscle group of trunk set of muscles of trunk uberon muscular system of trunk UBERON:0004479 musculature of trunk Any collection of muscles that is part of a trunk [Automatically generated definition]. OBOL:automatic muscle group of trunk FMA:50187 set of muscles of trunk FMA:50187 muscular system of trunk FMA:50187 Any collection of muscles that is part of a limb [Automatically generated definition]. currently defined by location rather than attachment UBERON:0005635 EHDAA2:0000995 EMAPA:32700 FMA:50188 limb muscle system limb musculature muscle group of limb set of muscles of limb uberon UBERON:0004480 musculature of limb Any collection of muscles that is part of a limb [Automatically generated definition]. OBOL:automatic limb muscle system EHDAA2:0000995 limb musculature FMA:50188 muscle group of limb FMA:50188 set of muscles of limb FMA:50188 Any collection of muscles that is part of a forelimb [Automatically generated definition]. currently defined by location rather than attachment FMA:50396 free upper limb musculature muscle group of free upper limb musculature of free upper limb set of muscles of free upper limb uberon UBERON:0004481 musculature of upper limb Any collection of muscles that is part of a forelimb [Automatically generated definition]. OBOL:automatic free upper limb musculature FMA:50396 muscle group of free upper limb FMA:50396 musculature of free upper limb FMA:50396 set of muscles of free upper limb FMA:50396 Any collection of muscles that is part of a hindlimb [Automatically generated definition]. currently defined by location rather than attachment FMA:50399 free lower limb musculature muscle group of free lower limb musculature of free lower limb set of muscles of free lower limb uberon UBERON:0004482 musculature of lower limb Any collection of muscles that is part of a hindlimb [Automatically generated definition]. OBOL:automatic free lower limb musculature FMA:50399 muscle group of free lower limb FMA:50399 musculature of free lower limb FMA:50399 set of muscles of free lower limb FMA:50399 Any collection of muscles that is part of a lower arm [Automatically generated definition]. FMA:39089 muscle group of forearm musculature of forearm set of muscles of forearm uberon UBERON:0004487 musculature of forelimb zeugopod Any collection of muscles that is part of a lower arm [Automatically generated definition]. OBOL:automatic muscle group of forearm FMA:39089 musculature of forearm FMA:39089 set of muscles of forearm FMA:39089 Any collection of muscles that is part of a foot [Automatically generated definition]. currently defined by location rather than attachment FMA:50214 foot musculature muscle group of foot musculature of foot set of muscles of foot uberon UBERON:0004488 musculature of pes Any collection of muscles that is part of a foot [Automatically generated definition]. OBOL:automatic foot musculature FMA:50214 muscle group of foot FMA:50214 musculature of foot FMA:50214 set of muscles of foot FMA:50214 Any collection of muscles that is part of a manus [Automatically generated definition]. currently defined by location rather than attachment FMA:42368 hand musculature muscle group of hand musculature of hand set of muscles of hand uberon UBERON:0004489 musculature of manus Any collection of muscles that is part of a manus [Automatically generated definition]. OBOL:automatic hand musculature FMA:42368 muscle group of hand FMA:42368 musculature of hand FMA:42368 set of muscles of hand FMA:42368 A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. FMA:7283 atrial cardiac muscle tissue atrial heart muscle cardiac atrium muscle uberon atrial myocardium UBERON:0004490 cardiac muscle tissue of atrium A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. OBOL:automatic in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. GO atrial cardiac muscle tissue GO:0055009 atrial heart muscle GO:0055009 cardiac atrium muscle GO:0055009 atrial myocardium GO:0055009 GOC:mtg_heart A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. FMA:84083 interatrial septum cardiac muscle tissue interatrial septum heart muscle interatrial septum muscle interatrial septum myocardium uberon UBERON:0004491 cardiac muscle tissue of interatrial septum A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. OBOL:automatic interatrial septum cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 interatrial septum heart muscle http://orcid.org/0000-0002-6601-2165 interatrial septum muscle http://orcid.org/0000-0002-6601-2165 interatrial septum myocardium http://orcid.org/0000-0002-6601-2165 A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. FMA:226279 cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium uberon UBERON:0004492 cardiac muscle tissue of cardiac septum A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. OBOL:automatic cardiac septum cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 cardiac septum heart muscle http://orcid.org/0000-0002-6601-2165 cardiac septum muscle http://orcid.org/0000-0002-6601-2165 cardiac septum myocardium http://orcid.org/0000-0002-6601-2165 A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 FMA:261726 MA:0002441 uberon UBERON:0004493 cardiac muscle tissue of myocardium MA A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. OBOL:automatic A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. FMA:261898 uberon UBERON:0004495 skeletal muscle tissue of diaphragm A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. OBOL:automatic A portion of skeletal muscle tissue that is part of a deltoid [Automatically generated definition]. FMA:261732 uberon skeletal muscle tissue of deltoid muscle UBERON:0004500 skeletal muscle tissue of deltoid A portion of skeletal muscle tissue that is part of a deltoid [Automatically generated definition]. OBOL:automatic skeletal muscle tissue of deltoid muscle FMA:261732 A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition]. FMA:261938 uberon skeletal muscle tissue of trapezius muscle UBERON:0004509 skeletal muscle tissue of trapezius A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition]. OBOL:automatic skeletal muscle tissue of trapezius muscle FMA:261938 A muscle that is attached to a vertebra of the vertebral column. FMA:22594 vertebral column muscle uberon UBERON:0004518 muscle of vertebral column A muscle that is attached to a vertebra of the vertebral column. https://orcid.org/0000-0002-6601-2165 vertebral column muscle FMA:22594 A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]. FMA:45716 uberon UBERON:0004520 striated muscle tissue of prostate A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]. OBOL:automatic A vasculature that is part of a muscle organ [Automatically generated definition]. FMA:87123 muscular organ vasculature uberon UBERON:0004521 vasculature of muscle organ A vasculature that is part of a muscle organ [Automatically generated definition]. OBOL:automatic muscular organ vasculature FMA:87123 A vasculature that is part of a musculoskeletal system [Automatically generated definition]. FMA:239607 uberon UBERON:0004522 vasculature of musculoskeletal system A vasculature that is part of a musculoskeletal system [Automatically generated definition]. OBOL:automatic A projection or outgrowth of tissue from a larger body or organ. should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs) Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] anatomical process process AAO:0010278 FMA:67601 HAO:0000822 NCIT:C61549 TAO:0001834 VSAO:0000180 Wikipedia:Process_(anatomy) XAO:0004020 galen:Ridge processus projection flange flanges lamella lamellae lamina laminae organ process papilla process of organ processes projection projections ridge ridges shelf shelves uberon anatomical protrusion protrusion spine UBERON:0004529 anatomical projection A projection or outgrowth of tissue from a larger body or organ. Wikipedia:Process_(anatomy) https://github.com/obophenotype/uberon/issues/39 Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] 2012-06-20 AAO:0010278 AAO AAO:BJB Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] 2012-08-14 TAO:0001834 TAO TAO:wd Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] 2012-08-14 VSAO:0000180 VSAO TAO:curator process VSAO:0000180 processus FMA:67601 FMA:TA flange VSAO:0000180 flanges VSAO:0000180 lamella VSAO:0000180 lamellae VSAO:0000180 lamina VSAO:0000180 laminae VSAO:0000180 processes VSAO:0000180 projection VSAO:0000180 projections VSAO:0000180 ridge VSAO:0000180 ridges VSAO:0000180 shelf VSAO:0000180 shelves VSAO:0000180 Anatomical projection that is composed of bone tissue. FMA:75433 ZFA:0001637 bone process projection of bone uberon bony projections UBERON:0004530 bony projection Anatomical projection that is composed of bone tissue. VSAO:wd bone process FMA:75433 bony projections ZFA:0001637 A testis that is in the left side of the genitalia [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37370 FMA:7212 MA:0001746 NCIT:C49323 SCTID:367720001 UMLS:C0227998 left testicle uberon UBERON:0004533 left testis A testis that is in the left side of the genitalia [Automatically generated definition]. OBOL:automatic EMAPA:37370 MA:th UMLS:C0227998 ncithesaurus:Left_Testis left testicle MA:0001746 A testis that is in the right side of the genitalia [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37371 FMA:7211 MA:0001747 NCIT:C49326 SCTID:367719007 UMLS:C0227997 right testicle uberon UBERON:0004534 right testis A testis that is in the right side of the genitalia [Automatically generated definition]. OBOL:automatic EMAPA:37371 MA:th UMLS:C0227997 ncithesaurus:Right_Testis right testicle MA:0001747 Anatomical system that has as its parts the heart and blood vessels. we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 NCIT:C12686 SCTID:278198007 TAO:0000010 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon CV system Herz und Gefaesssystem UBERON:0004535 cardiovascular system Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000302 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 http://bgee.unil.ch/ UMLS:C0007226 ncithesaurus:Cardiovascular_System CV system BTO:0000088 Herz und Gefaesssystem BTO:0000088 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. consider merging with parent A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] FMA:63815 TAO:0005105 ZFA:0005105 lymphatic trunks and ducts lymphatic vasculature lymphatic vessel network lymphatic vessels set set of lymphatic vessels trunci et ductus lymphatici uberon lymph vessels UBERON:0004536 lymph vasculature https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb trunci et ductus lymphatici FMA:63815 FMA:TA lymph vessels ZFA:0005105 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. ZFA:0005105 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] 2012-08-14 TAO:0005105 TAO ZFIN:curator lymphatic trunks and ducts FMA:63815 lymphatic vessels set FMA:63815 A vascular network consisting of blood vessels. TAO:0001079 ZFA:0001079 blood vascular network set of blood vessels uberon blood system blood vessel system blood vessels UBERON:0004537 blood vasculature https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb A vascular network consisting of blood vessels. https://orcid.org/0000-0002-6601-2165 blood vessels TAO:0001079 A kidney that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36589 FMA:7205 MA:0001655 NCIT:C34006 SCTID:362209008 UMLS:C0227614 uberon UBERON:0004538 left kidney https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Left.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb A kidney that is part of a left side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227614 ncithesaurus:Left_Kidney A kidney that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36590 FMA:7204 MA:0001683 NCIT:C34005 SCTID:362208000 UMLS:C0227613 uberon UBERON:0004539 right kidney https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Right.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb A kidney that is part of a right side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227613 ncithesaurus:Right_Kidney The layer of secretory cells which lines the epididymis. BTO:0005768 CALOHA:TS-2063 EMAPA:30445 FMA:19153 MA:0002825 epididymis epithelium epithelium of epididymis uberon UBERON:0004544 epididymis epithelium The layer of secretory cells which lines the epididymis. MGI:csmith MP:0004933 epididymis epithelium FMA:19153 epithelium of epididymis FMA:19153 An eye that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37362 FMA:12515 MA:0002949 NCIT:C119334 SCTID:362503005 left eyeball left orbital part of face left orbital region uberon UBERON:0004548 left eye https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb An eye that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37362 MA:th left eyeball FMA:12515 left orbital part of face FMA:54450 left orbital region FMA:54450 An eye that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37363 FMA:12514 MA:0002950 NCIT:C119333 SCTID:362502000 right eyeball right orbital part of face right orbital region uberon UBERON:0004549 right eye https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb An eye that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37363 MA:th right eyeball FMA:12514 right orbital part of face FMA:54449 right orbital region FMA:54449 The thick circular layer of smooth gastric musculature encircling the gastroesophageal junction that functions to reduce backflow into the esophagus from the stomach. TODO - split? check FMA:63048 ! circular muscle layer of abdominal part of esophagus EMAPA:18267 FMA:14915 MA:0002951 MESH:D049630 NCIT:C33009 SCTID:267809009 UMLS:C0227192 galen:LowerEsophagealSphincter cardiac sphincter gastroesophageal sphincter gastroesophageal sphincter muscle inferior esophageal sphincter uberon LES cardiac sphincter constrictor cardiae esophageal sphincter esophageal sphincter%2c lower esophageal-cardiac junction esophagogastric junction gastro-esophageal junction gastro-esophageal sphincter gastro-oesophageal junction gastroesophageal junction gastroesophageal sphincter lower esophageal sphincter UBERON:0004550 gastroesophageal sphincter MA The thick circular layer of smooth gastric musculature encircling the gastroesophageal junction that functions to reduce backflow into the esophagus from the stomach. ISBN:0-683-40008-8 MP:0010153 MESH:D049630 https://github.com/biopragmatics/biomappings UMLS:C0227192 ncithesaurus:Lower_Esophageal_Sphincter cardiac sphincter MA:0002951 MP:0010153 gastroesophageal sphincter FMA:14915 inferior esophageal sphincter FMA:14915 LES Wikipedia:Cardia cardiac sphincter Wikipedia:Cardia constrictor cardiae MP:0010153 esophageal sphincter Wikipedia:Cardia esophageal sphincter%2c lower Wikipedia:Cardia esophageal-cardiac junction Wikipedia:Cardia esophagogastric junction Wikipedia:Cardia gastro-esophageal junction Wikipedia:Cardia gastro-esophageal sphincter Wikipedia:Cardia gastro-oesophageal junction Wikipedia:Cardia gastroesophageal junction Wikipedia:Cardia gastroesophageal sphincter Wikipedia:Cardia lower esophageal sphincter MA:0002951 Wikipedia:Cardia An artery that is part of a digit [Automatically generated definition]. check part_of - do we need term for digit + metacarpal/tarsal bones? EMAPA:37076 MA:0001941 SCTID:181335004 uberon UBERON:0004552 digital artery An artery that is part of a digit [Automatically generated definition]. OBOL:automatic EMAPA:37076 MA:th A digital artery that is part of a forelimb [Automatically generated definition]. EMAPA:37210 MA:0001953 SCTID:265791006 digital artery of manus forelimb digital arteries wing digital artery uberon UBERON:0004553 forelimb digital artery A digital artery that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37210 MA:th forelimb digital arteries MA:0001953 wing digital artery NCBITaxon:8782 OBOL:automatic A digital artery that is part of a hindlimb [Automatically generated definition]. EMAPA:37214 FMA:69713 MA:0001964 digital artery of foot hindlimb digital arteries uberon UBERON:0004554 hindlimb digital artery A digital artery that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37214 MA:th digital artery of foot FMA:69713 hindlimb digital arteries MA:0001964 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. FMA:45623 Wikipedia:Systemic_circulation#Arteries systemic arterial circulatory system uberon UBERON:0004571 systemic arterial system MA-inferred The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. Wikipedia:Systemic_circulation#Arteries http://orcid.org/0000-0002-6601-2165 systemic arterial circulatory system FMA:45623 The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 SCTID:362030008 VHOG:0000273 uberon UBERON:0004572 arterial system MA The part of the cardiovascular system consisting of all arteries. https://orcid.org/0000-0002-6601-2165 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000273 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 FMA:66464 Wikipedia:Artery#Systemic_arteries systemic arterial subtree uberon UBERON:0004573 systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. Wikipedia:Artery#Systemic_arteries http://orcid.org/0000-0002-6601-2165 EMAPA:37126 MA:th systemic arterial subtree FMA:66464 The part of the venous system that drains the general body tissues[Kardong]. In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] FMA:45626 Wikipedia:Systemic_venous_system systemic venous circulatory system uberon UBERON:0004581 systemic venous system The part of the venous system that drains the general body tissues[Kardong]. ISBN:0073040584 Wikipedia:Systemic_venous_system In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Wikipedia:Systemic_venous_system Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] FMA FMA:45626 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ systemic venous circulatory system FMA:45626 The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 NCIT:C33858 SCTID:362060003 UMLS:C1267406 VHOG:0000277 vein system uberon UBERON:0004582 venous system MA The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. https://orcid.org/0000-0002-6601-2165 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ UMLS:C1267406 ncithesaurus:Venous_System A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA class is not a subtype of muscle FMA:75004 NCIT:C28381 UMLS:C1409894 Wikipedia:Sphincter sphincter uberon circular muscle UBERON:0004590 sphincter muscle A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. Wikipedia:Sphincter FMA class is not a subtype of muscle FMA UMLS:C1409894 ncithesaurus:Sphincter The third of the seven cervical vertebrae[ncit,modified]. under discussion: whether to generalize this beyond mammals, making it purely order-defined elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae 3 EMAPA:19433 FMA:12521 MA:0001423 NCIT:C32241 SCTID:181823007 UMLS:C0459939 C3 vertebra cervical vertebra 3 cervical vertebrae 3 third cervical vertebra third cervical vertebra of axial skeleton uberon UBERON:0004612 mammalian cervical vertebra 3 FMA The third of the seven cervical vertebrae[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:C3_Vertebra UMLS:C0459939 ncithesaurus:C3_Vertebra C3 vertebra FMA:12521 cervical vertebra 3 MA:0001423 third cervical vertebra FMA:12521 The fourth of the seven cervical vertebrae[ncit,modified]. elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae 4 EMAPA:19434 FMA:12522 MA:0001424 NCIT:C32242 SCTID:181824001 UMLS:C0459941 C4 vertebra cervical vertebra 4 fourth cervical vertebra uberon UBERON:0004613 mammalian cervical vertebra 4 FMA The fourth of the seven cervical vertebrae[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:C4_Vertebra UMLS:C0459941 ncithesaurus:C4_Vertebra C4 vertebra FMA:12522 cervical vertebra 4 MA:0001424 fourth cervical vertebra FMA:12522 The fifth of the seven cervical vertebrae[ncit,modified]. elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae 5 EMAPA:19435 FMA:12523 MA:0001425 NCIT:C32243 SCTID:181825000 UMLS:C0459943 C5 vertebra cervical vertebra 5 fifth cervical vertebra uberon UBERON:0004614 mammalian cervical vertebra 5 FMA The fifth of the seven cervical vertebrae[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:C5_Vertebra UMLS:C0459943 ncithesaurus:C5_Vertebra C5 vertebra FMA:12523 cervical vertebra 5 MA:0001425 fifth cervical vertebra FMA:12523 The sixth of the seven cervical vertebrae[ncit,modified]. elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae 6 EMAPA:19466 FMA:12524 MA:0001426 NCIT:C32244 SCTID:181826004 UMLS:C0459944 C6 vertebra cervical vertebra 6 sixth cervical vertebra uberon UBERON:0004615 mammalian cervical vertebra 6 FMA The sixth of the seven cervical vertebrae[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:C6_Vertebra UMLS:C0459944 ncithesaurus:C6_Vertebra C6 vertebra FMA:12524 cervical vertebra 6 MA:0001426 sixth cervical vertebra FMA:12524 Vertebra prominens is the proper name for the seventh cervical vertebra. The most distinctive characteristic of this vertebra is the existence of a long and prominent spinous process which is palpable from the skin surface, hence the name. This spinous process is thick, nearly horizontal in direction, not bifurcated, but terminating in a tubercle to which the lower end of the ligamentum nuchae is attached. The seventh cervical vertebra (C7) has the most prominent spinous process only in about 70% of people; in the remainder, either C6 or T1 (the first thoracic vertebra) will be the most prominent. The transverse processes are of considerable size, their posterior roots are large and prominent, while the anterior are small and faintly marked; the upper surface of each has usually a shallow sulcus for the eighth spinal nerve, and its extremity seldom presents more than a trace of bifurcation. The foramen transversarium may be as large as that in the other cervical vertebrae, but is generally smaller on one or both sides; occasionally it is double, sometimes it is absent. On the left side it occasionally gives passage to the vertebral artery; more frequently the vertebral vein traverses it on both sides; but the usual arrangement is for both artery and vein to pass in front of the transverse process, and not through the foramen. Sometimes the anterior root of the transverse process attains a large size and exists as a separate bone, which is known as a cervical rib. elements are to be defined spatially/topologically. all mammals have 7 cervical vertebrae 7 EMAPA:19467 FMA:12525 MA:0001427 NCIT:C32245 SCTID:181827008 UMLS:C0223176 Wikipedia:Vertebra_prominens C7 vertebra cervical vertebra 7 prominent vertebra seventh cervical vertebra vertebra prominens (CVII) vertebra prominens [C VII] uberon UBERON:0004616 mammalian cervical vertebra 7 FMA Vertebra prominens is the proper name for the seventh cervical vertebra. The most distinctive characteristic of this vertebra is the existence of a long and prominent spinous process which is palpable from the skin surface, hence the name. This spinous process is thick, nearly horizontal in direction, not bifurcated, but terminating in a tubercle to which the lower end of the ligamentum nuchae is attached. The seventh cervical vertebra (C7) has the most prominent spinous process only in about 70% of people; in the remainder, either C6 or T1 (the first thoracic vertebra) will be the most prominent. The transverse processes are of considerable size, their posterior roots are large and prominent, while the anterior are small and faintly marked; the upper surface of each has usually a shallow sulcus for the eighth spinal nerve, and its extremity seldom presents more than a trace of bifurcation. The foramen transversarium may be as large as that in the other cervical vertebrae, but is generally smaller on one or both sides; occasionally it is double, sometimes it is absent. On the left side it occasionally gives passage to the vertebral artery; more frequently the vertebral vein traverses it on both sides; but the usual arrangement is for both artery and vein to pass in front of the transverse process, and not through the foramen. Sometimes the anterior root of the transverse process attains a large size and exists as a separate bone, which is known as a cervical rib. Wikipedia:Vertebra_prominens UMLS:C0223176 ncithesaurus:C7_Vertebra C7 vertebra FMA:12525 cervical vertebra 7 MA:0001427 prominent vertebra FMA:12525 seventh cervical vertebra FMA:12525 vertebra prominens (CVII) FMA:12525 vertebra prominens [C VII] FMA:12525 FMA:TA The first lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19472 FMA:13072 MA:0001428 NCIT:C32899 SCTID:181841004 UMLS:C0223492 L1 vertebra first lumbar vertebra uberon UBERON:0004617 lumbar vertebra 1 The first lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:L1_Vertebra UMLS:C0223492 ncithesaurus:L1_Vertebra L1 vertebra FMA:13072 first lumbar vertebra FMA:13072 The second lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19570 FMA:13073 MA:0001429 NCIT:C32900 SCTID:181842006 UMLS:C0223507 L2 vertebra second lumbar vertebra uberon UBERON:0004618 lumbar vertebra 2 FMA The second lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:L2_Vertebra UMLS:C0223507 ncithesaurus:L2_Vertebra L2 vertebra FMA:13073 second lumbar vertebra FMA:13073 The third lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19571 FMA:13074 MA:0001430 NCIT:C32901 SCTID:181843001 UMLS:C0223522 L3 vertebra third lumbar vertebra uberon UBERON:0004619 lumbar vertebra 3 FMA The third lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:L3_Vertebra UMLS:C0223522 ncithesaurus:L3_Vertebra L3 vertebra FMA:13074 third lumbar vertebra FMA:13074 The fourth lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19572 FMA:13075 MA:0001431 NCIT:C32902 SCTID:181844007 UMLS:C0223537 L4 vertebra fourth lumbar vertebra uberon UBERON:0004620 lumbar vertebra 4 FMA The fourth lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:L4_Vertebra UMLS:C0223537 ncithesaurus:L4_Vertebra L4 vertebra FMA:13075 fourth lumbar vertebra FMA:13075 The fifth lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19573 FMA:13076 MA:0001432 NCIT:C32903 SCTID:181845008 UMLS:C0223552 L5 vertebra fifth lumbar vertebra uberon UBERON:0004621 lumbar vertebra 5 FMA The fifth lumbar vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:L5_Vertebra UMLS:C0223552 ncithesaurus:L5_Vertebra L5 vertebra FMA:13076 fifth lumbar vertebra FMA:13076 The first thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19542 FMA:9165 MA:0001438 NCIT:C33720 SCTID:181828003 UMLS:C0459933 T1 vertebra first dorsal vertebra first thoracic vertebra uberon UBERON:0004626 thoracic vertebra 1 The first thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T1_Vertebra UMLS:C0459933 ncithesaurus:T1_Vertebra T1 vertebra FMA:9165 first dorsal vertebra FMA:9165 first thoracic vertebra FMA:9165 The second thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19543 FMA:9187 MA:0001439 NCIT:C33724 SCTID:181829006 UMLS:C0459936 T2 vertebra second dorsal vertebra second thoracic vertebra uberon UBERON:0004627 thoracic vertebra 2 FMA The second thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T2_Vertebra UMLS:C0459936 ncithesaurus:T2_Vertebra T2 vertebra FMA:9187 second dorsal vertebra FMA:9187 second thoracic vertebra FMA:9187 The third thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19544 FMA:9209 MA:0001440 NCIT:C33725 SCTID:181830001 UMLS:C0459952 T3 vertebra third dorsal vertebra third thoracic vertebra uberon UBERON:0004628 thoracic vertebra 3 FMA The third thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T3_Vertebra UMLS:C0459952 ncithesaurus:T3_Vertebra T3 vertebra FMA:9209 third dorsal vertebra FMA:9209 third thoracic vertebra FMA:9209 The fourth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19545 FMA:9248 MA:0001441 NCIT:C33726 SCTID:181831002 UMLS:C0459951 T4 vertebra fourth dorsal vertebra fourth thoracic vertebra uberon UBERON:0004629 thoracic vertebra 4 FMA The fourth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T4_Vertebra UMLS:C0459951 ncithesaurus:T4_Vertebra T4 vertebra FMA:9248 fourth dorsal vertebra FMA:9248 fourth thoracic vertebra FMA:9248 The fifth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19546 FMA:9922 MA:0001442 NCIT:C33727 SCTID:181832009 UMLS:C0459950 T5 vertebra fifth dorsal vertebra fifth thoracic vertebra uberon UBERON:0004630 thoracic vertebra 5 FMA The fifth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T5_Vertebra UMLS:C0459950 ncithesaurus:T5_Vertebra T5 vertebra FMA:9922 fifth dorsal vertebra FMA:9922 fifth thoracic vertebra FMA:9922 The sixth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19547 FMA:9945 MA:0001443 NCIT:C33728 SCTID:181834005 UMLS:C0459949 T6 vertebra sixth dorsal vertebra sixth thoracic vertebra uberon UBERON:0004631 thoracic vertebra 6 FMA The sixth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T6_Vertebra UMLS:C0459949 ncithesaurus:T6_Vertebra T6 vertebra FMA:9945 sixth dorsal vertebra FMA:9945 sixth thoracic vertebra FMA:9945 The seventh thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19548 FMA:9968 MA:0001444 NCIT:C33729 SCTID:181835006 UMLS:C0459947 T7 vertebra seventh dorsal vertebra seventh thoracic vertebra uberon UBERON:0004632 thoracic vertebra 7 FMA The seventh thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T7_Vertebra UMLS:C0459947 ncithesaurus:T7_Vertebra T7 vertebra FMA:9968 seventh dorsal vertebra FMA:9968 seventh thoracic vertebra FMA:9968 The ninth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19550 FMA:10014 MA:0001446 NCIT:C33731 SCTID:181837003 UMLS:C0459954 Ninth dorsal vertebra T9 vertebra ninth thoracic vertebra uberon UBERON:0004633 thoracic vertebra 9 FMA The ninth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T9_Vertebra UMLS:C0459954 ncithesaurus:T9_Vertebra Ninth dorsal vertebra FMA:10014 T9 vertebra FMA:10014 ninth thoracic vertebra FMA:10014 The tenth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19551 FMA:10037 MA:0001447 NCIT:C33721 SCTID:181838008 UMLS:C0459955 T10 vertebra tenth dorsal vertebra tenth thoracic vertebra uberon UBERON:0004634 thoracic vertebra 10 FMA The tenth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T10_Vertebra UMLS:C0459955 ncithesaurus:T10_Vertebra T10 vertebra FMA:10037 tenth dorsal vertebra FMA:10037 tenth thoracic vertebra FMA:10037 The eleventh thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19552 FMA:10059 MA:0001448 NCIT:C33722 SCTID:181839000 UMLS:C0459956 T11 vertebra eleventh dorsal vertebra eleventh thoracic vertebra uberon UBERON:0004635 thoracic vertebra 11 FMA The eleventh thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T11_Vertebra UMLS:C0459956 ncithesaurus:T11_Vertebra T11 vertebra FMA:10059 eleventh dorsal vertebra FMA:10059 eleventh thoracic vertebra FMA:10059 The twelfth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. elements are to be defined spatially/topologically EMAPA:19553 FMA:10081 MA:0001449 NCIT:C33723 SCTID:181840003 UMLS:C0459957 T12 vertebra twelfth dorsal vertebra twelfth thoracic vertebra uberon UBERON:0004636 thoracic vertebra 12 FMA The twelfth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T12_Vertebra UMLS:C0459957 ncithesaurus:T12_Vertebra T12 vertebra FMA:10081 twelfth dorsal vertebra FMA:10081 twelfth thoracic vertebra FMA:10081 An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart. BTO:0000766 CALOHA:TS-2155 EMAPA:35176 MA:0000709 NCIT:C53395 TAO:0005257 UMLS:C1706972 ZFA:0005257 uberon UBERON:0004638 blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart. https://orcid.org/0000-0002-6601-2165 UMLS:C1706972 ncithesaurus:Blood_Vessel_Endothelium The blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism. EMAPA:28230 EMAPA:28266 FMA:77042 MA:0002579 SCTID:67498004 TAO:0002139 Wikipedia:Afferent_arterioles ZFA:0005307 afferent arteriole afferent glomerular arteriole afferent glomerular arteriole of kidney arteriola glomerularis afferens renis kidney afferent arteriole uberon arteriola glomerularis afferens UBERON:0004639 renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png Wikipedia The blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism. ISBN:0-683-40008-8 MGI:csmith MP:0011312 afferent arteriole MA:0002579 afferent glomerular arteriole ZFA:0005307 afferent glomerular arteriole of kidney FMA:77042 arteriola glomerularis afferens renis FMA:77042 FMA:TA kidney afferent arteriole MP:0011312 arteriola glomerularis afferens Wikipedia:Afferent_arterioles The connective tissue that surrounds the spleen. EMAPA:35802 FMA:15849 MA:0000753 NCIT:C33598 SCTID:329635002 UMLS:C0229681 Malpighian capsule capsula splenica capsule of spleen fibroelastic coat of spleen fibrous capsule of spleen splenic capsule tunica fibrosa (splen)(lien) tunica fibrosa splenica uberon UBERON:0004641 spleen capsule The connective tissue that surrounds the spleen. MGI:cwg MP:0002227 UMLS:C0229681 ncithesaurus:Splenic_Capsule Malpighian capsule FMA:15849 capsula splenica FMA:15849 FMA:TA capsule of spleen FMA:15849 fibroelastic coat of spleen FMA:15849 fibrous capsule of spleen FMA:15849 splenic capsule FMA:15849 tunica fibrosa (splen)(lien) FMA:15849 tunica fibrosa splenica FMA:15849 FMA:TA The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein. should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP] EMAPA:35499 FMA:14471 MA:0002494 NCIT:C32732 SCTID:362194004 UMLS:C0227518 Wikipedia:Lobules_of_liver hepatic lobule lobuli hepatici lobulus hepaticus uberon lobules of liver lobuli hepatis UBERON:0004647 liver lobule FMA FMA MA The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein. ISBN:0-683-40008-8 MP:0008987 UMLS:C0227518 ncithesaurus:Hepatic_Lobule hepatic lobule FMA:14471 lobuli hepatici lobulus hepaticus FMA:14471 lobules of liver Wikipedia:Lobules_of_liver lobuli hepatis Wikipedia:Lobules_of_liver A keratinized stratified squamous epithelium that is part of a tongue. FMA:74865 MA:0002787 keratinized epithelium of tongue uberon UBERON:0004650 tongue keratinized epithelium A keratinized stratified squamous epithelium that is part of a tongue. OBOL:automatic keratinized epithelium of tongue FMA:74865 The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces. EMAPA:25051 FMA:13305 MA:0002807 NCIT:C120671 SCTID:181927007 Wikipedia:Body_of_humerus body of humerus corpus humeri diaphysis of humerus humeral diaphysis shaft of humerus uberon body of the humerus medial humerus shaft of the humerus UBERON:0004652 humerus diaphysis The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces. Wikipedia:Body_of_humerus body of humerus FMA:13305 corpus humeri FMA:13305 FMA:TA diaphysis of humerus FMA:13305 humeral diaphysis FMA:13305 shaft of humerus FMA:13305 body of the humerus Wikipedia:Body_of_humerus medial humerus Wikipedia:Body_of_humerus shaft of the humerus Wikipedia:Body_of_humerus An anatomical wall that is part of an aorta, enclosing the luminal space. EMAPA:35139 FMA:14156 MA:0002901 aortic wall wall of aorta uberon UBERON:0004663 aorta wall An anatomical wall that is part of an aorta, enclosing the luminal space. http://orcid.org/0000-0002-6601-2165 aortic wall FMA:14156 wall of aorta FMA:14156 The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers. EMAPA:35136 FMA:14283 MA:0002902 SCTID:24996002 tunica adventitia of aorta uberon UBERON:0004664 aorta tunica adventitia The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers. ISBN:0-683-40008-8 MP:0009871 tunica adventitia of aorta FMA:14283 A muscular coat that is part of a seminal vesicle [Automatically generated definition]. EMAPA:29773 FMA:19404 MA:0002913 muscle layer of seminal vesicle muscular coat of seminal gland muscular layer of seminal gland tunica muscularis (vesicula seminalis) tunica muscularis glandulae vesiculosae uberon UBERON:0004665 muscular coat of seminal vesicle A muscular coat that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic muscle layer of seminal vesicle FMA:19404 muscular coat of seminal gland FMA:19404 muscular layer of seminal gland FMA:19404 tunica muscularis (vesicula seminalis) FMA:19404 tunica muscularis glandulae vesiculosae FMA:19404 FMA:TA The membranous portion of the wall between the two lower chambers of the heart. The membranous septum is the upper part of ventricular septum[GO:0003149]. UBERON:0004143 membranous septum ventricle membranous septum ventricular membranous septum EHDAA2:0004596 EMAPA:18246 FMA:7135 MA:0002939 SCTID:278228007 VHOG:0000927 cardiac ventricular membranous septum membranous interventricular septum membranous part interventricular septum membranous part of interventricular septum membranous portion of interventricular septum pars membranacea (septi interventricularis) pars membranacea septi interventricularis uberon membranous interventricular septum UBERON:0004666 interventricular septum membranous part Wikipedia The membranous portion of the wall between the two lower chambers of the heart. MP:0008823 The membranous septum is the upper part of ventricular septum[GO:0003149]. GO:0003149 membranous septum GO:0003149 ventricle membranous septum VT:0000018 ventricular membranous septum MP:0008823 cardiac ventricular membranous septum http://orcid.org/0000-0002-6601-2165 membranous interventricular septum FMA:7135 membranous part interventricular septum VHOG:0000927 membranous part of interventricular septum FMA:7135 membranous portion of interventricular septum FMA:7135 pars membranacea (septi interventricularis) FMA:7135 pars membranacea septi interventricularis FMA:7135 FMA:TA membranous interventricular septum MA:0002939 The muscular portion of the wall between the two lower chambers of the heart. The muscular septum is the lower part of the ventricular septum[GO] UBERON:0004144 muscular septum EHDAA2:0000885 EHDAA:2607 EMAPA:18247 FMA:7134 MA:0002940 RETIRED_EHDAA2:0000888 cardiac ventricular muscular septum muscular interventricular septum muscular part interventricular septum muscular part of interventricular septum pars muscularis (septi interventricularis) pars muscularis septi interventricularis septum membranaceum ventricular muscular septum uberon muscular interventricular septum UBERON:0004667 interventricular septum muscular part The muscular portion of the wall between the two lower chambers of the heart. Wikipedia:Interventricular_septum#Portions http://orcid.org/0000-0002-6601-2165 The muscular septum is the lower part of the ventricular septum[GO] GO:0003150 muscular septum GO:0003150 cardiac ventricular muscular septum http://orcid.org/0000-0002-6601-2165 muscular interventricular septum FMA:7134 muscular part of interventricular septum FMA:7134 pars muscularis (septi interventricularis) FMA:7134 pars muscularis septi interventricularis FMA:7134 FMA:TA septum membranaceum muscular interventricular septum MA:0002940 One of: the 4th ventricle median or lateral apertures. FMA:242766 MA:0002945 aperture of 4th ventricle aperture of fourth ventricle uberon UBERON:0004668 fourth ventricle aperture One of: the 4th ventricle median or lateral apertures. https://orcid.org/0000-0002-6601-2165 aperture of fourth ventricle FMA:242766 The sensory system for the sense of balance. The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]. FMA and NIF have no part information for this class. This is a GAT in FMA BTO:0003381 EMAPA:37986 FMA:7193 NLXANAT:090819 SCTID:361533001 Wikipedia:Vestibular_system vestibular organ system vestibular system equilibrioception system vestibulomotor system uberon UBERON:0004681 vestibular system The sensory system for the sense of balance. NLXANAT:090819 The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]. Wikipedia:Vestibular_system FMA and NIF have no part information for this class. This is a GAT in FMA FMA EMAPA:37986 MA:th vestibular organ system FMA:7193 vestibular system NLXANAT:090819 The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 FMA:84017 MA:0003147 MESH:D011903 NCIT:C97335 NLXANAT:20090205 TAO:0001429 UMLS:C0034671 Wikipedia:Raphe_nuclei ZFA:0001429 neuronames:2495 nuclei raphes raphe nuclei raphe nuclei set uberon nuclei raphes raphe cluster raphe nucleus raphe of mesenchephalon set of raphe nuclei UBERON:0004684 we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei' raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png GO Wikipedia Wikipedia The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. NLXANAT:20090205 https://sourceforge.net/tracker/?func=detail&aid=3248146&group_id=36855&atid=440764 UMLS:C0034671 ncithesaurus:Raphe_Nuclei nuclei raphes FMA:84017 FMA:TA raphe nuclei FMA:84017 NLXANAT:20090205 raphe nuclei set FMA:84017 nuclei raphes Wikipedia:Raphe_nuclei raphe cluster Wikipedia:Raphe_nuclei raphe nucleus ZFA:0001429 raphe of mesenchephalon BAMS:RA set of raphe nuclei FMA:84017 The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 FMA:10636 MA:0001939 SCTID:244225009 Wikipedia:Costocervical_trunk costocervical trunk trunk of costocervical artery uberon truncus costocervicalis UBERON:0004688 costo-cervical trunk http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. Wikipedia:Costocervical_trunk EMAPA:37496 MA:th costocervical trunk FMA:10636 trunk of costocervical artery FMA:10636 truncus costocervicalis Wikipedia:Costocervical_trunk An epithelium that is part of an external naris [Automatically generated definition]. EMAPA:18596 MA:0001321 uberon UBERON:0004692 external naris epithelium An epithelium that is part of an external naris [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. EMAPA:36503 MA:0000704 uberon UBERON:0004695 arterial system smooth muscle A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. EMAPA:36613 MA:0000715 uberon UBERON:0004696 venous system smooth muscle A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. OBOL:automatic An endothelium that is part of a vena cava [Automatically generated definition]. EMAPA:37800 MA:0000713 NCIT:C49318 UMLS:C1710623 uberon UBERON:0004698 vena cava endothelium An endothelium that is part of a vena cava [Automatically generated definition]. OBOL:automatic EMAPA:37800 MA:th UMLS:C1710623 ncithesaurus:Vena_Cava_Endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] MA:0000490 VHOG:0001524 uberon UBERON:0004699 outflow tract endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] 2012-09-17 VHOG:0001524 VHOG DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001) http://bgee.unil.ch/ An endothelium that is part of an arterial system [Automatically generated definition]. EMAPA:35145 MA:0000703 NCIT:C49329 UMLS:C1706849 uberon UBERON:0004700 arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. OBOL:automatic UMLS:C1706849 ncithesaurus:Arterial_System_Endothelium An endothelium that is part of a venous system [Automatically generated definition]. EMAPA:35907 MA:0000714 NCIT:C49320 UMLS:C1710626 uberon UBERON:0004701 venous system endothelium An endothelium that is part of a venous system [Automatically generated definition]. OBOL:automatic UMLS:C1710626 ncithesaurus:Venous_System_Endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:35732 MA:0001805 uberon UBERON:0004702 respiratory system blood vessel endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic A depression or hollow in a bone[WP]. Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO] General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here fossa AAO:0010439 FMA:45791 TAO:0001743 UMLS:C0836913 VSAO:0005069 Wikipedia:Fossa#Anatomy ZFA:0005388 uberon concavities concavity depression depressions fossae groove UBERON:0004704 bone fossa FMA-implied A depression or hollow in a bone[WP]. Wikipedia:Fossa#Anatomy Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO] 2012-08-14 TAO:0001743 TAO TAO:wd General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here FMA UMLS:C0836913 ncithesaurus:Fossa concavities TAO:0001743 concavity TAO:0001743 depression TAO:0001743 depressions TAO:0001743 fossae TAO:0001743 groove TAO:0001743 A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches. TODO - check relationship to bulbus arteriosus A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] EHDAA2:0000197 EHDAA:438 EHDAA:768 EMAPA:16333 FMA:70300 NCIT:C34114 SCTID:361525002 UMLS:C1284055 Wikipedia:Bulbus_cordis primitive right ventricle endocardium uberon UBERON:0004706 bulbus cordis http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches. ISBN:0-683-40008-8 MP:0010568 A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] 2012-08-14 TAO:0000173 TAO ZFIN:curator UMLS:C1284055 ncithesaurus:Bulbus_Cordis primitive right ventricle endocardium EHDAA2:0000197 A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities. Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001) DrerDO:0000052 EFO:0001310 OGES:000006 Wikipedia:Pharyngula ZFS:0000050 phylotypic stage uberon pharyngula UBERON:0004707 pharyngula stage A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities. Wikipedia:Pharyngula An appendage that is part of an appendage girdle complex. this class is the union of the classes limb, pectoral fin and pelvic fin. UBERON:0009872 VSAO:0000067 girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage uberon UBERON:0004708 paired limb/fin VSAO VSAO definitional An appendage that is part of an appendage girdle complex. UBERON:cjm https://github.com/geneontology/go-ontology/issues/9029 girdle-associated appendage https://orcid.org/0000-0002-6601-2165 limb or fin https://orcid.org/0000-0002-6601-2165 limb/fin https://orcid.org/0000-0002-6601-2165 pectoral or pelvic appendage https://orcid.org/0000-0002-6601-2165 pelvic/pectoral appendage https://orcid.org/0000-0002-6601-2165 jointed paired lateral appendage https://orcid.org/0000-0002-6601-2165 paired appendage VSAO:0000067 Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0009876 posterior appendage VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior limb/fin posterior paired appendage uberon UBERON:0004709 pelvic appendage definitional lexical Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. VSAO:0000150 hindlimb/pelvic fin https://orcid.org/0000-0002-6601-2165 pelvic appendage VSAO:0000126 pelvic limb/fin https://orcid.org/0000-0002-6601-2165 posterior paired appendage VSAO:0000126 Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] UBERON:0009875 anterior appendage VHOG:0001753 VSAO:0000125 anterior limb/fin anterior paired appendage forelimb - pectoral fin forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin uberon UBERON:0004710 pectoral appendage definitional Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. VSAO:0000150-modified While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001753 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) http://bgee.unil.ch/ anterior limb/fin https://orcid.org/0000-0002-6601-2165 anterior paired appendage VSAO:0000148 forelimb - pectoral fin VHOG:0001753 forelimb or pectoral fin https://orcid.org/0000-0002-6601-2165 forelimb/pectoral fin https://orcid.org/0000-0002-6601-2165 pectoral limb/fin https://orcid.org/0000-0002-6601-2165 The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. BTO:0001744 CALOHA:TS-0497 EMAPA:18638 GAID:536 MA:0002154 MESH:D007601 NCIT:C12738 SCTID:244403000 UMLS:C0022427 Wikipedia:Jugular_vein uberon jugular vena jugularis UBERON:0004711 jugular vein http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. Wikipedia:Jugular_vein UMLS:C0022427 ncithesaurus:Jugular_Vein vena jugularis BTO:0001744 The ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised. annulus fibrosus BTO:0003629 EMAPA:32670 FMA:13551 MA:0000111 Wikipedia:Annulus_fibrosus_disci_intervertebralis anulus fibrosus (diskus intervertebralis) anulus fibrosus of intervertebral disk uberon annulus fibrosus of intervertebral disc fibrous ring of intervertebral disc UBERON:0004715 annulus fibrosus disci intervertebralis http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png The ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised. BTO:0003629 Wikipedia:Annulus_fibrosus_disci_intervertebralis annulus fibrosus MA:0000111 anulus fibrosus (diskus intervertebralis) FMA:13551 anulus fibrosus of intervertebral disk FMA:13551 annulus fibrosus of intervertebral disc BTO:0003629 fibrous ring of intervertebral disc BTO:0003629 The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus AEO:0000194 BTO:0003834 EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 NCIT:C34131 UMLS:C1516779 Wikipedia:Conceptus embryo plus adnexa uberon UBERON:0004716 conceptus The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. BTO:0003834 Wikipedia:Conceptus UMLS:C1516779 ncithesaurus:Conceptus The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule. EMAPA:28212 FMA:70498 MA:0002584 NCIT:C32826 SCTID:76147008 UMLS:C1512856 Wikipedia:Interlobular_arteries interlobular renal artery kidney interlobular artery uberon arteriae corticales radiatae arteriae interlobulares renis cortical radial arteries interlobular renal interlobular artery UBERON:0004723 interlobular artery http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png Wikipedia:Renal_circulation The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule. MP:0011316 Wikipedia:Interlobular_arteries UMLS:C1512856 ncithesaurus:Interlobular_Artery interlobular renal artery FMA:70498 kidney interlobular artery MP:0011316 arteriae corticales radiatae Wikipedia:Interlobular_arteries arteriae interlobulares renis Wikipedia:Interlobular_arteries cortical radial arteries Wikipedia:Interlobular_arteries interlobular Wikipedia:Interlobular_arteries renal interlobular artery FMA:70498 A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted A metameric segment of the central nervous system.[ZFA] 2009-06-18T09:00:04Z NLX:147842 TAO:0001328 Wikipedia:Neuromere ZFA:0001328 neural tube metameric segment neural tube segment neuromere neuromeres uberon neural metamere neural segment UBERON:0004731 neuromere A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). DOI:10.1016/j.tins.2013.06.004 https://github.com/obophenotype/uberon/issues/318 A metameric segment of the central nervous system.[ZFA] 2012-08-14 TAO:0001328 TAO ZFIN:curator neural tube metameric segment http://orcid.org/0000-0002-6601-2165 neuromeres TAO:0001328 Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) uberon neuromere UBERON:0004732 segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 http://orcid.org/0000-0002-6601-2165 neuromere FBbt:00005140 An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 hindbrain segment segment of hindbrain uberon UBERON:0004733 segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. OBOL:automatic hindbrain segment FMA:61998 segment of hindbrain FMA:61998 Organism at the gastrula stage. We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 MIAA:0000179 NCIT:C34057 NCIT:C34058 UMLS:C0017199 UMLS:C1284022 Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst gastrula embryo uberon blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ UBERON:0004734 gastrula Organism at the gastrula stage. Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst We explicitly merge the NCITA terms here NCIT FBbt:00005317 UMLS:C0017199 ncithesaurus:Gastrula UMLS:C1284022 ncithesaurus:Trilaminar_Embryonic_Disc gastrula embryo BILA:0000060 blastocystis trilaminaris https://orcid.org/0000-0002-6601-2165 tri-laminar disc https://orcid.org/0000-0002-6601-2165 tri-laminar disk https://orcid.org/0000-0002-6601-2165 trilaminar blastocyst https://orcid.org/0000-0002-6601-2165 trilaminar blastoderm https://orcid.org/0000-0002-6601-2165 trilaminar disc https://orcid.org/0000-0002-6601-2165 trilaminar disk https://orcid.org/0000-0002-6601-2165 trilaminar germ https://orcid.org/0000-0002-6601-2165 Glomerulus of the mature vertebrate kidney, or metanephros. VHOG:0001242 glomerulus of metanephros uberon UBERON:0004736 metanephric glomerulus Glomerulus of the mature vertebrate kidney, or metanephros. GO:0072224 A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]. VHOG:0000983 collecting duct of metanephros uberon metanephric collecting tubule UBERON:0004737 metanephric collecting duct true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Wikipedia-abduced A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]. OBOL:automatic metanephric collecting tubule VHOG:0000983 The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment. a glomus differs from a glomerulus in that each vascular glomus services several tubules Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO] The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG] GO treats glomus and pronephric glomerulus differently UBERON:0004191 AAO:0011049 SCTID:360548001 TAO:0001557 VHOG:0001237 XAO:0000318 ZFA:0001557 glomerulus of pronephros glomus uberon corpuscle glomera pronephric glomera pronephric glomeruli pronephric glomus UBERON:0004739 pronephric glomerulus XAO The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment. DOI:10.1371/journal.pone.0099864 GO:0072013 GOC:mtg_kidney_jan10 PMID:10572058 PMID:15647339 PMID:9268568 XAO:0000318 a glomus differs from a glomerulus in that each vascular glomus services several tubules ISBN:0073040584 Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO] 2012-08-14 TAO:0001557 TAO ZFIN:curator The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001237 VHOG PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636 http://bgee.unil.ch/ GO treats glomus and pronephric glomerulus differently GO glomus XAO:0000318 corpuscle XAO:0000318 glomera XAO:0000318 pronephric glomera VHOG:0001237 pronephric glomeruli VHOG:0001237 pronephric glomus VHOG:0001237 The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO] Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO] The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG] relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG] In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular. AAO:0000124 EFO:0003508 TAO:0000191 VHOG:0001022 ZFA:0000191 http://palaeos.com/vertebrates/bones/dermal/images/Dentary1.gif dentaries dentary bone uberon dentale os dentale sur-angulaire UBERON:0004742 dentary ZFA mandibular series ISBN:0073040584 ZFA EHDAA2 EHDAA2-modified The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. VHOG:0001022 Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO] 2012-08-14 TAO:0000191 TAO TAO:GA_TG Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO] 2012-06-20 AAO:0000124 AAO AAO:LAP The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG] 2012-09-17 VHOG:0001022 VHOG http://bgee.unil.ch/ relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] 2012-08-14 TAO:0000191 TAO Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG] 2012-09-17 VHOG:0001022 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248 http://bgee.unil.ch/ dentaries TAO:0000191 dentary bone ZFA:0000191 dentale AAO:0000124 os dentale AAO:0000124 sur-angulaire AAO:0000124 Skeletal element that consists of the scapula and the coracoid[VSAO, modified]. todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO] Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO] either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos] relationship loss: part_of scapular area (AAO:0000935)[AAO] ZFA defines as precursor to scapula and coracoid. Cartilage in TAO AAO:0000781 TAO:0001455 VSAO:0005002 Wikipedia:Scapulocoracoid ZFA:0001455 scapulocoracoideum coraco-scapular cartilage scapulo-coracoid cartilage scapulocoracoid cartilage uberon UBERON:0004753 scapulocoracoid VSAO Skeletal element that consists of the scapula and the coracoid[VSAO, modified]. VSAO:0005002 Wikipedia:Scapulocoracoid https://github.com/obophenotype/uberon/issues/125 https://github.com/obophenotype/uberon/issues/66 Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO] 2012-06-20 AAO:0000781 AAO AAO:LAP Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO] 2012-08-14 TAO:0001455 TAO TAO:GA_TG ZFIN:curator either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos] 2012-09-10 http://palaeos.com/vertebrates/glossary/glossaryS.html relationship loss: part_of scapular area (AAO:0000935)[AAO] 2012-06-20 AAO:0000781 AAO ZFA defines as precursor to scapula and coracoid. Cartilage in TAO ZFA scapulocoracoideum VSAO:0005002 coraco-scapular cartilage ZFA:0001455 scapulo-coracoid cartilage TAO:0001455 scapulocoracoid cartilage TAO:0001455 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon UBERON:0004755 Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue VSAO 2012-08-14 VSAO:0000015 VSAO A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. GO_REF:0000034 PSPUB:0000170 VSAO:0000015 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] 2012-08-14 VSAO:0000015 taken from version of VSAO used in TAO and used directly in Uberon VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 EMAPA:37744 MA:th Dermis-derived entity that is made of skeletal tissue. dermal element uberon UBERON:0004756 dermal skeletal element Dermis-derived entity that is made of skeletal tissue. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/206 dermal element VSAO:curator A gland that is part of an anal canal [Automatically generated definition]. EMAPA:27221 EMAPA:27233 EMAPA:27543 FMA:15720 FMA:15724 NCIT:C32068 SCTID:245448005 UMLS:C0162322 Wikipedia:Anal_gland gland of anal canal uberon anal gland anal sac gland of anus rectal gland UBERON:0004760 gland of anal canal A gland that is part of an anal canal [Automatically generated definition]. OBOL:automatic Wikipedia:Anal_gland UMLS:C0162322 ncithesaurus:Anal_Gland gland of anal canal OBOL:automatic anal sac Wikipedia:Anal_gland The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 AAO:0010153 EHDAA:6031 FMA:76621 NCIT:C34121 SCTID:155540009 UMLS:C1516496 Wikipedia:Chondrocranium XAO:0003059 cartilaginous chondocranium cartiligionous skeletal structure of skull uberon cartilaginous skull chondocranium embryonic chondocranium neurocranium UBERON:0004761 cartilaginous neurocranium FMA PMC1571569 The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. Wikipedia:Chondrocranium in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) FMA UMLS:C1516496 ncithesaurus:Chondrocranium chondocranium Wikipedia:Chondrocranium neurocranium Replacement bone tissue that forms within cartilage[VSAO, modified]. the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type EMAPA:35304 MA:0002836 Wikipedia:Endochondral_ossification uberon UBERON:0004763 endochondral bone tissue Replacement bone tissue that forms within cartilage[VSAO, modified]. GO:0001958 VSAO:0000145 Wikipedia:Endochondral_ossification the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type MA Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) MA:0002837 Wikipedia:Intramembranous_ossification uberon UBERON:0004764 intramembranous bone tissue Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. GO:0001957 Wikipedia:Intramembranous_ossification note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) MA Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon UBERON:0004765 skeletal element VSAO Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 VSAO:0000128 VSAO PSPUB:0000170 Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 TAO:0001890 TAO TAO:VSAO_workshop A bone that is part of a cranium. here cranium = skull - mandible SCTID:181792001 cranium bone uberon UBERON:0004766 cranial bone A bone that is part of a cranium. UBERON:automatic cranium bone UBERON:automatic A tooth that is on the vomer. Tooth that is attached to the vomer.[TAO] relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO] AAO:0000635 TAO:0001631 uberon UBERON:0004767 vomerine tooth A tooth that is on the vomer. http://www.encyclo.co.uk/define/Vomerine%20teeth Tooth that is attached to the vomer.[TAO] 2012-08-14 TAO:0001631 TAO TAO:wd relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO] 2012-08-14 TAO:0001631 TAO Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. Do not manually classify under here - bones are automatically classified lower jaw bone uberon UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular. https://orcid.org/0000-0002-6601-2165 Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified]. Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA]. The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis]. EMAPA:35504 FMA:24013 GAID:189 MESH:D018483 SCTID:361729006 Wikipedia:Diaphysis body of long bone long bone diaphysis shaft of long bone uberon UBERON:0004769 diaphysis http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified]. FMA:24013 Wikipedia:Diaphysis Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA]. FMA:24013 The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis]. FMA:24013, Wikipedia:Diaphysis Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 SCTID:361827000 VSAO:0000181 joint system set of all joints of body uberon set of all joints set of joints of body UBERON:0004770 articular system FMA Anatomical system that consists of all the joints of the body. VSAO:0000181 joint system FMA:23878 set of all joints of body FMA:23878 set of joints of body FMA:23878 Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP]. One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Opening between the nasal cavity and the nasopharynx.[AAO] The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] Fish don't have choanae, instead they have two pairs of external nostrils In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity. choana internal naris AAO:0000093 EHDAA2:0000242 EHDAA:7842 EMAPA:17849 FMA:53143 MA:0001323 SCTID:244507001 VHOG:0000545 Wikipedia:Posterior_nasal_apertures XAO:0000277 posterior nasal apperture uberon choanae nasopharyngeal naris posterior choana posterior naris UBERON:0004771 posterior nasal aperture http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP]. AAO:0000093 Wikipedia:Posterior_nasal_apertures One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000545 VHOG http://bgee.unil.ch/ Opening between the nasal cavity and the nasopharynx.[AAO] 2012-06-20 AAO:0000093 AAO AAO:LAP The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] 2012-09-17 VHOG:0000545 VHOG DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004) http://bgee.unil.ch/ Fish don't have choanae, instead they have two pairs of external nostrils WP choana Wikipedia:Choane XAO:0000277 internal naris MA:0001323 posterior nasal apperture XAO:0000277 choanae VHOG:0000545 posterior choana HP:0004496 posterior naris VHOG:0000545 A submucosa that is part of a respiratory system [Automatically generated definition]. EMAPA:37578 MA:0001822 apparatus respiratorius submucosa submucosa of apparatus respiratorius submucosa of respiratory system uberon UBERON:0004777 respiratory system submucosa A submucosa that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37578 MA:th apparatus respiratorius submucosa OBOL:automatic submucosa of apparatus respiratorius OBOL:automatic submucosa of respiratory system OBOL:automatic A submucosa that is part of a larynx [Automatically generated definition]. EMAPA:35474 FMA:321584 MA:0002728 SCTID:361941005 submucosa of larynx uberon laryngeal submucosa UBERON:0004778 larynx submucosa A submucosa that is part of a larynx [Automatically generated definition]. OBOL:automatic submucosa of larynx OBOL:automatic laryngeal submucosa EMAPA:35474 A lamina propria that is part of a respiratory system [Automatically generated definition]. EMAPA:37576 MA:0001821 apparatus respiratorius lamina propria apparatus respiratorius lamina propria mucosa lamina propria mucosa of apparatus respiratorius lamina propria mucosa of respiratory system lamina propria of apparatus respiratorius lamina propria of respiratory system respiratory system lamina propria mucosa uberon UBERON:0004779 respiratory system lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37576 MA:th apparatus respiratorius lamina propria OBOL:automatic apparatus respiratorius lamina propria mucosa OBOL:automatic lamina propria mucosa of apparatus respiratorius OBOL:automatic lamina propria mucosa of respiratory system OBOL:automatic lamina propria of apparatus respiratorius OBOL:automatic lamina propria of respiratory system OBOL:automatic respiratory system lamina propria mucosa OBOL:automatic A lamina propria that is part of a gastrointestinal system. MA:0001899 NCIT:C49299 UMLS:C1708197 uberon UBERON:0004780 gastrointestinal system lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a gastrointestinal system. OBOL:automatic UMLS:C1708197 ncithesaurus:Gastrointestinal_Tract_Lamina_Propria A lamina propria that is part of a gallbladder [Automatically generated definition]. EMAPA:35371 FMA:278594 MA:0001633 NCIT:C49228 UMLS:C1708175 gall bladder lamina propria gall bladder lamina propria mucosa gallbladder lamina propria mucosa lamina propria mucosa of gall bladder lamina propria mucosa of gallbladder lamina propria of gall bladder lamina propria of gallbladder uberon biliary lamina propria UBERON:0004781 gallbladder lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708175 ncithesaurus:Gallbladder_Lamina_Propria gall bladder lamina propria OBOL:automatic gall bladder lamina propria mucosa OBOL:automatic lamina propria mucosa of gall bladder OBOL:automatic lamina propria mucosa of gallbladder OBOL:automatic lamina propria of gall bladder OBOL:automatic lamina propria of gallbladder OBOL:automatic biliary lamina propria MA:0001633 A serous membrane that is part of a digestive system [Automatically generated definition]. EMAPA:37592 MA:0001522 digestive system serosa digestive system serous membrane gastrointestinal system serous membrane serosa of digestive system serosa of gastrointestinal system serous membrane of digestive system serous membrane of gastrointestinal system uberon UBERON:0004782 gastrointestinal system serosa A serous membrane that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37592 MA:th digestive system serosa OBOL:automatic digestive system serous membrane OBOL:automatic gastrointestinal system serous membrane OBOL:automatic serosa of digestive system OBOL:automatic serosa of gastrointestinal system OBOL:automatic serous membrane of digestive system OBOL:automatic serous membrane of gastrointestinal system OBOL:automatic A serous membrane that is part of a gallbladder [Automatically generated definition]. EMAPA:35372 FMA:14659 MA:0001634 SCTID:362197006 gall bladder serosa gall bladder serous membrane gallbladder serous membrane serosa of gall bladder serosa of gallbladder serous coat of gallbladder serous membrane of gall bladder serous membrane of gallbladder tunica serosa (vesica biliaris) tunica serosa vesicae biliaris uberon biliary serosa UBERON:0004783 gallbladder serosa A serous membrane that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder serosa OBOL:automatic gallbladder serous membrane OBOL:automatic serosa of gall bladder OBOL:automatic serosa of gallbladder OBOL:automatic serous coat of gallbladder FMA:14659 serous membrane of gall bladder OBOL:automatic serous membrane of gallbladder OBOL:automatic tunica serosa (vesica biliaris) FMA:14659 tunica serosa vesicae biliaris FMA:14659 FMA:TA biliary serosa MA:0001634 An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. FMA:13884 MA:0002791 NCIT:C119295 anatomical wall of cardiac ventricle anatomical wall of heart ventricle anatomical wall of lower chamber of heart anatomical wall of ventricle of heart cardiac ventricle anatomical wall cardiac ventricle wall heart ventricle anatomical wall lower chamber of heart anatomical wall lower chamber of heart wall ventricle of heart anatomical wall ventricle of heart wall ventricular wall wall of cardiac ventricle wall of heart ventricle wall of lower chamber of heart wall of ventricle of heart uberon wall of ventricle UBERON:0004784 heart ventricle wall An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. OBOL:automatic anatomical wall of cardiac ventricle OBOL:automatic anatomical wall of heart ventricle OBOL:automatic anatomical wall of lower chamber of heart OBOL:automatic anatomical wall of ventricle of heart OBOL:automatic cardiac ventricle anatomical wall OBOL:automatic cardiac ventricle wall OBOL:automatic heart ventricle anatomical wall OBOL:automatic lower chamber of heart anatomical wall OBOL:automatic lower chamber of heart wall OBOL:automatic ventricle of heart anatomical wall OBOL:automatic ventricle of heart wall OBOL:automatic ventricular wall FMA:13884 wall of cardiac ventricle OBOL:automatic wall of heart ventricle OBOL:automatic wall of lower chamber of heart OBOL:automatic wall of ventricle of heart OBOL:automatic wall of ventricle MA:0002791 The mucous membrane lining the respiratory tract. TODO - split respiratory tract mucosa from respiratory system mucosa BTO:0000973 EMAPA:18334 EMAPA:37577 FMA:302092 GAID:304 MA:0001827 MESH:D020545 apparatus respiratorius mucosa apparatus respiratorius mucosa of organ apparatus respiratorius mucous membrane mucosa of apparatus respiratorius mucosa of organ of apparatus respiratorius mucosa of organ of respiratory system mucosa of respiratory system mucous membrane of apparatus respiratorius mucous membrane of respiratory system respiratory system mucosa of organ respiratory system mucous membrane uberon laryngeal mucous membrane respiratory mucosa respiratory tract mucosa UBERON:0004785 respiratory system mucosa The mucous membrane lining the respiratory tract. MESH:A04.760 MGI:cwg MP:0002277 EMAPA:37577 MA:th apparatus respiratorius mucosa OBOL:automatic apparatus respiratorius mucosa of organ OBOL:automatic apparatus respiratorius mucous membrane OBOL:automatic mucosa of apparatus respiratorius OBOL:automatic mucosa of organ of apparatus respiratorius OBOL:automatic mucosa of organ of respiratory system OBOL:automatic mucosa of respiratory system OBOL:automatic mucous membrane of apparatus respiratorius OBOL:automatic mucous membrane of respiratory system OBOL:automatic respiratory system mucosa of organ OBOL:automatic respiratory system mucous membrane OBOL:automatic laryngeal mucous membrane EMAPA:18334 respiratory mucosa BTO:0000973 A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 SCTID:410433007 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon UBERON:0004786 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa PMID:16417468 PMID:16417468 PMID:16417468 BTO-modified A mucosa that is part of a gastrointestinal system. OBOL:automatic digestive tract mucosa https://orcid.org/0000-0002-6601-2165 gut mucosa BTO:0000546 gut mucuous membrane https://orcid.org/0000-0002-6601-2165 mucosa of gut https://orcid.org/0000-0002-6601-2165 A mucous gland that is part of a larynx [Automatically generated definition]. EMAPA:37631 MA:0001767 mucous gland of larynx uberon UBERON:0004789 larynx mucous gland A mucous gland that is part of a larynx [Automatically generated definition]. OBOL:automatic EMAPA:37631 MA:th mucous gland of larynx OBOL:automatic A mucous gland that is part of the skin. See comments for 'skin mucus' EMAPA:35775 MA:0000148 mucous gland of entire skin mucous gland of skin of body skin mucus gland skin of body mucous gland uberon UBERON:0004790 skin mucous gland A mucous gland that is part of the skin. http://orcid.org/0000-0002-6601-2165 mucous gland of entire skin OBOL:automatic mucous gland of skin of body OBOL:automatic skin mucus gland OBOL:automatic skin of body mucous gland OBOL:automatic The thymic connective tissue which extends into the parenchyma. MA:0002674 NCIT:C33773 UMLS:C1515431 thymic trabecula thymus gland trabecula thymus trabeculae trabecula of thymus trabecula of thymus gland uberon UBERON:0004791 thymus trabecula MA The thymic connective tissue which extends into the parenchyma. ISBN:0-397-51047-0 MGI:cwg MP:0002370 UMLS:C1515431 ncithesaurus:Thymic_Trabecula thymic trabecula OBOL:automatic thymus gland trabecula OBOL:automatic thymus trabeculae trabecula of thymus OBOL:automatic trabecula of thymus gland OBOL:automatic A secretion that is part of a endocrine pancreas [Automatically generated definition]. MA:0002517 NCIT:C33255 UMLS:C1518866 endocrine pancreas secretion pancreatic endocrine secretion pars endocrina pancreatis secretion secretion of pars endocrina pancreatis uberon UBERON:0004792 secretion of endocrine pancreas A secretion that is part of a endocrine pancreas [Automatically generated definition]. OBOL:automatic UMLS:C1518866 ncithesaurus:Pancreatic_Endocrine_Secretion endocrine pancreas secretion OBOL:automatic pancreatic endocrine secretion ncithesaurus:Pancreatic_Endocrine_Secretion pars endocrina pancreatis secretion OBOL:automatic secretion of pars endocrina pancreatis OBOL:automatic A secretion that is part of a exocrine pancreas [Automatically generated definition]. MA:0002518 NCIT:C33256 UMLS:C1518867 exocrine pancreas secretion pancreatic exocrine secretion pars exocrina pancreatis secretion secretion of pars exocrina pancreatis uberon UBERON:0004793 secretion of exocrine pancreas A secretion that is part of a exocrine pancreas [Automatically generated definition]. OBOL:automatic UMLS:C1518867 ncithesaurus:Pancreatic_Exocrine_Secretion exocrine pancreas secretion OBOL:automatic pancreatic exocrine secretion ncithesaurus:Pancreatic_Exocrine_Secretion pars exocrina pancreatis secretion OBOL:automatic secretion of pars exocrina pancreatis OBOL:automatic A secretion that is part of a esophagus [Automatically generated definition]. FMA:79662 MA:0002514 NCIT:C52555 UMLS:C0227179 esophageal secretion gullet secretion oesophagus secretion secretion of esophagus secretion of gullet secretion of oesophagus uberon UBERON:0004794 esophagus secretion A secretion that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C0227179 ncithesaurus:Esophagus_Secretion esophageal secretion FMA:79662 gullet secretion OBOL:automatic oesophagus secretion OBOL:automatic secretion of esophagus OBOL:automatic secretion of gullet OBOL:automatic secretion of oesophagus OBOL:automatic A secretion that is part of a pancreas [Automatically generated definition]. MA:0002516 NCIT:C13270 UMLS:C0030296 pancreatic secretion secretion of pancreas uberon UBERON:0004795 pancreas secretion A secretion that is part of a pancreas [Automatically generated definition]. OBOL:automatic UMLS:C0030296 ncithesaurus:Pancreatic_Secretion pancreatic secretion OBOL:automatic secretion of pancreas OBOL:automatic A bodily secretion that is produced by the prostate gland. Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline. A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions] UBERON:0010142 EMAPA:36545 FMA:66884 MA:0002525 NCIT:C52553 UMLS:C1709733 Wikipedia:Prostate#Secretions prostate secretion prostatic fluid secretion of prostate secretion of prostate gland uberon prostate fluid UBERON:0004796 prostate gland secretion FMA A bodily secretion that is produced by the prostate gland. http://orcid.org/0000-0002-6601-2165 UMLS:C1709733 ncithesaurus:Prostate_Gland_Secretion prostate secretion OBOL:automatic prostatic fluid FMA:66884 secretion of prostate OBOL:automatic secretion of prostate gland OBOL:automatic prostate fluid BTO:0001232 Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. EMAPA:36296 MA:0002854 uberon UBERON:0004797 blood vessel layer https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. http://orcid.org/0000-0002-6601-2165 An epithelium that is part of a uterine cervix [Automatically generated definition]. The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium BTO:0000241 CALOHA:TS-0137 EFO:0001913 EMAPA:29929 MA:0001724 NCIT:C49218 UMLS:C1711358 cervical canal epithelial tissue cervical canal epithelium cervical epithelium cervix epithelial tissue epithelium of cervix uberon UBERON:0004801 cervix epithelium An epithelium that is part of a uterine cervix [Automatically generated definition]. OBOL:automatic The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium Wikipedia:Cervix#Histology UMLS:C1711358 ncithesaurus:Cervix_Epithelium cervical canal epithelial tissue OBOL:automatic cervical canal epithelium OBOL:automatic cervical epithelium BTO:0000241 cervix epithelial tissue OBOL:automatic epithelium of cervix OBOL:automatic The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 SCTID:321764001 VHOG:0000981 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue uberon airway epithelium respiratory epithelium UBERON:0004802 respiratory tract epithelium The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. ISBN:0-683-40008-8 MGI:anna MP:0010942 epithelial tissue of respiratory tract OBOL:automatic epithelium of respiratory tract OBOL:automatic respiratory tract epithelial tissue OBOL:automatic airway epithelium BTO:0000419 respiratory epithelium BTO:0000419 An epithelium that is part of a penis [Automatically generated definition]. EHDAA2:0004039 EMAPA:35674 MA:0001742 epithelial tissue of penis epithelium of penis penis epithelial tissue uberon UBERON:0004803 penis epithelium An epithelium that is part of a penis [Automatically generated definition]. OBOL:automatic epithelial tissue of penis OBOL:automatic epithelium of penis OBOL:automatic penis epithelial tissue OBOL:automatic An epithelium that is part of a oviduct [Automatically generated definition]. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label BTO:0002402 CALOHA:TS-1316 EMAPA:29043 MA:0001718 epithelial tissue of oviduct epithelium of fallopian tube epithelium of oviduct epithelium of uterine tube oviduct epithelial tissue uberon columnar epithelium of the fallopian tube columnar epithelium of the oviduct fallopian tube epithelium UBERON:0004804 oviduct epithelium An epithelium that is part of a oviduct [Automatically generated definition]. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelial tissue of oviduct OBOL:automatic epithelium of fallopian tube OBOL:automatic epithelium of oviduct OBOL:automatic epithelium of uterine tube FMA:62016 oviduct epithelial tissue OBOL:automatic columnar epithelium of the fallopian tube BTO:0002402 columnar epithelium of the oviduct BTO:0002402 fallopian tube epithelium BTO:0002402 An epithelium that is part of a seminal vesicle [Automatically generated definition]. CALOHA:TS-2069 EMAPA:29771 MA:0001745 NCIT:C49295 UMLS:C1710049 epithelial tissue of seminal gland epithelial tissue of seminal vesicle epithelium of seminal gland epithelium of seminal vesicle seminal gland epithelial tissue seminal gland epithelium seminal vesicle epithelial tissue uberon UBERON:0004805 seminal vesicle epithelium An epithelium that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic UMLS:C1710049 ncithesaurus:Seminal_Vesicle_Epithelium epithelial tissue of seminal gland OBOL:automatic epithelial tissue of seminal vesicle OBOL:automatic epithelium of seminal gland OBOL:automatic epithelium of seminal vesicle OBOL:automatic seminal gland epithelial tissue OBOL:automatic seminal gland epithelium OBOL:automatic seminal vesicle epithelial tissue OBOL:automatic An epithelium that is part of a vas deferens [Automatically generated definition]. EMAPA:29274 FMA:225317 MA:0001749 NCIT:C49315 UMLS:C1710617 deferent duct epithelial tissue deferent duct epithelium ductus deferens epithelial tissue ductus deferens epithelium epithelial tissue of deferent duct epithelial tissue of ductus deferens epithelial tissue of sperm duct epithelial tissue of vas deferen epithelial tissue of vas deferens epithelium of deferent duct epithelium of ductus deferens epithelium of sperm duct epithelium of vas deferen epithelium of vas deferens sperm duct epithelial tissue sperm duct epithelium vas deferen epithelial tissue vas deferen epithelium vas deferens epithelial tissue uberon UBERON:0004806 vas deferens epithelium An epithelium that is part of a vas deferens [Automatically generated definition]. OBOL:automatic UMLS:C1710617 ncithesaurus:Vas_Deferens_Epithelium deferent duct epithelial tissue OBOL:automatic deferent duct epithelium OBOL:automatic ductus deferens epithelial tissue OBOL:automatic ductus deferens epithelium OBOL:automatic epithelial tissue of deferent duct OBOL:automatic epithelial tissue of ductus deferens OBOL:automatic epithelial tissue of sperm duct OBOL:automatic epithelial tissue of vas deferen OBOL:automatic epithelial tissue of vas deferens OBOL:automatic epithelium of deferent duct OBOL:automatic epithelium of ductus deferens OBOL:automatic epithelium of sperm duct OBOL:automatic epithelium of vas deferen OBOL:automatic epithelium of vas deferens OBOL:automatic sperm duct epithelial tissue OBOL:automatic sperm duct epithelium OBOL:automatic vas deferen epithelial tissue OBOL:automatic vas deferen epithelium OBOL:automatic vas deferens epithelial tissue OBOL:automatic An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue uberon UBERON:0004807 respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius epithelial tissue OBOL:automatic apparatus respiratorius epithelium OBOL:automatic epithelial tissue of apparatus respiratorius OBOL:automatic epithelial tissue of respiratory system OBOL:automatic epithelium of apparatus respiratorius OBOL:automatic epithelium of respiratory system OBOL:automatic respiratory system epithelial tissue OBOL:automatic An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon UBERON:0004808 gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. OBOL:automatic digestive system epithelial tissue OBOL:automatic digestive system epithelium OBOL:automatic epithelial tissue of digestive system OBOL:automatic epithelial tissue of gastrointestinal system OBOL:automatic epithelium of digestive system OBOL:automatic epithelium of gastrointestinal system OBOL:automatic gastrointestinal system epithelial tissue OBOL:automatic An epithelium that is part of a salivary gland [Automatically generated definition]. BTO:0004421 CALOHA:TS-2067 EMAPA:32816 MA:0001587 epithelial tissue of salivary gland epithelium of salivary gland salivary gland epithelial tissue uberon UBERON:0004809 salivary gland epithelium An epithelium that is part of a salivary gland [Automatically generated definition]. OBOL:automatic epithelial tissue of salivary gland OBOL:automatic epithelium of salivary gland OBOL:automatic salivary gland epithelial tissue OBOL:automatic The cellular avascular layer of the renal tubule luminar surfaces. See https://github.com/obophenotype/uberon/issues/1305 BTO:0005239 EMAPA:36524 MA:0001681 NCIT:C49276 UMLS:C1709902 kidney tubule epithelium uberon UBERON:0004810 nephron tubule epithelium The cellular avascular layer of the renal tubule luminar surfaces. MGI:csmith MP:0009640 UMLS:C1709902 ncithesaurus:Renal_Tubule_Epithelium kidney tubule epithelium MA:0001681 An epithelium that is part of an endometrium [Automatically generated definition]. In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) EMAPA:35307 MA:0002731 SCTID:253526009 endometrium epithelial tissue epithelial tissue of endometrium epithelium of endometrium epithelium of tunica mucosa of endometrium uberon uterine epithelium UBERON:0004811 endometrium epithelium An epithelium that is part of an endometrium [Automatically generated definition]. OBOL:automatic In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) PMID:19829370 endometrium epithelial tissue OBOL:automatic epithelial tissue of endometrium OBOL:automatic epithelium of endometrium OBOL:automatic epithelium of tunica mucosa of endometrium OBOL:automatic uterine epithelium PMID:19829370 An epithelium that is part of a prepuce of penis [Automatically generated definition]. NCITA term may be sex-neutral epithelial tissue of prepuce epithelium of prepuce prepuce epithelial tissue prepuce of penis epithelium EMAPA:30655 MA:0001753 NCIT:C49270 UMLS:C1709639 epithelial tissue of foreskin epithelial tissue of penile prepuce epithelial tissue of prepuce of penis epithelium of foreskin epithelium of penile prepuce epithelium of prepuce of penis foreskin epithelial tissue foreskin epithelium penile prepuce epithelial tissue penile prepuce epithelium prepuce epithelium prepuce of penis epithelial tissue uberon UBERON:0004812 male prepuce epithelium An epithelium that is part of a prepuce of penis [Automatically generated definition]. OBOL:automatic epithelial tissue of prepuce OBOL:automatic epithelium of prepuce OBOL:automatic prepuce epithelial tissue OBOL:automatic prepuce of penis epithelium OBOL:automatic UMLS:C1709639 ncithesaurus:Prepuce_Epithelium epithelial tissue of foreskin OBOL:automatic epithelial tissue of penile prepuce OBOL:automatic epithelial tissue of prepuce of penis OBOL:automatic epithelium of foreskin OBOL:automatic epithelium of penile prepuce OBOL:automatic epithelium of prepuce of penis OBOL:automatic foreskin epithelial tissue OBOL:automatic foreskin epithelium OBOL:automatic penile prepuce epithelial tissue OBOL:automatic penile prepuce epithelium OBOL:automatic prepuce epithelium MA:0001753 prepuce of penis epithelial tissue OBOL:automatic The stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule. BTO:0001811 CALOHA:TS-0920 EHDAA:8148 EMAPA:35761 FMA:19885 GAID:401 MA:0001748 MESH:D012670 NCIT:C49296 RETIRED_EHDAA2:0002009 UMLS:C0036629 VHOG:0000631 Wikipedia:Germinal_epithelium_(male) epithelial tissue of seminiferous tubule epithelial tissue of seminiferous tubule of testis epithelium of seminiferous tubule epithelium of seminiferous tubule of testis germinal epithelium (male) male germinal epithelium seminiferous epithelium seminiferous tubule epithelial tissue testis germinal epithelium wall of seminiferous tubule uberon UBERON:0004813 seminiferous tubule epithelium The stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule. MGI:csmith MP:0011750 UMLS:C0036629 ncithesaurus:Seminiferous_Epithelium epithelial tissue of seminiferous tubule OBOL:automatic epithelial tissue of seminiferous tubule of testis OBOL:automatic epithelium of seminiferous tubule OBOL:automatic epithelium of seminiferous tubule of testis OBOL:automatic germinal epithelium (male) Wikipedia:Germinal_epithelium_(male) male germinal epithelium Wikipedia:Germinal_epithelium_(male) seminiferous epithelium BTO:0001811 seminiferous tubule epithelial tissue OBOL:automatic testis germinal epithelium VHOG:0000631 wall of seminiferous tubule Wikipedia:Germinal_epithelium_(male) An epithelium that is part of a upper respiratory tract [Automatically generated definition]. EMAPA:35894 MA:0001912 epithelial tissue of upper respiratory tract epithelium of upper respiratory tract upper respiratory tract epithelial tissue uberon UBERON:0004814 upper respiratory tract epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. OBOL:automatic epithelial tissue of upper respiratory tract OBOL:automatic epithelium of upper respiratory tract OBOL:automatic upper respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37549 MA:0001481 epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue uberon UBERON:0004815 lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37549 MA:th epithelial tissue of lower respiratory tract OBOL:automatic epithelium of lower respiratory tract OBOL:automatic lower respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a larynx [Automatically generated definition]. composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] EHDAA2:0004065 EMAPA:35472 MA:0001765 NCIT:C49247 UMLS:C0751258 epithelial tissue of larynx epithelium of larynx laryngeal epithelium larynx epithelial tissue uberon UBERON:0004816 larynx epithelium An epithelium that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C0751258 ncithesaurus:Laryngeal_Epithelium epithelial tissue of larynx OBOL:automatic epithelium of larynx OBOL:automatic laryngeal epithelium OBOL:automatic larynx epithelial tissue OBOL:automatic An epithelium that is part of a lacrimal gland [Automatically generated definition]. EMAPA:36515 MA:0001297 epithelial tissue of lacrimal gland epithelium of lacrimal gland lacrimal gland epithelial tissue uberon UBERON:0004817 lacrimal gland epithelium An epithelium that is part of a lacrimal gland [Automatically generated definition]. OBOL:automatic epithelial tissue of lacrimal gland OBOL:automatic epithelium of lacrimal gland OBOL:automatic lacrimal gland epithelial tissue OBOL:automatic The cellular avascular layer of the kidney luminar surfaces. BTO:0000059 CALOHA:TS-0505 EMAPA:35457 MA:0002846 epithelial tissue of kidney epithelium of kidney kidney epithelial tissue uberon renal epithelium UBERON:0004819 kidney epithelium The cellular avascular layer of the kidney luminar surfaces. MGI:csmith MP:0004967 epithelial tissue of kidney OBOL:automatic epithelium of kidney OBOL:automatic kidney epithelial tissue OBOL:automatic renal epithelium EMAPA:35457 Any epithelium that lines one of the bile ducts. The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. BTO:0000417 MA:0001629 NCIT:C43616 UMLS:C1711208 biliary duct epithelium epithelium of bile duct epithelium of biliary duct uberon UBERON:0004820 bile duct epithelium Any epithelium that lines one of the bile ducts. http://orcid.org/0000-0002-6601-2165 The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. BTO:0000417 UMLS:C1711208 ncithesaurus:Bile_Duct_Epithelium biliary duct epithelium OBOL:automatic epithelium of bile duct OBOL:automatic epithelium of biliary duct OBOL:automatic An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]. EHDAA2:0000742 EHDAA:3051 MA:0002661 NCIT:C43618 UMLS:C1711347 epithelial tissue of extrahepatic bile duct epithelium of extrahepatic bile duct extrahepatic bile duct epithelial tissue uberon UBERON:0004822 extrahepatic bile duct epithelium An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]. OBOL:automatic UMLS:C1711347 ncithesaurus:Extrahepatic_Bile_Duct_Epithelium epithelial tissue of extrahepatic bile duct OBOL:automatic epithelium of extrahepatic bile duct OBOL:automatic extrahepatic bile duct epithelial tissue OBOL:automatic An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]. EHDAA2:0000743 EHDAA:3053 MA:0002662 NCIT:C43617 UMLS:C1708552 epithelial tissue of intrahepatic bile duct epithelium of intrahepatic bile duct intrahepatic bile duct epithelial tissue uberon UBERON:0004823 intrahepatic bile duct epithelium An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]. OBOL:automatic UMLS:C1708552 ncithesaurus:Intrahepatic_Bile_Duct_Epithelium epithelial tissue of intrahepatic bile duct OBOL:automatic epithelium of intrahepatic bile duct OBOL:automatic intrahepatic bile duct epithelial tissue OBOL:automatic A medulla that is part of a thyroid [Automatically generated definition]. EMAPA:37768 MA:0000132 medulla of thyroid medulla of thyroid follicle medulla of thyroid gland medulla of thyroid gland follicle thyroid follicle medulla thyroid gland follicle medulla thyroid medulla uberon UBERON:0004827 thyroid gland medulla A medulla that is part of a thyroid [Automatically generated definition]. OBOL:automatic EMAPA:37768 MA:th medulla of thyroid OBOL:automatic medulla of thyroid follicle OBOL:automatic medulla of thyroid gland OBOL:automatic medulla of thyroid gland follicle OBOL:automatic thyroid follicle medulla OBOL:automatic thyroid gland follicle medulla OBOL:automatic thyroid medulla OBOL:automatic A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:37788 MA:0001690 skeletal muscle of urethra skeletal muscle tissue of urethra urethra skeletal muscle tissue uberon urethra skeletal muscle urethral skeletal muscle UBERON:0004829 urethra skeletal muscle tissue A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37788 MA:th skeletal muscle of urethra OBOL:automatic skeletal muscle tissue of urethra OBOL:automatic urethra skeletal muscle tissue OBOL:automatic urethra skeletal muscle MA:0001690 urethral skeletal muscle MA:0001690 A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37583 MA:0001829 respiratory system skeletal muscle tissue skeletal muscle of apparatus respiratorius skeletal muscle of respiratory system skeletal muscle tissue of apparatus respiratorius skeletal muscle tissue of respiratory system uberon UBERON:0004830 respiratory system skeletal muscle A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37583 MA:th respiratory system skeletal muscle tissue OBOL:automatic skeletal muscle of apparatus respiratorius OBOL:automatic skeletal muscle of respiratory system OBOL:automatic skeletal muscle tissue of apparatus respiratorius OBOL:automatic skeletal muscle tissue of respiratory system OBOL:automatic A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:36523 MA:0001572 esophagus skeletal muscle tissue skeletal muscle of esophagus uberon UBERON:0004831 Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal esophagus skeletal muscle A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus skeletal muscle tissue OBOL:automatic skeletal muscle of esophagus OBOL:automatic A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37393 MA:0001530 anal part of perineum skeletal muscle anal part of perineum skeletal muscle tissue anal region skeletal muscle tissue anal triangle skeletal muscle anal triangle skeletal muscle tissue skeletal muscle of anal part of perineum skeletal muscle of anal region skeletal muscle of anal triangle skeletal muscle tissue of anal part of perineum skeletal muscle tissue of anal region skeletal muscle tissue of anal triangle uberon UBERON:0004832 anal region skeletal muscle A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37393 MA:th anal part of perineum skeletal muscle OBOL:automatic anal part of perineum skeletal muscle tissue OBOL:automatic anal region skeletal muscle tissue OBOL:automatic anal triangle skeletal muscle OBOL:automatic anal triangle skeletal muscle tissue OBOL:automatic skeletal muscle of anal part of perineum OBOL:automatic skeletal muscle of anal region OBOL:automatic skeletal muscle of anal triangle OBOL:automatic skeletal muscle tissue of anal part of perineum OBOL:automatic skeletal muscle tissue of anal region OBOL:automatic skeletal muscle tissue of anal triangle OBOL:automatic A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips EMAPA:37642 MA:0001578 lip skeletal muscle tissue skeletal muscle of lip skeletal muscle tissue of lip uberon UBERON:0004833 lip skeletal muscle A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37642 MA:th lip skeletal muscle tissue OBOL:automatic skeletal muscle of lip OBOL:automatic skeletal muscle tissue of lip OBOL:automatic Smooth muscle tissue in all or part of a hepatic duct. EMAPA:37598 MA:0001640 uberon UBERON:0004834 hepatic duct smooth muscle Smooth muscle tissue in all or part of a hepatic duct. http://orcid.org/0000-0002-6601-2165 EMAPA:37598 MA:th A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]. EMAPA:30747 MA:0001736 epididymis involuntary muscle epididymis non-striated muscle epididymis smooth muscle tissue involuntary muscle of epididymis non-striated muscle of epididymis smooth muscle of epididymis smooth muscle tissue of epididymis uberon UBERON:0004835 epididymis smooth muscle A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]. OBOL:automatic epididymis involuntary muscle OBOL:automatic epididymis non-striated muscle OBOL:automatic epididymis smooth muscle tissue OBOL:automatic involuntary muscle of epididymis OBOL:automatic non-striated muscle of epididymis OBOL:automatic smooth muscle of epididymis OBOL:automatic smooth muscle tissue of epididymis OBOL:automatic An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 MA:0001801 apparatus respiratorius arterial endothelium apparatus respiratorius artery endothelium apparatus respiratorius endothelium of artery arterial endothelium of apparatus respiratorius arterial endothelium of respiratory system artery endothelium of apparatus respiratorius artery endothelium of respiratory system endothelium of artery of apparatus respiratorius endothelium of artery of respiratory system respiratory system artery endothelium respiratory system endothelium of artery uberon UBERON:0004848 respiratory system arterial endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An endothelium of artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37566 MA:th apparatus respiratorius arterial endothelium OBOL:automatic apparatus respiratorius artery endothelium OBOL:automatic apparatus respiratorius endothelium of artery OBOL:automatic arterial endothelium of apparatus respiratorius OBOL:automatic arterial endothelium of respiratory system OBOL:automatic artery endothelium of apparatus respiratorius OBOL:automatic artery endothelium of respiratory system OBOL:automatic endothelium of artery of apparatus respiratorius OBOL:automatic endothelium of artery of respiratory system OBOL:automatic respiratory system artery endothelium OBOL:automatic respiratory system endothelium of artery OBOL:automatic An endothelium of vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37585 MA:0001811 apparatus respiratorius endothelium of vein apparatus respiratorius vein endothelium apparatus respiratorius venous endothelium endothelium of vein of apparatus respiratorius endothelium of vein of respiratory system respiratory system endothelium of vein respiratory system vein endothelium vein endothelium of apparatus respiratorius vein endothelium of respiratory system venous endothelium of apparatus respiratorius venous endothelium of respiratory system uberon UBERON:0004849 respiratory system venous endothelium An endothelium of vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37585 MA:th apparatus respiratorius endothelium of vein OBOL:automatic apparatus respiratorius vein endothelium OBOL:automatic apparatus respiratorius venous endothelium OBOL:automatic endothelium of vein of apparatus respiratorius OBOL:automatic endothelium of vein of respiratory system OBOL:automatic respiratory system endothelium of vein OBOL:automatic respiratory system vein endothelium OBOL:automatic vein endothelium of apparatus respiratorius OBOL:automatic vein endothelium of respiratory system OBOL:automatic venous endothelium of apparatus respiratorius OBOL:automatic venous endothelium of respiratory system OBOL:automatic An endothelium that is part of a lymph node [Automatically generated definition]. EMAPA:35526 MA:0000741 endothelium of lymph node uberon UBERON:0004850 lymph node endothelium An endothelium that is part of a lymph node [Automatically generated definition]. OBOL:automatic endothelium of lymph node OBOL:automatic The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall. BTO:0000394 CALOHA:TS-0047 EFO:0002597 EMAPA:35134 MA:0000701 NCIT:C49190 UMLS:C1706824 adult aorta endothelium endothelium of adult aorta endothelium of aorta endothelium of trunk of aortic tree endothelium of trunk of systemic arterial tree trunk of aortic tree endothelium trunk of systemic arterial tree endothelium uberon aortic endothelium UBERON:0004851 aorta endothelium The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall. MGI:csmith MP:0009864 UMLS:C1706824 ncithesaurus:Aorta_Endothelium adult aorta endothelium OBOL:automatic endothelium of adult aorta OBOL:automatic endothelium of aorta OBOL:automatic endothelium of trunk of aortic tree OBOL:automatic endothelium of trunk of systemic arterial tree OBOL:automatic trunk of aortic tree endothelium OBOL:automatic trunk of systemic arterial tree endothelium OBOL:automatic aortic endothelium BTO:0000394 An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 MA:0000717 MESH:D004730 NCIT:C13053 TAO:0002171 UMLS:C0014261 VHOG:0001217 XAO:0000356 ZFA:0001639 uberon endothelia vascular endothelia UBERON:0004852 cardiovascular system endothelium An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001217 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C0014261 ncithesaurus:Vascular_Endothelium endothelia ZFA:0001639 vascular endothelia XAO:0000356 A mesentery that is part of a digestive system [Automatically generated definition]. EMAPA:37068 MA:0001900 digestive system mesentery mesentery of digestive system mesentery of gastrointestinal system uberon UBERON:0004854 gastrointestinal system mesentery A mesentery that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37068 MA:th digestive system mesentery OBOL:automatic mesentery of digestive system OBOL:automatic mesentery of gastrointestinal system OBOL:automatic A connective tissue that surrounds a skeletal muscle tissue. EMAPA:37743 MA:0002868 connective tissue of skeletal muscle connective tissue of skeletal muscle tissue portion of connective tissue of skeletal muscle portion of connective tissue of skeletal muscle tissue skeletal muscle portion of connective tissue skeletal muscle textus connectivus skeletal muscle tissue connective tissue skeletal muscle tissue portion of connective tissue skeletal muscle tissue textus connectivus textus connectivus of skeletal muscle textus connectivus of skeletal muscle tissue uberon skeletal muscle interstitial tissue skeletal muscle interstitum UBERON:0004857 skeletal muscle connective tissue A connective tissue that surrounds a skeletal muscle tissue. OBOL:automatic EMAPA:37743 MA:th connective tissue of skeletal muscle OBOL:automatic connective tissue of skeletal muscle tissue OBOL:automatic portion of connective tissue of skeletal muscle OBOL:automatic portion of connective tissue of skeletal muscle tissue OBOL:automatic skeletal muscle portion of connective tissue OBOL:automatic skeletal muscle textus connectivus OBOL:automatic skeletal muscle tissue connective tissue OBOL:automatic skeletal muscle tissue portion of connective tissue OBOL:automatic skeletal muscle tissue textus connectivus OBOL:automatic textus connectivus of skeletal muscle OBOL:automatic textus connectivus of skeletal muscle tissue OBOL:automatic skeletal muscle interstitial tissue MA:0002868 skeletal muscle interstitum MA:0002868 A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. EMAPA:35334 MA:0000267 eye-associated gland gland of eye uberon UBERON:0004859 Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. http://orcid.org/0000-0002-6601-2165 eye-associated gland http://orcid.org/0000-0002-6601-2165 gland of eye OBOL:automatic A sympathetic nerve trunk that is part of a thorax [Automatically generated definition]. EMAPA:37657 FMA:6262 MA:0001165 NCIT:C52827 UMLS:C1710393 nerve trunk of sympathetic nervous system of thorax nerve trunk of sympathetic part of autonomic division of nervous system of thorax sympathetic nerve trunk of thorax sympathetic nervous system nerve trunk of thorax thoracic part of sympathetic trunk thoracic sympathetic chain thorax nerve trunk of sympathetic nervous system thorax nerve trunk of sympathetic part of autonomic division of nervous system thorax sympathetic nerve trunk thorax sympathetic nervous system nerve trunk uberon thoracic sympathetic trunk UBERON:0004863 thoracic sympathetic nerve trunk A sympathetic nerve trunk that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37657 MA:th UMLS:C1710393 ncithesaurus:Thoracic_Sympathetic_Nerve_Trunk nerve trunk of sympathetic nervous system of thorax OBOL:automatic nerve trunk of sympathetic part of autonomic division of nervous system of thorax OBOL:automatic sympathetic nerve trunk of thorax OBOL:automatic sympathetic nervous system nerve trunk of thorax OBOL:automatic thoracic part of sympathetic trunk FMA:6262 thoracic sympathetic chain FMA:6262 thorax nerve trunk of sympathetic nervous system OBOL:automatic thorax nerve trunk of sympathetic part of autonomic division of nervous system OBOL:automatic thorax sympathetic nerve trunk OBOL:automatic thorax sympathetic nervous system nerve trunk OBOL:automatic thoracic sympathetic trunk FMA:6262 A vasculature that is part of a retina [Automatically generated definition]. FMA:76552 MESH:D012171 XAO:0004153 retina vasculature retina vasculature of camera-type eye retinal blood vessels retinal blood vessels set retinal vasculature set of blood vessels of retina set of retinal blood vessels vasa sanguinea retinae uberon UBERON:0004864 vasculature of retina A vasculature that is part of a retina [Automatically generated definition]. OBOL:automatic PMID:21622558 PMID:2772405 michaelerice retina vasculature GO:0061298 retina vasculature of camera-type eye GO:0061298 retinal blood vessels FMA:76552 retinal blood vessels set FMA:76552 retinal vasculature OBOL:automatic set of blood vessels of retina OBOL:automatic set of retinal blood vessels FMA:76552 vasa sanguinea retinae FMA:76552 FMA:TA Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye. note that the AAO and ZFA class is a cavity AAO:0000343 FMA:84961 SCTID:280541000 Wikipedia:Orbit_(anatomy) ZFA:0005558 uberon orbit UBERON:0004867 orbital cavity Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye. http://orcid.org/0000-0002-6601-2165 note that the AAO and ZFA class is a cavity AAO https://github.com/obophenotype/uberon/issues/462 orbit AAO:0000343 A part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation. The parietal eye is a part of the epithalamus, which can be divided into two major parts; the epiphysis (the pineal organ, or pineal gland if mostly endocrine) and the parietal organ (often called the parietal eye, or third eye if it is photoreceptive). It arises as an anterior evagination of the pineal organ or as a separate outgrowth of the roof of the diencephalon. In some species, it protrudes through the skull.[4] The parietal eye uses a different biochemical method of detecting light than rod cells or cone cells in a normal vertebrate eye[WP]. Wikipedia:Parietal_eye parietal eye uberon third eye UBERON:0004869 parietal organ cjm cjm A part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation. The parietal eye is a part of the epithalamus, which can be divided into two major parts; the epiphysis (the pineal organ, or pineal gland if mostly endocrine) and the parietal organ (often called the parietal eye, or third eye if it is photoreceptive). It arises as an anterior evagination of the pineal organ or as a separate outgrowth of the roof of the diencephalon. In some species, it protrudes through the skull.[4] The parietal eye uses a different biochemical method of detecting light than rod cells or cone cells in a normal vertebrate eye[WP]. Wikipedia:Parietal_eye parietal eye Wikipedia:Parietal_eye third eye Wikipedia:Parietal_eye Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. check BILA AAO:0011100 BILA:0000047 FMA:295570 Wikipedia:Lateral_plate_mesoderm#Division_into_layers XAO:0000271 outer layer of lateral plate mesoderm uberon parietal mesoderm somatic mesoderm UBERON:0004871 somatic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers parietal mesoderm ISBN:9780878932504 somatic mesoderm BILA:0000047 Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 FMA:295568 Wikipedia:Lateral_plate_mesoderm#Division_into_layers XAO:0000276 inner layer of lateral plate mesoderm uberon splanchnic mesoderm UBERON:0004872 splanchnic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors BILA visceral mesoderm BILA:0000044 http://www.drugs.com/dict/visceral-mesoderm.html http://www.stedmans.com/ splanchnic mesoderm ISBN:9780878932504 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. TODO - check relationship to LPM EHDAA2:0001903 EHDAA:383 EMAPA:16181 FMA:295564 NCIT:C34303 UMLS:C1519472 VHOG:0000558 Wikipedia:Splanchnopleure uberon ventral splanchnic mesoderm UBERON:0004873 splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. Wikipedia:Splanchnopleure UMLS:C1519472 ncithesaurus:Splanchnopleure ventral splanchnic mesoderm Wikipedia:Intraembryonic_coelom A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 NCIT:C34301 UMLS:C1519423 VHOG:0000557 Wikipedia:Somatopleure uberon UBERON:0004874 somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Wikipedia:Somatopleure UMLS:C1519423 ncithesaurus:Somatopleure A portion of the urogenital ridge which is the source of much of the urinary system[WP]. FMA:72168 NCIT:C34219 SCTID:361405003 UMLS:C1283944 Wikipedia:Nephrogenic_cord uberon chorda nephrogenica UBERON:0004875 part_of or develops_from urogenital ridge? nephrogenic cord A portion of the urogenital ridge which is the source of much of the urinary system[WP]. Wikipedia:Nephrogenic_cord UMLS:C1283944 ncithesaurus:Nephrogenic_Cord chorda nephrogenica Wikipedia:Nephrogenic_cord One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] EHDAA2:0004022 EMAPA:30888 FMA:321919 Wikipedia:Urogenital_folds urethral fold urogenital fold uberon urogenital ridge UBERON:0004876 urogenital fold EHDAA2 Wikipedia EHDAA2 One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. MP:0011835 MP:anna Wikipedia:Urogenital_folds urethral fold EMAPA:30888 urogenital fold EHDAA2:0004022 MP:0011835 urogenital ridge MP:0011835 The central region of trunk mesoderm. This tissue forms the notochord. Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon UBERON:0004880 chordamesoderm The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 axial chorda mesoderm ZFA:0000091 dorsal mesoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest presumptive notochord ZFA:0000091 The mass of tissue made up of mesenchymal cells in the lung. EMAPA:32866 lung-associated mesenchyme mesenchyme of lung pulmonary mesenchyme uberon UBERON:0004883 lung mesenchyme The mass of tissue made up of mesenchymal cells in the lung. GO:0060484 lung-associated mesenchyme GO:0060484 mesenchyme of lung OBOL:automatic pulmonary mesenchyme GO:0060484 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra. we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2:0004061 EMAPA:31509 UGE epithelium of urogenital sinus uberon UBERON:0004902 urogenital sinus epithelium EHDAA2 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra. PMID:18977204 we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2 UGE PMID:18977204 epithelium of urogenital sinus OBOL:automatic A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila. optic nerve BTO:0000966 EV:0100351 FBbt:00001956 TADS:0000232 optic nerve (generic) uberon UBERON:0004904 for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila. http://orcid.org/0000-0002-6601-2165 optic nerve BTO:0000966 FBbt:00001956 Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 FBbt:00005811 A portion of the gut that is derived from ectoderm. ectodermal gut gut ectoderm uberon UBERON:0004906 ectodermal part of digestive tract A portion of the gut that is derived from ectoderm. GO:0007439 gut ectoderm EMAPA:32930 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L gut FMA:49179 NCIT:C33010 SCTID:279973004 UMLS:C0226875 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract galen:LowerGastrointestinalTract lower GI tract lower gastrointestinal tract uberon UBERON:0004907 lower digestive tract The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 MA WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L FMA gut GO:0048565 UMLS:C0226875 ncithesaurus:Lower_Gastrointestinal_Tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA:49177 NCIT:C33837 SCTID:181244000 UMLS:C0226874 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract galen:UpperGastrointestinalTract upper GI tract upper gastrointestinal tract uberon UBERON:0004908 upper digestive tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA UMLS:C0226874 ncithesaurus:Upper_Gastrointestinal_Tract An epithelium surrounding a gonad. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts EHDAA:4032 EHDAA:5931 NCIT:C32676 UMLS:C1517534 gonad epithelium gonadal epithelium uberon gonadal sheath UBERON:0004909 epithelium of gonad An epithelium surrounding a gonad. OBOL:automatic UMLS:C1517534 ncithesaurus:Germinal_Epithelium gonad epithelium OBOL:automatic gonadal epithelium OBOL:automatic gonadal sheath FBbt:00004859 An epithelium surrounding a testis. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0001364 EMAPA:17973 testis epithelium uberon UBERON:0004910 epithelium of male gonad An epithelium surrounding a testis. OBOL:automatic testis epithelium OBOL:automatic An epithelium surrounding an ovary. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0003661 ovarian epithelium ovary epithelium ovarian sheath uberon UBERON:0004911 epithelium of female gonad An epithelium surrounding an ovary. OBOL:automatic ovarian epithelium OBOL:automatic ovary epithelium OBOL:automatic ovarian sheath FBbt:00004896 EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 VHOG:0001351 uberon hepatic diverticulum UBERON:0004912 biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png EHDAA2 EHDAA2 EHDAA2-modified hepatic diverticulum EMAPA:16561 A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] CALOHA:TS-2348 FMA:15076 GAID:283 MESH:D014670 NCIT:C13011 SCTID:362200007 TAO:0005167 UMLS:C0042425 Wikipedia:Ampulla_of_Vater ZFA:0005167 galen:AmpullaOfVater Vater's ampulla ampulla biliaropancreatica ampulla of Vater ampulla of bile duct biliaropancreatic ampulla papilla Vateri uberon ampulla Vaterii ampulla hepatopancreatica papilla duodeni major UBERON:0004913 hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Wikipedia:Ampulla_of_Vater Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] 2012-08-14 TAO:0005167 TAO ZFIN:ZDB-PUB-070212-11 ZFIN:ZDB-PUB-080414-12 UMLS:C0042425 ncithesaurus:Ampulla_of_Vater ampulla biliaropancreatica FMA:15076 FMA:TA ampulla of bile duct FMA:15076 papilla Vateri ZFA:0005167 ampulla Vaterii Wikipedia:Ampulla_of_Vater ampulla hepatopancreatica Wikipedia:Ampulla_of_Vater papilla duodeni major ZFA:0005167 One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. EMAPA:18662 FMA:15953 MA:0003107 NCIT:C119578 SCTID:245389007 papilla duodenalis papilla of duodenum uberon papilla duodeni UBERON:0004914 duodenal papilla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. http://medical-dictionary.thefreedictionary.com/duodenal+papilla papilla duodeni Wikipedia:Major_duodenal_papilla Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]. EMAPA:18663 FMA:15077 GAID:285 MESH:D009803 NCIT:C13065 SCTID:181271000 UMLS:C0028872 Wikipedia:Sphincter_of_ampulla Oddi's sphincter hepatopancreatic ampullary sphincter musculus sphincter ampullae musculus sphincter ampullae hepatopancreatica sphincter of Oddi sphincter of ampulla of vater uberon UBERON:0004915 sphincter of hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]. Wikipedia:Sphincter_of_ampulla UMLS:C0028872 ncithesaurus:Sphincter_of_Oddi hepatopancreatic ampullary sphincter FMA:15077 musculus sphincter ampullae FMA:15077 musculus sphincter ampullae hepatopancreatica FMA:15077 FMA:TA sphincter of ampulla of vater FMA:15077 A sphincter muscle that is part of a anal region. EMAPA:36052 anal region sphincter sphincter analia uberon UBERON:0004916 anal sphincter A sphincter muscle that is part of a anal region. OBOL:automatic A sphincter muscle surrounding the urethra. EMAPA:37789 MA:0002650 SCTID:277855007 SCTID:277857004 Wikipedia:Urethral_sphincter sphincter muscle of urethra sphincter of urethra sphincter urethrae urethral sphincter muscle uberon UBERON:0004917 urethral sphincter A sphincter muscle surrounding the urethra. Wikipedia:Urethral_sphincter EMAPA:37789 MA:th A proximal-distal subdivision of the digestive tract. intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. FBbt:00100315 FMA:71131 uberon alimentary system subdivision gut section intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 FBbt:00100315 alimentary system subdivision FMA:71131 gut section FBbt:00100315 subdivision of alimentary system FMA:71131 A part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer A part of a wall of an organ that forms a layer. http://orcid.org/0000-0002-6601-2165 The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 FMA:75144 SCTID:19594009 pharyngeal submucosa pharynx submucosa tela submucosa pharyngea tela submucosa pharyngis uberon pharyngobasilar fascia submucous coat of pharynx submucous layer of pharynx UBERON:0004924 submucosa of pharynx The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 pharyngeal submucosa FMA:75144 pharynx submucosa OBOL:automatic tela submucosa pharyngea FMA:75144 FMA:TA tela submucosa pharyngis BTO:0002113 submucous coat of pharynx BTO:0002113 submucous layer of pharynx BTO:0002113 A submucosa that is part of a hypopharynx [Automatically generated definition]. FMA:55072 SCTID:47496006 hypopharynx submucosa laryngeal pharynx submucosa laryngopharynx submucosa submucosa of hypopharynx submucosa of laryngeal pharynx tela submucosa (pars laryngea pharyngis) uberon UBERON:0004925 submucosa of laryngopharynx A submucosa that is part of a hypopharynx [Automatically generated definition]. OBOL:automatic hypopharynx submucosa OBOL:automatic laryngeal pharynx submucosa OBOL:automatic laryngopharynx submucosa OBOL:automatic submucosa of hypopharynx OBOL:automatic submucosa of laryngeal pharynx OBOL:automatic tela submucosa (pars laryngea pharyngis) FMA:55072 A submucosa that is part of a cystic duct [Automatically generated definition]. FMA:18013 cystic duct submucosa cystic ductal submucosa uberon UBERON:0004926 submucosa of cystic duct A submucosa that is part of a cystic duct [Automatically generated definition]. OBOL:automatic cystic duct submucosa OBOL:automatic cystic ductal submucosa FMA:18013 A submucosa that is part of a cecum [Automatically generated definition]. FMA:14999 caecum submucosa cecum submucosa intestinum crassum caecum submucosa submucosa of caecum submucosa of intestinum crassum caecum uberon UBERON:0004927 submucosa of cecum A submucosa that is part of a cecum [Automatically generated definition]. OBOL:automatic caecum submucosa OBOL:automatic cecum submucosa OBOL:automatic intestinum crassum caecum submucosa OBOL:automatic submucosa of caecum OBOL:automatic submucosa of intestinum crassum caecum OBOL:automatic A submucosa that is part of an appendix [Automatically generated definition]. FMA:14992 SCTID:86833001 appendiceal submucosa appendix submucosa caecal appendix submucosa submucosa of caecal appendix submucosa of vermiform appendix submucosa of vermix vermiform appendix submucosa vermix submucosa uberon UBERON:0004928 submucosa of appendix A submucosa that is part of an appendix [Automatically generated definition]. OBOL:automatic appendiceal submucosa FMA:14992 appendix submucosa OBOL:automatic caecal appendix submucosa OBOL:automatic submucosa of caecal appendix OBOL:automatic submucosa of vermiform appendix OBOL:automatic submucosa of vermix OBOL:automatic vermiform appendix submucosa OBOL:automatic vermix submucosa OBOL:automatic A submucosa that is part of an ascending colon [Automatically generated definition]. FMA:15006 ascending colon submucosa uberon UBERON:0004929 submucosa of ascending colon A submucosa that is part of an ascending colon [Automatically generated definition]. OBOL:automatic ascending colon submucosa OBOL:automatic A submucosa that is part of a transverse colon [Automatically generated definition]. FMA:15013 transverse colon submucosa uberon UBERON:0004930 submucosa of transverse colon A submucosa that is part of a transverse colon [Automatically generated definition]. OBOL:automatic transverse colon submucosa OBOL:automatic A submucosa that is part of a descending colon [Automatically generated definition]. FMA:15020 descending colon submucosa uberon UBERON:0004931 submucosa of descending colon A submucosa that is part of a descending colon [Automatically generated definition]. OBOL:automatic descending colon submucosa OBOL:automatic A submucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15027 sigmoid colon submucosa uberon UBERON:0004932 submucosa of sigmoid colon A submucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic sigmoid colon submucosa OBOL:automatic A submucosa that is part of a body of stomach [Automatically generated definition]. FMA:17059 body of stomach submucosa corpus gastricum (ventriculare) submucosa gastric body submucosa stomach body submucosa submucosa of corpus gastricum (ventriculare) submucosa of gastric body submucosa of stomach body uberon UBERON:0004934 submucosa of body of stomach A submucosa that is part of a body of stomach [Automatically generated definition]. OBOL:automatic body of stomach submucosa OBOL:automatic corpus gastricum (ventriculare) submucosa OBOL:automatic gastric body submucosa OBOL:automatic stomach body submucosa OBOL:automatic submucosa of corpus gastricum (ventriculare) OBOL:automatic submucosa of gastric body OBOL:automatic submucosa of stomach body OBOL:automatic A submucosa that is part of a cardia of stomach [Automatically generated definition]. FMA:17457 cardia of stomach submucosa cardial part of stomach submucosa gastric cardia submucosa pars cardiaca (gaster) submucosa stomach cardiac region submucosa submucosa of cardial part of stomach submucosa of gastric cardia submucosa of pars cardiaca (gaster) submucosa of stomach cardiac region uberon UBERON:0004935 submucosa of cardia of stomach A submucosa that is part of a cardia of stomach [Automatically generated definition]. OBOL:automatic cardia of stomach submucosa OBOL:automatic cardial part of stomach submucosa OBOL:automatic gastric cardia submucosa OBOL:automatic pars cardiaca (gaster) submucosa OBOL:automatic stomach cardiac region submucosa OBOL:automatic submucosa of cardial part of stomach OBOL:automatic submucosa of gastric cardia OBOL:automatic submucosa of pars cardiaca (gaster) OBOL:automatic submucosa of stomach cardiac region OBOL:automatic A submucosa that is part of a pyloric antrum [Automatically generated definition]. FMA:17060 antrum of stomach submucosa pyloric antrum submucosa stomach pyloric antrum submucosa submucosa of antrum of stomach submucosa of stomach pyloric antrum uberon UBERON:0004936 submucosa of pyloric antrum A submucosa that is part of a pyloric antrum [Automatically generated definition]. OBOL:automatic antrum of stomach submucosa OBOL:automatic pyloric antrum submucosa OBOL:automatic stomach pyloric antrum submucosa OBOL:automatic submucosa of antrum of stomach OBOL:automatic submucosa of stomach pyloric antrum OBOL:automatic A submucosa that is part of a pylorus [Automatically generated definition]. EMAPA:27201 FMA:17462 pyloric part of stomach submucosa pyloric submucosa pylorus submucosa stomach pyloric region submucosa submucosa of pyloric part of stomach submucosa of stomach pyloric region uberon UBERON:0004937 submucosa of pylorus A submucosa that is part of a pylorus [Automatically generated definition]. OBOL:automatic pyloric part of stomach submucosa OBOL:automatic pylorus submucosa FMA:17462 OBOL:automatic stomach pyloric region submucosa OBOL:automatic submucosa of pyloric part of stomach OBOL:automatic submucosa of stomach pyloric region OBOL:automatic A submucosa that is part of a biliary tree [Automatically generated definition]. FMA:18009 biliary tract submucosa biliary tree submucosa submucosa of biliary tract uberon UBERON:0004938 submucosa of biliary tree A submucosa that is part of a biliary tree [Automatically generated definition]. OBOL:automatic biliary tract submucosa OBOL:automatic biliary tree submucosa OBOL:automatic submucosa of biliary tract OBOL:automatic A submucosa that is part of a common bile duct [Automatically generated definition]. FMA:18011 common bile duct submucosa common bile ductal submucosa ductus choledochus (biliaris) submucosa submucosa of ductus choledochus (biliaris) uberon UBERON:0004939 submucosa of common bile duct A submucosa that is part of a common bile duct [Automatically generated definition]. OBOL:automatic common bile duct submucosa OBOL:automatic common bile ductal submucosa FMA:18011 ductus choledochus (biliaris) submucosa OBOL:automatic submucosa of ductus choledochus (biliaris) OBOL:automatic A submucosa that is part of a common hepatic duct [Automatically generated definition]. FMA:18014 common hepatic duct submucosa common hepatic ductal submucosa hepatic duct submucosa submucosa of hepatic duct uberon UBERON:0004940 submucosa of common hepatic duct A submucosa that is part of a common hepatic duct [Automatically generated definition]. OBOL:automatic common hepatic duct submucosa OBOL:automatic common hepatic ductal submucosa FMA:18014 hepatic duct submucosa OBOL:automatic submucosa of hepatic duct OBOL:automatic A submucosa that is part of a right hepatic duct [Automatically generated definition]. FMA:18015 right hepatic duct submucosa right hepatic ductal submucosa uberon UBERON:0004941 submucosa of right hepatic duct A submucosa that is part of a right hepatic duct [Automatically generated definition]. OBOL:automatic right hepatic duct submucosa OBOL:automatic right hepatic ductal submucosa FMA:18015 A submucosa that is part of a left hepatic duct [Automatically generated definition]. FMA:18017 left hepatic duct submucosa left hepatic ductal submucosa uberon UBERON:0004942 submucosa of left hepatic duct A submucosa that is part of a left hepatic duct [Automatically generated definition]. OBOL:automatic left hepatic duct submucosa OBOL:automatic left hepatic ductal submucosa FMA:18017 The submucous layer of the wall of the urinary bladder. BTO:0002117 EMAPA:32275 FMA:15929 SCTID:88384001 bladder submucosa submucosa of bladder tela submucosa (vesica urinaria) tela submucosa vesicae tela submucosa vesicae urinariae urinary bladder submucosa uberon submucous layer of urinary bladder UBERON:0004943 submucosa of urinary bladder https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The submucous layer of the wall of the urinary bladder. BTO:0002117 bladder submucosa OBOL:automatic submucosa of bladder OBOL:automatic tela submucosa (vesica urinaria) FMA:15929 FMA:TA tela submucosa vesicae FMA:15929 FMA:TA tela submucosa vesicae urinariae BTO:0002117 urinary bladder submucosa OBOL:automatic submucous layer of urinary bladder BTO:0002117 A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:32276 FMA:17851 bladder neck submucosa neck of bladder submucosa neck of urinary bladder submucosa submucosa of bladder neck submucosa of neck of bladder submucosa of urinary bladder neck submucosa of vesical neck urinary bladder neck submucosa vesical neck submucosa uberon UBERON:0004945 submucosa of neck of urinary bladder A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck submucosa OBOL:automatic neck of bladder submucosa OBOL:automatic neck of urinary bladder submucosa OBOL:automatic submucosa of bladder neck OBOL:automatic submucosa of neck of bladder OBOL:automatic submucosa of urinary bladder neck OBOL:automatic submucosa of vesical neck OBOL:automatic urinary bladder neck submucosa OBOL:automatic vesical neck submucosa OBOL:automatic A submucosa that is part of a ileum [Automatically generated definition]. FMA:14957 SCTID:65374006 ileal submucosa ileum submucosa uberon UBERON:0004946 submucosa of ileum A submucosa that is part of a ileum [Automatically generated definition]. OBOL:automatic ileal submucosa FMA:14957 ileum submucosa OBOL:automatic A mucosa that is part of a ureter [Automatically generated definition]. FMA:15894 SCTID:40476001 galen:MucousMembraneOfUreter mucosa of organ of ureter mucosal layer of ureter mucous membrane of ureter organ mucosa of ureter tunica mucosa (ureter) tunica mucosa ureteris ureter mucosa ureter mucosa of organ ureter mucous membrane ureter organ mucosa ureteral mucosa ureteric mucosa uberon UBERON:0004980 mucosa of ureter https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A mucosa that is part of a ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of ureter OBOL:automatic mucosal layer of ureter FMA:15894 mucous membrane of ureter OBOL:automatic organ mucosa of ureter OBOL:automatic tunica mucosa (ureter) FMA:15894 tunica mucosa ureteris FMA:15894 FMA:TA ureter mucosa OBOL:automatic ureter mucosa of organ OBOL:automatic ureter mucous membrane OBOL:automatic ureter organ mucosa OBOL:automatic ureteral mucosa FMA:15894 ureteric mucosa FMA:15894 A mucosa that is part of a vagina [Automatically generated definition]. BTO:0005676 FMA:19975 SCTID:362245006 mucosa of organ of vagina mucous membrane of vagina organ mucosa of vagina tunica mucosa vaginae vagina mucosa vagina mucosa of organ vagina mucous membrane vagina organ mucosa vaginal mucosa uberon UBERON:0004983 mucosa of vagina A mucosa that is part of a vagina [Automatically generated definition]. OBOL:automatic mucosa of organ of vagina OBOL:automatic mucous membrane of vagina OBOL:automatic organ mucosa of vagina OBOL:automatic tunica mucosa vaginae FMA:19975 FMA:TA vagina mucosa OBOL:automatic vagina mucosa of organ OBOL:automatic vagina mucous membrane OBOL:automatic vagina organ mucosa OBOL:automatic vaginal mucosa FMA:19975 A mucosa that is part of a seminal vesicle [Automatically generated definition]. FMA:19405 SCTID:252260007 mucosa of organ of seminal gland mucosa of organ of seminal vesicle mucosa of seminal gland mucous membrane of seminal gland mucous membrane of seminal vesicle organ mucosa of seminal gland organ mucosa of seminal vesicle seminal gland mucosa seminal gland mucosa of organ seminal gland mucous membrane seminal gland organ mucosa seminal vesicle mucosa seminal vesicle mucosa of organ seminal vesicle mucous membrane seminal vesicle organ mucosa tunica mucosa glandulae vesiculosae uberon UBERON:0004984 mucosa of seminal vesicle A mucosa that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic mucosa of organ of seminal gland OBOL:automatic mucosa of organ of seminal vesicle OBOL:automatic mucosa of seminal gland OBOL:automatic mucous membrane of seminal gland OBOL:automatic mucous membrane of seminal vesicle OBOL:automatic organ mucosa of seminal gland OBOL:automatic organ mucosa of seminal vesicle OBOL:automatic seminal gland mucosa OBOL:automatic seminal gland mucosa of organ OBOL:automatic seminal gland mucous membrane OBOL:automatic seminal gland organ mucosa OBOL:automatic seminal vesicle mucosa OBOL:automatic seminal vesicle mucosa of organ OBOL:automatic seminal vesicle mucous membrane OBOL:automatic seminal vesicle organ mucosa OBOL:automatic tunica mucosa glandulae vesiculosae FMA:19405 FMA:TA A mucosa that is part of a ejaculatory duct [Automatically generated definition]. FMA:19373 ejaculatory duct mucosa ejaculatory duct mucosa of organ ejaculatory duct mucous membrane ejaculatory duct organ mucosa ejaculatory ductal mucosa mucosa of organ of ejaculatory duct mucous membrane of ejaculatory duct organ mucosa of ejaculatory duct uberon UBERON:0004985 mucosa of ejaculatory duct A mucosa that is part of a ejaculatory duct [Automatically generated definition]. OBOL:automatic ejaculatory duct mucosa OBOL:automatic ejaculatory duct mucosa of organ OBOL:automatic ejaculatory duct mucous membrane OBOL:automatic ejaculatory duct organ mucosa OBOL:automatic ejaculatory ductal mucosa FMA:19373 mucosa of organ of ejaculatory duct OBOL:automatic mucous membrane of ejaculatory duct OBOL:automatic organ mucosa of ejaculatory duct OBOL:automatic A mucosa that is part of a vas deferens [Automatically generated definition]. FMA:19240 SCTID:299626000 deferent duct mucosa deferent duct mucosa of organ deferent duct mucous membrane deferent duct organ mucosa deferent ductal mucosa ductus deferens mucosa ductus deferens mucosa of organ ductus deferens mucous membrane ductus deferens organ mucosa mucosa of ductus deferens mucosa of organ of deferent duct mucosa of organ of ductus deferens mucosa of organ of sperm duct mucosa of organ of vas deferen mucosa of organ of vas deferens mucosa of sperm duct mucosa of vas deferen mucosa of vas deferens mucous membrane of deferent duct mucous membrane of ductus deferens mucous membrane of sperm duct mucous membrane of vas deferen mucous membrane of vas deferens organ mucosa of deferent duct organ mucosa of ductus deferens organ mucosa of sperm duct organ mucosa of vas deferen organ mucosa of vas deferens sperm duct mucosa sperm duct mucosa of organ sperm duct mucous membrane sperm duct organ mucosa tunica mucosa (ductus deferens) tunica mucosa ductus deferentis vas deferen mucosa vas deferen mucosa of organ vas deferen mucous membrane vas deferen organ mucosa vas deferens mucosa vas deferens mucosa of organ vas deferens mucous membrane vas deferens organ mucosa uberon UBERON:0004986 mucosa of deferent duct A mucosa that is part of a vas deferens [Automatically generated definition]. OBOL:automatic deferent duct mucosa OBOL:automatic deferent duct mucosa of organ OBOL:automatic deferent duct mucous membrane OBOL:automatic deferent duct organ mucosa OBOL:automatic deferent ductal mucosa FMA:19240 ductus deferens mucosa OBOL:automatic ductus deferens mucosa of organ OBOL:automatic ductus deferens mucous membrane OBOL:automatic ductus deferens organ mucosa OBOL:automatic mucosa of ductus deferens OBOL:automatic mucosa of organ of deferent duct OBOL:automatic mucosa of organ of ductus deferens OBOL:automatic mucosa of organ of sperm duct OBOL:automatic mucosa of organ of vas deferen OBOL:automatic mucosa of organ of vas deferens OBOL:automatic mucosa of sperm duct OBOL:automatic mucosa of vas deferen OBOL:automatic mucosa of vas deferens OBOL:automatic mucous membrane of deferent duct OBOL:automatic mucous membrane of ductus deferens OBOL:automatic mucous membrane of sperm duct OBOL:automatic mucous membrane of vas deferen OBOL:automatic mucous membrane of vas deferens OBOL:automatic organ mucosa of deferent duct OBOL:automatic organ mucosa of ductus deferens OBOL:automatic organ mucosa of sperm duct OBOL:automatic organ mucosa of vas deferen OBOL:automatic organ mucosa of vas deferens OBOL:automatic sperm duct mucosa OBOL:automatic sperm duct mucosa of organ OBOL:automatic sperm duct mucous membrane OBOL:automatic sperm duct organ mucosa OBOL:automatic tunica mucosa (ductus deferens) FMA:19240 tunica mucosa ductus deferentis FMA:19240 FMA:TA vas deferen mucosa OBOL:automatic vas deferen mucosa of organ OBOL:automatic vas deferen mucous membrane OBOL:automatic vas deferen organ mucosa OBOL:automatic vas deferens mucosa OBOL:automatic vas deferens mucosa of organ OBOL:automatic vas deferens mucous membrane OBOL:automatic vas deferens organ mucosa OBOL:automatic A mucosa that is part of a hypopharynx [Automatically generated definition]. FMA:55030 SCTID:362126008 hypopharynx mucosa hypopharynx mucosa of organ hypopharynx mucous membrane hypopharynx organ mucosa laryngeal pharynx mucosa laryngeal pharynx mucosa of organ laryngeal pharynx mucous membrane laryngeal pharynx organ mucosa laryngopharynx mucosa laryngopharynx mucosa of organ laryngopharynx mucous membrane laryngopharynx organ mucosa mucosa of hypopharynx mucosa of laryngeal pharynx mucosa of organ of hypopharynx mucosa of organ of laryngeal pharynx mucosa of organ of laryngopharynx mucous membrane of hypopharynx mucous membrane of laryngeal pharynx mucous membrane of laryngopharynx organ mucosa of hypopharynx organ mucosa of laryngeal pharynx organ mucosa of laryngopharynx uberon UBERON:0004987 mucosa of laryngopharynx A mucosa that is part of a hypopharynx [Automatically generated definition]. OBOL:automatic hypopharynx mucosa OBOL:automatic hypopharynx mucosa of organ OBOL:automatic hypopharynx mucous membrane OBOL:automatic hypopharynx organ mucosa OBOL:automatic laryngeal pharynx mucosa OBOL:automatic laryngeal pharynx mucosa of organ OBOL:automatic laryngeal pharynx mucous membrane OBOL:automatic laryngeal pharynx organ mucosa OBOL:automatic laryngopharynx mucosa OBOL:automatic laryngopharynx mucosa of organ OBOL:automatic laryngopharynx mucous membrane OBOL:automatic laryngopharynx organ mucosa OBOL:automatic mucosa of hypopharynx OBOL:automatic mucosa of laryngeal pharynx OBOL:automatic mucosa of organ of hypopharynx OBOL:automatic mucosa of organ of laryngeal pharynx OBOL:automatic mucosa of organ of laryngopharynx OBOL:automatic mucous membrane of hypopharynx OBOL:automatic mucous membrane of laryngeal pharynx OBOL:automatic mucous membrane of laryngopharynx OBOL:automatic organ mucosa of hypopharynx OBOL:automatic organ mucosa of laryngeal pharynx OBOL:automatic organ mucosa of laryngopharynx OBOL:automatic A mucosa that is part of a cystic duct [Automatically generated definition]. FMA:14690 cystic duct mucosa cystic duct mucosa of organ cystic duct mucous membrane cystic duct organ mucosa cystic ductal mucosa mucosa of organ of cystic duct mucous membrane of cystic duct organ mucosa of cystic duct uberon UBERON:0004988 mucosa of cystic duct A mucosa that is part of a cystic duct [Automatically generated definition]. OBOL:automatic cystic duct mucosa OBOL:automatic cystic duct mucosa of organ OBOL:automatic cystic duct mucous membrane OBOL:automatic cystic duct organ mucosa OBOL:automatic cystic ductal mucosa FMA:14690 mucosa of organ of cystic duct OBOL:automatic mucous membrane of cystic duct OBOL:automatic organ mucosa of cystic duct OBOL:automatic A mucosa that is part of an appendix [Automatically generated definition]. CALOHA:TS-2022 FMA:14991 SCTID:362155000 appendiceal mucous membrane appendix mucosa appendix mucosa of organ appendix mucous membrane appendix organ mucosa caecal appendix mucosa caecal appendix mucosa of organ caecal appendix mucous membrane caecal appendix organ mucosa mucosa of caecal appendix mucosa of organ of appendix mucosa of organ of caecal appendix mucosa of organ of vermiform appendix mucosa of organ of vermix mucosa of vermiform appendix mucosa of vermix mucous membrane of appendix mucous membrane of caecal appendix mucous membrane of vermiform appendix mucous membrane of vermix organ mucosa of appendix organ mucosa of caecal appendix organ mucosa of vermiform appendix organ mucosa of vermix vermiform appendix mucosa vermiform appendix mucosa of organ vermiform appendix mucous membrane vermiform appendix organ mucosa vermix mucosa vermix mucosa of organ vermix mucous membrane vermix organ mucosa uberon UBERON:0004989 mucosa of appendix A mucosa that is part of an appendix [Automatically generated definition]. OBOL:automatic appendiceal mucous membrane FMA:14991 appendix mucosa OBOL:automatic appendix mucosa of organ OBOL:automatic appendix mucous membrane OBOL:automatic appendix organ mucosa OBOL:automatic caecal appendix mucosa OBOL:automatic caecal appendix mucosa of organ OBOL:automatic caecal appendix mucous membrane OBOL:automatic caecal appendix organ mucosa OBOL:automatic mucosa of caecal appendix OBOL:automatic mucosa of organ of appendix OBOL:automatic mucosa of organ of caecal appendix OBOL:automatic mucosa of organ of vermiform appendix OBOL:automatic mucosa of organ of vermix OBOL:automatic mucosa of vermiform appendix OBOL:automatic mucosa of vermix OBOL:automatic mucous membrane of appendix OBOL:automatic mucous membrane of caecal appendix OBOL:automatic mucous membrane of vermiform appendix OBOL:automatic mucous membrane of vermix OBOL:automatic organ mucosa of appendix OBOL:automatic organ mucosa of caecal appendix OBOL:automatic organ mucosa of vermiform appendix OBOL:automatic organ mucosa of vermix OBOL:automatic vermiform appendix mucosa OBOL:automatic vermiform appendix mucosa of organ OBOL:automatic vermiform appendix mucous membrane OBOL:automatic vermiform appendix organ mucosa OBOL:automatic vermix mucosa OBOL:automatic vermix mucosa of organ OBOL:automatic vermix mucous membrane OBOL:automatic vermix organ mucosa OBOL:automatic A mucosa that is part of an ascending colon [Automatically generated definition]. FMA:15005 ascending colon mucosa ascending colon mucosa of organ ascending colon mucous membrane ascending colon organ mucosa mucosa of organ of ascending colon mucous membrane of ascending colon organ mucosa of ascending colon uberon UBERON:0004990 mucosa of ascending colon A mucosa that is part of an ascending colon [Automatically generated definition]. OBOL:automatic ascending colon mucosa OBOL:automatic ascending colon mucosa of organ OBOL:automatic ascending colon mucous membrane OBOL:automatic ascending colon organ mucosa OBOL:automatic mucosa of organ of ascending colon OBOL:automatic mucous membrane of ascending colon OBOL:automatic organ mucosa of ascending colon OBOL:automatic A mucosa that is part of a transverse colon [Automatically generated definition]. FMA:15012 mucosa of organ of transverse colon mucous membrane of transverse colon organ mucosa of transverse colon transverse colon mucosa transverse colon mucosa of organ transverse colon mucous membrane transverse colon organ mucosa uberon UBERON:0004991 mucosa of transverse colon A mucosa that is part of a transverse colon [Automatically generated definition]. OBOL:automatic mucosa of organ of transverse colon OBOL:automatic mucous membrane of transverse colon OBOL:automatic organ mucosa of transverse colon OBOL:automatic transverse colon mucosa OBOL:automatic transverse colon mucosa of organ OBOL:automatic transverse colon mucous membrane OBOL:automatic transverse colon organ mucosa OBOL:automatic A mucosa that is part of a descending colon [Automatically generated definition]. FMA:15019 descending colon mucosa descending colon mucosa of organ descending colon mucous membrane descending colon organ mucosa mucosa of organ of descending colon mucous membrane of descending colon organ mucosa of descending colon uberon UBERON:0004992 mucosa of descending colon A mucosa that is part of a descending colon [Automatically generated definition]. OBOL:automatic descending colon mucosa OBOL:automatic descending colon mucosa of organ OBOL:automatic descending colon mucous membrane OBOL:automatic descending colon organ mucosa OBOL:automatic mucosa of organ of descending colon OBOL:automatic mucous membrane of descending colon OBOL:automatic organ mucosa of descending colon OBOL:automatic A mucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15026 mucosa of organ of sigmoid colon mucous membrane of sigmoid colon organ mucosa of sigmoid colon sigmoid colon mucosa sigmoid colon mucosa of organ sigmoid colon mucous membrane sigmoid colon organ mucosa uberon UBERON:0004993 mucosa of sigmoid colon A mucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic mucosa of organ of sigmoid colon OBOL:automatic mucous membrane of sigmoid colon OBOL:automatic organ mucosa of sigmoid colon OBOL:automatic sigmoid colon mucosa OBOL:automatic sigmoid colon mucosa of organ OBOL:automatic sigmoid colon mucous membrane OBOL:automatic sigmoid colon organ mucosa OBOL:automatic A mucosa that is part of a body of stomach [Automatically generated definition]. FMA:17054 body of stomach mucosa body of stomach mucosa of organ body of stomach mucous membrane body of stomach organ mucosa corpus gastricum (ventriculare) mucosa corpus gastricum (ventriculare) mucosa of organ corpus gastricum (ventriculare) mucous membrane corpus gastricum (ventriculare) organ mucosa gastric body mucosa gastric body mucosa of organ gastric body mucous membrane gastric body organ mucosa mucosa of corpus gastricum (ventriculare) mucosa of gastric body mucosa of organ of body of stomach mucosa of organ of corpus gastricum (ventriculare) mucosa of organ of gastric body mucosa of organ of stomach body mucosa of stomach body mucous membrane of body of stomach mucous membrane of corpus gastricum (ventriculare) mucous membrane of gastric body mucous membrane of stomach body organ mucosa of body of stomach organ mucosa of corpus gastricum (ventriculare) organ mucosa of gastric body organ mucosa of stomach body stomach body mucosa stomach body mucosa of organ stomach body mucous membrane stomach body organ mucosa uberon UBERON:0004995 mucosa of body of stomach A mucosa that is part of a body of stomach [Automatically generated definition]. OBOL:automatic body of stomach mucosa OBOL:automatic body of stomach mucosa of organ OBOL:automatic body of stomach mucous membrane OBOL:automatic body of stomach organ mucosa OBOL:automatic corpus gastricum (ventriculare) mucosa OBOL:automatic corpus gastricum (ventriculare) mucosa of organ OBOL:automatic corpus gastricum (ventriculare) mucous membrane OBOL:automatic corpus gastricum (ventriculare) organ mucosa OBOL:automatic gastric body mucosa OBOL:automatic gastric body mucosa of organ OBOL:automatic gastric body mucous membrane OBOL:automatic gastric body organ mucosa OBOL:automatic mucosa of corpus gastricum (ventriculare) OBOL:automatic mucosa of gastric body OBOL:automatic mucosa of organ of body of stomach OBOL:automatic mucosa of organ of corpus gastricum (ventriculare) OBOL:automatic mucosa of organ of gastric body OBOL:automatic mucosa of organ of stomach body OBOL:automatic mucosa of stomach body OBOL:automatic mucous membrane of body of stomach OBOL:automatic mucous membrane of corpus gastricum (ventriculare) OBOL:automatic mucous membrane of gastric body OBOL:automatic mucous membrane of stomach body OBOL:automatic organ mucosa of body of stomach OBOL:automatic organ mucosa of corpus gastricum (ventriculare) OBOL:automatic organ mucosa of gastric body OBOL:automatic organ mucosa of stomach body OBOL:automatic stomach body mucosa OBOL:automatic stomach body mucosa of organ OBOL:automatic stomach body mucous membrane OBOL:automatic stomach body organ mucosa OBOL:automatic A mucosa that is part of a cardia of stomach [Automatically generated definition]. FMA:17456 cardia of stomach mucosa cardia of stomach mucosa of organ cardia of stomach mucous membrane cardia of stomach organ mucosa cardial part of stomach mucosa cardial part of stomach mucosa of organ cardial part of stomach mucous membrane cardial part of stomach organ mucosa gastric cardia mucosa gastric cardia mucosa of organ gastric cardia mucous membrane gastric cardia organ mucosa mucosa of cardial part of stomach mucosa of gastric cardia mucosa of organ of cardia of stomach mucosa of organ of cardial part of stomach mucosa of organ of gastric cardia mucosa of organ of pars cardiaca (gaster) mucosa of organ of stomach cardiac region mucosa of pars cardiaca (gaster) mucosa of stomach cardiac region mucous membrane of cardia of stomach mucous membrane of cardial part of stomach mucous membrane of gastric cardia mucous membrane of pars cardiaca (gaster) mucous membrane of stomach cardiac region organ mucosa of cardia of stomach organ mucosa of cardial part of stomach organ mucosa of gastric cardia organ mucosa of pars cardiaca (gaster) organ mucosa of stomach cardiac region pars cardiaca (gaster) mucosa pars cardiaca (gaster) mucosa of organ pars cardiaca (gaster) mucous membrane pars cardiaca (gaster) organ mucosa stomach cardiac region mucosa stomach cardiac region mucosa of organ stomach cardiac region mucous membrane stomach cardiac region organ mucosa uberon UBERON:0004996 mucosa of cardia of stomach A mucosa that is part of a cardia of stomach [Automatically generated definition]. OBOL:automatic cardia of stomach mucosa OBOL:automatic cardia of stomach mucosa of organ OBOL:automatic cardia of stomach mucous membrane OBOL:automatic cardia of stomach organ mucosa OBOL:automatic cardial part of stomach mucosa OBOL:automatic cardial part of stomach mucosa of organ OBOL:automatic cardial part of stomach mucous membrane OBOL:automatic cardial part of stomach organ mucosa OBOL:automatic gastric cardia mucosa OBOL:automatic gastric cardia mucosa of organ OBOL:automatic gastric cardia mucous membrane OBOL:automatic gastric cardia organ mucosa OBOL:automatic mucosa of cardial part of stomach OBOL:automatic mucosa of gastric cardia OBOL:automatic mucosa of organ of cardia of stomach OBOL:automatic mucosa of organ of cardial part of stomach OBOL:automatic mucosa of organ of gastric cardia OBOL:automatic mucosa of organ of pars cardiaca (gaster) OBOL:automatic mucosa of organ of stomach cardiac region OBOL:automatic mucosa of pars cardiaca (gaster) OBOL:automatic mucosa of stomach cardiac region OBOL:automatic mucous membrane of cardia of stomach OBOL:automatic mucous membrane of cardial part of stomach OBOL:automatic mucous membrane of gastric cardia OBOL:automatic mucous membrane of pars cardiaca (gaster) OBOL:automatic mucous membrane of stomach cardiac region OBOL:automatic organ mucosa of cardia of stomach OBOL:automatic organ mucosa of cardial part of stomach OBOL:automatic organ mucosa of gastric cardia OBOL:automatic organ mucosa of pars cardiaca (gaster) OBOL:automatic organ mucosa of stomach cardiac region OBOL:automatic pars cardiaca (gaster) mucosa OBOL:automatic pars cardiaca (gaster) mucosa of organ OBOL:automatic pars cardiaca (gaster) mucous membrane OBOL:automatic pars cardiaca (gaster) organ mucosa OBOL:automatic stomach cardiac region mucosa OBOL:automatic stomach cardiac region mucosa of organ OBOL:automatic stomach cardiac region mucous membrane OBOL:automatic stomach cardiac region organ mucosa OBOL:automatic A mucosa that is part of a pyloric antrum [Automatically generated definition]. BTO:0004107 FMA:17055 antral mucosa antrum of stomach mucosa antrum of stomach mucosa of organ antrum of stomach mucous membrane antrum of stomach organ mucosa mucosa of antrum of stomach mucosa of organ of antrum of stomach mucosa of organ of pyloric antrum mucosa of organ of stomach pyloric antrum mucosa of stomach pyloric antrum mucous membrane of antrum of stomach mucous membrane of pyloric antrum mucous membrane of stomach pyloric antrum organ mucosa of antrum of stomach organ mucosa of pyloric antrum organ mucosa of stomach pyloric antrum pyloric antrum mucosa pyloric antrum mucosa of organ pyloric antrum mucous membrane pyloric antrum organ mucosa stomach pyloric antrum mucosa stomach pyloric antrum mucosa of organ stomach pyloric antrum mucous membrane stomach pyloric antrum organ mucosa uberon gastric antrum mucosa UBERON:0004997 mucosa of pyloric antrum BTO A mucosa that is part of a pyloric antrum [Automatically generated definition]. OBOL:automatic antral mucosa BTO:0004107 antrum of stomach mucosa OBOL:automatic antrum of stomach mucosa of organ OBOL:automatic antrum of stomach mucous membrane OBOL:automatic antrum of stomach organ mucosa OBOL:automatic mucosa of antrum of stomach OBOL:automatic mucosa of organ of antrum of stomach OBOL:automatic mucosa of organ of pyloric antrum OBOL:automatic mucosa of organ of stomach pyloric antrum OBOL:automatic mucosa of stomach pyloric antrum OBOL:automatic mucous membrane of antrum of stomach OBOL:automatic mucous membrane of pyloric antrum OBOL:automatic mucous membrane of stomach pyloric antrum OBOL:automatic organ mucosa of antrum of stomach OBOL:automatic organ mucosa of pyloric antrum OBOL:automatic organ mucosa of stomach pyloric antrum OBOL:automatic pyloric antrum mucosa OBOL:automatic pyloric antrum mucosa of organ OBOL:automatic pyloric antrum mucous membrane OBOL:automatic pyloric antrum organ mucosa OBOL:automatic stomach pyloric antrum mucosa OBOL:automatic stomach pyloric antrum mucosa of organ OBOL:automatic stomach pyloric antrum mucous membrane OBOL:automatic stomach pyloric antrum organ mucosa OBOL:automatic gastric antrum mucosa BTO:0004107 A mucosa that is part of a pylorus [Automatically generated definition]. BTO:0004110 EMAPA:27199 FMA:17461 mucosa of organ of pyloric part of stomach mucosa of organ of pylorus mucosa of organ of stomach pyloric region mucosa of pyloric part of stomach mucosa of stomach pyloric region mucous membrane of pyloric part of stomach mucous membrane of pylorus mucous membrane of stomach pyloric region organ mucosa of pyloric part of stomach organ mucosa of pylorus organ mucosa of stomach pyloric region pyloric part of stomach mucosa pyloric part of stomach mucosa of organ pyloric part of stomach mucous membrane pyloric part of stomach organ mucosa pylorus mucosa pylorus mucosa of organ pylorus mucous membrane pylorus organ mucosa stomach pyloric region mucosa stomach pyloric region mucosa of organ stomach pyloric region mucous membrane stomach pyloric region organ mucosa uberon antropyloric mucosa UBERON:0004998 mucosa of pylorus A mucosa that is part of a pylorus [Automatically generated definition]. OBOL:automatic mucosa of organ of pyloric part of stomach OBOL:automatic mucosa of organ of pylorus OBOL:automatic mucosa of organ of stomach pyloric region OBOL:automatic mucosa of pyloric part of stomach OBOL:automatic mucosa of stomach pyloric region OBOL:automatic mucous membrane of pyloric part of stomach OBOL:automatic mucous membrane of pylorus OBOL:automatic mucous membrane of stomach pyloric region OBOL:automatic organ mucosa of pyloric part of stomach OBOL:automatic organ mucosa of pylorus OBOL:automatic organ mucosa of stomach pyloric region OBOL:automatic pyloric part of stomach mucosa OBOL:automatic pyloric part of stomach mucosa of organ OBOL:automatic pyloric part of stomach mucous membrane OBOL:automatic pyloric part of stomach organ mucosa OBOL:automatic pylorus mucosa OBOL:automatic pylorus mucosa of organ OBOL:automatic pylorus mucous membrane OBOL:automatic pylorus organ mucosa OBOL:automatic stomach pyloric region mucosa OBOL:automatic stomach pyloric region mucosa of organ OBOL:automatic stomach pyloric region mucous membrane OBOL:automatic stomach pyloric region organ mucosa OBOL:automatic antropyloric mucosa BTO:0002984 A mucosa that is part of a biliary tree [Automatically generated definition]. FMA:14695 biliary tract mucosa biliary tract mucosa of organ biliary tract mucous membrane biliary tract organ mucosa biliary tree mucosa biliary tree mucosa of organ biliary tree mucous membrane biliary tree organ mucosa mucosa of biliary tract mucosa of organ of biliary tract mucosa of organ of biliary tree mucous membrane of biliary tract mucous membrane of biliary tree organ mucosa of biliary tract organ mucosa of biliary tree uberon UBERON:0004999 mucosa of biliary tree A mucosa that is part of a biliary tree [Automatically generated definition]. OBOL:automatic biliary tract mucosa OBOL:automatic biliary tract mucosa of organ OBOL:automatic biliary tract mucous membrane OBOL:automatic biliary tract organ mucosa OBOL:automatic biliary tree mucosa OBOL:automatic biliary tree mucosa of organ OBOL:automatic biliary tree mucous membrane OBOL:automatic biliary tree organ mucosa OBOL:automatic mucosa of biliary tract OBOL:automatic mucosa of organ of biliary tract OBOL:automatic mucosa of organ of biliary tree OBOL:automatic mucous membrane of biliary tract OBOL:automatic mucous membrane of biliary tree OBOL:automatic organ mucosa of biliary tract OBOL:automatic organ mucosa of biliary tree OBOL:automatic A mucosa that is part of a common bile duct [Automatically generated definition]. FMA:14688 common bile duct mucosa common bile duct mucosa of organ common bile duct mucous membrane common bile duct organ mucosa common bile ductal mucosa ductus choledochus (biliaris) mucosa ductus choledochus (biliaris) mucosa of organ ductus choledochus (biliaris) mucous membrane ductus choledochus (biliaris) organ mucosa mucosa of ductus choledochus (biliaris) mucosa of organ of common bile duct mucosa of organ of ductus choledochus (biliaris) mucous membrane of common bile duct mucous membrane of ductus choledochus (biliaris) organ mucosa of common bile duct organ mucosa of ductus choledochus (biliaris) uberon UBERON:0005000 mucosa of common bile duct A mucosa that is part of a common bile duct [Automatically generated definition]. OBOL:automatic common bile duct mucosa OBOL:automatic common bile duct mucosa of organ OBOL:automatic common bile duct mucous membrane OBOL:automatic common bile duct organ mucosa OBOL:automatic common bile ductal mucosa FMA:14688 ductus choledochus (biliaris) mucosa OBOL:automatic ductus choledochus (biliaris) mucosa of organ OBOL:automatic ductus choledochus (biliaris) mucous membrane OBOL:automatic ductus choledochus (biliaris) organ mucosa OBOL:automatic mucosa of ductus choledochus (biliaris) OBOL:automatic mucosa of organ of common bile duct OBOL:automatic mucosa of organ of ductus choledochus (biliaris) OBOL:automatic mucous membrane of common bile duct OBOL:automatic mucous membrane of ductus choledochus (biliaris) OBOL:automatic organ mucosa of common bile duct OBOL:automatic organ mucosa of ductus choledochus (biliaris) OBOL:automatic A mucosa that is part of a common hepatic duct [Automatically generated definition]. FMA:14691 common hepatic duct mucosa common hepatic duct mucosa of organ common hepatic duct mucous membrane common hepatic duct organ mucosa common hepatic ductal mucosa hepatic duct mucosa hepatic duct mucosa of organ hepatic duct mucous membrane hepatic duct organ mucosa mucosa of hepatic duct mucosa of organ of common hepatic duct mucosa of organ of hepatic duct mucous membrane of common hepatic duct mucous membrane of hepatic duct organ mucosa of common hepatic duct organ mucosa of hepatic duct uberon UBERON:0005001 mucosa of common hepatic duct A mucosa that is part of a common hepatic duct [Automatically generated definition]. OBOL:automatic common hepatic duct mucosa OBOL:automatic common hepatic duct mucosa of organ OBOL:automatic common hepatic duct mucous membrane OBOL:automatic common hepatic duct organ mucosa OBOL:automatic common hepatic ductal mucosa FMA:14691 hepatic duct mucosa OBOL:automatic hepatic duct mucosa of organ OBOL:automatic hepatic duct mucous membrane OBOL:automatic hepatic duct organ mucosa OBOL:automatic mucosa of hepatic duct OBOL:automatic mucosa of organ of common hepatic duct OBOL:automatic mucosa of organ of hepatic duct OBOL:automatic mucous membrane of common hepatic duct OBOL:automatic mucous membrane of hepatic duct OBOL:automatic organ mucosa of common hepatic duct OBOL:automatic organ mucosa of hepatic duct OBOL:automatic A mucosa that is part of a right hepatic duct [Automatically generated definition]. FMA:14692 mucosa of organ of right hepatic duct mucous membrane of right hepatic duct organ mucosa of right hepatic duct right hepatic duct mucosa right hepatic duct mucosa of organ right hepatic duct mucous membrane right hepatic duct organ mucosa right hepatic ductal mucosa uberon UBERON:0005002 mucosa of right hepatic duct A mucosa that is part of a right hepatic duct [Automatically generated definition]. OBOL:automatic mucosa of organ of right hepatic duct OBOL:automatic mucous membrane of right hepatic duct OBOL:automatic organ mucosa of right hepatic duct OBOL:automatic right hepatic duct mucosa OBOL:automatic right hepatic duct mucosa of organ OBOL:automatic right hepatic duct mucous membrane OBOL:automatic right hepatic duct organ mucosa OBOL:automatic right hepatic ductal mucosa FMA:14692 A mucosa that is part of a left hepatic duct [Automatically generated definition]. FMA:14693 left hepatic duct mucosa left hepatic duct mucosa of organ left hepatic duct mucous membrane left hepatic duct organ mucosa left hepatic ductal mucosa mucosa of organ of left hepatic duct mucous membrane of left hepatic duct organ mucosa of left hepatic duct uberon UBERON:0005003 mucosa of left hepatic duct A mucosa that is part of a left hepatic duct [Automatically generated definition]. OBOL:automatic left hepatic duct mucosa OBOL:automatic left hepatic duct mucosa of organ OBOL:automatic left hepatic duct mucous membrane OBOL:automatic left hepatic duct organ mucosa OBOL:automatic left hepatic ductal mucosa FMA:14693 mucosa of organ of left hepatic duct OBOL:automatic mucous membrane of left hepatic duct OBOL:automatic organ mucosa of left hepatic duct OBOL:automatic A mucosa that is part of a right ureter [Automatically generated definition]. FMA:17806 mucosa of organ of right ureter mucous membrane of right ureter organ mucosa of right ureter right ureter mucosa right ureter mucosa of organ right ureter mucous membrane right ureter organ mucosa right ureteral mucosa uberon UBERON:0005004 mucosa of right ureter A mucosa that is part of a right ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of right ureter OBOL:automatic mucous membrane of right ureter OBOL:automatic organ mucosa of right ureter OBOL:automatic right ureter mucosa OBOL:automatic right ureter mucosa of organ OBOL:automatic right ureter mucous membrane OBOL:automatic right ureter organ mucosa OBOL:automatic right ureteral mucosa FMA:17806 A mucosa that is part of a left ureter [Automatically generated definition]. FMA:17807 left ureter mucosa left ureter mucosa of organ left ureter mucous membrane left ureter organ mucosa left ureteral mucosa mucosa of organ of left ureter mucous membrane of left ureter organ mucosa of left ureter uberon UBERON:0005005 mucosa of left ureter A mucosa that is part of a left ureter [Automatically generated definition]. OBOL:automatic left ureter mucosa OBOL:automatic left ureter mucosa of organ OBOL:automatic left ureter mucous membrane OBOL:automatic left ureter organ mucosa OBOL:automatic left ureteral mucosa FMA:17807 mucosa of organ of left ureter OBOL:automatic mucous membrane of left ureter OBOL:automatic organ mucosa of left ureter OBOL:automatic A mucosa that is part of a renal pelvis [Automatically generated definition]. FMA:17931 SCTID:243482002 kidney pelvis mucosa kidney pelvis mucosa of organ kidney pelvis mucous membrane kidney pelvis organ mucosa mucosa of kidney pelvis mucosa of organ of kidney pelvis mucosa of organ of pelvis of ureter mucosa of organ of renal pelvis mucosa of pelvis of ureter mucous membrane of kidney pelvis mucous membrane of pelvis of ureter mucous membrane of renal pelvis organ mucosa of kidney pelvis organ mucosa of pelvis of ureter organ mucosa of renal pelvis pelvis of ureter mucosa pelvis of ureter mucosa of organ pelvis of ureter mucous membrane pelvis of ureter organ mucosa renal pelvic mucosa renal pelvis mucosa renal pelvis mucosa of organ renal pelvis mucous membrane renal pelvis organ mucosa tunica mucosa pelvis renalis uberon UBERON:0005006 mucosa of renal pelvis A mucosa that is part of a renal pelvis [Automatically generated definition]. OBOL:automatic kidney pelvis mucosa OBOL:automatic kidney pelvis mucosa of organ OBOL:automatic kidney pelvis mucous membrane OBOL:automatic kidney pelvis organ mucosa OBOL:automatic mucosa of kidney pelvis OBOL:automatic mucosa of organ of kidney pelvis OBOL:automatic mucosa of organ of pelvis of ureter OBOL:automatic mucosa of organ of renal pelvis OBOL:automatic mucosa of pelvis of ureter OBOL:automatic mucous membrane of kidney pelvis OBOL:automatic mucous membrane of pelvis of ureter OBOL:automatic mucous membrane of renal pelvis OBOL:automatic organ mucosa of kidney pelvis OBOL:automatic organ mucosa of pelvis of ureter OBOL:automatic organ mucosa of renal pelvis OBOL:automatic pelvis of ureter mucosa OBOL:automatic pelvis of ureter mucosa of organ OBOL:automatic pelvis of ureter mucous membrane OBOL:automatic pelvis of ureter organ mucosa OBOL:automatic renal pelvic mucosa FMA:17931 renal pelvis mucosa OBOL:automatic renal pelvis mucosa of organ OBOL:automatic renal pelvis mucous membrane OBOL:automatic renal pelvis organ mucosa OBOL:automatic tunica mucosa pelvis renalis FMA:17931 FMA:TA A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. FMA:17846 bladder neck mucosa bladder neck mucosa of organ bladder neck mucous membrane bladder neck organ mucosa mucosa of bladder neck mucosa of neck of bladder mucosa of organ of bladder neck mucosa of organ of neck of bladder mucosa of organ of neck of urinary bladder mucosa of organ of urinary bladder neck mucosa of organ of vesical neck mucosa of urinary bladder neck mucosa of vesical neck mucous membrane of bladder neck mucous membrane of neck of bladder mucous membrane of neck of urinary bladder mucous membrane of urinary bladder neck mucous membrane of vesical neck neck of bladder mucosa neck of bladder mucosa of organ neck of bladder mucous membrane neck of bladder organ mucosa neck of urinary bladder mucosa neck of urinary bladder mucosa of organ neck of urinary bladder mucous membrane neck of urinary bladder organ mucosa organ mucosa of bladder neck organ mucosa of neck of bladder organ mucosa of neck of urinary bladder organ mucosa of urinary bladder neck organ mucosa of vesical neck urinary bladder neck mucosa urinary bladder neck mucosa of organ urinary bladder neck mucous membrane vesical neck mucosa vesical neck mucosa of organ vesical neck mucous membrane vesical neck organ mucosa uberon UBERON:0005010 mucosa of neck of urinary bladder A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck mucosa OBOL:automatic bladder neck mucosa of organ OBOL:automatic bladder neck mucous membrane OBOL:automatic bladder neck organ mucosa OBOL:automatic mucosa of bladder neck OBOL:automatic mucosa of neck of bladder OBOL:automatic mucosa of organ of bladder neck OBOL:automatic mucosa of organ of neck of bladder OBOL:automatic mucosa of organ of neck of urinary bladder OBOL:automatic mucosa of organ of urinary bladder neck OBOL:automatic mucosa of organ of vesical neck OBOL:automatic mucosa of urinary bladder neck OBOL:automatic mucosa of vesical neck OBOL:automatic mucous membrane of bladder neck OBOL:automatic mucous membrane of neck of bladder OBOL:automatic mucous membrane of neck of urinary bladder OBOL:automatic mucous membrane of urinary bladder neck OBOL:automatic mucous membrane of vesical neck OBOL:automatic neck of bladder mucosa OBOL:automatic neck of bladder mucosa of organ OBOL:automatic neck of bladder mucous membrane OBOL:automatic neck of bladder organ mucosa OBOL:automatic neck of urinary bladder mucosa OBOL:automatic neck of urinary bladder mucosa of organ OBOL:automatic neck of urinary bladder mucous membrane OBOL:automatic neck of urinary bladder organ mucosa OBOL:automatic organ mucosa of bladder neck OBOL:automatic organ mucosa of neck of bladder OBOL:automatic organ mucosa of neck of urinary bladder OBOL:automatic organ mucosa of urinary bladder neck OBOL:automatic organ mucosa of vesical neck OBOL:automatic urinary bladder neck mucosa OBOL:automatic urinary bladder neck mucosa of organ OBOL:automatic urinary bladder neck mucous membrane OBOL:automatic vesical neck mucosa OBOL:automatic vesical neck mucosa of organ OBOL:automatic vesical neck mucous membrane OBOL:automatic vesical neck organ mucosa OBOL:automatic A mucosa that is part of a right uterine tube [Automatically generated definition]. FMA:18452 mucosa of organ of right fallopian tube mucosa of organ of right oviduct mucosa of organ of right uterine tube mucosa of right fallopian tube mucosa of right oviduct mucous membrane of right fallopian tube mucous membrane of right oviduct mucous membrane of right uterine tube organ mucosa of right fallopian tube organ mucosa of right oviduct organ mucosa of right uterine tube right fallopian tube mucosa right fallopian tube mucosa of organ right fallopian tube mucous membrane right fallopian tube organ mucosa right oviduct mucosa right oviduct mucosa of organ right oviduct mucous membrane right oviduct organ mucosa right uterine tube mucosa right uterine tube mucosa of organ right uterine tube mucous membrane right uterine tube organ mucosa uberon UBERON:0005011 mucosa of right uterine tube A mucosa that is part of a right uterine tube [Automatically generated definition]. OBOL:automatic mucosa of organ of right fallopian tube OBOL:automatic mucosa of organ of right oviduct OBOL:automatic mucosa of organ of right uterine tube OBOL:automatic mucosa of right fallopian tube OBOL:automatic mucosa of right oviduct OBOL:automatic mucous membrane of right fallopian tube OBOL:automatic mucous membrane of right oviduct OBOL:automatic mucous membrane of right uterine tube OBOL:automatic organ mucosa of right fallopian tube OBOL:automatic organ mucosa of right oviduct OBOL:automatic organ mucosa of right uterine tube OBOL:automatic right fallopian tube mucosa OBOL:automatic right fallopian tube mucosa of organ OBOL:automatic right fallopian tube mucous membrane OBOL:automatic right fallopian tube organ mucosa OBOL:automatic right oviduct mucosa OBOL:automatic right oviduct mucosa of organ OBOL:automatic right oviduct mucous membrane OBOL:automatic right oviduct organ mucosa OBOL:automatic right uterine tube mucosa OBOL:automatic right uterine tube mucosa of organ OBOL:automatic right uterine tube mucous membrane OBOL:automatic right uterine tube organ mucosa OBOL:automatic A mucosa that is part of a left uterine tube [Automatically generated definition]. FMA:18453 left fallopian tube mucosa left fallopian tube mucosa of organ left fallopian tube mucous membrane left fallopian tube organ mucosa left oviduct mucosa left oviduct mucosa of organ left oviduct mucous membrane left oviduct organ mucosa left uterine tube mucosa left uterine tube mucosa of organ left uterine tube mucous membrane left uterine tube organ mucosa mucosa of left fallopian tube mucosa of left oviduct mucosa of organ of left fallopian tube mucosa of organ of left oviduct mucosa of organ of left uterine tube mucous membrane of left fallopian tube mucous membrane of left oviduct mucous membrane of left uterine tube organ mucosa of left fallopian tube organ mucosa of left oviduct organ mucosa of left uterine tube uberon UBERON:0005012 mucosa of left uterine tube A mucosa that is part of a left uterine tube [Automatically generated definition]. OBOL:automatic left fallopian tube mucosa OBOL:automatic left fallopian tube mucosa of organ OBOL:automatic left fallopian tube mucous membrane OBOL:automatic left fallopian tube organ mucosa OBOL:automatic left oviduct mucosa OBOL:automatic left oviduct mucosa of organ OBOL:automatic left oviduct mucous membrane OBOL:automatic left oviduct organ mucosa OBOL:automatic left uterine tube mucosa OBOL:automatic left uterine tube mucosa of organ OBOL:automatic left uterine tube mucous membrane OBOL:automatic left uterine tube organ mucosa OBOL:automatic mucosa of left fallopian tube OBOL:automatic mucosa of left oviduct OBOL:automatic mucosa of organ of left fallopian tube OBOL:automatic mucosa of organ of left oviduct OBOL:automatic mucosa of organ of left uterine tube OBOL:automatic mucous membrane of left fallopian tube OBOL:automatic mucous membrane of left oviduct OBOL:automatic mucous membrane of left uterine tube OBOL:automatic organ mucosa of left fallopian tube OBOL:automatic organ mucosa of left oviduct OBOL:automatic organ mucosa of left uterine tube OBOL:automatic A mucosa that is part of a male urethra [Automatically generated definition]. FMA:239937 male urethra mucosa male urethra mucosa of organ male urethra mucous membrane male urethra organ mucosa mucosa of organ of male urethra mucous membrane of male urethra organ mucosa of male urethra uberon UBERON:0005013 mucosa of male urethra A mucosa that is part of a male urethra [Automatically generated definition]. OBOL:automatic male urethra mucosa OBOL:automatic male urethra mucosa of organ OBOL:automatic male urethra mucous membrane OBOL:automatic male urethra organ mucosa OBOL:automatic mucosa of organ of male urethra OBOL:automatic mucous membrane of male urethra OBOL:automatic organ mucosa of male urethra OBOL:automatic A mucosa that is part of a female urethra [Automatically generated definition]. FMA:239940 female urethra mucosa female urethra mucosa of organ female urethra mucous membrane female urethra organ mucosa mucosa of organ of female urethra mucous membrane of female urethra organ mucosa of female urethra uberon UBERON:0005014 mucosa of female urethra A mucosa that is part of a female urethra [Automatically generated definition]. OBOL:automatic female urethra mucosa OBOL:automatic female urethra mucosa of organ OBOL:automatic female urethra mucous membrane OBOL:automatic female urethra organ mucosa OBOL:automatic mucosa of organ of female urethra OBOL:automatic mucous membrane of female urethra OBOL:automatic organ mucosa of female urethra OBOL:automatic A mucosa that is part of a lacrimal sac [Automatically generated definition]. FMA:72061 lacrimal sac mucosa lacrimal sac mucosa of organ lacrimal sac mucous membrane lacrimal sac organ mucosa mucosa of organ of lacrimal sac mucous membrane of lacrimal sac organ mucosa of lacrimal sac uberon UBERON:0005017 mucosa of lacrimal sac A mucosa that is part of a lacrimal sac [Automatically generated definition]. OBOL:automatic lacrimal sac mucosa OBOL:automatic lacrimal sac mucosa of organ OBOL:automatic lacrimal sac mucous membrane OBOL:automatic lacrimal sac organ mucosa OBOL:automatic mucosa of organ of lacrimal sac OBOL:automatic mucous membrane of lacrimal sac OBOL:automatic organ mucosa of lacrimal sac OBOL:automatic A mucosa that is part of a nasal septum [Automatically generated definition]. EMAPA:36028 FMA:60113 mucosa of organ of nasal septum mucous membrane of nasal septum nasal septum mucosa nasal septum mucosa of organ nasal septum mucous membrane nasal septum organ mucosa organ mucosa of nasal septum uberon UBERON:0005018 mucosa of nasal septum A mucosa that is part of a nasal septum [Automatically generated definition]. OBOL:automatic mucosa of organ of nasal septum OBOL:automatic mucous membrane of nasal septum OBOL:automatic nasal septum mucosa OBOL:automatic nasal septum mucosa of organ OBOL:automatic nasal septum mucous membrane OBOL:automatic nasal septum organ mucosa OBOL:automatic organ mucosa of nasal septum OBOL:automatic A mucosa that is part of a palate [Automatically generated definition]. FMA:59765 mucosa of oral roof mucosa of organ of oral roof mucosa of organ of palate mucosa of organ of roof of mouth mucosa of roof of mouth mucous membrane of oral roof mucous membrane of palate mucous membrane of roof of mouth oral roof mucosa oral roof mucosa of organ oral roof mucous membrane oral roof organ mucosa organ mucosa of oral roof organ mucosa of palate organ mucosa of roof of mouth palate mucosa palate mucosa of organ palate mucous membrane palate organ mucosa roof of mouth mucosa roof of mouth mucosa of organ roof of mouth mucous membrane roof of mouth organ mucosa uberon UBERON:0005019 mucosa of palate A mucosa that is part of a palate [Automatically generated definition]. OBOL:automatic mucosa of oral roof OBOL:automatic mucosa of organ of oral roof OBOL:automatic mucosa of organ of palate OBOL:automatic mucosa of organ of roof of mouth OBOL:automatic mucosa of roof of mouth OBOL:automatic mucous membrane of oral roof OBOL:automatic mucous membrane of palate OBOL:automatic mucous membrane of roof of mouth OBOL:automatic oral roof mucosa OBOL:automatic oral roof mucosa of organ OBOL:automatic oral roof mucous membrane OBOL:automatic oral roof organ mucosa OBOL:automatic organ mucosa of oral roof OBOL:automatic organ mucosa of palate OBOL:automatic organ mucosa of roof of mouth OBOL:automatic palate mucosa OBOL:automatic palate mucosa of organ OBOL:automatic palate mucous membrane OBOL:automatic palate organ mucosa OBOL:automatic roof of mouth mucosa OBOL:automatic roof of mouth mucosa of organ OBOL:automatic roof of mouth mucous membrane OBOL:automatic roof of mouth organ mucosa OBOL:automatic A mucosa that is part of a tongue [Automatically generated definition]. EFO:0002553 FMA:54807 SCTID:362092002 lingual mucosa mucosa of organ of tongue mucous membrane of tongue organ mucosa of tongue tongue mucosa tongue mucosa of organ tongue mucous membrane tongue organ mucosa tunica mucosa linguae uberon UBERON:0005020 mucosa of tongue A mucosa that is part of a tongue [Automatically generated definition]. OBOL:automatic lingual mucosa FMA:54807 mucosa of organ of tongue OBOL:automatic mucous membrane of tongue OBOL:automatic organ mucosa of tongue OBOL:automatic tongue mucosa OBOL:automatic tongue mucosa of organ OBOL:automatic tongue mucous membrane OBOL:automatic tongue organ mucosa OBOL:automatic tunica mucosa linguae FMA:54807 FMA:TA A mucosa that is part of a nasopharynx [Automatically generated definition]. FMA:54971 SCTID:361938001 mucosa of nasal part of pharynx mucosa of organ of nasal part of pharynx mucosa of organ of nasopharynx mucosa of organ of rhinopharynx mucosa of rhinopharynx mucous membrane of nasal part of pharynx mucous membrane of nasopharynx mucous membrane of rhinopharynx nasal part of pharynx mucosa nasal part of pharynx mucosa of organ nasal part of pharynx mucous membrane nasal part of pharynx organ mucosa nasopharynx mucosa nasopharynx mucosa of organ nasopharynx mucous membrane nasopharynx organ mucosa organ mucosa of nasal part of pharynx organ mucosa of nasopharynx organ mucosa of rhinopharynx rhinopharynx mucosa rhinopharynx mucosa of organ rhinopharynx mucous membrane rhinopharynx organ mucosa uberon UBERON:0005022 mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic mucosa of nasal part of pharynx OBOL:automatic mucosa of organ of nasal part of pharynx OBOL:automatic mucosa of organ of nasopharynx OBOL:automatic mucosa of organ of rhinopharynx OBOL:automatic mucosa of rhinopharynx OBOL:automatic mucous membrane of nasal part of pharynx OBOL:automatic mucous membrane of nasopharynx OBOL:automatic mucous membrane of rhinopharynx OBOL:automatic nasal part of pharynx mucosa OBOL:automatic nasal part of pharynx mucosa of organ OBOL:automatic nasal part of pharynx mucous membrane OBOL:automatic nasal part of pharynx organ mucosa OBOL:automatic nasopharynx mucosa OBOL:automatic nasopharynx mucosa of organ OBOL:automatic nasopharynx mucous membrane OBOL:automatic nasopharynx organ mucosa OBOL:automatic organ mucosa of nasal part of pharynx OBOL:automatic organ mucosa of nasopharynx OBOL:automatic organ mucosa of rhinopharynx OBOL:automatic rhinopharynx mucosa OBOL:automatic rhinopharynx mucosa of organ OBOL:automatic rhinopharynx mucous membrane OBOL:automatic rhinopharynx organ mucosa OBOL:automatic A mucosa that is part of a oropharynx [Automatically generated definition]. FMA:54933 SCTID:144632009 mucosa of oral part of pharynx mucosa of organ of oral part of pharynx mucosa of organ of oropharynx mucous membrane of oral part of pharynx mucous membrane of oropharynx oral part of pharynx mucosa oral part of pharynx mucosa of organ oral part of pharynx mucous membrane oral part of pharynx organ mucosa organ mucosa of oral part of pharynx organ mucosa of oropharynx oropharynx mucosa oropharynx mucosa of organ oropharynx mucous membrane oropharynx organ mucosa uberon UBERON:0005023 mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. OBOL:automatic mucosa of oral part of pharynx OBOL:automatic mucosa of organ of oral part of pharynx OBOL:automatic mucosa of organ of oropharynx OBOL:automatic mucous membrane of oral part of pharynx OBOL:automatic mucous membrane of oropharynx OBOL:automatic oral part of pharynx mucosa OBOL:automatic oral part of pharynx mucosa of organ OBOL:automatic oral part of pharynx mucous membrane OBOL:automatic oral part of pharynx organ mucosa OBOL:automatic organ mucosa of oral part of pharynx OBOL:automatic organ mucosa of oropharynx OBOL:automatic oropharynx mucosa OBOL:automatic oropharynx mucosa of organ OBOL:automatic oropharynx mucous membrane OBOL:automatic oropharynx organ mucosa OBOL:automatic A mucosa that is part of a middle ear [Automatically generated definition]. CALOHA:TS-0631 FMA:59663 middle ear mucosa middle ear mucosa of organ middle ear mucous membrane middle ear organ mucosa mucosa of organ of middle ear mucosa of tympanic cavity mucous membrane of middle ear organ mucosa of middle ear tunica mucosa cavitatis tympanicae uberon UBERON:0005026 mucosa of middle ear A mucosa that is part of a middle ear [Automatically generated definition]. OBOL:automatic middle ear mucosa OBOL:automatic middle ear mucosa of organ OBOL:automatic middle ear mucous membrane OBOL:automatic middle ear organ mucosa OBOL:automatic mucosa of organ of middle ear OBOL:automatic mucosa of tympanic cavity FMA:59663 mucous membrane of middle ear OBOL:automatic organ mucosa of middle ear OBOL:automatic tunica mucosa cavitatis tympanicae FMA:59663 FMA:TA A mucosa that is part of a upper lip [Automatically generated definition]. FMA:59832 NCIT:C12224 SCTID:362088009 UMLS:C0226933 mucosa of organ of upper lip mucous membrane of upper lip organ mucosa of upper lip upper labial mucosa upper lip mucosa upper lip mucosa of organ upper lip mucous membrane upper lip organ mucosa uberon UBERON:0005031 mucosa of upper lip A mucosa that is part of a upper lip [Automatically generated definition]. OBOL:automatic UMLS:C0226933 ncithesaurus:Mucosa_of_the_Upper_Lip mucosa of organ of upper lip OBOL:automatic mucous membrane of upper lip OBOL:automatic organ mucosa of upper lip OBOL:automatic upper labial mucosa UBERON:cjm upper lip mucosa OBOL:automatic upper lip mucosa of organ OBOL:automatic upper lip mucous membrane OBOL:automatic upper lip organ mucosa OBOL:automatic A mucosa that is part of a lower lip [Automatically generated definition]. FMA:59833 NCIT:C12225 SCTID:362089001 UMLS:C0226939 lower labial mucosa lower lip mucosa lower lip mucosa of organ lower lip mucous membrane lower lip organ mucosa mucosa of organ of lower lip mucous membrane of lower lip organ mucosa of lower lip uberon UBERON:0005032 mucosa of lower lip A mucosa that is part of a lower lip [Automatically generated definition]. OBOL:automatic UMLS:C0226939 ncithesaurus:Mucosa_of_the_Lower_Lip lower labial mucosa UBERON:cjm lower lip mucosa OBOL:automatic lower lip mucosa of organ OBOL:automatic lower lip mucous membrane OBOL:automatic lower lip organ mucosa OBOL:automatic mucosa of organ of lower lip OBOL:automatic mucous membrane of lower lip OBOL:automatic organ mucosa of lower lip OBOL:automatic A mucosa that is part of a gallbladder [Automatically generated definition]. FMA:14662 SCTID:362196002 gall bladder mucosa gall bladder mucosa of organ gall bladder mucous membrane gall bladder organ mucosa gallbladder mucosa gallbladder mucosa of organ gallbladder mucous membrane gallbladder organ mucosa mucosa of gall bladder mucosa of organ of gall bladder mucosa of organ of gallbladder mucous membrane of gall bladder mucous membrane of gallbladder organ mucosa of gall bladder organ mucosa of gallbladder tunica mucosa (vesica biliaris) tunica mucosa vesicae biliaris uberon UBERON:0005033 mucosa of gallbladder A mucosa that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder mucosa OBOL:automatic gall bladder mucosa of organ OBOL:automatic gall bladder mucous membrane OBOL:automatic gall bladder organ mucosa OBOL:automatic gallbladder mucosa OBOL:automatic gallbladder mucosa of organ OBOL:automatic gallbladder mucous membrane OBOL:automatic gallbladder organ mucosa OBOL:automatic mucosa of gall bladder OBOL:automatic mucosa of organ of gall bladder OBOL:automatic mucosa of organ of gallbladder OBOL:automatic mucous membrane of gall bladder OBOL:automatic mucous membrane of gallbladder OBOL:automatic organ mucosa of gall bladder OBOL:automatic organ mucosa of gallbladder OBOL:automatic tunica mucosa (vesica biliaris) FMA:14662 tunica mucosa vesicae biliaris FMA:14662 FMA:TA A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane. in FMA this is classified as a mucosa FMA:56844 SCTID:36411006 mucosa of tympanic membrane mucous layer of tympanic membrane mucous stratum of tympanic membrane tympanic membrane external middle ear cavity epithelial component tympanic membrane mucosa uberon UBERON:0005042 inner epithelial layer of tympanic membrane A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane. PMID:11237469 https://orcid.org/0000-0002-6601-2165 in FMA this is classified as a mucosa FMA mucosa of tympanic membrane FMA:56844 mucous layer of tympanic membrane FMA:56844 mucous stratum of tympanic membrane FMA:56844 tympanic membrane external middle ear cavity epithelial component https://orcid.org/0000-0002-6601-2165 tympanic membrane mucosa FMA:56844 A mucosa that is part of a nasolacrimal duct [Automatically generated definition]. FMA:59664 mucosa of organ of nasolacrimal duct mucous membrane of nasolacrimal duct nasolacrimal duct mucosa nasolacrimal duct mucosa of organ nasolacrimal duct mucous membrane nasolacrimal duct organ mucosa nasolacrimal ductal mucosa organ mucosa of nasolacrimal duct uberon UBERON:0005043 mucosa of nasolacrimal duct A mucosa that is part of a nasolacrimal duct [Automatically generated definition]. OBOL:automatic mucosa of organ of nasolacrimal duct OBOL:automatic mucous membrane of nasolacrimal duct OBOL:automatic nasolacrimal duct mucosa OBOL:automatic nasolacrimal duct mucosa of organ OBOL:automatic nasolacrimal duct mucous membrane OBOL:automatic nasolacrimal duct organ mucosa OBOL:automatic nasolacrimal ductal mucosa FMA:59664 organ mucosa of nasolacrimal duct OBOL:automatic A mucosa that is part of a fallopian tube [Automatically generated definition]. FMA:18319 fallopian tube mucosa fallopian tube mucosa of organ fallopian tube mucous membrane fallopian tube organ mucosa mucosa of fallopian tube mucosa of organ of fallopian tube mucosa of organ of uterine tube mucosa of oviduct mucous membrane of fallopian tube mucous membrane of uterine tube organ mucosa of fallopian tube organ mucosa of uterine tube tunica mucosa tubae uterinae uterine tubal mucosa uterine tube mucosa uterine tube mucosa of organ uterine tube mucous membrane uterine tube organ mucosa uberon UBERON:0005048 mucosa of uterine tube A mucosa that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube mucosa OBOL:automatic fallopian tube mucosa of organ OBOL:automatic fallopian tube mucous membrane OBOL:automatic fallopian tube organ mucosa OBOL:automatic mucosa of fallopian tube OBOL:automatic mucosa of organ of fallopian tube OBOL:automatic mucosa of organ of uterine tube OBOL:automatic mucosa of oviduct FMA:18319 mucous membrane of fallopian tube OBOL:automatic mucous membrane of uterine tube OBOL:automatic organ mucosa of fallopian tube OBOL:automatic organ mucosa of uterine tube OBOL:automatic tunica mucosa tubae uterinae FMA:18319 FMA:TA uterine tubal mucosa FMA:18319 uterine tube mucosa OBOL:automatic uterine tube mucosa of organ OBOL:automatic uterine tube mucous membrane OBOL:automatic uterine tube organ mucosa OBOL:automatic A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. FMA:18357 mucosa of infundibulum of fallopian tube mucosa of infundibulum of oviduct mucosa of organ of uterine tube infundibulum mucosa of uterine tube infundibulum mucous membrane of uterine tube infundibulum organ mucosa of uterine tube infundibulum uterine tube infundibulum mucosa uterine tube infundibulum mucosa of organ uterine tube infundibulum mucous membrane uterine tube infundibulum organ mucosa uberon UBERON:0005049 mucosa of infundibulum of uterine tube A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. OBOL:automatic mucosa of infundibulum of fallopian tube FMA:18357 mucosa of infundibulum of oviduct FMA:18357 mucosa of organ of uterine tube infundibulum OBOL:automatic mucosa of uterine tube infundibulum OBOL:automatic mucous membrane of uterine tube infundibulum OBOL:automatic organ mucosa of uterine tube infundibulum OBOL:automatic uterine tube infundibulum mucosa OBOL:automatic uterine tube infundibulum mucosa of organ OBOL:automatic uterine tube infundibulum mucous membrane OBOL:automatic uterine tube infundibulum organ mucosa OBOL:automatic The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP]. EMAPA:18331 FMA:19812 MA:0003240 SCTID:362279007 Wikipedia:Mediastinum_testis body of highmore hilum of testicle mediastinum of testis testis mediastinum uberon UBERON:0005051 mediastinum testis http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP]. Wikipedia:Mediastinum_testis body of highmore FMA:19812 mediastinum of testis FMA:19812 testis mediastinum FMA:19812 An organ part that is part of a long bone [Automatically generated definition]. FMA:24008 long bone zone uberon UBERON:0005055 zone of long bone An organ part that is part of a long bone [Automatically generated definition]. OBOL:automatic An external genitalia that is part of a female reproductive system [Automatically generated definition]. in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126] BTO:0003100 EMAPA:30984 FMA:45649 SCTID:362234008 galen:FemaleExternalGenitalia external female genital organ external genitalia of female reproductive system female external genitalia uberon organa genitalia feminina externa UBERON:0005056 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external female genitalia An external genitalia that is part of a female reproductive system [Automatically generated definition]. OBOL:automatic external female genital organ BTO:0003100 external genitalia of female reproductive system OBOL:automatic female external genitalia FMA:45649 organa genitalia feminina externa BTO:0003100 An organ that is part of a immune system [Automatically generated definition]. immune system organ uberon UBERON:0005057 immune organ An organ that is part of a immune system [Automatically generated definition]. OBOL:automatic A gland that is part of a hemolymphoid system [Automatically generated definition]. hemopoietic or lymphoid organ EMAPA:18766 MA:0002962 hemopoietic or lymphoid gland uberon haemolymphoid system gland UBERON:0005058 hemolymphoid system gland A gland that is part of a hemolymphoid system [Automatically generated definition]. OBOL:automatic hemopoietic or lymphoid organ GO:0048534 hemopoietic or lymphoid gland http://orcid.org/0000-0002-6601-2165 haemolymphoid system gland EMAPA:18766 The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 NCIT:C34224 SCTID:361463007 UMLS:C0814992 Wikipedia:Neural_groove XAO:0000248 neuronames:1363 uberon UBERON:0005061 neural groove The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. GO:0001842 Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. Wikipedia:Neural_groove UMLS:C0814992 ncithesaurus:Neural_Groove One of the two elevated edges of the neural groove[GO,MP]. In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 SCTID:361461009 UMLS:C0814993 Wikipedia:Neural_fold XAO:0004087 neuronames:1364 medullary fold uberon UBERON:0005062 neural fold One of the two elevated edges of the neural groove[GO,MP]. GO:0001842 MP:0011256 Wikipedia:Neural_fold In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. Wikipedia:Neural_fold UMLS:C0814993 ncithesaurus:Neural_Fold medullary fold MP:0011256 Missing definition for term UBERON:0005064. Please replace it using linked reference. uberon UBERON:0005064 left ventricular trabecular myocardium GO Missing definition for term UBERON:0005064. Please replace it using linked reference. GO:0003225 Missing definition for term UBERON:0005066. Please replace it using linked reference. uberon UBERON:0005066 right ventricular trabecular myocardium GO Missing definition for term UBERON:0005066. Please replace it using linked reference. GO:0003227 A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 uberon neural tube rod UBERON:0005068 neural rod A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. GO:0014024 ZFA:0000133 An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000133 TAO ZFIN:curator neural tube rod GO:0014027 An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. The boundary between the diencephalon and the mesencephalon.[TAO] relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] EMAPA:36449 TAO:0001367 ZFA:0001367 diencephalic-mesencephalic boundary forebrain midbrain boundary forebrain-midbrain boundary region uberon UBERON:0005075 forebrain-midbrain boundary definitional An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. OBOL:automatic The boundary between the diencephalon and the mesencephalon.[TAO] 2012-08-14 TAO:0001367 TAO ZFIN:curator relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] 2012-08-14 TAO:0001367 TAO diencephalic-mesencephalic boundary ZFA:0001367 forebrain midbrain boundary ZFA:0001367 forebrain-midbrain boundary region EMAPA:36449 An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. hindbrain-spinal cord boundary region uberon UBERON:0005076 hindbrain-spinal cord boundary An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. OBOL:automatic The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. uberon UBERON:0005080 metanephric ureteric bud The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. GO:0035502 The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. uberon UBERON:0005081 ureter ureteric bud The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. GO:0035503 A hole in a tube[GO]. AEO:0000078 EHDAA2:0004618 RETIRED_EHDAA2:0003078 uberon UBERON:0005082 tube lumen A hole in a tube[GO]. GO:0060609 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode UBERON:0005085 ectodermal placode An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. GO:0060788 in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures GO https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347 epithelial placode AEO:0000112 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. EMAPA:36479 hair placode vibrissa placode uberon hair gem hair germ hair peg UBERON:0005086 hair follicle placode Wikipathways:WP2062 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. DOI:10.1016/j.cub.2008.12.005 An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. GO:0060789 hair placode DOI:10.1016/j.cub.2008.12.005 hair gem ISBN:9780878932504 hair germ DOI:10.1016/j.cub.2008.12.005 hair peg ISBN:9780878932504 An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO]. Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO] In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs. BTO:0001511 TAO:0001153 ZFA:0001153 dental anlage dental placode dental primordium odontogenic placode tooth anlage tooth primordium uberon tooth germ UBERON:0005087 tooth placode NCBIBook:NBK53175 check for other species Wikipedia:Tooth_development An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO]. GO:0060790 Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO] 2012-08-14 TAO:0001153 TAO ZFIN:curator dental placode OBOL:automatic dental primordium ZFA:0001153 odontogenic placode OBOL:automatic tooth anlage MP:0000117 tooth primordium MP:0000117 tooth germ ZFA:0001153 A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]. TODO - add bud uberon UBERON:0005088 sebaceous gland placode NCBIBook:NBK53175 Wikipathways:WP2062 A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]. GO:0060791 An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO]. TODO - add bud uberon UBERON:0005089 sweat gland placode NCBIBook:NBK53175 Wikipathways:WP2062 An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO]. GO:0060793 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila EMAPA:32715 FMA:30316 musculus uberon muscle muscle element UBERON:0005090 muscle structure Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. GO:0061061 musculus FMA:30316 Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] EHDAA2:0001841 EHDAA:484 EMAPA:16239 FMA:70318 VHOG:0000489 sinus venosus right horn uberon UBERON:0005092 right horn of sinus venosus FMA Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] 2012-09-17 VHOG:0000489 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003 http://bgee.unil.ch/ sinus venosus right horn VHOG:0000489 Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon kidney anlage UBERON:0005095 kidney rudiment GO Missing definition for term UBERON:0005095. Please replace it using linked reference. GO:0072003 kidney anlage GOC:mtg_kidney_jan10 An epithelium that is part of a mesonephros [Automatically generated definition]. uberon UBERON:0005103 mesonephric epithelium An epithelium that is part of a mesonephros [Automatically generated definition]. OBOL:automatic A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] VHOG:0001526 uberon UBERON:0005106 metanephric tubule A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. GO:0072173 The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0001526 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 http://bgee.unil.ch/ An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. uberon UBERON:0005108 metanephric epithelium An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. GO:0072207 Any smooth muscle tissue that is part of a metanephros. uberon UBERON:0005109 metanephric smooth muscle tissue Any smooth muscle tissue that is part of a metanephros. GO:0072208 https://orcid.org/0000-0002-6601-2165 A metanephric nephron is the functional unit of the metanephros[GO]. The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG] UBERON:0005142 VHOG:0000719 uberon UBERON:0005110 metanephric nephron Wikipedia Wikipedia:Nephron Bgee:AN A metanephric nephron is the functional unit of the metanephros[GO]. GO:0072273 The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG] 2012-09-17 VHOG:0000719 VHOG DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994) http://bgee.unil.ch/ Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]. uberon UBERON:0005111 metanephric pyramid Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]. GO:0072211 EHDAA2:0001140 uberon UBERON:0005113 metanephric cortex mesenchyme EHDAA2 The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]. uberon UBERON:0005115 metanephric cortical collecting duct true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]. GO:0072219 The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO]. UBERON:0005143 uberon UBERON:0005133 metanephric glomerulus vasculature true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO]. GO:0072239 The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]. uberon UBERON:0005134 metanephric nephron epithelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]. GO:0072243 A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO]. uberon UBERON:0005135 metanephric glomerular epithelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO]. GO:0072244 The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO]. uberon UBERON:0005136 metanephric glomerular endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO]. GO:0072264 The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. UBERON:0005112 uberon UBERON:0005137 metanephric capsule The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. GO:0072213 This process pertains to the initial formation of a structure from unspecified parts[GO]. uberon UBERON:0005144 metanephric glomerular capillary true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships This process pertains to the initial formation of a structure from unspecified parts[GO]. GO:0072277 The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. uberon UBERON:0005145 metanephric comma-shaped body The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. GO:0072278 A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]. UBERON:0005128 UBERON:0005152 uberon UBERON:0005146 metanephric nephron tubule ISBN:9780878932504 A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]. GO:0072282 The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. EHDAA2:0001245 EHDAA:9346 EMAPA:27678 metanephric vesicle uberon UBERON:0005147 metanephric renal vesicle EHDAA2 The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. GO:0072283 The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. uberon UBERON:0005148 metanephric S-shaped body true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]. GO:0072284 A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 uberon UBERON:0005153 epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. GO:0060572 A cord of epithelial cells without a lumen and usually several cells thick. AEO:0000216 EHDAA2:0004052 uberon UBERON:0005154 epithelial cord AEO A cord of epithelial cells without a lumen and usually several cells thick. AEO:0000216 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure uberon UBERON:0005156 reproductive structure Any anatomical structure that is part of the reproductive system. http://orcid.org/0000-0002-6601-2165 An epithelial sheet bent on a linear axis. uberon UBERON:0005157 epithelial fold An epithelial sheet bent on a linear axis. GO:0060571 The functional tissue of the central nervous system consisting of neurons and glial cells. CNS parenchyma central nervous system parenchyma parenchyma of CNS parenchyma of central nervous system uberon UBERON:0005158 parenchyma of central nervous system The functional tissue of the central nervous system consisting of neurons and glial cells. CL:tm https://github.com/obophenotype/uberon/issues/8 CNS parenchyma OBOL:automatic central nervous system parenchyma OBOL:automatic parenchyma of CNS OBOL:automatic A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure uberon cell part cluster UBERON:0005162 multi cell part structure A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' CARO FMA FBbt:00007060 multi-cell-component structure CARO:0001000 multi-cell-part structure CARO:0001000 cell part cluster FMA:83115 Connective tissue between the cellular elements of a structure. specify differentia from stroma interstital FMA:86301 SCTID:85293002 interstitium uberon UBERON:0005169 interstitial tissue FMA Connective tissue between the cellular elements of a structure. http://medical-dictionary.thefreedictionary.com/tissue Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same A duct that carries bile from the liver to the small intestine.[TAO] The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] The hepatic duct is the duct that leads from the liver to the bile duct[GO]. EHDAA2:0000741 EHDAA:3049 EMAPA:16843 FMA:71891 MA:0000357 NCIT:C32730 SCTID:245399002 UMLS:C0917710 VHOG:0000219 galen:HepaticDuct uberon UBERON:0005171 hepatic duct Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). http://orcid.org/0000-0002-6601-2165 A duct that carries bile from the liver to the small intestine.[TAO] 2012-08-14 TAO:0001100 TAO ZFIN:curator The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] 2012-09-17 VHOG:0000219 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/hepatic+duct The hepatic duct is the duct that leads from the liver to the bile duct[GO]. GO:0061011 UMLS:C0917710 ncithesaurus:Hepatic_Duct An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 SCTID:272631008 abdomen organ uberon UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. http://orcid.org/0000-0002-6601-2165 abdomen organ MA:0000522 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ uberon UBERON:0005173 abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. http://orcid.org/0000-0002-6601-2165 EMAPA:37062 MA:th abdominal segment organ MA:0000529 An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:0001901 back organ dorsal region organ uberon UBERON:0005174 dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. http://orcid.org/0000-0002-6601-2165 EMAPA:37274 MA:th back organ MA:0001901 An organ that is part of a chest [Automatically generated definition]. EMAPA:37272 MA:0000552 uberon UBERON:0005175 chest organ An organ that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37272 MA:th A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth. A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO] NOT develops_from NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation BTO:0001722 CALOHA:TS-0271 EMAPA:32888 FMA:312389 MA:0001604 MESH:D004658 SCTID:362863002 TAO:0005138 Wikipedia:Enamel_organ ZFA:0005138 dental organ enamel organ uberon odontogenic organ organum enameleum UBERON:0005176 . Alternate definition: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla. tooth enamel organ A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth. ISBN:0-683-40008-8 MP:0010747 Wikipedia:Enamel_organ https://github.com/cerivs/zebrafish-anatomical-ontology/issues/107 https://github.com/obophenotype/uberon/issues/1313 A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO] 2012-08-14 TAO:0005138 TAO ZFIN:curator dental organ ZFA:0005138 enamel organ MP:0010747 organum enameleum Wikipedia:Enamel_organ An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ uberon UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. http://orcid.org/0000-0002-6601-2165 EMAPA:37270 MA:th trunk organ MA:0000516 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. http://orcid.org/0000-0002-6601-2165 EMAPA:37273 MA:th thoracic cavity organ MA:0000557 An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:0000543 pelvic element pelvis organ pelvis region organ uberon UBERON:0005179 pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. http://orcid.org/0000-0002-6601-2165 EMAPA:37275 MA:th pelvis organ MA:0000543 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. http://orcid.org/0000-0002-6601-2165 EMAPA:37271 MA:th upper body organ MA:0000563 Innermost layer of the hair shaft. BTO:0004671 EMAPA:35389 MA:0000158 SCTID:318929009 Wikipedia:Bone_marrow_of_ovary_(hair) uberon medulla of hair shaft UBERON:0005184 hair medulla Innermost layer of the hair shaft. Wikipedia:Bone_marrow_of_ovary_(hair) medulla of hair shaft BTO:0004671 The portion of the collecting duct that resides in the renal medulla. BTO:0004536 EMAPA:28061 EMAPA:35459 MA:0002935 kidney medulla collecting duct medullary collecting duct uberon UBERON:0005185 renal medulla collecting duct The portion of the collecting duct that resides in the renal medulla. http://orcid.org/0000-0002-6601-2165 kidney medulla collecting duct MA:0002935 medullary collecting duct EMAPA:28061 An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]. EMAPA:37513 FMA:18930 MA:0001940 SCTID:279659005 Wikipedia:Artery_to_the_ductus_deferens arteria ductus deferentis artery of ductus deferens ductus deferens artery vas deferens artery uberon UBERON:0005192 deferent duct artery Wikipedia An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]. Wikipedia:Artery_to_the_ductus_deferens EMAPA:37513 MA:th arteria ductus deferentis Wikipedia:Artery_to_the_ductus_deferens artery of ductus deferens FMA:18930 ductus deferens artery FMA:18930 A vein that is part of a thorax [Automatically generated definition]. EMAPA:37197 MA:0002235 NCIT:C53142 SCTID:281472008 UMLS:C0226629 uberon UBERON:0005194 thoracic vein A vein that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37197 MA:th UMLS:C0226629 ncithesaurus:Thoracic_Vein A vein that is part of a vas deferens [Automatically generated definition]. EMAPA:37514 MA:0002100 uberon UBERON:0005195 deferent duct vein A vein that is part of a vas deferens [Automatically generated definition]. OBOL:automatic EMAPA:37514 MA:th A mammary gland that is part of a cervical region. mice have a single pair of cervical mammary glands MA:0000789 uberon UBERON:0005199 cervical mammary gland A mammary gland that is part of a cervical region. OBOL:automatic A lactiferous gland that is located in the thoracic region/breast. Most primates have one pair of mammary glands, which are thoracic. lactiferous gland mammary gland EHDAA2:0001056 EHDAA:6524 EMAPA:36633 FMA:62088 MA:0000797 SCTID:31448001 Wikipedia:Mammary_gland#Other_mammals breast mammary gland uberon anterior mammary gland UBERON:0005200 thoracic mammary gland BTO A lactiferous gland that is located in the thoracic region/breast. Wikipedia:Mammary_gland#Other_mammals https://orcid.org/0000-0002-6601-2165 lactiferous gland FMA:62088 mammary gland FMA:62088 anterior mammary gland Wikipedia:Mammary_gland#Other_mammals A tubuloacinar seromucous gland that is located principally in the submucosa of the trachea. Excretory ducts from this gland pass through the lamina propria to the tracheal lumen. These glands secrete mucus, lysozyme, defensins, and other agents that help protect the lungs from particles and infectious agents. EMAPA:36574 FMA:7473 MA:0002937 SCTID:197423006 glandula trachealis tracheal gland uberon tubular seromucous gland of trachea UBERON:0005203 trachea gland A tubuloacinar seromucous gland that is located principally in the submucosa of the trachea. Excretory ducts from this gland pass through the lamina propria to the tracheal lumen. ISBN:1451113412 MGI:Anna PMID:15973734 http://medical-dictionary.thefreedictionary.com/tracheal+glands https://github.com/obophenotype/uberon/issues/1197 glandula trachealis FMA:7473 tracheal gland FMA:7473 tubular seromucous gland of trachea FMA:7473 A gland that is part of a larynx submucosa [Automatically generated definition]. EMAPA:35475 MA:0002729 uberon laryngeal submucosa gland UBERON:0005204 larynx submucosa gland A gland that is part of a larynx submucosa [Automatically generated definition]. OBOL:automatic laryngeal submucosa gland EMAPA:35475 EMAPA:35902 FMA:19979 MA:0002737 uberon vagina stroma UBERON:0005205 lamina propria of vagina vagina stroma MA:0002737 Stromal matrix surrounding blood vessels within the choroid plexus. EMAPA:36609 MA:0000825 choroid plexus stromal matrix uberon UBERON:0005206 choroid plexus stroma Stromal matrix surrounding blood vessels within the choroid plexus. PMCID:PMC3496674 choroid plexus stromal matrix PMCID:PMC3496674 A capsule that is part of a tonsil [Automatically generated definition]. FMA:294647 MA:0000776 uberon UBERON:0005207 tonsil capsule A capsule that is part of a tonsil [Automatically generated definition]. OBOL:automatic A valve that is part of a right atrium [Automatically generated definition]. EHDAA2:0000302 EMAPA:17327 MA:0001871 valve of right atrium uberon right atrium valves superior vena cava valve UBERON:0005208 right atrium valve A valve that is part of a right atrium [Automatically generated definition]. OBOL:automatic valve of right atrium EMAPA:17327 right atrium valves EHDAA2:0000302 superior vena cava valve EMAPA:17327 Tissue surrounding the loop of Henle in the renal medulla. It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct. EMAPA:18326 MA:0002619 SCTID:245693005 Wikipedia:Bone_marrow_of_ovaryry_interstitium kidney medulla interstitium renal medullary interstitial tissue renal medullary interstitium medullary interstitium uberon medullary stroma UBERON:0005211 renal medulla interstitium MA Tissue surrounding the loop of Henle in the renal medulla. Wikipedia:Bone_marrow_of_ovaryry_interstitium kidney medulla interstitium MA:0002619 renal medullary interstitium EMAPA:18326 medullary interstitium Wikipedia:Medullary_interstitium medullary stroma EMAPA:18326 The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes. See https://sourceforge.net/p/geneontology/ontology-requests/10941/ The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment. The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue. EMAPA:28518 FMA:70983 MA:0002616 NCIT:C33459 SCTID:362210003 interstitial tissue of kidney renal interstitial tissue renal interstitium renal stroma stroma of kidney uberon kidney interstitium group UBERON:0005215 kidney interstitium The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes. DOI:10.1038/ki.1991.49 PMID:18575881 http://orcid.org/0000-0002-6601-2165 renal interstitium FMA:70983 renal stroma FMA:70983 stroma of kidney FMA:70983 kidney interstitium group EMAPA:28518 An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 VHOG:0000520 uberon UBERON:0005216 optic eminence surface ectoderm true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An external ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic A subarachnoid space that is part of a midbrain [Automatically generated definition]. Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG] EMAPA:19055 VHOG:0001304 subarachnoid space midbrain uberon subarachnoid space mesencephalon UBERON:0005217 midbrain subarachnoid space A subarachnoid space that is part of a midbrain [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001304 VHOG http://bgee.unil.ch/ subarachnoid space midbrain VHOG:0001304 subarachnoid space mesencephalon VHOG:0001304 A subarachnoid space that is part of a diencephalon [Automatically generated definition]. Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG] EMAPA:19053 VHOG:0001302 subarachnoid space diencephalon uberon UBERON:0005218 diencephalon subarachnoid space A subarachnoid space that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001302 VHOG http://bgee.unil.ch/ subarachnoid space diencephalon VHOG:0001302 A subarachnoid space that is part of a hindbrain [Automatically generated definition]. Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG] EMAPA:18211 VHOG:0001303 subarachnoid space hindbrain uberon subarachnoid space rhombencephalon UBERON:0005219 hindbrain subarachnoid space A subarachnoid space that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001303 VHOG http://bgee.unil.ch/ subarachnoid space hindbrain VHOG:0001303 subarachnoid space rhombencephalon VHOG:0001303 A parenchyma that is part of a right lobe of liver [Automatically generated definition]. EHDAA2:0001010 EMAPA:18317 FMA:71657 VHOG:0000840 parenchyma of right lobe of liver uberon UBERON:0005221 liver right lobe parenchyma A parenchyma that is part of a right lobe of liver [Automatically generated definition]. OBOL:automatic parenchyma of right lobe of liver FMA:71657 A parenchyma that is part of a left lobe of liver [Automatically generated definition]. EHDAA2:0001002 EMAPA:18310 FMA:71658 VHOG:0000839 parenchyma of left lobe of liver uberon UBERON:0005222 liver left lobe parenchyma A parenchyma that is part of a left lobe of liver [Automatically generated definition]. OBOL:automatic parenchyma of left lobe of liver FMA:71658 An epithelium that is part of a hindlimb stylopod [Automatically generated definition]. EHDAA2:0002131 EMAPA:17500 VHOG:0001041 uberon UBERON:0005225 upper leg epithelium EHDAA2 An epithelium that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic An epithelium that is part of a toe [Automatically generated definition]. EMAPA:32946 VHOG:0001031 hind limb digit epithelium toe epithelium foot digit epithelium uberon UBERON:0005226 pedal digit epithelium EHDAA2 EHDAA2 An epithelium that is part of a toe [Automatically generated definition]. OBOL:automatic hind limb digit epithelium OBOL:accepted foot digit epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a finger [Automatically generated definition]. EHDAA2:0000406 EMAPA:32647 VHOG:0001032 finger epithelium fore limb digit epithelium hand digit epithelium uberon UBERON:0005227 manual digit epithelium EHDAA2 An epithelium that is part of a finger [Automatically generated definition]. OBOL:automatic fore limb digit epithelium OBOL:accepted hand digit epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a forelimb stylopod [Automatically generated definition]. EHDAA2:0002113 EMAPA:17425 VHOG:0000990 uberon UBERON:0005228 upper arm epithelium EHDAA2 An epithelium that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic An epithelium that is part of a lower leg [Automatically generated definition]. EHDAA2:0001031 EMAPA:17497 VHOG:0001050 uberon UBERON:0005229 lower leg epithelium EHDAA2 An epithelium that is part of a lower leg [Automatically generated definition]. OBOL:automatic An ectoderm that is part of a medial nasal prominence [Automatically generated definition]. EHDAA2:0001078 EMAPA:16809 FMA:312675 VHOG:0000803 uberon UBERON:0005233 medial-nasal process ectoderm An ectoderm that is part of a medial nasal prominence [Automatically generated definition]. OBOL:automatic An ectoderm that is part of a optic eminence [Automatically generated definition]. EHDAA:940 EMAPA:16539 RETIRED_EHDAA2:0001309 VHOG:0001105 uberon UBERON:0005234 optic eminence ectoderm An ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] EHDAA2:0001154 EMAPA:17078 VHOG:0000320 metencephalon basal plate uberon UBERON:0005239 basal plate metencephalon The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] 2012-09-17 VHOG:0000320 VHOG http://bgee.unil.ch/ metencephalon basal plate EHDAA2:0001154 An endocardium that is part of a interventricular septum [Automatically generated definition]. TODO - split? EHDAA2:0000886 EHDAA2:0000887 FMA:83584 VHOG:0000615 endocardium of interventricular septum uberon interventricular septum endocardial tissue UBERON:0005243 interventricular septum endocardium An endocardium that is part of a interventricular septum [Automatically generated definition]. OBOL:automatic endocardium of interventricular septum FMA:83584 interventricular septum endocardial tissue VHOG:0000615 A myocardium that is part of a bulbus cordis [Automatically generated definition]. EMAPA:36488 VHOG:0000609 uberon bulbus cordis cardiac muscle UBERON:0005248 bulbus cordis myocardium A myocardium that is part of a bulbus cordis [Automatically generated definition]. OBOL:automatic bulbus cordis cardiac muscle VHOG:0000609 A renal pelvis that is part of a metanephros. The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] VHOG:0000945 metanephros pelvis uberon UBERON:0005249 metanephric renal pelvis A renal pelvis that is part of a metanephros. OBOL:automatic The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] 2012-09-17 VHOG:0000945 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 http://bgee.unil.ch/ metanephros pelvis VHOG:0000945 A gland that is part of a stomodeum. check this VHOG:0000658 stomatodaeum gland uberon UBERON:0005250 stomatodeum gland A gland that is part of a stomodeum. OBOL:automatic stomatodaeum gland VHOG:0000658 An anatomical cavity that is part of a yolk sac [Automatically generated definition]. In mammals, the yolk sac cavity contains fluid rather than platelets in EHDAA2, there are separate primary and secondary yolk sac cavities EMAPA:16055 FMA:63942 VHOG:0000843 cavity of yolk sac yolk sac lumen uberon yolk sac space UBERON:0005251 yolk sac cavity An anatomical cavity that is part of a yolk sac [Automatically generated definition]. OBOL:automatic In mammals, the yolk sac cavity contains fluid rather than platelets ISBN:0073040584 in EHDAA2, there are separate primary and secondary yolk sac cavities EHDAA2 cavity of yolk sac FMA:63942 yolk sac space FMA:63942 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 TAO:0000113 VHOG:0000332 ZFA:0000113 cephalic mesenchyme uberon cranial mesenchyme desmocranium UBERON:0005253 head mesenchyme EHDAA2 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. ISBN:0683400088 MP:0011260 Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000113 TAO ZFIN:curator cephalic mesenchyme MP:0011260 cranial mesenchyme MGI:anna desmocranium FMA:76622 Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]. EHDAA2:0002132 EMAPA:17501 VHOG:0000506 uberon UBERON:0005254 upper leg mesenchyme Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]. OBOL:automatic Mesenchyme that is part of a developing toe [Automatically generated definition]. EMAPA:32947 VHOG:0000463 hind limb digit mesenchyme toe mesenchyme foot digit mesenchyme uberon finger ray mesenchyme pedal digital ray mesenchyme UBERON:0005255 pedal digit mesenchyme EHDAA2 Mesenchyme that is part of a developing toe [Automatically generated definition]. OBOL:automatic hind limb digit mesenchyme OBOL:accepted foot digit mesenchyme NCBITaxon:9606 OBOL:accepted finger ray mesenchyme https://orcid.org/0000-0002-6601-2165 pedal digital ray mesenchyme https://orcid.org/0000-0002-6601-2165 Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 TAO:0000081 VHOG:0000281 ZFA:0000081 uberon trunk and cervical mesenchyme UBERON:0005256 trunk mesenchyme EHDAA2 Mesenchyme that is part of a developing trunk. OBOL:automatic trunk and cervical mesenchyme EHDAA2:0002092 Mesenchyme that is part of a developing finger [Automatically generated definition]. In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation EHDAA2:0000407 EMAPA:32645 VHOG:0001416 finger mesenchyme fore limb digit mesenchyme hand digit mesenchyme uberon anterior limb digital ray mesenchyme finger ray mesenchyme manual digital ray mesenchyme UBERON:0005257 manual digit mesenchyme Mesenchyme that is part of a developing finger [Automatically generated definition]. OBOL:automatic fore limb digit mesenchyme OBOL:accepted hand digit mesenchyme NCBITaxon:9606 OBOL:accepted anterior limb digital ray mesenchyme https://orcid.org/0000-0002-6601-2165 finger ray mesenchyme https://orcid.org/0000-0002-6601-2165 manual digital ray mesenchyme https://orcid.org/0000-0002-6601-2165 Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition]. EHDAA2:0002114 EMAPA:17426 VHOG:0000505 uberon UBERON:0005258 upper arm mesenchyme Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition]. OBOL:automatic Mesenchyme that is part of a developing lower leg [Automatically generated definition]. EHDAA2:0001032 EMAPA:17498 VHOG:0000752 uberon UBERON:0005259 lower leg mesenchyme Mesenchyme that is part of a developing lower leg [Automatically generated definition]. OBOL:automatic An artery that supplies the renal cortex. EMAPA:28147 MA:0002582 kidney cortex artery renal cortex artery uberon renal cortex arterial system UBERON:0005268 renal cortex artery MA An artery that supplies the renal cortex. http://orcid.org/0000-0002-6601-2165 kidney cortex artery MP:0011314 renal cortex artery MA:0002582 renal cortex arterial system MA:0002582 Artery that receives blood from the renal cortex[MP, modified]. EMAPA:28152 MA:0002592 uberon kidney cortex vein renal cortex venous system UBERON:0005269 renal cortex vein MA Artery that receives blood from the renal cortex[MP, modified]. MGI:csmith kidney cortex vein MP:0011322 renal cortex venous system MA:0002592 A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells. In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c. EMAPA:28136 MA:0002608 SCTID:243707006 Wikipedia:Medullary_interstitium kidney cortex interstitium renal cortical interstitial tissue uberon cortical stroma UBERON:0005270 renal cortex interstitium MA MA A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells. PMID:18575881 In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c. PMID:18575881 kidney cortex interstitium MA:0002608 cortical stroma EMAPA:28136 A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity' EFO:0003650 EHDAA2:0004362 EV:0100306 FMA:242675 MBA:73 TAO:0001261 Wikipedia:Ventricular_system ZFA:0001261 neuronames:2497 CNS ventricular system ventricular system ventricular system of neuraxis uberon ventricle system ventriculi cerebri UBERON:0005281 ventricular system of central nervous system http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png ZFA A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. Wikipedia:Ventricular_system CNS ventricular system EHDAA2:0004362 ventricular system ZFA:0001261 ventricular system of neuraxis FMA:242675 ventricle system Wikipedia:Ventricular_system ventriculi cerebri Wikipedia:Ventricular_system The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] CALOHA:TS-1295 EMAPA:37447 FMA:242787 VHOG:0000005 brain ventricular system uberon UBERON:0005282 ventricular system of brain The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000005 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ EMAPA:37447 MA:th brain ventricular system VHOG:0000005 A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. Vascularized tela choroidea is choroid plexus. Note that the structure in ZFA may be different FMA:242849 TAO:0000447 Wikipedia:Tela_chorioidea ZFA:0000447 neuronames:1378 uberon tela chorioidea UBERON:0005283 tela choroidea FMA A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. ISBN:0471888893 Wikipedia:Tela_chorioidea http://isc.temple.edu/neuroanatomy/lab/embryo_new/choroid/ Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. ZFA:0000447 Note that the structure in ZFA may be different ZFA tela chorioidea FMA:242849 Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]. Tela chorioidea that lines the fourth ventricle.[TAO] tela choroidea BAMS:tc4v FMA:78493 SCTID:362321009 TAO:0005158 Wikipedia:Tela_chorioidea_of_fourth_ventricle ZFA:0005158 neuronames:639 choroid membrane choroid membrane of fourth ventricle tela chorioidea fourth ventricle tela choroidea fourth ventricle tela choroidea of fourth ventricle tela choroidea ventriculi quarti uberon tela choroidea ventriculi quarti UBERON:0005287 tela choroidea of fourth ventricle Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]. Wikipedia:Tela_chorioidea_of_fourth_ventricle ZFIN:curator Tela chorioidea that lines the fourth ventricle.[TAO] 2012-08-14 TAO:0005158 TAO ZFIN:curator tela choroidea FMA:78493 FMA:TA choroid membrane FMA:78493 choroid membrane of fourth ventricle FMA:78493 tela choroidea ventriculi quarti FMA:78493 FMA:TA tela choroidea ventriculi quarti Wikipedia:Tela_chorioidea_of_fourth_ventricle Tela chorioidea that lines the telencephalic ventricle. BAMS:tclv FMA:83712 SCTID:362319004 TAO:0005160 ZFA:0005160 neuronames:219 tela chorioidea of lateral ventricle tela chorioidea of telencephalic ventricle tela chorioidea telencephalic ventricle tela choroidea (ventriculi lateralis) tela choroidea of lateral ventricle tela choroidea telencephalic ventricle uberon UBERON:0005289 tela choroidea of telencephalic ventricle Tela chorioidea that lines the telencephalic ventricle. ZFIN:curator tela chorioidea telencephalic ventricle ZFA:0005160 tela choroidea (ventriculi lateralis) FMA:83712 FMA:TA tela choroidea of lateral ventricle FMA:83712 The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 MESH:D054024 VHOG:0000456 Wikipedia:Myelencephalon uberon myelencephalon (medulla oblongata) UBERON:0005290 myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. BTO:0000758 Wikipedia:Myelencephalon The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] 2012-09-17 VHOG:0000456 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/myelencephalon The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000456 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ MESH:D054024 https://github.com/biopragmatics/biomappings myelencephalon (medulla oblongata) DHBA:10662 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue uberon developing tissue UBERON:0005291 embryonic tissue A portion of tissue that is part of an embryo. OBOL:automatic portion of embryonic tissue OBOL:automatic Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061 MIAA:0000061 extra-embryonic tissue uberon UBERON:0005292 extraembryonic tissue Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. https://orcid.org/0000-0002-6601-2165 The elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary. TODO - check developmental relationships. merge with urogenital ridge? in eutherians, SRY transforms the indifferent gonad into testes AAO:0011047 BTO:0001402 EFO:0001414 EHDAA2:0004044 EMAPA:35899 FMA:321917 NCIT:C34184 NCIT:C34321 SCTID:308801004 SCTID:361399001 UMLS:C0231047 UMLS:C1512243 Wikipedia:Gonadal_ridge XAO:0000018 genital ridge gonadal ridge indifferent gonadal ridge uberon crista gonadalis genital cord UBERON:0005294 gonadal ridge http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png The elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary. MGI:anna MP:0011411 UMLS:C0231047 ncithesaurus:Urogenital_Ridge UMLS:C1512243 ncithesaurus:Gonadal_Ridge genital ridge MP:0011411 Wikipedia:Gonadal_ridge gonadal ridge Wikipedia:Gonadal_ridge indifferent gonadal ridge http://orcid.org/0000-0002-6601-2165 crista gonadalis Wikipedia:Gonadal_ridge genital cord MP:0011411 Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female. EHDAA2:0004051 NCIT:C34183 RETIRED_EHDAA2:0001523 SCTID:343823004 UMLS:C1512242 Wikipedia:Sex_cords uberon genital cord gonad cord gonadal cord primitive sex cord UBERON:0005295 sex cord EHDAA2 Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female. Wikipedia:Sex_cords http://www.answers.com/topic/sex-cord UMLS:C1512242 ncithesaurus:Gonadal_Cord Structures that develop from sex cords in the female. After further development they become the ovarian follicles. TODO check secondary vs cortical vs ovary EHDAA2:0001363 EHDAA:8130 EMAPA:31058 NCIT:C34134 UMLS:C1511527 VHOG:0001339 Wikipedia:Cortical_cords ovigerous cord ovigerous cords uberon cortical cord cortical sex cord ovary primitive sex cord secondary cord UBERON:0005296 ovary sex cord Structures that develop from sex cords in the female. After further development they become the ovarian follicles. Wikipedia:Cortical_cords UMLS:C1511527 ncithesaurus:Cortical_Cord ovigerous cords VHOG:0001339 The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]. TODO - check primary vs testis EHDAA2:0002011 EHDAA:8152 EMAPA:29098 VHOG:0001321 Wikipedia:Testis_cords testis cord testis primary sex cords uberon primary sex cord testis primitive sex cord UBERON:0005297 testis sex cord Bgee:AN The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]. Wikipedia:Testis_cords testis cord MP:0006424 testis primary sex cords EHDAA2:0002011 A zone of skin that is part of a clitoris [Automatically generated definition]. FMA:20168 SCTID:361374002 clitoris skin uberon UBERON:0005298 skin of clitoris A zone of skin that is part of a clitoris [Automatically generated definition]. OBOL:automatic A retractable double-layered fold of skin and mucous membrane that covers the clitoral glans. FMA has FMA:27886 skin of prepuce of clitoris EMAPA:30699 FMA:20169 NCIT:C32590 SCTID:362242009 UMLS:C0227771 Wikipedia:Clitoral_hood clitoral hood clitoral prepuce clitoris prepuce prepuce of female prepuce of the clitoris preputium clitoridis uberon UBERON:0005299 prepuce of clitoris http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif A retractable double-layered fold of skin and mucous membrane that covers the clitoral glans. Wikipedia:Clitoral_hood http://orcid.org/0000-0002-6601-2165 UMLS:C0227771 ncithesaurus:Female_Prepuce clitoral hood Wikipedia:Clitoral_hood prepuce of female EMAPA:30699 preputium clitoridis Wikipedia:Clitoral_hood A pronephric nephron is the functional unit of the pronephros[GO]. The structure that is the basic functional unit of the pronephros.[AAO] AAO:0011091 XAO:0000285 uberon UBERON:0005309 pronephric nephron A pronephric nephron is the functional unit of the pronephros[GO]. GO:0039019 The structure that is the basic functional unit of the pronephros.[AAO] 2012-06-20 AAO:0011091 AAO UBERON:0005309 The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]. Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO] TAO:0001558 XAO:0004105 ZFA:0001558 pronephric tubule uberon ciliated neck segment UBERON:0005310 pronephric nephron tubule GO The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]. GO:0039020 ISBN:0073040584 Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO] 2012-08-14 TAO:0001558 TAO ZFIN:curator pronephric tubule ZFA:0001558 ciliated neck segment ZFA:0001558 The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO]. TODO develops_from in mouse, five pairs of symmetrically positioned mammary placodes (three thoracic and two inguinal) form at reproducible locations along the mammary line at E11.5; the individual pairs develop asynchronously and in a distinct order; pair 3 is first, followed by pair 4, then by pairs 1 and 5 (which develop together), and finally by pair 2; the orientation of placodal cells is not uniform, suggesting that placodes are formed by migration of cells from the mammary line; between E11.5 and E12.5, each mammary placode expands and invaginates into the underlying mesenchyme to form an early bulb-shaped mammary bud[MP] EMAPA:35541 uberon mammary anlage UBERON:0005311 mammary placode NCBIBook:NBK53175 PMID:20484386 Stedmans The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO]. GO:0060596 The endothelial lining of the endocardium. FMA:83596 endocardium endothelium endothelium of endocardium uberon UBERON:0005316 endocardial endothelium The endothelial lining of the endocardium. UBERON:cjm endocardium endothelium FMA:83596 endothelium of endocardium FMA:83596 An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. BTO:0000137 pulmonary artery endothelial tube uberon UBERON:0005317 pulmonary artery endothelium An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. GO:0061155 pulmonary artery endothelial tube GO:0061155 The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]. AAO:0010390 XAO:0000151 uberon UBERON:0005319 mesonephric collecting duct true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]. GO:0061211 Missing definition for term UBERON:0005321. Please replace it using linked reference. uberon UBERON:0005321 mesonephric smooth muscle tissue Missing definition for term UBERON:0005321. Please replace it using linked reference. GO:0061214 A nephron that is part of a mesonephros. The structure that is the basic functional unit of the kidney.[AAO] AAO:0010387 XAO:0000292 ZFA:0005592 nephron of mesonephros uberon stage IV nephron UBERON:0005322 mesonephric nephron XAO A nephron that is part of a mesonephros. http://orcid.org/0000-0002-6601-2165 The structure that is the basic functional unit of the kidney.[AAO] 2012-06-20 AAO:0010387 AAO PMID:9268568 stage IV nephron ZFA:0005592 Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. AAO:0011062 EHDAA2:0001132 EMAPA:16745 XAO:0000291 uberon UBERON:0005323 mesonephric mesenchyme Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. GO:0061219 The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO]. A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO] In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG] XAO/AAO class belongs here, as it refers to mesonephric structure glomerulus AAO:0010388 EMAPA:30568 SCTID:362217000 VHOG:0001238 XAO:0000146 uberon UBERON:0005325 mesonephric glomerulus The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO]. GO:0061224 A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO] 2012-06-20 AAO:0010388 AAO AAO:BJB In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG] 2012-09-17 VHOG:0001238 VHOG ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3 http://bgee.unil.ch/ XAO/AAO class belongs here, as it refers to mesonephric structure XAO glomerulus AAO:0010388 The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO]. uberon UBERON:0005326 mesonephric glomerulus vasculature true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO]. GO:0061231 A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO]. uberon UBERON:0005327 mesonephric glomerular epithelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO]. GO:0061232 The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. uberon UBERON:0005328 mesonephric comma-shaped body The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. GO:0061236 The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]. uberon UBERON:0005330 mesonephric nephron epithelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]. GO:0061241 The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. SCTID:361407006 ZFA:0005586 mesonephric vesicle uberon UBERON:0005331 mesonephric renal vesicle ZFA The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. GO:0061243 The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. uberon UBERON:0005332 mesonephric S-shaped body The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]. GO:0061244 A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland. produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts UBERON:0004181 EMAPA:35536 lactiferous gland bud mammary gland bud uberon mammary primordium milk bud UBERON:0005333 mammary bud A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland. http://orcid.org/0000-0002-6601-2165 produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts http://medical-dictionary.thefreedictionary.com/mammary+bud mammary gland bud GO:0060648 A lamina propria that is part of a mucosa of oral region. EMAPA:26947 lamina propria of oral mucosa uberon UBERON:0005334 oral lamina propria A lamina propria that is part of a mucosa of oral region. OBOL:automatic A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. FMA:13225 Wikipedia:Ventricular_outflow_tract XAO:0004140 heart ventricle outflow tract outflow part of ventricle ventricular outflow tract uberon UBERON:0005337 outflow tract of ventricle A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. Wikipedia:Ventricular_outflow_tract heart ventricle outflow tract MP:0010224 ventricular outflow tract Wikipedia:Ventricular_outflow_tract An outflow tract that is part of a aorta. merge with LVOT? EHDAA2:0001353 EMAPA:17329 MA:0000101 VHOG:0001394 uberon UBERON:0005338 outflow tract aortic component An outflow tract that is part of a aorta. OBOL:automatic merge with RVOT? EHDAA2:0001359 EHDAA:4401 EMAPA:17330 MA:0000102 VHOG:0001395 uberon UBERON:0005339 outflow tract pulmonary component The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047] in humans develops into cortical layers II-VI CP CxP BAMS:CTXpl DHBA:10515 EMAPA:32711 MBA:695 MESH:D002540 PBA:294021914 neuronames:2702 cerebral cortex cortical plate future cortical layers II-VI neocortex cortical plate uberon future neocortex UBERON:0005343 cortical plate NCBIBook:NBK10047 The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. MP:0008439 http://www.ncbi.nlm.nih.gov/books/NBK10047 CP BRAINSPAN:BRAINSPAN CxP PMID:23375746 MESH:D002540 https://github.com/biopragmatics/biomappings future cortical layers II-VI http://orcid.org/0000-0002-6601-2165 future neocortex http://orcid.org/0000-0002-6601-2165 The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]. FMA:19937 GAID:395 MESH:D013085 NCIT:C12329 SCTID:181433005 UMLS:C0037855 Wikipedia:Spermatic_cord uberon funiculus spermaticus spermatic chord UBERON:0005352 spermatic cord https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]. MP:0010145 Wikipedia:Spermatic_cord UMLS:C0037855 ncithesaurus:Spermatic_Cord funiculus spermaticus Wikipedia:Spermatic_cord A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP]. A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke's pouch and perhaps to Hatschek 's pit (amphioxus). EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium. AAO:0011094 EHDAA2:0001588 EMAPA:16725 FMA:302929 NCIT:C34281 NCIT:C54098 SCTID:362583008 SCTID:61127000 UMLS:C0229548 UMLS:C1709841 VHOG:0000674 Wikipedia:Rathke's_pouch XAO:0000430 neuronames:1516 Rathke pouch pouch of Rathke Rathkes pouch epithelium adenohypophysial pouch uberon Rathke's cleft Rathke's cyst Rathke's pocket craniobuccal pouch craniopharyngeal pouch hypophyseal diverticulum hypophyseal pouch nasohypophyseal pouch pituitary diverticulum UBERON:0005356 Rathke's pouch EHDAA2 MP NCBIBook:NBK53175 A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP]. MP:0003817 Wikipedia:Rathke's_pouch A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG] 2012-09-17 VHOG:0000674 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/rathke's+pouch It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000674 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 http://bgee.unil.ch/ median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke's pouch and perhaps to Hatschek 's pit (amphioxus). http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium. EHDAA2 UMLS:C0229548 ncithesaurus:Rathke_s_Pouch UMLS:C1709841 ncithesaurus:Rathke_Pouch_Epithelium Rathkes pouch epithelium EHDAA2:0001473 adenohypophysial pouch EHDAA2:0001588 Rathke's pocket MP:0003817 hypophyseal diverticulum https://orcid.org/0000-0002-6601-2165 hypophyseal pouch ISBN:0073040584 nasohypophyseal pouch http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html pituitary diverticulum MP:0003817 A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. EMAPA:35209 FMA:242770 ventricular layer uberon region of wall of ventricular system of neuraxis UBERON:0005358 ventricle of nervous system A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. https://github.com/obophenotype/uberon/issues/300 ventricular layer EMAPA:35209 region of wall of ventricular system of neuraxis FMA:242770 The group of sensory neuron cell bodies associated with the vagus nerve. gX EMAPA:16798 FMA:53472 MA:0001081 SCTID:244452001 TAO:0007067 VHOG:0000684 Wikipedia:Vagus_ganglion ZFA:0007067 ganglion of vagus nerve right glossopharyngeal ganglion vagal ganglion vagus ganglion vagus neural ganglion uberon vagus X UBERON:0005362 vagus X ganglion ZFA The group of sensory neuron cell bodies associated with the vagus nerve. ISBN:0-683-40008-8 MP:0001100 gX ZFA:0007067 ganglion of vagus nerve FMA:53472 right glossopharyngeal ganglion FMA:53472 vagal ganglion ZFA:0007067 vagus neural ganglion FMA:53472 vagus X EMAPA:16798 An epithelium that lines the nasal cavity. this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism CALOHA:TS-0656 EHDAA2:0001227 EHDAA:6803 EMAPA:17605 FMA:63140 MA:0001324 NCIT:C49261 UMLS:C1709151 VHOG:0000501 nasal epithelium uberon nasal mucosa UBERON:0005384 nasal cavity epithelium An epithelium that lines the nasal cavity. http://orcid.org/0000-0002-6601-2165 UMLS:C1709151 ncithesaurus:Nasal_Cavity_Epithelium nasal epithelium FMA:63140 nasal mucosa MA:0001324 An epithelium that is part of the respiratory segment of the nasal mucosa [Automatically generated definition]. EHDAA2:0001230 EHDAA:6807 EMAPA:17607 MA:0001326 NCIT:C49262 UMLS:C1709152 uberon UBERON:0005385 nasal cavity respiratory epithelium An epithelium that is part of the respiratory segment of the nasal mucosa [Automatically generated definition]. OBOL:automatic https://github.com/obophenotype/uberon/issues/50 UMLS:C1709152 ncithesaurus:Nasal_Cavity_Respiratory_Epithelium An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 photoreceptor array An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 FBbt:00004200 A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. directing or focusing light onto light receptors lens uberon UBERON:0005389 transparent eye structure A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. http://orcid.org/0000-0002-6601-2165 One of: the common carotid artery, or its branches, the external and internal carotid arteries. This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] AAO:0010217 BTO:0000168 CALOHA:TS-0116 EFO:0000818 EHDAA:6385 EMAPA:18609 EV:0100379 FMA:70504 GAID:478 MA:0001925 MAT:0000501 MESH:D002339 NCIT:C12687 SCTID:362040006 SCTID:69105007 TAO:0000097 UMLS:C0007272 VHOG:0000266 Wikipedia:Carotid_artery ZFA:0000097 galen:CarotidArtery carotid carotid artery subdivision of common carotid artery uberon common carotid arterial subdivision UBERON:0005396 carotid artery segment FMA One of: the common carotid artery, or its branches, the external and internal carotid arteries. Wikipedia:Carotid_artery https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764 Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000097 TAO ZFIN:curator UMLS:C0007272 ncithesaurus:Carotid_Artery carotid AAO:0010217 carotid artery MA:0001925 subdivision of common carotid artery FMA:70504 common carotid arterial subdivision FMA:70504 An arachnoid mater that surrounds a brain. The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32661 FMA:83981 MA:0000814 NCIT:C49331 UMLS:C1707346 VHOG:0000230 arachnoidea mater cranialis arachnoidea mater encephali brain arachnoid matter cranial arachnoid mater uberon UBERON:0005397 brain arachnoid mater An arachnoid mater that surrounds a brain. OBOL:automatic The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000230 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/arachnoid+mater In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000230 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 http://bgee.unil.ch/ arachnoidea mater cranialis FMA:83981 FMA:TA arachnoidea mater encephali FMA:83981 FMA:TA brain arachnoid matter MA:0000814 cranial arachnoid mater FMA:83981 A sex gland that is part of a female reproductive system. BTO:0000254 MA:0000383 uberon UBERON:0005398 female reproductive gland A sex gland that is part of a female reproductive system. OBOL:automatic A sex gland that is part of a male reproductive system. BTO:0000080 EMAPA:19285 MA:0000399 uberon accessory sex gland UBERON:0005399 male reproductive gland A sex gland that is part of a male reproductive system. OBOL:automatic accessory sex gland EMAPA:19285 An arachnoid mater that is part of a telencephalon. EMAPA:17775 MA:0000980 telencephalon arachnoid matter uberon UBERON:0005400 telencephalon arachnoid mater An arachnoid mater that is part of a telencephalon. OBOL:automatic telencephalon arachnoid matter MA:0000980 A gray matter that is part of a cerebral hemisphere. BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO:0000823 CALOHA:TS-2361 EMAPA:37477 FMA:61821 MA:0000944 cerebral gray matter cerebral grey matter cerebral hemisphere grey matter uberon UBERON:0005401 cerebral hemisphere gray matter A gray matter that is part of a cerebral hemisphere. OBOL:automatic BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO EMAPA:37477 MA:th cerebral gray matter BTO:0000823 cerebral grey matter MA:0000944 Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow. All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330) CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances BTO:0006267 EMAPA:35243 FMA:84081 MA:0002942 MESH:D066280 NLXANAT:20090312 Wikipedia:Circumventricular_organs neuronames:1242 CVO circumventricular organ circumventricular organ of neuraxis uberon UBERON:0005408 circumventricular organ http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow. MP:0013562 BTO:0006267 https://github.com/biopragmatics/biomappings MESH:D066280 https://github.com/biopragmatics/biomappings CVO NLXANAT:20090312 circumventricular organ NLXANAT:20090312 circumventricular organ of neuraxis FMA:84081 The part of the digestive system that excludes the hepatobiliary system. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 MA:0000323 MESH:D041981 NCIT:C12378 SCTID:373871007 UMLS:C0012240 VHOG:0000412 galen:GastrointestinalTract uberon GI tract alimentary system alimentary tract gastro-intestinal system gastroenterological system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract UBERON:0005409 alimentary part of gastrointestinal system The part of the digestive system that excludes the hepatobiliary system. http://orcid.org/0000-0002-6601-2165 The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. ncithesaurus:Gastrointestinal_System All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] 2012-09-17 VHOG:0000412 VHOG ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3 http://bgee.unil.ch/ that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. MA UMLS:C0012240 ncithesaurus:Gastrointestinal_System GI tract GAID:294 alimentary system MA:0000323 alimentary tract MA:0000323 gastro-intestinal system FMA:71132 gastroenterological system UBERON:cjm gastrointestinal (GI) tract GAID:294 gastrointestinal system FMA:71132 gastrointestinal tract FMA:71132 A limb bud that develops into a forelimb. AAO:0010381 BTO:0001645 EHDAA:1699 EMAPA:16406 FMA:296782 MIAA:0000065 RETIRED_EHDAA2:0003198 SCTID:346062002 XAO:0003065 anterior limb bud limb bud - forelimb upper limb bud wing bud uberon arm bud UBERON:0005417 Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995) forelimb bud lexical A limb bud that develops into a forelimb. http://orcid.org/0000-0002-6601-2165 limb bud - forelimb MIAA:0000065 upper limb bud RETIRED_EHDAA2:0003198 wing bud NCBITaxon:8782 OBOL:automatic A limb bud that develops into a hindlimb. The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] AAO:0010382 EHDAA:2358 EMAPA:16779 MIAA:0000256 RETIRED_EHDAA2:0003197 SCTID:346164003 XAO:0003066 hind limb bud posterior limb bud uberon leg bud limb bud - hindlimb UBERON:0005418 Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. hindlimb bud A limb bud that develops into a hindlimb. http://orcid.org/0000-0002-6601-2165 The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] 2012-06-20 AAO:0010382 AAO XAO:curator hind limb bud XAO:0003066 A limb bud that develops into a forelimb or pectoral fin. Fin bud that develops into the pectoral fin.[TAO] While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] EFO:0003430 TAO:0000141 VHOG:0001754 VHOG_RETIRED:0001259 ZFA:0000141 forelimb - pectoral fin bud uberon pectoral fin bud pectoral fin buds UBERON:0005419 at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future pectoral appendage bud A limb bud that develops into a forelimb or pectoral fin. OBOL:automatic Fin bud that develops into the pectoral fin.[TAO] 2012-08-14 TAO:0000141 TAO ZFIN:curator While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001754 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) http://bgee.unil.ch/ forelimb - pectoral fin bud VHOG:0001754 pectoral fin bud TAO:0000141 pectoral fin buds TAO:0000141 A limb bud that develops into a hindlimb or pelvic fin. Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] EFO:0003469 TAO:0001384 VHOG:0001260 ZFA:0001384 hindlimb/pelvic fin bud uberon pelvic fin bud pelvic fin buds UBERON:0005420 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. OBOL:automatic PMID:15893975 Fin bud that develops into the pelvic fin.[TAO] 2012-08-14 TAO:0001384 TAO ZFIN:curator Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001260 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ hindlimb/pelvic fin bud VHOG:0001260 pelvic fin bud TAO:0001384 pelvic fin buds ZFA:0001384 An apical ectodermal ridge that is part of a pectoral appendage bud. An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003487 EHDAA2:0000138 EMAPA:16778 TAO:0000085 TAO:0000736 VHOG:0001064 ZFA:0000085 AER forelimb apical ectodermal ridge forelimb apical ectodermal ridge pectoral fin bud upper limb bud apical ectodermal ridge wing AER wing apical ectodermal ridge uberon aer pectoral fin apical ectodermal ridge pectoral fin apical fold pectoral fin UBERON:0005421 pectoral appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pectoral appendage bud. OBOL:automatic An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001064 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000085 TAO ZFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001064 VHOG DOI:10.1111/j.1440-169X.2007.00942.x http://bgee.unil.ch/ AER forelimb VHOG:0001064 apical ectodermal ridge forelimb VHOG:0001064 apical ectodermal ridge pectoral fin bud ZFA:0000085 upper limb bud apical ectodermal ridge EHDAA2:0000138 wing AER Giesha:syn wing apical ectodermal ridge aer pectoral fin TAO:0000085 apical ectodermal ridge pectoral fin TAO:0000085 apical fold pectoral fin TAO:0000085 An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003681 EHDAA2:0003194 EMAPA:16892 TAO:0001385 VHOG:0001066 ZFA:0001385 apical ectodermal ridge hind limb apical ectodermal ridge hindlimb lower lmb bud apical ectodermal ridge uberon AER hindlimb apical ectodermal ridge pelvic fin bud leg AER UBERON:0005422 pelvic appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pelvic appendage bud. OBOL:automatic An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001066 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] 2012-08-14 TAO:0001385 TAO ZIFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001066 VHOG DOI:10.1111/j.1440-169X.2007.00942.x http://bgee.unil.ch/ apical ectodermal ridge hind limb VHOG:0001066 apical ectodermal ridge hindlimb VHOG:0001066 lower lmb bud apical ectodermal ridge EHDAA2:0003194 AER hindlimb VHOG:0001066 apical ectodermal ridge pelvic fin bud TAO:0001385 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure FBbt:00007006 developmental tissue MIAA:0000019 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 VHOG:0000490 ZFA:0001071 future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retinas uberon future NR future neural epithelium future neural layer presumptive retina UBERON:0005425 presumptive neural retina Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000490 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ inner layer optic cup ZFA:0001071 optic cup inner layer EHDAA2:0001304 presumptive retinas ZFA:0001071 future neural epithelium EMAPA:16675 future neural layer EMAPA:16675 presumptive retina TAO:0001071 Portion of tissue that gives rise to the lens. A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 SCTID:361510002 TAO:0002205 VHOG:0001163 ZFA:0001679 hollow lens vesicle solid lens vesicle uberon immature lens lens mass presumptive lens UBERON:0005426 lens vesicle Portion of tissue that gives rise to the lens. ZFIN:curator https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834 A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] 2012-09-17 VHOG:0001163 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/lens+vesicle (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0001163 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals ZFA hollow lens vesicle solid lens vesicle ZFA:0001679 immature lens ZFA:0001679 lens mass ZFA:0001679 ZFIN:ZDB-PUB-091023-49 presumptive lens ZFA:0001679 Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 uberon UBERON:0005427 corneal primordium ZFA Obol ZFA Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. ZFIN:ZDB-PUB-061010-3 Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) EHDAA2:0002156 EHDAA:669 TAO:0000818 VHOG:0001208 XAO:0004191 ZFA:0000818 VNC uberon enteric neural crest post-otic neural crest UBERON:0005428 vagal neural crest Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. ZFIN:curator Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] 2012-08-14 TAO:0000818 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001208 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) filemaps.com VNC XAO:0004191 post-otic neural crest ZFA:0000818 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates. the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 EHDAA:9826 EMAPA:36461 FMA:71008 RETIRED_EHDAA2:0000133 SCTID:361527005 saccus aorticus uberon UBERON:0005432 aortic sac EHDAA2 EHDAA2 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates. MP:0012510 the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. http://medical-dictionary.thefreedictionary.com/aortic+sac saccus aorticus FMA:24219 SCTID:123958008 cervical region neck subdivision region of neck subdivision of neck uberon UBERON:0005434 cervical region cervical region FMA:24219 neck subdivision FMA:24219 region of neck FMA:24219 subdivision of neck FMA:24219 In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:. EHDAA2:0000308 EHDAA:8570 EMAPA:37206 FMA:14771 MA:0003094 SCTID:244263001 Wikipedia:Common_hepatic_artery galen:CommonHepaticArtery uberon arteria hepatica communis common hepatic UBERON:0005436 common hepatic artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:. Wikipedia:Common_hepatic_artery EMAPA:37206 MA:th arteria hepatica communis Wikipedia:Common_hepatic_artery common hepatic Wikipedia:Common_hepatic_artery The short trunk that recieves most of the cardiac veins carrying the blood from the myocardium and delivers it to the right atrium, with the sinoatrial connection occurring between the inferior vena cava and the atrioventricular orifice. The sinus, before entering the auricle, is considerably dilated - nearly to the size of the end of the little finger. Its wall is partly muscular, and at its junction with the great coronary vein is somewhat constricted and furnished with a valve consisting of two unequal segments EHDAA2:0000320 EHDAA:9884 EMAPA:37836 FMA:4706 MESH:D054326 NCIT:C32378 SCTID:244386006 UMLS:C0456944 Wikipedia:Coronary_sinus sinus coronarius uberon sinus coronarius UBERON:0005438 coronary sinus http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray491.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The short trunk that recieves most of the cardiac veins carrying the blood from the myocardium and delivers it to the right atrium, with the sinoatrial connection occurring between the inferior vena cava and the atrioventricular orifice. ISBN:0-683-40008-8 MP:0010436 The sinus, before entering the auricle, is considerably dilated - nearly to the size of the end of the little finger. Its wall is partly muscular, and at its junction with the great coronary vein is somewhat constricted and furnished with a valve consisting of two unequal segments WP EMAPA:37836 MA:th MESH:D054326 https://github.com/biopragmatics/biomappings UMLS:C0456944 ncithesaurus:Coronary_Sinus sinus coronarius Wikipedia:Coronary_sinus A segment of autopod that is part of a pes. foot region FMA:24993 SCTID:362887000 foot subdivision regio pedis segment of foot subdivision of foot uberon UBERON:0005445 segment of pes A segment of autopod that is part of a pes. OBOL:automatic foot region FMA:24993 foot subdivision FMA:24993 regio pedis FMA:24993 FMA:TA segment of foot FMA:24993 subdivision of foot FMA:24993 The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa. A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG] It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG] todo - check placement of AAO class AAO:0000194 EHDAA2:0000552 EHDAA:10629 EMAPA:18712 FMA:53154 SCTID:369439002 VHOG:0001543 Wikipedia:Foramen_rotundum uberon foramen rotundum of the skull foramen rotundum ossis sphenoidalis round foramen UBERON:0005446 foramen rotundum http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa. Wikipedia:Foramen_rotundum A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG] 2012-09-17 VHOG:0001543 VHOG http://bgee.unil.ch/ It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG] 2012-09-17 VHOG:0001543 VHOG PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976) http://bgee.unil.ch/ todo - check placement of AAO class AAO foramen rotundum of the skull Wikipedia:Foramen_rotundum foramen rotundum ossis sphenoidalis Wikipedia:Foramen_rotundum round foramen VHOG:0001543 A segment of autopod that is part of a manus. hand region FMA:24945 SCTID:127950000 hand subdivision regio manus segment of hand subdivision of hand uberon UBERON:0005451 segment of manus A segment of autopod that is part of a manus. OBOL:automatic hand region FMA:24945 hand subdivision FMA:24945 regio manus segment of hand FMA:24945 subdivision of hand FMA:24945 The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side. Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] AAO:0000249 EHDAA2:0000893 EHDAA:10631 EMAPA:18713 FMA:56432 MESH:D000080869 NCIT:C12496 SCTID:361735006 UMLS:C0222712 VHOG:0001113 Wikipedia:Jugular_foramen Posterior lacerate foramen uberon foramen jugulare UBERON:0005456 jugular foramen http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side. Wikipedia:Jugular_foramen Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] 2012-06-20 AAO:0000249 AAO AAO:LAP One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] 2012-09-17 VHOG:0001113 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/jugular+foramen relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] 2012-06-20 AAO:0000249 AAO MESH:D000080869 https://github.com/biopragmatics/biomappings UMLS:C0222712 ncithesaurus:Jugular_Foramen Posterior lacerate foramen FMA:56432 foramen jugulare Wikipedia:Jugular_foramen A thymus lobe that is in the left side of a thymus. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:71195 RETIRED_EHDAA2:0000964 SCTID:188079002 left lobe of thymus left thymic lobe uberon UBERON:0005457 left thymus lobe https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb A thymus lobe that is in the left side of a thymus. OBOL:automatic left lobe of thymus FMA:71195 left thymic lobe FMA:71195 EHDAA2:0000966 EMAPA:16544 FMA:18822 VHOG:0000522 embryonic left umbilical artery uberon UBERON:0005458 left umbilical artery check this EHDAA2 check this EHDAA2 embryonic left umbilical artery VHOG:0000522 A vitelline vein that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000971 EMAPA:16380 EMAPA:16698 FMA:70307 SCTID:361446008 uberon UBERON:0005460 left vitelline vein A vitelline vein that is in the left side of a multicellular organism. OBOL:automatic An axial muscle that originates in the cervical vertebraae inserts on the scapula. AAO:0010689 EHDAA2:0000992 EHDAA:8309 FMA:32519 SCTID:279236008 Wikipedia:Levator_scapulae_muscle levator scapulae uberon levator scapula levator scapulae muscle levator scapulæ musculus levator scapulae UBERON:0005461 Axial muscle group[Kardong] levator scapulae muscle https://upload.wikimedia.org/wikipedia/commons/b/bc/Levator_scapulae.png EHDAA2 cervical nerve and dorsal scapular nerve dbpedia EHDAA2 Posterior tubercles of transverse processes of C1 - C4 vertebrae dbpedia Superior part of medial border of scapula dbpedia An axial muscle that originates in the cervical vertebraae inserts on the scapula. http://orcid.org/0000-0002-6601-2165 levator scapulae FMA:32519 levator scapula Wikipedia:Levator_scapulae_muscle levator scapulae muscle Wikipedia:Levator_scapulae_muscle levator scapulæ Wikipedia:Levator_scapulae_muscle musculus levator scapulae Wikipedia:Levator_scapulae_muscle Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]. lumbar lumbar region BTO:0001505 EMAPA:36623 FMA:61681 MA:0000027 NCIT:C34004 SCTID:182343007 UMLS:C0024090 abdominal back back of abdomen dorsum of abdomen lower back lumbar part of back lumbar region of back posterior part of abdomen regio lumbalis uberon loin lombus lumbos UBERON:0005462 overlaps with region sometimes called 'loin' lower back MA Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]. FMA:61681 lumbar region FMA:61681 UMLS:C0024090 ncithesaurus:Lumbar_Region abdominal back FMA:61681 back of abdomen FMA:61681 dorsum of abdomen FMA:61681 lower back MA:0000027 lumbar part of back FMA:61681 lumbar region of back https://orcid.org/0000-0002-6601-2165 posterior part of abdomen FMA:61681 regio lumbalis FMA:61681 FMA:TA loin BTO:0001505 Wikipedia:Loin A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae. marginal sinus EMAPA:37662 FMA:312355 MA:0003027 NCIT:C33033 NCIT:C33642 UMLS:C1518051 UMLS:C1518052 Wikipedia:Subcapsular_sinus lymph node subcortical sinus uberon lymph path lymph sinus marginal sinus of lymph node subcapsular sinus UBERON:0005463 subcapsular sinus of lymph node http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae. Wikipedia:Lymph_node#Subcapsular_sinus marginal sinus Wikipedia:Subcapsular_sinus EMAPA:37662 MA:th UMLS:C1518051 ncithesaurus:Lymph_Node_Sinus UMLS:C1518052 ncithesaurus:Lymph_Node_Subcapsular_Sinus lymph node subcortical sinus MA:0003027 lymph path Wikipedia:Subcapsular_sinus lymph sinus Wikipedia:Subcapsular_sinus marginal sinus of lymph node Wikipedia:Subcapsular_sinus subcapsular sinus Wikipedia:Subcapsular_sinus A thymus lobe that is in the right side of a thymus. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:71194 RETIRED_EHDAA2:0001758 SCTID:187981000 right lobe of thymus right thymic lobe uberon UBERON:0005469 right thymus lobe https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb A thymus lobe that is in the right side of a thymus. OBOL:automatic right lobe of thymus FMA:71194 right thymic lobe FMA:71194 EHDAA2:0001760 EMAPA:16545 FMA:18821 VHOG:0000523 embryonic right umbilical artery uberon UBERON:0005470 right umbilical artery check this EHDAA2 check this EHDAA2 embryonic right umbilical artery VHOG:0000523 A vitelline vein that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001766 EMAPA:16381 EMAPA:16699 FMA:70306 SCTID:361445007 uberon UBERON:0005472 right vitelline vein A vitelline vein that is in the right side of a multicellular organism. OBOL:automatic A subdivision of an organism along the anterior-posterior axis in the pelvic region immediately posterior to the lumbar region and anterior to the caudal region. Sometimes an intermediate region is defined between the sacral and caudal. pygal sacral Amphibians - 1 sacral vertebra; Living reptiles & most birds - 2 sacral vertebrae; Most mammals - 3 to 5 sacral vertebrae. TODO - split sacral from sacrococcygeal FMA:24228 SCTID:182344001 Wikipedia:Sacrum back of pelvis pelvic back posterior part of pelvis regio sacralis sacral part of pelvis croup hindquarter rump uberon UBERON:0005473 sacral region A subdivision of an organism along the anterior-posterior axis in the pelvic region immediately posterior to the lumbar region and anterior to the caudal region. Sometimes an intermediate region is defined between the sacral and caudal. http://orcid.org/0000-0002-6601-2165 back of pelvis FMA:24228 pelvic back FMA:24228 posterior part of pelvis FMA:24228 regio sacralis FMA:24228 FMA:TA sacral part of pelvis FMA:24228 croup Wikipedia:Rump_(animal) hindquarter Wikipedia:Rump_(animal) rump Wikipedia:Rump_(animal) Trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami. EHDAA2:0001900 FMA:5929 spinal nerve (trunk) spinal neural trunk trunk of spinal nerve uberon UBERON:0005476 spinal nerve trunk Trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami. http://orcid.org/0000-0002-6601-2165 spinal nerve (trunk) FMA:5929 spinal neural trunk FMA:5929 trunk of spinal nerve FMA:5929 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim BAMS:slm neuronames:629 neural tube lateral wall sulcus limitans uberon UBERON:0005478 sulcus limitans of neural tube EHDAA2 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. http://medical-dictionary.thefreedictionary.com/Sulcus+limitans http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube lateral wall sulcus limitans EHDAA2:0001265 Either of the two lateral lobes that constitute the thymus. each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP] FMA:71193 RETIRED_EHDAA2:0002021 lateral lobe of thymus lobe of thymus uberon UBERON:0005483 thymus lobe FMA-abduced-lr Either of the two lateral lobes that constitute the thymus. http://orcid.org/0000-0002-6601-2165 lateral lobe of thymus http://orcid.org/0000-0002-6601-2165 lobe of thymus FMA:71193 A valve leaflet that is part of a tricuspid valve. Leaf of caridac valve which has as its parts the anterior, posterior and septal leaflets that is is attached to the chorda tendinea of the right ventricle and the fibrous ring of tricuspid valve. The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG] EMAPA:18630 FMA:7237 MA:0003180 RETIRED_EHDAA2:0002082 SCTID:276830008 VHOG:0000821 leaflet of tricuspid valve tricuspid valve leaflet tricuspid valve leaflets tricuspid valvular leaflet uberon UBERON:0005484 tricuspid valve leaflet A valve leaflet that is part of a tricuspid valve. http://orcid.org/0000-0002-6601-2165 Leaf of caridac valve which has as its parts the anterior, posterior and septal leaflets that is is attached to the chorda tendinea of the right ventricle and the fibrous ring of tricuspid valve. FMA:7237 The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG] 2012-09-17 VHOG:0000821 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ leaflet of tricuspid valve FMA:7237 tricuspid valve leaflet FMA:7237 tricuspid valve leaflets VHOG:0000821 tricuspid valvular leaflet FMA:7237 A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein. the MA placement should be checked EHDAA2:0002169 EHDAA:6491 EMAPA:18634 FMA:50762 MA:0002113 NCIT:C102627 SCTID:54944003 VHOG:0001004 Wikipedia:Dural_venous_sinuses cranial dural venous sinus dural sinus dural vein dural venous sinus venous dural venous dural sinus uberon s. durae matris UBERON:0005486 venous dural sinus https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif FMA A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein. Wikipedia:Dural_venous_sinuses cranial dural venous sinus FMA:50762 dural sinus FMA:50762 dural vein MA:0002113 dural venous sinus FMA:50762 venous dural EHDAA:6491 venous dural sinus EHDAA2:0002169 s. durae matris Wikipedia:Dural_venous_sinuses The paired veins that carry blood from the yolk sac back to the embryo. One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO] Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG] check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO EMAPA:36021 FMA:70305 NCIT:C34329 RETIRED_EHDAA2:0002209 SCTID:2730004 SCTID:308832003 UMLS:C0231091 VHOG:0000401 Wikipedia:Vitelline_veins XAO:0000376 XAO:0004147 embryonic vitelline vein vascular vitelline network vena vitellina uberon omphalomesenteric vein vein of omphalomesenteric system vitelline veins UBERON:0005487 vitelline vein http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png The paired veins that carry blood from the yolk sac back to the embryo. MGI:csmith MP:0010666 One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO] XAO XAO:0004147 Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG] 2012-09-17 VHOG:0000401 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 http://bgee.unil.ch/ check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO XAO UMLS:C0231091 ncithesaurus:Vitelline_Vein embryonic vitelline vein VHOG:0000401 vascular vitelline network XAO:0004147 vena vitellina Wikipedia:Vitelline_veins omphalomesenteric vein EMAPA:16244 vitelline veins XAO:0004147 Cranial neural crest which gives rise to the glossopharyngeal ganglion. EHDAA2:0000714 EHDAA:660 TAO:0007066 ZFA:0007066 uberon UBERON:0005491 glossopharyngeal neural crest Cranial neural crest which gives rise to the glossopharyngeal ganglion. ZFA:0007066 Portion of tissue on the side of the lumen of the neural tube. EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16166 TAO:0001435 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon UBERON:0005496 neural tube lateral wall Portion of tissue on the side of the lumen of the neural tube. ZFA:0001435 lateral wall neural tube ZFA:0001435 todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 RETIRED_EHDAA2:0001273 TAO:0001178 VHOG:0001372 XAO:0004091 ZFA:0001178 non neural ectoderm epidermal ectoderm epithelial ectoderm uberon surface ectoderm ventral ectoderm UBERON:0005497 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). non-neural ectoderm ZFA In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] 2012-09-17 VHOG:0001372 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ non neural ectoderm ZFA:0001178 epidermal ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest epithelial ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest surface ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest ventral ectoderm ZFA:0001178 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16215 FMA:321916 SCTID:361522004 TAO:0000149 Wikipedia:Primitive_heart_tube ZFA:0000149 primitive heart tube early primitive heart tube uberon UBERON:0005498 primitive heart tube ZFA Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 BTO:0006179 https://github.com/biopragmatics/biomappings primitive heart tube EMAPA:16215 early primitive heart tube EMAPA:16208 A neural tube lateral wall that is part of a rhombomere. EMAPA:32819 EMAPA:35364 uberon future hindbrain lateral wall UBERON:0005501 rhombomere lateral wall A neural tube lateral wall that is part of a rhombomere. OBOL:automatic future hindbrain lateral wall EMAPA:35364 A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]. we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO] variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals EFO:0003622 EHDAA2:0002023 EHDAA:2969 EMAPA:17523 TAO:0001077 ZFA:0001077 thymic primordium thymic rudiment uberon UBERON:0005562 thymus primordium ZFA EHDAA2 mesenchymal ZFA https://github.com/obophenotype/uberon/wiki/The-neural-crest A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]. ZFA:0001077 we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. ISBN:0781714125 A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO] 2012-08-14 TAO:0001077 TAO ZFIN:curator variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals ISBN:0781714125 thymic primordium OBOL:automatic thymic rudiment ZFA:0001077 Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003484 EHDAA2:0002083 EHDAA:667 EMAPA:16170 TAO:0000080 VHOG:0000269 ZFA:0000080 uberon UBERON:0005563 trigeminal neural crest ZFA EHDAA2 EHDAA2 Cranial neural crest which gives rise to the trigeminal ganglion. ZFA:0000080 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000269 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ Portion of tissue that gives rise to the immature gonad. Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 RETIRED_EHDAA2:0002148 TAO:0001262 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium primitive gonad undifferentiated gonad uberon immature gonad UBERON:0005564 gonad primordium Obol ZFA Portion of tissue that gives rise to the immature gonad. ZFA:0001262 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] 2012-08-14 TAO:0001262 TAO ZFIN:curator future gonad http://orcid.org/0000-0002-6601-2165 gonadal primordium ZFA:0001262 primitive gonad http://orcid.org/0000-0002-6601-2165 undifferentiated gonad ZFA:0001262 immature gonad http://orcid.org/0000-0002-6601-2165 Cranial neural crest that gives rise to the facio-acoustic ganglion. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0000492 EHDAA:658 EMAPA:16312 TAO:0000762 VHOG:0000268 ZFA:0000762 facio acoustic neural crest uberon UBERON:0005565 facio-acoustic neural crest EHDAA2 EHDAA2 Cranial neural crest that gives rise to the facio-acoustic ganglion. ZFA:0000762 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000268 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ facio acoustic neural crest ZFA:0000762 Somite located in the head region, caudal to the otic vesicle. in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2:0003437 EMAPA:16172 XAO:0000313 occipital somite uberon cranial somite UBERON:0005594 head somite EHDAA2 EHDAA2 Somite located in the head region, caudal to the otic vesicle. PMID:11830559 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) PMID:11830559 EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2 occipital somite PMID:11830559 XAO:0000313 cranial somite XAO:0000313 A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. AAO:0011059 EFO:0002578 EMAPA:36007 XAO:0001002 uberon lateral diverticula lung diverticulum lung endoderm UBERON:0005597 lung primordium XAO XAO A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. XAO:0001002 lateral diverticula XAO:0001002 lung diverticulum AAO:3010717 lung endoderm EFO:0002578 A somite that is part of a trunk. AAO:0010385 EHDAA2:0003438 EMAPA:16184 XAO:0000314 uberon UBERON:0005598 trunk somite A somite that is part of a trunk. OBOL:automatic The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] EHDAA2:0000416 EHDAA:3001 EMAPA:17025 MA:0001618 NCIT:C34142 UMLS:C1512038 VHOG:0000352 Wikipedia:Dorsal_mesentery uberon dorsal mesentery UBERON:0005602 dorsal mesogastrium MA EHDAA2 EHDAA2 The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. Wikipedia:Dorsal_mesentery The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] 2012-09-17 VHOG:0000352 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mesogastrium UMLS:C1512038 ncithesaurus:Dorsal_Mesogastrium dorsal mesentery Wikipedia:Dorsal_mesentery EMAPA:16844 MA:0001636 VHOG:0000215 extrahepatic part of the hepatic duct hepatic duct extrahepatic part uberon UBERON:0005604 extrahepatic part of hepatic duct MA MA extrahepatic part of the hepatic duct VHOG:0000215 hepatic duct extrahepatic part MA:0001636 A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] EHDAA2:0000789 EHDAA:4733 EMAPA:17302 FMA:312291 MA:0000272 VHOG:0001477 uberon UBERON:0005606 hyaloid cavity A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] 2012-09-17 VHOG:0001477 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/hyaloid+fossa Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery. this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific BTO:0004665 EHDAA:2551 EMAPA:17309 MA:0001971 MESH:D007083 NCIT:C12733 RETIRED_EHDAA2:0000807 SCTID:244330006 UMLS:C0020887 Wikipedia:Iliac_artery XAO:0000361 galen:IliacArtery uberon UBERON:0005609 iliac artery Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery. Wikipedia:Iliac_artery https://orcid.org/0000-0002-6601-2165 we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific XAO UMLS:C0020887 ncithesaurus:Iliac_Artery Any of the three veins including the common, external and internal iliac veins. EHDAA2:0000811 EMAPA:37151 MA:0002142 MESH:D007084 NCIT:C12734 SCTID:281481002 UMLS:C0020888 uberon pelvic vein UBERON:0005610 iliac vein Any of the three veins including the common, external and internal iliac veins. ncithesaurus:Iliac_Vein EMAPA:37151 MA:th UMLS:C0020888 ncithesaurus:Iliac_Vein A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Contributes to the arch of aorta in humans EHDAA2:0000936 EHDAA:404 EMAPA:16205 MA:0000478 SCTID:361403005 VHOG:0000484 uberon UBERON:0005613 left dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000484 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 http://bgee.unil.ch/ Contributes to the arch of aorta in humans http://emedicine.medscape.com/article/899609-overview A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm lens epithelium EHDAA2:0000984 EHDAA:9059 EMAPA:17304 EMAPA:17839 FMA:70612 MA:0001302 NCIT:C33641 RETIRED_EHDAA2:0000976 SCTID:362521008 UMLS:C1182652 VHOG:0001425 lens subcapsular epithelium subcapsular lens epithelium uberon anterior epithelium of lens vesicle anterior surface of lens UBERON:0005614 lens anterior epithelium A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. http://orcid.org/0000-0002-6601-2165 UMLS:C1182652 ncithesaurus:Subcapsular_Epithelium_of_the_Lens lens subcapsular epithelium http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm subcapsular lens epithelium FMA:70612 anterior epithelium of lens vesicle EMAPA:17304 anterior surface of lens FMA:58889 Arteries which arise from the abdominal aorta and distribute to most of the intestines. includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries BTO:0000779 EHDAA2:0001123 EHDAA:4343 EMAPA:17312 MA:0002003 MESH:D008638 NCIT:C52975 SCTID:281084003 UMLS:C0025465 VHOG:0001117 Wikipedia:Mesenteric_artery XAO:0000370 uberon UBERON:0005616 mesenteric artery Arteries which arise from the abdominal aorta and distribute to most of the intestines. MESH:A07.231.114.565 Wikipedia:Mesenteric_artery UMLS:C0025465 ncithesaurus:Mesenteric_Artery A vein that returns blood from the intestines. In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein BTO:0002781 EHDAA:4442 EMAPA:17348 MA:0002177 MESH:D008642 NCIT:C53055 RETIRED_EHDAA2:0001125 SCTID:304045008 UMLS:C0025473 Wikipedia:Mesenteric_vein uberon intestinal vein UBERON:0005617 mesenteric vein A vein that returns blood from the intestines. MESH:A07.231.908.670.385 Wikipedia:Mesenteric_vein UMLS:C0025473 ncithesaurus:Mesenteric_Vein intestinal vein http://orcid.org/0000-0002-6601-2165 The outgrowths of the embryonic maxillary prominences that come together during prenatal development to form the secondary palate. consider splitting into embryonic/fully formed The outgrowths of the embryonic maxillae that come together during prenatal development to form the secondary palate. [TFD][VHOG] EHDAA2:0001364 EHDAA:9283 EMAPA:17362 FMA:295948 MA:0001581 VHOG:0000378 lateral palatine process palatal shelf secondary palatal shelf uberon palatal shelves palatine shelf UBERON:0005619 secondary palatal shelf EHDAA2 cjm The outgrowths of the embryonic maxillary prominences that come together during prenatal development to form the secondary palate. http://medical-dictionary.thefreedictionary.com/palatal+shelves http://www.indiana.edu/~anat550/hnanim/face/face.html The outgrowths of the embryonic maxillae that come together during prenatal development to form the secondary palate. [TFD][VHOG] 2012-09-17 VHOG:0000378 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/palatal lateral palatine process http://medical-dictionary.thefreedictionary.com/palatal+shelf palatal shelf MA:0001581 palatal shelves palatine shelf VHOG:0000378 A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Normally regresses in humans EHDAA2:0001720 EHDAA:406 EMAPA:16206 MA:0000479 SCTID:361404004 VHOG:0000485 uberon UBERON:0005622 right dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000485 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 http://bgee.unil.ch/ Normally regresses in humans http://emedicine.medscape.com/article/899609-overview The valves that gate the flow of blood from the ventricles into the aorta and pulmonary trunk. Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG] Lacks chordae tendinae EHDAA2:0001823 EHDAA:4408 EMAPA:35760 MA:0002790 VHOG:0001393 semilunar valve semilunar valves uberon UBERON:0005623 semi-lunar valve The valves that gate the flow of blood from the ventricles into the aorta and pulmonary trunk. MGI:pvb MP:0002746 Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG] 2012-09-17 VHOG:0001393 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ semilunar valve MA:0002790 semilunar valves MA:0002790 Artery that supplies blood to the adrenal glands. EHDAA2:0001965 EHDAA:8596 EMAPA:37124 MA:0001914 NCIT:C33708 SCTID:181342004 Wikipedia:Adrenal_artery ncithesaurus:Adrenal_Artery uberon adrenal artery UBERON:0005624 suprarenal artery Artery that supplies blood to the adrenal glands. Wikipedia:Adrenal_artery EMAPA:37124 MA:th adrenal artery MA:0001914 Wikipedia:Adrenal_artery The cavity formed by the tubotympanic recess epithelium. EHDAA2:0002095 cavity of tubotympanic recess tubotympanic recess cavity tubotympanic recess space uberon tubotympanic recess UBERON:0005625 tubotympanic recess lumen MA ISBN:0073040584 The cavity formed by the tubotympanic recess epithelium. https://orcid.org/0000-0002-6601-2165 tubotympanic recess EHDAA2:0002095 Portion of ventral mesentery closest to the stomach. The mesentery that originates from the ventral side of the peritoneal cavity.[TAO] The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG] EHDAA2:0002176 EHDAA:3005 EMAPA:17026 MA:0001621 NCIT:C34327 TAO:0005133 UMLS:C1519967 VHOG:0000351 ZFA:0005133 uberon foregut ventral mesentery UBERON:0005626 "The primitive gut is enveloped by a mesentery that has a dorsal and a ventral aspect. The ventral mesentery degenerates during development with the exception of the foregut ventral mesentery, which develops into specialized structures (see foregut embryology)." [http://sprojects.mmi.mcgill.ca/embryology/gi/pgm.htm]. todo - check ventral mesogastrium http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png EHDAA2 Portion of ventral mesentery closest to the stomach. Wikipedia:Ventral_mesentery The mesentery that originates from the ventral side of the peritoneal cavity.[TAO] 2012-08-14 TAO:0005133 TAO ZFIN:curator The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG] 2012-09-17 VHOG:0000351 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/mesogastrium UMLS:C1519967 ncithesaurus:Ventral_Mesogastrium foregut ventral mesentery Wikipedia:Ventral_mesentery A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. AEO:0000219 EHDAA2:0004112 EMAPA:35904 FMA:5900 XAO:0004143 plexus vasculosus uberon UBERON:0005629 vascular plexus A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. http://www.medilexicon.com/medicaldictionary.php?t=70052 In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. Wikipedia:Plexus#Circulatory_system plexus vasculosus Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)] EHDAA2 is a mereological sum. EHDAA2:0004714 FMA:305915 MESH:D005321 SCTID:362840007 uberon UBERON:0005631 extraembryonic membrane https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. ISBN:0073040584 EHDAA2 is a mereological sum. EHDAA2 MESH:D005321 https://github.com/biopragmatics/biomappings An epithelium that is part of a caecum. EHDAA2:0000209 uberon UBERON:0005636 caecum epithelium An epithelium that is part of a caecum. OBOL:automatic An epithelium that is part of a pylorus. EHDAA2:0001582 EMAPA:17633 RETIRED_EHDAA2:0001927 uberon UBERON:0005637 pyloric region epithelium An epithelium that is part of a pylorus. OBOL:automatic An epithelium that is part of a anterior chamber of eyeball. EHDAA2:0000130 uberon UBERON:0005638 anterior chamber epithelium An epithelium that is part of a anterior chamber of eyeball. OBOL:automatic An epithelium that is part of a manual digit 5. EHDAA2:0000536 EMAPA:17442 fore limb digit 5 epithelium manual digit V epithelium hand digit 5 epithelium uberon UBERON:0005648 manual digit 5 epithelium An epithelium that is part of a manual digit 5. OBOL:automatic fore limb digit 5 epithelium OBOL:accepted manual digit V epithelium https://github.com/obophenotype/uberon/issues/458 hand digit 5 epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a pedal digit 5. EHDAA2:0002058 EMAPA:17473 hind limb digit 5 epithelium pedal digit V epithelium foot digit 5 epithelium uberon UBERON:0005652 pedal digit 5 epithelium An epithelium that is part of a pedal digit 5. OBOL:automatic hind limb digit 5 epithelium OBOL:accepted pedal digit V epithelium https://github.com/obophenotype/uberon/issues/458 foot digit 5 epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a lens vesicle. EHDAA2:0000987 EMAPA:17165 VHOG:0000532 uberon UBERON:0005656 lens vesicle epithelium An epithelium that is part of a lens vesicle. OBOL:automatic An epithelium that is part of a secondary palatal shelf. EHDAA2:0001365 EMAPA:17363 FMA:312465 VHOG:0001040 uberon palatal shelf epithelium UBERON:0005658 secondary palatal shelf epithelium An epithelium that is part of a secondary palatal shelf. OBOL:automatic palatal shelf epithelium VHOG:0001040 An ectoderm that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000055 EMAPA:16277 EMAPA:16397 EMAPA:16398 RETIRED_EHDAA2:0000064 VHOG:0001062 2nd pharyngeal arch ectoderm uberon UBERON:0005660 2nd arch ectoderm An ectoderm that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001062 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 2nd pharyngeal arch ectoderm VHOG:0001062 An ectoderm that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000072 EMAPA:16400 EMAPA:16582 EMAPA:16584 RETIRED_EHDAA2:0000079 VHOG:0000946 3rd pharyngeal arch ectoderm uberon UBERON:0005661 3rd arch ectoderm An ectoderm that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000946 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch ectoderm VHOG:0000946 An ectoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004032 EMAPA:16762 EMAPA:16764 EMAPA:16768 RETIRED_EHDAA2:0000094 VHOG:0001095 4th pharyngeal arch ectoderm uberon UBERON:0005662 4th arch ectoderm An ectoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001095 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch ectoderm VHOG:0001095 An endoderm that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000061 EMAPA:16274 EMAPA:16276 EMAPA:16278 RETIRED_EHDAA2:0000065 VHOG:0001108 2nd pharyngeal arch endoderm uberon UBERON:0005664 2nd arch endoderm An endoderm that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001108 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 2nd pharyngeal arch endoderm VHOG:0001108 An endoderm that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000075 EMAPA:16401 EMAPA:16585 EMAPA:16587 RETIRED_EHDAA2:0000080 VHOG:0001081 3rd pharyngeal arch endoderm uberon UBERON:0005665 3rd arch endoderm An endoderm that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001081 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch endoderm VHOG:0001081 An endoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004033 EMAPA:16765 EMAPA:16767 EMAPA:16769 RETIRED_EHDAA2:0000095 VHOG:0001092 4th pharyngeal arch endoderm uberon UBERON:0005666 4th arch endoderm An endoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001092 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch endoderm VHOG:0001092 EHDAA2:0000314 uberon UBERON:0005667 connecting stalk mesoderm EHDAA2 EHDAA2 A mesothelium that is part of a peritoneal cavity. we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood peritoneum BTO:0003156 EHDAA2:0001447 EMAPA:16139 FMA:18147 SCTID:34073007 mesothelium of peritoneal component mesothelium of peritoneum peritoneal mesothelium peritoneum mesothelium uberon UBERON:0005669 peritoneal cavity mesothelium A mesothelium that is part of a peritoneal cavity. OBOL:automatic we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood EMAPA peritoneum EMAPA:16139 mesothelium of peritoneal component EMAPA:16139 mesothelium of peritoneum FMA:18147 peritoneal mesothelium BTO:0003156 EMAPA:16139 peritoneum mesothelium FMA:18147 An endothelium that is part of a right lung. EHDAA2:0001755 uberon UBERON:0005672 right lung endothelium An endothelium that is part of a right lung. OBOL:automatic An endothelium that is part of a left lung. EHDAA2:0000961 uberon UBERON:0005673 left lung endothelium An endothelium that is part of a left lung. OBOL:automatic A mesentery that is part of a caecum. RETIRED_EHDAA2:0000210 uberon UBERON:0005677 caecum mesentery A mesentery that is part of a caecum. OBOL:automatic A dorsal mesentery that is part of a midgut. EMAPA:16722 EMAPA:17040 EMAPA:18671 RETIRED_EHDAA2:0001187 SCTID:361434009 uberon UBERON:0005685 midgut dorsal mesentery A dorsal mesentery that is part of a midgut. OBOL:automatic A dorsal mesentery that is part of a caecum. RETIRED_EHDAA2:0000208 uberon UBERON:0005686 caecum dorsal mesentery A dorsal mesentery that is part of a caecum. OBOL:automatic An anatomical cavity that is part of a lens vesicle. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] cavity of lens lens cavity EHDAA2:0000986 EMAPA:17164 VHOG:0000531 cavity of lens vesicle uberon UBERON:0005688 lens vesicle cavity An anatomical cavity that is part of a lens vesicle. OBOL:automatic (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000531 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ lens cavity EHDAA2:0000986 cavity of lens vesicle EMAPA:17164 Mesenchyme that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000066 EHDAA:625 EMAPA:16279 FMA:295698 VHOG:0001102 2nd pharyngeal arch mesenchyme uberon 2nd branchial arch mesenchyme pharyngeal arch 2 mesenchyme UBERON:0005689 2nd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001102 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 2nd pharyngeal arch mesenchyme VHOG:0001102 Mesenchyme that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000081 EHDAA:1094 EMAPA:16402 FMA:295700 VHOG:0001083 3rd pharyngeal arch mesenchyme uberon 3rd branchial arch mesenchyme pharyngeal arch 3 mesenchyme UBERON:0005690 3rd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001083 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch mesenchyme VHOG:0001083 Mesenchyme that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000096 EHDAA:1677 EMAPA:16770 FMA:295702 VHOG:0001052 4th pharyngeal arch mesenchyme uberon 4th branchial arch mesenchyme pharyngeal arch 4 mesenchyme UBERON:0005691 4th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001052 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch mesenchyme VHOG:0001052 Mesenchyme that is part of a developing manual digit 5. EHDAA2:0000537 EMAPA:17443 fore limb digit 5 mesenchyme manual digit V mesenchyme hand digit 5 mesenchyme uberon UBERON:0005695 manual digit 5 mesenchyme Mesenchyme that is part of a developing manual digit 5. OBOL:automatic fore limb digit 5 mesenchyme OBOL:accepted manual digit V mesenchyme https://github.com/obophenotype/uberon/issues/458 hand digit 5 mesenchyme NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a developing pedal digit 5. EHDAA2:0002059 EMAPA:17474 hind limb digit 5 mesenchyme pedal digit V mesenchyme foot digit 5 mesenchyme uberon UBERON:0005699 pedal digit 5 mesenchyme Mesenchyme that is part of a developing pedal digit 5. OBOL:automatic hind limb digit 5 mesenchyme OBOL:accepted pedal digit V mesenchyme https://github.com/obophenotype/uberon/issues/458 foot digit 5 mesenchyme NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a optic eminence. EHDAA:942 EMAPA:16324 RETIRED_EHDAA2:0001310 VHOG:0001073 uberon UBERON:0005702 optic eminence mesenchyme Mesenchyme that is part of a optic eminence. OBOL:automatic Mesenchyme that is part of a developing secondary palatal shelf. EHDAA2:0001366 EHDAA:9287 EMAPA:17364 VHOG:0001063 uberon palatal shelf mesenchyme UBERON:0005704 secondary palatal shelf mesenchyme Mesenchyme that is part of a developing secondary palatal shelf. OBOL:automatic palatal shelf mesenchyme VHOG:0001063 A mesentery of duodenum that is part of a foregut. EHDAA2:0000564 uberon UBERON:0005711 foregut duodenum mesentery A mesentery of duodenum that is part of a foregut. OBOL:automatic A mesentery of duodenum that is part of a midgut. EHDAA2:0001193 uberon UBERON:0005712 midgut duodenum mesentery A mesentery of duodenum that is part of a midgut. OBOL:automatic An apical ectodermal ridge that is part of a footplate. EHDAA2:0000547 EMAPA:17251 uberon UBERON:0005719 footplate apical ectodermal ridge true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An apical ectodermal ridge that is part of a footplate. OBOL:automatic A venous system that is part of a hindbrain. EHDAA2:0000776 EMAPA:18632 VHOG:0001322 uberon rhombencephalon venous system UBERON:0005720 hindbrain venous system A venous system that is part of a hindbrain. OBOL:automatic rhombencephalon venous system VHOG:0001322 A mesoderm that has the potential to develop into a pronephros. Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] AAO:0011090 EFO:0003479 TAO:0000067 VHOG:0001239 XAO:0000264 ZFA:0000067 uberon pronephric anlage pronephric bulge pronephric mesenchyme pronephric primordium UBERON:0005721 the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm ZFA Bgee:AN A mesoderm that has the potential to develop into a pronephros. OBOL:automatic Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] 2012-06-20 AAO:0011090 AAO XAO:curator pronephric anlage XAO:0000264 pronephric bulge XAO:0000264 pronephric mesenchyme XAO:0000264 pronephric primordium XAO:0000264 A sensory system that is capable of olfaction (the sensory perception of smell). consider splitting into main and accessory. See also: vomeronasal organ we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]. The sensory system used for olfaction (the sense of smell).[AAO] In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP]. AAO:0000334 AAO:0000978 BILA:0000144 EFO:0001973 EMAPA:36004 FMA:7190 MA:0002445 NCIT:C94501 NLXANAT:090806 SCTID:362290002 TAO:0001149 UMLS:C0228065 Wikipedia:Olfactory_system XAO:0003196 ZFA:0001149 uberon UBERON:0005725 olfactory system A sensory system that is capable of olfaction (the sensory perception of smell). http://orcid.org/0000-0002-6601-2165 The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]. Wikipedia:Olfactory_system The sensory system used for olfaction (the sense of smell).[AAO] 2012-06-20 AAO:0000978 AAO AAO:EJS UMLS:C0228065 ncithesaurus:Olfactory_System BILA:0000139 uberon UBERON:0005726 chemosensory system EHDAA2:0000474 EMAPA:31862 EMAPA:31863 FMA:296719 VHOG:0000616 extra-embryonic mesoderm extraembryonic mesenchyme uberon UBERON:0005728 extraembryonic mesoderm EHDAA2 EHDAA2 A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. Embryonic region that develops into the pectoral fin bud.[TAO] TAO:0001453 ZFA:0001453 pectoral appendage field of lateral plate mesoderm pectoral fin field uberon UBERON:0005729 pectoral appendage field A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pectoral fin bud.[TAO] 2012-08-14 TAO:0001453 TAO ZFIN:curator pectoral fin field ZFA:0001453 A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon UBERON:0005730 pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pelvic fin bud.[TAO] 2012-08-14 TAO:0001454 TAO ZFIN:curator pelvic fin field ZFA:0001454 A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb/fin field of lateral plate mesoderm paired limb/fin field uberon UBERON:0005732 paired limb/fin field ISBN:9780878932504 ZFA-inferred A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. ISBN:9780878932504 A ring of cells capable of forming a limb. limb field of lateral plate mesoderm uberon UBERON:0005733 the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995) limb field A ring of cells capable of forming a limb. ISBN:9780878932504 The outermost layer of a blood vessel, composed mainly of fibrous tissue. TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. BTO:0002010 EMAPA:36299 NCIT:C33818 SCTID:61066005 UMLS:C0225342 Wikipedia:Tunica_externa_(vessels) adventitia externa tunica adventitia tunica adventitia of vessel uberon external coat tunica adventitia vasorum tunica externa vasorum UBERON:0005734 tunica adventitia of blood vessel https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg cjm The outermost layer of a blood vessel, composed mainly of fibrous tissue. ISBN:0073040584 Wikipedia:Tunica_externa_(vessels) The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. Wikipedia:Tunica_externa_(vessels) UMLS:C0225342 ncithesaurus:Tunica_Adventitia adventitia externa Wikipedia:Tunica_externa_(vessels) tunica adventitia Wikipedia:Tunica_externa_(vessels) tunica adventitia of vessel Wikipedia:Tunica_externa_(vessels) external coat Wikipedia:Tunica_externa_(vessels) tunica adventitia vasorum Wikipedia:Tunica_externa_(vessels) tunica externa vasorum Wikipedia:Tunica_externa_(vessels) A tunica intima that is part of a artery. EMAPA:36293 EV:0100028 FMA:14272 SCTID:40022005 galen:IntimaOfArtery arterial intima tunica interna (intima)(arteriae) uberon UBERON:0005740 tunica intima of artery A tunica intima that is part of a artery. OBOL:automatic arterial intima EV:0100028 tunica interna (intima)(arteriae) FMA:14272 An outermost connective tissue covering of an organ, vessel, or other structure[WP]. BTO:0002010 FMA:45635 MESH:D063194 SCTID:30180000 Wikipedia:Adventitia tunica advetitia tunica externa uberon UBERON:0005742 adventitia http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg An outermost connective tissue covering of an organ, vessel, or other structure[WP]. Wikipedia:Adventitia MESH:D063194 https://github.com/biopragmatics/biomappings tunica advetitia Wikipedia:Adventitia tunica externa FMA:45635 Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). foramen AAO:0010438 TAO:0001736 VHOG:0001760 ZFA:0005386 uberon UBERON:0005744 bone foramen http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. TAO:curator in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). FMA foramen ZFA:0005386 The capillary loops of the kidney that normally function as a filtration unit[MP]. ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus EMAPA:28239 SCTID:362217000 Wikipedia:Glomerulus uberon glomerular capillary tuft glomerulus UBERON:0005749 glomerular tuft Wikipedia The capillary loops of the kidney that normally function as a filtration unit[MP]. MP:0005325 Wikipedia:Glomerulus http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus GudMap glomerulus EMAPA:28239 The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord caudal region of nephrogenic cord rear part of nephrogenic cord rear portion of nephrogenic cord uberon UBERON:0005753 caudal part of nephrogenic cord The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron caudal portion of nephrogenic cord OBOL:automatic caudal region of nephrogenic cord OBOL:automatic rear part of nephrogenic cord OBOL:automatic rear portion of nephrogenic cord Wikipedia:Metanephros#Metanephros The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. uberon UBERON:0005754 rostral part of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron An acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane An acellular anatomical structure that is the bounding layer of a anatomical structure. OBOL:automatic An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 GAID:915 NCIT:C13191 SCTID:68989006 UMLS:C0004799 Wikipedia:Basement_membrane basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium FMA An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. Wikipedia:Basement_membrane http://orcid.org/0000-0002-6601-2165 http://palaeos.com/metazoa/porifera/homoscleromorpha.html UMLS:C0004799 ncithesaurus:Basement_Membrane basement membrane of connective tissue FMA:63872 membrana basalis Wikipedia:Basement_membrane basement membrane FMA:63872 The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter. Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] GBM EMAPA:28251 EMAPA:30965 FMA:74274 MA:0001659 MESH:D050533 NCIT:C32683 SCTID:243897006 TAO:0005285 UMLS:C0599297 Wikipedia:Glomerular_basement_membrane ZFA:0005285 glomerular capillary basement membrane glomerular filtration membrane uberon UBERON:0005777 glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter. MGI:anna MP:0011348 Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] 2012-08-14 TAO:0005285 TAO ZFIN:ZDB-PUB-000824-1 GBM MESH:D050533 https://github.com/biopragmatics/biomappings UMLS:C0599297 ncithesaurus:Glomerular_Basement_Membrane glomerular capillary basement membrane MA:0001659 glomerular filtration membrane ZFA:0005285 Layer of the glomerular basement membrane adjacent to the glomerular capillary. FMA:74277 NCIT:C32920 TAO:0005287 UMLS:C1517719 ZFA:0005287 internal layer of glomerular basement membrane lamina interna of glomerular basement membrane uberon UBERON:0005788 lamina rara interna Layer of the glomerular basement membrane adjacent to the glomerular capillary. ZFIN:curator UMLS:C1517719 ncithesaurus:Lamina_Rara_Interna internal layer of glomerular basement membrane FMA:74277 lamina interna of glomerular basement membrane FMA:74277 Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. TODO - check ridge vs cord vs nephrogenic cord vs blastema EHDAA2:0001242 EHDAA:1015 EMAPA:16368 VHOG:0001240 uberon nephric cord UBERON:0005792 nephric ridge Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter27/custom2/deluxe-content.html nephric cord VHOG:0001240 FMA:72173 SCTID:255782009 fetal uterus uberon UBERON:0005795 embryonic uterus fetal uterus FMA:72173 Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. FMA:13087 NCIT:C34027 SCTID:119203005 UMLS:C0506947 aortic section uberon aortic segment portion of aorta segment of aorta UBERON:0005800 section of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. ncithesaurus:Aortic_Segment UMLS:C0506947 ncithesaurus:Aortic_Segment aortic segment FMA:13087 segment of aorta FMA:13087 The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch relationship loss: part_of axial vasculature (TAO:0001073)[TAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] AAO:0011029 BTO:0004673 EHDAA:402 EMAPA:18606 SCTID:338637006 TAO:0000014 VHOG:0000264 Wikipedia:Dorsal_aorta XAO:0000051 ZFA:0000014 DA aorta dorsalis uberon aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ UBERON:0005805 dorsal aorta http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GO:0035907 https://sourceforge.net/p/geneontology/ontology-requests/8525/ Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Wikipedia:Dorsal_aorta Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000014 TAO ZFIN:curator The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch BTO:0004673 relationship loss: part_of axial vasculature (TAO:0001073)[TAO] 2012-08-14 TAO:0000014 TAO When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000264 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ DA ZFA:0000014 aorta dorsalis XAO:0000051 aortae dorsales Wikipedia:Dorsal_aorta dorsal aorta root VHOG:0000264 dorsal aortae Wikipedia:Dorsal_aorta dorsal aortic root VHOG:0000264 dorsal aortæ Wikipedia:Dorsal_aorta In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. FMA:45628 MESH:D011168 NCIT:C33344 SCTID:362063001 UMLS:C0226727 Wikipedia:Portal_venous_system portal venous system uberon UBERON:0005806 portal system In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. Wikipedia:Portal_venous_system UMLS:C0226727 ncithesaurus:Portal_Venous_System portal venous system FMA:45628 A bone tissue that is part of a long bone. FMA:83117 SCTID:425475006 uberon osseous tissue of long bone UBERON:0005808 bone tissue of long bone A bone tissue that is part of a long bone. OBOL:automatic osseous tissue of long bone FMA:83117 A round nodule, small eminence, or warty outgrowth on an anatomical surface, such as bones, skin, or within the lungs (in the case of tuberculosis). They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP]. AAO:0010605 BTO:0002173 FMA:75429 Wikipedia:Tubercle_(anatomy) uberon tuber UBERON:0005813 tubercle A round nodule, small eminence, or warty outgrowth on an anatomical surface, such as bones, skin, or within the lungs (in the case of tuberculosis). They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP]. Wikipedia:Tubercle_(anatomy) A vertebral arch that is part of the first cervical vertebra. FMA:23975 SCTID:272708001 Wikipedia:Arch_of_the_atlas atlas arch uberon UBERON:0005814 arch of atlas A vertebral arch that is part of the first cervical vertebra. http://orcid.org/0000-0002-6601-2165 atlas arch FMA:23975 A spinal cord segment that adjacent_to a sacral region. BIRNLEX:1275 FMA:256623 MA:0003085 NCIT:C12896 SCTID:244438003 UMLS:C0581669 UMLS:C1280196 pars sacralis medullae spinalis sacral segment of spinal cord sacral segments of spinal cord [1-5] segmenta sacralia medullae spinalis [1-5] uberon UBERON:0005843 sacral spinal cord A spinal cord segment that adjacent_to a sacral region. OBOL:automatic UMLS:C0581669 BIRNLEX:1275 ncithesaurus:Sacral_Spinal_Cord UMLS:C1280196 BIRNLEX:1275 pars sacralis medullae spinalis FMA:256623 FMA:TA sacral segment of spinal cord FMA:256623 sacral segments of spinal cord [1-5] FMA:256623 segmenta sacralia medullae spinalis [1-5] FMA:256623 FMA:TA This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term BIRNLEX:2665 FMA:62420 MA:0003080 SCTID:278748001 axial part of spinal cord axial regional part of spinal cord segment of spinal cord uberon spinal neuromeres UBERON:0005844 spinal cord segment axial part of spinal cord BIRNLEX:2665 axial regional part of spinal cord BIRNLEX:2665 segment of spinal cord FMA:62420 spinal neuromeres TAO:0001332 A spinal cord segment that adjacent_to a caudal region. FMA:256635 MA:0003084 SCTID:278753006 neuronames:1656 coccygeal segment of spinal cord coccygeal segments of spinal cord [1-3] pars coccygea medullae spinalis segmenta coccygea medullae spinalis [1-3] uberon segmenta coccygea UBERON:0005845 for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned caudal segment of spinal cord A spinal cord segment that adjacent_to a caudal region. OBOL:automatic coccygeal segment of spinal cord FMA:256635 coccygeal segments of spinal cord [1-3] FMA:256635 pars coccygea medullae spinalis FMA:256635 FMA:TA segmenta coccygea medullae spinalis [1-3] FMA:256635 FMA:TA segmenta coccygea NeuroNames:1656 A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 mesenchyme condensation uberon UBERON:0005856 developing mesenchymal condensation AEO cjm AEO-modified-relation A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 mesenchyme condensation EMAPA:25351 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. isa cell condensation in VSAO; has_part chondroblast in AEO AEO:0000147 EHDAA2_RETIRED:0003147 EMAPA:32731 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation uberon UBERON:0005863 cartilaginous condensation AEO AEO Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. GO:curator isa cell condensation in VSAO; has_part chondroblast in AEO VSAO cartilage condensation EMAPA:25353 cartilagenous condensation EHDAA2:0003147 chondrogenic condensation VSAO:0000092 UBERON:0008714 AEO:0000149 EHDAA2_RETIRED:0003149 pre muscle mass premuscle mass uberon UBERON:0005865 pre-muscle condensation AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. AEO:0000150 EHDAA2:0003150 EMAPA:32736 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon UBERON:0005866 pre-cartilage condensation AEO AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 AEO:JB A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. http://dictionary.reference.com/browse/precartilage The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip. check develops_from EHDAA2:0001061 EHDAA:5871 EMAPA:17355 FMA:293051 NCIT:C34204 UMLS:C1512982 Wikipedia:Mandibular_prominence uberon mandibular process mandibular swelling prominentia mandibularis UBERON:0005867 mandibular prominence The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip. ISBN:0-683-40008-8 MP:0010939 UMLS:C1512982 ncithesaurus:Mandibular_Prominence mandibular process Wikipedia:Mandibular_prominence mandibular swelling https://orcid.org/0000-0002-6601-2165 prominentia mandibularis Wikipedia:Mandibular_prominence The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw. EHDAA2:0001070 EHDAA:5877 EMAPA:17359 FMA:293049 NCIT:C34206 SCTID:346355001 UMLS:C1513037 Wikipedia:Maxillary_prominence embryonic maxillary process maxillary process maxillary process of embryo uberon prominentia maxilaris UBERON:0005868 maxillary prominence http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw. ISBN:0-683-40008-8 MP:0010940 UMLS:C1513037 ncithesaurus:Maxillary_Prominence maxillary process EHDAA2:0001070 prominentia maxilaris Wikipedia:Maxillary_prominence An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. AAO:0011068 EFO:0003496 EHDAA2:0001295 EHDAA:4772 EMAPA:16800 FMA:295840 SCTID:361485001 Wikipedia:Nasal_pit XAO:0000275 XAO:0004073 nasal pit uberon UBERON:0005870 olfactory pit EHDAA2 EMAPA EHDAA2 XAO:0000275 nasal pit An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. GO:0060166 Wikipedia:Nasal_pit By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. Wikipedia:Nasal_pit nasal pit XAO:0000275 A groove that is situated between the 1st and 2nd pharyngeal arch. In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] EHDAA2:0000009 EHDAA:575 EMAPA:16119 VHOG:0000554 VHOG:0000969 1st arch branchial groove 1st arch groove ectoderm 1st pharyngeal groove 1st pharyngeal groove ectoderm branchial groove of 1st arch uberon 1st branchial cleft 1st pharyngeal cleft UBERON:0005872 1st arch pharyngeal cleft A groove that is situated between the 1st and 2nd pharyngeal arch. ISBN:0124020607 VHOG:OG In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] 2012-09-17 VHOG:0000969 VHOG DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010) http://bgee.unil.ch/ 1st arch branchial groove EHDAA2:0000008 1st arch groove ectoderm EHDAA2:0000009 1st pharyngeal groove VHOG:0000969 1st pharyngeal groove ectoderm VHOG:0000554 branchial groove of 1st arch EMAPA:16119 1st branchial cleft EMAPA:16119 1st pharyngeal cleft VHOG:0000969 A groove that is situated between the 2nd and 3rd pharyngeal arch. EHDAA2:0000057 EHDAA:613 EMAPA:16396 VHOG:0000568 VHOG:0000972 2nd arch branchial groove 2nd arch groove ectoderm 2nd pharyngeal groove 2nd pharyngeal groove ectoderm branchial groove of 2nd arch uberon 2nd branchial cleft 2nd pharyngeal cleft UBERON:0005873 2nd arch pharyngeal cleft A groove that is situated between the 2nd and 3rd pharyngeal arch. ISBN:0124020607 VHOG:OG 2nd arch branchial groove EHDAA2:0000054 2nd arch groove ectoderm EHDAA2:0000057 2nd pharyngeal groove VHOG:0000972 2nd pharyngeal groove ectoderm VHOG:0000568 branchial groove of 2nd arch EMAPA:16396 2nd branchial cleft EMAPA:16396 2nd pharyngeal cleft VHOG:0000972 A groove that is situated between the 3rd and 4th pharyngeal arch. EHDAA2:0000074 EHDAA:1082 EMAPA:16581 VHOG:0000572 VHOG:0000973 3rd arch branchial groove 3rd arch groove ectoderm 3rd pharyngeal groove 3rd pharyngeal groove ectoderm branchial groove of 3rd arch uberon 3rd branchial cleft 3rd pharyngeal cleft UBERON:0005874 3rd arch pharyngeal cleft A groove that is situated between the 3rd and 4th pharyngeal arch. ISBN:0124020607 VHOG:OG 3rd arch branchial groove EHDAA2:0000071 3rd arch groove ectoderm EHDAA2:0000074 3rd pharyngeal groove VHOG:0000973 3rd pharyngeal groove ectoderm VHOG:0000572 branchial groove of 3rd arch EMAPA:16581 3rd branchial cleft EMAPA:16581 3rd pharyngeal cleft VHOG:0000973 A groove that is situated between the 4th and 5th pharyngeal arch. EHDAA2:0000089 EHDAA:1665 EMAPA:16761 RETIRED_EHDAA2:0000088 VHOG:0000577 VHOG:0000968 4th arch branchial groove 4th arch pharyngeal groove ectoderm 4th pharyngeal groove 4th pharyngeal groove ectoderm branchial groove of 4th arch uberon 4th branchial cleft 4th pharyngeal cleft UBERON:0005875 4th arch pharyngeal cleft A groove that is situated between the 4th and 5th pharyngeal arch. ISBN:0124020607 VHOG:OG 4th arch branchial groove RETIRED_EHDAA2:0000088 4th arch pharyngeal groove ectoderm EHDAA2:0000089 4th pharyngeal groove VHOG:0000968 4th pharyngeal groove ectoderm VHOG:0000577 branchial groove of 4th arch EMAPA:16761 4th branchial cleft EMAPA:16761 4th pharyngeal cleft VHOG:0000968 The embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin. The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG] embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP] In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG] All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313] GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771] todo - add taxon constraints we assume the EMAPA class is the undifferentiated form based on TS timings EHDAA2:0000705 EHDAA:5925 EMAPA:17382 FMA:302888 SCTID:308798005 VHOG:0000583 Wikipedia:Genital_tubercle undifferentiated genital tubercle uberon genital tubercle phallic tubercle tuberculum genitale tuberculum phallicum UBERON:0005876 undifferentiated genital tubercle http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png EHDAA2 https://github.com/obophenotype/uberon/issues/1230 The embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin. MGI:anna MP:0011771 https://github.com/obophenotype/uberon/issues/1230 The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG] 2012-09-17 VHOG:0000583 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/genital+tubercle embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP] MP In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG] 2012-09-17 VHOG:0000583 VHOG DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009) http://bgee.unil.ch/ we assume the EMAPA class is the undifferentiated form based on TS timings EMAPA undifferentiated genital tubercle VHOG:0000583 genital tubercle EMAPA:17382 tuberculum genitale Wikipedia:Genital_tubercle tuberculum phallicum Wikipedia:Genital_tubercle An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches. Note we use overlaps as the relationship to the arches EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former pharyngeal groove AAO:0010623 EMAPA:32750 FMA:295672 NCIT:C34250 UMLS:C1280559 Wikipedia:Pharyngeal_groove pharyngeal groove ectoderm gill cleft uberon Kiemenspalten branchial cleft branchial groove pharyngeal ectodermal cleft pharyngeal slit sulcus pharyngei UBERON:0005879 pharyngeal cleft http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg EHDAA2 An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches. PMID:23020903 http://orcid.org/0000-0002-6601-2165 EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former EMAPA pharyngeal groove Wikipedia:Pharyngeal_groove UMLS:C1280559 ncithesaurus:Pharyngeal_Groove pharyngeal groove ectoderm https://orcid.org/0000-0002-6601-2165 branchial cleft Wikipedia:Pharyngeal_groove branchial groove AAO:0010623 Wikipedia:Pharyngeal_groove pharyngeal slit sulcus pharyngei Wikipedia:Pharyngeal_groove A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. uberon digit or predigit limb outgrowth UBERON:0005881 encompasses digits and prepollex. requires review autopodial extension A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. http://orcid.org/0000-0002-6601-2165 A subdivision of skeleton that supports pharyngeal arch 2. it's not clear where AAO:'hyobranchial skeleton' belongs AAO:0000665 AAO:0010370 TAO:0001276 XAO:0003177 ZFA:0001276 hyoid arch skeleton pharyngeal arch 2 skeleton hyoid bars uberon hyoid arch visceral arch 2 UBERON:0005884 hyoid arch skeleton ZFA cjm A subdivision of skeleton that supports pharyngeal arch 2. OBOL:automatic it's not clear where AAO:'hyobranchial skeleton' belongs AAO hyoid arch skeleton ZFA:0001276 pharyngeal arch 2 skeleton ZFA:0001276 hyoid bars TAO:0001276 hyoid arch TAO:0001276 visceral arch 2 TAO:0001276 The epithelial lining of the surface of the coelom. EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium' Wikipedia:Coelomic_epithelium XAO:0000329 celomic epithelium germinal epithelium of Waldeyer uberon UBERON:0005891 coelomic epithelium XAO XAO The epithelial lining of the surface of the coelom. Wikipedia:Coelomic_epithelium XAO:0000329 EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium' EHDAA2 germinal epithelium of Waldeyer Wikipedia:Coelomic_epithelium A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx. EMAPA:37304 MA:0000670 MESH:D007867 uberon UBERON:0005893 leg bone A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx. https://orcid.org/0000-0002-6601-2165 EMAPA:37304 MA:th A bone that is part of the manus skeleton. Note that this includes the carpal bones. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35391 MA:0000619 SCTID:426741001 bone of hand bone of hand skeleton bone of manus bone of pectoral limb autopod bone of pectoral limb autopodium forelimb autopod bone forelimb autopodium bone hand bone uberon UBERON:0005897 manus bone A bone that is part of the manus skeleton. Note that this includes the carpal bones. https://orcid.org/0000-0002-6601-2165 hand bone MA:0000619 A bone that is part of the pes skeleton. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35354 GAID:192 MA:0000643 MESH:D005529 NCIT:C13068 SCTID:361371005 UMLS:C0016505 bone of foor proper or tarsal skeleton bone of foot bone of pedal skeleton bone of pes foot bone uberon UBERON:0005899 pes bone A bone that is part of the pes skeleton. https://orcid.org/0000-0002-6601-2165 UMLS:C0016505 ncithesaurus:Foot_Bone foot bone MA:0000643 Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TODO - check An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] AAO:0010199 BTO:0004675 FMA:49187 MESH:D009778 SCTID:362618001 TAO:0001414 XAO:0003173 ZFA:0001414 neuronames:2431 basicranial region occipital part of head occipital region of head uberon back of head UBERON:0005902 occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TAO:0001414 UBERONREF:0000007 An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] 2012-06-20 AAO:0010199 AAO AAO:EJS Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] 2012-08-14 TAO:0001414 TAO TAO:MAH MESH:D009778 https://github.com/biopragmatics/biomappings basicranial region ZFA:0001414 occipital part of head FMA:49187 occipital region of head FMA:49187 back of head FMA:49187 Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]. EMAPA:29282 FMA:19473 SCTID:279675008 Wikipedia:Excretory_duct_of_seminal_gland ductus excretorius (vesicula seminalis) ductus excretorius glandulae vesiculosae excretory duct of seminal gland seminal vesicle duct uberon ductus excretorius glandulae vesiculosae UBERON:0005903 duct of seminal vesicle http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]. Wikipedia:Excretory_duct_of_seminal_gland ductus excretorius (vesicula seminalis) FMA:19473 ductus excretorius glandulae vesiculosae FMA:19473 FMA:TA excretory duct of seminal gland FMA:19473 seminal vesicle duct FMA:19473 ductus excretorius glandulae vesiculosae Wikipedia:Excretory_duct_of_seminal_gland Any of the ducts that are part of a male reproductive system. this class groups the individual ducts in a variety of species uberon UBERON:0005904 duct of male reproductive system Any of the ducts that are part of a male reproductive system. http://orcid.org/0000-0002-6601-2165 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]. FMA:9689 SCTID:362890006 uberon UBERON:0005906 See notes for serous membrane serous sac Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]. FMA:9689 https://github.com/obophenotype/uberon/issues/86 Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]. FMA:69065 endoderm-derived epithelium endoepithelium uberon UBERON:0005911 endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]. FMA:69065 FMA:10483 bone organ zone uberon UBERON:0005913 zone of bone organ FMA bone organ zone FMA:10483 A naris that provides one of the small external openings of the head that give passage to air for breathing. Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO] relationship loss: subclass nasal opening (AAO:0000316)[AAO] In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG] Fish have two pairs of external nostrils. naris AAO:0000024 AAO:0000983 AAO:0010358 EHDAA2:0001275 EHDAA:9085 EMAPA:17848 FMA:59645 MA:0001320 NCIT:C33178 SCTID:276165005 TAO:0000550 UMLS:C0595944 VHOG:0000544 Wikipedia:Nostril XAO:0003033 ZFA:0000550 external nares nostril blowhole uberon anterior nares anterior naris UBERON:0005928 external naris ZFA A naris that provides one of the small external openings of the head that give passage to air for breathing. Wikipedia:Nostril http://orcid.org/0000-0002-6601-2165 Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO] 2012-06-20 AAO:0000024 AAO AAO:LAP relationship loss: subclass nasal opening (AAO:0000316)[AAO] 2012-06-20 AAO:0000024 AAO In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG] 2012-09-17 VHOG:0000544 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27 http://bgee.unil.ch/ naris ZFA:0000550 UMLS:C0595944 ncithesaurus:Nostril external nares nostril FMA:59645 XAO:0003033 blowhole Wikipedia:Blowhole_(anatomy) anterior nares VHOG:0000544 anterior naris ZFA:0001427 Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 UMLS:C0222645 VSAO:0000056 Wikipedia:Axial_skeleton XAO:0004011 uberon skeleton axiale UBERON:0005944 axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. FMA:71221 VSAO:0000056 Wikipedia:Axial_skeleton https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000056 VSAO PSPUB:0000170 UMLS:C0222645 ncithesaurus:Axial_Skeleton skeleton axiale Wikipedia:Axial_skeleton trabecula trabecular cartilage EFO:0003677 TAO:0001321 ZFA:0001321 neurocranial trabeculae uberon UBERON:0005945 neurocranial trabecula ZFA ZFA trabecula ZFA:0001321 trabecular cartilage ZFA:0001321 neurocranial trabeculae ZFA:0001321 An outflow tract that is part of a cardiac atrium. FMA:14141 outflow part of atrium uberon UBERON:0005946 outflow tract of atrium An outflow tract that is part of a cardiac atrium. OBOL:automatic outflow part of atrium FMA:14141 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. infundibulum EMAPA:37926 FMA:7216 NCIT:C61368 SCTID:244379003 UMLS:C1881209 RVOT conus arteriosus (infundibulum) infundibulum of right ventricle outflow tract of right ventricle pulmonary conus right ventricle pulmonary outflow tract right ventricular outflow tract uberon arterial cone conus arteriosus pulmonary cone pulmonary conus UBERON:0005953 outflow part of right ventricle PMID:17276708 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk. MP:0010428 infundibulum Wikipedia:Conus_arteriosus EMAPA:37926 MA:th UMLS:C1881209 ncithesaurus:Infundibulum RVOT MP:0010428 conus arteriosus (infundibulum) FMA:7216 infundibulum of right ventricle FMA:7216 MP:0010428 outflow tract of right ventricle FMA:7216 pulmonary conus FMA:7216 right ventricle pulmonary outflow tract MP:0010428 right ventricular outflow tract MP:0010428 arterial cone MP:0010428 conus arteriosus MP:0010428 pulmonary cone MP:0010428 pulmonary conus MP:0010428 Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. EMAPA:37925 FMA:9473 SCTID:264070001 Wikipedia:Aortic_vestibule LVOT Sibson vestibule aortic vestibule heart left ventricle outflow tract left ventricular outflow left ventricular outflow tract outflow tract of left ventricle vestibulum aortae uberon UBERON:0005956 outflow part of left ventricle Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. MP:0010429 EMAPA:37925 MA:th LVOT MP:0010429 Sibson vestibule MP:0010429 aortic vestibule FMA:9473 MP:0010429 heart left ventricle outflow tract MP:0010429 left ventricular outflow FMA:9473 left ventricular outflow tract HP:0011103 outflow tract of left ventricle FMA:9473 vestibulum aortae FMA:9473 FMA:TA Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]. FMA:9550 main part of right atrium outflow tract of right atrium uberon UBERON:0005965 outflow part of right atrium Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]. FMA:9550 FMA:FMA main part of right atrium FMA:9550 outflow tract of right atrium FMA:9550 An outflow tract of atrium that is part of a left atrium. FMA:9551 main part of left atrium outflow tract of left atrium uberon UBERON:0005966 outflow part of left atrium An outflow tract of atrium that is part of a left atrium. OBOL:automatic main part of left atrium FMA:9551 outflow tract of left atrium FMA:9551 A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP]. TODO check syns - ligaments UBERON:0004028 BTO:0001605 CALOHA:TS-1058 EFO:0003077 EV:0100352 FMA:77660 GAID:897 MA:0003086 MESH:D014129 NCIT:C12803 SCTID:280694002 UMLS:C0040573 Wikipedia:Trabecular_meshwork eye trabecular meshwork reticulum trabeculare trabecular meshwork of the eye uberon Hueck's ligament cribiform ligament iridis ligamentum peactin-tum iridis ligamentum pectinatum ligamentum pectinatum anguli iridocornealis ligamentum pectinatum iridis pectinate ligament pectinate ligament of iris reticulum trabeculare sclerae scleral trabeculae scleral trabecular scleral trabecule scribiform ligament trabecular mesh trabecular meshwork UBERON:0005969 eye trabecular meshwork http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP]. MP:0005203 Wikipedia:Trabecular_meshwork UMLS:C0040573 ncithesaurus:Trabecular_Meshwork eye trabecular meshwork MA:0003086 reticulum trabeculare BTO:0001605 trabecular meshwork of the eye Wikipedia:Trabecular_meshwork Hueck's ligament BTO:0001605 cribiform ligament Wikipedia:Trabecular_meshwork iridis Wikipedia:Trabecular_meshwork ligamentum peactin-tum iridis Wikipedia:Trabecular_meshwork ligamentum pectinatum Wikipedia:Trabecular_meshwork ligamentum pectinatum anguli iridocornealis BTO:0001605 ligamentum pectinatum iridis Wikipedia:Trabecular_meshwork pectinate ligament BTO:0001605 pectinate ligament of iris BTO:0001605 reticulum trabeculare sclerae Wikipedia:Trabecular_meshwork scleral trabeculae Wikipedia:Trabecular_meshwork scleral trabecular Wikipedia:Trabecular_meshwork scleral trabecule Wikipedia:Trabecular_meshwork scribiform ligament Wikipedia:Trabecular_meshwork trabecular mesh Wikipedia:Trabecular_meshwork trabecular meshwork BTO:0001605 GO:0002930 A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. EMAPA:16076 amnionic fold uberon UBERON:0005971 amniotic fold ISBN:0073040584 A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. ISBN:0073040584 amnionic fold http://placentation.ucsd.edu/glossfs.html The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium. EMAPA:37837 FMA:9236 SCTID:277693004 Wikipedia:Crista_terminalis crista terminalis atrii dextri crista terminalis cordis crista terminalis of right atrium uberon UBERON:0005979 crista terminalis The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium. MP:0010495 EMAPA:37837 MA:th crista terminalis atrii dextri FMA:9236 FMA:TA crista terminalis cordis FMA:9236 crista terminalis of right atrium FMA:9236 The laminar structure of the heart. uberon UBERON:0005983 heart layer The laminar structure of the heart. MP:0010545 Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation. TODO - change relation from part_of MESH:D003331 Wikipedia:Coronary_circulation uberon UBERON:0005985 coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation. MP:0010551 The supporting bundles of muscular fibers lining the walls of the atrial myocardium. EMAPA:37432 ZFA:0005810 atrial trabecula atrium myocardial trabeculae trabecula of atrium trabecular layer of atrium trabecular layer of the atrium uberon UBERON:0005988 atrium myocardial trabecula ZFA The supporting bundles of muscular fibers lining the walls of the atrial myocardium. MP:0010581 ZFA:0005810 EMAPA:37432 MA:th atrium myocardial trabeculae MP:0010581 trabecular layer of the atrium ZFA:0005810 The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve. EMAPA:37431 FMA:7136 SCTID:280151006 Wikipedia:Atrioventricular_septum membranous atrioventricular septum uberon UBERON:0005989 atrioventricular septum PMID:15797462 Wikipedia The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve. MP:0010592 EMAPA:37431 MA:th membranous atrioventricular septum FMA:7136 The three fibrous triangular components and associated flap of the pulmonary valve. FMA:7248 cusp of pulmonary valve pulmonary semilunar valvule pulmonary valvular cusp semilunar cusp of pulmonary valve semilunar valvule of pulmonary valve uberon UBERON:0005992 pulmonary valve cusp The three fibrous triangular components and associated flap of the pulmonary valve. MP:0010602 cusp of pulmonary valve FMA:7248 pulmonary semilunar valvule FMA:7248 pulmonary valvular cusp FMA:7248 semilunar cusp of pulmonary valve FMA:7248 semilunar valvule of pulmonary valve FMA:7248 The fibrous ring of the pulmonary valve that attaches the cusps of pulmonary valve to the wall of right ventricle, and which consists of portions of the fibrous scallops of the anterior, right posterior and left posterior cusps. EMAPA:37420 FMA:9503 anulus of pulmonary valve fibrous ring of pulmonary valve pulmonary anulus pulmonary valvar anulus uberon UBERON:0005993 pulmonary valve anulus The fibrous ring of the pulmonary valve that attaches the cusps of pulmonary valve to the wall of right ventricle, and which consists of portions of the fibrous scallops of the anterior, right posterior and left posterior cusps. MP:0010606 EMAPA:37420 MA:th anulus of pulmonary valve FMA:9503 fibrous ring of pulmonary valve FMA:9503 pulmonary anulus FMA:9503 pulmonary valvar anulus FMA:9503 The tendinous strands that connect the papillary muscles on the wall of the ventricles to the leaflets of the atrioventricular valves; the chordae tendineae serve to prevent the AV valves from prolapsing back into the atria. EMAPA:36322 FMA:12225 GAID:564 MESH:D002815 NCIT:C32307 SCTID:279330004 UMLS:C0008484 Wikipedia:Chordae_tendineae uberon chordae tendinea chordae tendineae cordis UBERON:0005994 chorda tendineae http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png FMA-abduced The tendinous strands that connect the papillary muscles on the wall of the ventricles to the leaflets of the atrioventricular valves; the chordae tendineae serve to prevent the AV valves from prolapsing back into the atria. MP:0010608 Wikipedia:Chordae_tendineae UMLS:C0008484 ncithesaurus:Chordae_Tendineae chordae tendinea FMA:12225 chordae tendineae cordis Wikipedia:Chordae_tendineae The fibrous ring of the mitral valve that attaches the cusps of mitral valve to the heart, and which consists of portions of the fibrous scallops of the anterior and posterior cusps. EMAPA:37419 FMA:9498 Wikipedia:Mitral_annulus anulus of mitral valve fibrous ring of mitral valve mitral annulus mitral anulus mitral valvar anulus uberon UBERON:0005995 mitral valve anulus The fibrous ring of the mitral valve that attaches the cusps of mitral valve to the heart, and which consists of portions of the fibrous scallops of the anterior and posterior cusps. MP:0010613 EMAPA:37419 MA:th anulus of mitral valve FMA:9498 fibrous ring of mitral valve FMA:9498 mitral annulus Wikipedia:Mitral_annulus mitral anulus FMA:9498 mitral valvar anulus FMA:9498 The two fibrous components and associated flaps of the mitral valve. uberon UBERON:0005996 mitral valve cusp The two fibrous components and associated flaps of the mitral valve. MP:0010614 The fibrous ring of the tricuspid valve that attaches the cusps of tricuspid valve to the heart, and which consists of portions of the fibrous scallops of the anterior cusp (infundibular cusp), the posterior cusp (marginal cusp), and the septal cusp (medial cusp). EMAPA:37421 FMA:9500 anulus of tricuspid valve fibrous ring of tricuspid valve tricuspid anulus tricuspid valvar anulus uberon UBERON:0005997 tricuspid valve anulus The fibrous ring of the tricuspid valve that attaches the cusps of tricuspid valve to the heart, and which consists of portions of the fibrous scallops of the anterior cusp (infundibular cusp), the posterior cusp (marginal cusp), and the septal cusp (medial cusp). MP:0010621 EMAPA:37421 MA:th anulus of tricuspid valve FMA:9500 fibrous ring of tricuspid valve FMA:9500 tricuspid anulus FMA:9500 tricuspid valvar anulus FMA:9500 The three fibrous triangular components and associated flaps of the tricuspid valve. check whether we need to separate cusp/leaflet/valve FMA:7240 SCTID:261417002 cuspis septalis (valva tricuspidalis) cuspis septalis valvae atrioventricularis dextrae septal cusp of right atrioventricular valve septal cusp of tricuspid valve septal leaflet of right-sided tricuspid valve septal leaflet of tricuspid valve septal tricuspid leaflet uberon UBERON:0005998 tricuspid valve cusp FMA The three fibrous triangular components and associated flaps of the tricuspid valve. MP:0010622 cuspis septalis (valva tricuspidalis) FMA:7240 FMA:TA cuspis septalis valvae atrioventricularis dextrae FMA:7240 FMA:TA septal cusp of right atrioventricular valve FMA:7240 septal cusp of tricuspid valve FMA:7240 septal leaflet of right-sided tricuspid valve https://orcid.org/0000-0003-3308-6245 septal leaflet of tricuspid valve FMA:7240 septal tricuspid leaflet FMA:7240 The paired arteries that carry blood to the yolk sac from the dorsal aorta. EHDAA2:0002208 EMAPA:16207 Wikipedia:Vitelline_arteries uberon UBERON:0006002 Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664] vitelline artery http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png ventral branch The paired arteries that carry blood to the yolk sac from the dorsal aorta. MP:0010664 Wikipedia:Vitelline_arteries Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] EMAPA:37883 Wikipedia:Skin_appendage body hair or bristle uberon adnexae cutis skin adnexa skin adnexal structure skin appendage UBERON:0006003 integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. http://code.google.com/p/caro2/issues/detail?id=5 http://orcid.org/0000-0002-6601-2165 the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] MP:0010678 EMAPA:37883 MA:th body hair or bristle GO:GO adnexae cutis Wikipedia:Skin_appendage skin adnexa Wikipedia:Skin_appendage skin appendage Wikipedia:Skin_appendage A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices. TODO - compare with ZFA atrioventricular ring, part of the conduction system BTO:0003628 EMAPA:37422 FMA:9497 Wikipedia:Fibrous_rings_of_heart anulus fibrosus of heart uberon Lower's ring annulus fibrosus cordis anulus fibrosus cordis aortic annulus atrioventricular ring coronary tendon fibrous ring of heart UBERON:0006008 fibrous ring of heart A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices. Wikipedia:Fibrous_rings_of_heart http://orcid.org/0000-0002-6601-2165 EMAPA:37422 MA:th anulus fibrosus of heart FMA:9497 Lower's ring BTO:0003628 annulus fibrosus cordis Wikipedia:Fibrous_rings_of_heart anulus fibrosus cordis Wikipedia:Fibrous_rings_of_heart aortic annulus Wikipedia:Fibrous_rings_of_heart atrioventricular ring BTO:0003628 coronary tendon BTO:0003628 fibrous ring of heart Wikipedia:Fibrous_rings_of_heart The part of the heart valves that serves to seal the heart valves when closed. There are three cusps for each valve except for the mitral valve, which has only two (hence its alternate name, 'bicuspid valve'). 'Nodules' are located at the tip of the valve, to form a tighter seal[WP]. FMA:7232 NCIT:C33849 SCTID:30822008 UMLS:C0225923 Wikipedia:Cusps_of_heart_valves cardiac valve cusp cardiac valvular cusp cardiac valvule cardial valve cusp semilunar valvule uberon UBERON:0006009 cusp of cardiac valve http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png The part of the heart valves that serves to seal the heart valves when closed. There are three cusps for each valve except for the mitral valve, which has only two (hence its alternate name, 'bicuspid valve'). 'Nodules' are located at the tip of the valve, to form a tighter seal[WP]. Wikipedia:Cusps_of_heart_valves UMLS:C0225923 ncithesaurus:Cardiac_Valve_Cusp cardiac valve cusp FMA:7232 cardiac valvular cusp FMA:7232 cardiac valvule FMA:7232 semilunar valvule FMA:7232 A digit that is part of a digit 1 plus metapodial segment. 1 EMAPA:37285 MA:0003023 autopod digit 1 digit I limb digit 1 dewclaw uberon UBERON:0006048 digit 1 A digit that is part of a digit 1 plus metapodial segment. OBOL:automatic EMAPA:37285 MA:th digit I https://github.com/obophenotype/uberon/issues/458 limb digit 1 MA:0003023 dewclaw Wikipedia:Dewclaw A digit that is part of a digit 5 plus metapodial segment. 5 EMAPA:17441 EMAPA:37289 autopod digit 5 digit V fifth digit limb digit 5 uberon digiti minimi UBERON:0006052 digit 5 A digit that is part of a digit 5 plus metapodial segment. OBOL:automatic EMAPA:37289 MA:th digit V https://github.com/obophenotype/uberon/issues/458 uberon UBERON:0006056 posterior surface of head A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). uberon UBERON:0006058 multi-limb segment region https://github.com/obophenotype/uberon/issues/514 A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). https://orcid.org/0000-0002-6601-2165 A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses). AAO:0000739 FMA:24530 NCIT:C116112 Wikipedia:Vertebral_column#Structure_of_individual_vertebrae vertebra process vertebral process spinous process uberon UBERON:0006061 process of vertebra A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses). Wikipedia:Vertebral_column#Structure_of_individual_vertebrae vertebral process FMA:24530 spinous process AAO:0000739 One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch. BTO:0001763 uberon neural arch primordium UBERON:0006063 cartilaginous neural arch One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch. BTO:0001763 Any collection of muscles that is part of a hindlimb zeugopod. FMA:50211 leg musculature muscle group of leg set of muscles of leg uberon UBERON:0006067 musculature of hindlimb zeugopod Any collection of muscles that is part of a hindlimb zeugopod. OBOL:automatic leg musculature FMA:50211 muscle group of leg FMA:50211 set of muscles of leg FMA:50211 A bone that is part of a post-anal tail. MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. EMAPA:18042 MA:0000696 uberon tail bone tail vertebra UBERON:0006068 bone of tail A bone that is part of a post-anal tail. OBOL:automatic MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. MA tail bone MA:0000696 tail vertebra http://orcid.org/0000-0002-6601-2165 Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. This region is reduced in humans and corresponds to the coccyx We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO:0000087 uberon post-anal caudal region post-anal tail region postsacral region tail region UBERON:0006071 caudal region Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. http://orcid.org/0000-0002-6601-2165 We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO post-anal caudal region http://orcid.org/0000-0002-6601-2165 post-anal tail region http://orcid.org/0000-0002-6601-2165 postsacral region AAO:0000082 tail region AAO:0000082 That portion of the spine comprising the cervical vertebrae. The neck area of the spine. Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] AAO:0000092 BTO:0004148 EHDAA2:0000238 EHDAA:5051 EMAPA:17215 FMA:24138 MA:0003154 NCIT:C69313 SCTID:260488005 UMLS:C0728985 axial skeleton cervical region cervical skeleton cervical spinal column cervical spine cervical vertebrae series cervical vertebral column uberon skeletal system of neck UBERON:0006072 cervical region of vertebral column FMA That portion of the spine comprising the cervical vertebrae. The neck area of the spine. http://medical-dictionary.thefreedictionary.com/ Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] 2012-06-20 AAO:0000092 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0728985 ncithesaurus:Cervical_Spine axial skeleton cervical region MA:0003154 cervical skeleton EHDAA2:0000238 cervical spinal column FMA:24138 cervical spine FMA:24138 cervical vertebral column FMA:24138 skeletal system of neck FMA:24138 That part of the spine comprising the thoracic vertebrae. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 BTO:0004150 EHDAA:5063 EMAPA:17396 FMA:9140 MA:0003155 NCIT:C69315 SCTID:243931006 UMLS:C0581269 axial skeleton thoracic region columna vertebralis thoracicus thoracic spine thoracic vertebrae series thoracic vertebral column uberon UBERON:0006073 thoracic region of vertebral column FMA That part of the spine comprising the thoracic vertebrae. http://medical-dictionary.thefreedictionary.com/ Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0581269 ncithesaurus:Thoracic_Spine axial skeleton thoracic region MA:0003155 columna vertebralis thoracicus FMA:9140 thoracic spine FMA:9140 thoracic vertebral column FMA:9140 Subdivision of vertebral column that corresponds to the lumbar subdivision of the body, containing the lumbar vertebrae. lumbar BTO:0004147 EHDAA2:0001037 EHDAA:5055 EMAPA:17393 FMA:16203 GAID:31 MA:0003156 NCIT:C69314 SCTID:243932004 axial skeleton lumbar region lumbar skeleton lumbar spine lumbar vertebrae series lumbar vertebral column uberon UBERON:0006074 lumbar region of vertebral column Subdivision of vertebral column that corresponds to the lumbar subdivision of the body, containing the lumbar vertebrae. UBERONREF:0000006 axial skeleton lumbar region MA:0003156 lumbar skeleton EHDAA2:0001037 lumbar spine BTO:0004147 lumbar vertebral column FMA:16203 Subdivision of vertebral column that corresponds to the sacral subdivision of the body, containing the sacral vertebrae or sacrum. Region of the vertebral column represented by one or two vertebrae.[AAO] In adult humans, the sacral skeleton is fused and called the sacrum AAO:0000724 EHDAA2:0001772 EHDAA:5059 EMAPA:17676 GAID:32 MA:0003157 NCIT:C33508 Wikipedia:Sacrum axial skeleton sacral region sacral skeleton sacral vertebrae series sacrum uberon UBERON:0006075 sacral region of vertebral column Subdivision of vertebral column that corresponds to the sacral subdivision of the body, containing the sacral vertebrae or sacrum. UBERONREF:0000006 Region of the vertebral column represented by one or two vertebrae.[AAO] 2012-06-20 AAO:0000724 AAO AAO:Duellman_and_Trueb_1994 axial skeleton sacral region MA:0003157 sacral skeleton EHDAA2:0001772 Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] in AAO, this is posterior to the caudal-sacral region AAO:0000082 EMAPA:18043 MA:0003158 axial skeleton tail region caudal skeleton caudal vertebrae series uberon caudal region postsacral region tail region UBERON:0006076 caudal region of vertebral column Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. UBERONREF:0000006 Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] 2012-06-20 AAO:0000082 AAO AAO:Duellman_and_Trueb_1994 in AAO, this is posterior to the caudal-sacral region AAO axial skeleton tail region MA:0003158 caudal skeleton UBERONREF:0000006 caudal vertebrae series http://purl.bioontology.org/ontology/provisional/a047a2d5-418f-4d9c-ad21-ee0b7c29c29d caudal region AAO:0000082 postsacral region AAO:0000082 tail region AAO:0000082 A collection of all skeletal elements in some subdivision of the vertebral column. FMA:16201 subdivision of vertebral skeleton vertebrae series vertebral column subdivision vertebral series uberon vertebral region vertebral subdivision UBERON:0006077 subdivision of vertebral column FMA A collection of all skeletal elements in some subdivision of the vertebral column. https://orcid.org/0000-0002-6601-2165 subdivision of vertebral skeleton https://orcid.org/0000-0002-6601-2165 vertebral column subdivision FMA:16201 The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. uberon UBERON:0006170 mesonephric capsule The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. DOI:10.1371/journal.pone.0099864 GO:0061285 GOC:mtg_kidney_jan10 Missing definition for term UBERON:0006183. Please replace it using linked reference. uberon UBERON:0006183 mesonephric glomerular capillary https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Missing definition for term UBERON:0006183. Please replace it using linked reference. GO:0061249 Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP]. FMA:58577 SCTID:244498000 anterior chamber angle uberon UBERON:0006206 iridocorneal angle Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP]. MP:0004221 anterior chamber angle FMA:58577 The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. UBERON:0005999 CALOHA:TS-2409 EHDAA2:0000136 EHDAA:2592 EMAPA:16827 VHOG:0000502 Wikipedia:Aorticopulmonary_septum aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale uberon aortic septum spiral septum UBERON:0006207 aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png PMID:6844926 Wikipedia The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. MP:0010650 Wikipedia:Aorticopulmonary_septum aortico-pulmonary septum Wikipedia:Aorticopulmonary_septum aorticopulmonary septum Wikipedia:Aorticopulmonary_septum septum aorticopulmonale Wikipedia:Aorticopulmonary_septum aortic septum Wikipedia:Aorticopulmonary_septum spiral septum Wikipedia:Aorticopulmonary_septum A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head. EHDAA2:0000155 EHDAA:4685 EMAPA:17280 NCIT:C34110 VHOG:0001364 auditory hillock of Hiss uberon auditory tubercles auricular hillock hillock of Hiss UBERON:0006208 auditory hillocks A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head. Wikipedia:Pinna_(anatomy)#Development auditory tubercles VHOG:0001364 EHDAA2:0000179 EHDAA:3217 EMAPA:16893 uberon UBERON:0006210 body-wall mesenchyme The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. EHDAA2:0000189 EHDAA:536 EMAPA:16259 FMA:313607 SCTID:361412007 VHOG:0000380 Wikipedia:Buccopharyngeal_membrane uberon oral membrane oral plate oropharyngeal membrane pharyngeal membrane UBERON:0006211 buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png EHDAA2 The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. MP:0012521 oral membrane MP:0012521 oral plate MP:0012521 oropharyngeal membrane Wikipedia:Buccopharyngeal_membrane pharyngeal membrane MP:0012521 A cartilaginous condensation that has the potential to develop into a carpal bone. EHDAA2:0000221 EHDAA:8544 EMAPA:18102 VHOG:0001123 uberon carpal cartilage condensation UBERON:0006213 carpus cartilage element A cartilaginous condensation that has the potential to develop into a carpal bone. OBOL:automatic carpal cartilage condensation EMAPA:18102 A pre-cartilage condensation that has the potential to develop into a carpal bone. EHDAA2:0000222 EHDAA:6324 EMAPA:17724 VHOG:0000955 uberon carpal pre-cartilage condensation UBERON:0006214 carpus pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a carpal bone. OBOL:automatic carpal pre-cartilage condensation EMAPA:17724 The posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system. The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] UBERON:0013163 DHBA:10664 EHDAA2:0000231 EMAPA:17074 TAO:0001440 Wikipedia:Rhombic_lips XAO:0004135 ZFA:0001440 uberon cerebellar anlage cerebellar primordium cerebellum primordium dorsal part of alar plate of metencephalon future cerebellum presumptive cerebellum rostral rhombic lip UBERON:0006215 rhombic lip EHDAA2 Wikipedia The posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system. MGI:anna MP:0012525 The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] 2012-08-14 TAO:0001440 TAO ZFIN:curator cerebellar anlage MGI:anna cerebellar primordium EMAPA:17074 cerebellum primordium EHDAA2:0000231 EMAPA:17074 dorsal part of alar plate of metencephalon EMAPA:17074 future cerebellum http://orcid.org/0000-0002-6601-2165 presumptive cerebellum MGI:anna rostral rhombic lip MGI:anna The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 EMAPA:16832 FMA:295525 NCIT:C34128 SCTID:308826008 UMLS:C0231056 VHOG:0001198 Wikipedia:Cloacal_membrane embryonic cloacal membrane uberon membrana cloacalis UBERON:0006217 cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png Wikipedia The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. MP:0011837 MP:anna Wikipedia:Cloacal_membrane A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0001198 VHOG http://bgee.unil.ch/ In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] 2012-09-17 VHOG:0001198 VHOG PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002) http://bgee.unil.ch/ UMLS:C0231056 ncithesaurus:Cloacal_Membrane membrana cloacalis Wikipedia:Cloacal_membrane EHDAA:1267 EMAPA:16342 RETIRED_EHDAA2:0000268 uberon UBERON:0006218 common atrial chamber EHDAA2:0000340 EHDAA:6002 EMAPA:17749 uberon UBERON:0006219 deltoid pre-muscle mass EHDAA2 EHDAA2 EHDAA2 The foremost region of the future forebrain that develops into the diencephalon. EFO:0003442 EHDAA2:0000600 EHDAA:844 EMAPA:16514 RETIRED_EHDAA2:0000386 TAO:0000574 ZFA:0000574 presumptive diencephalon uberon UBERON:0006222 future diencephalon EHDAA2 The foremost region of the future forebrain that develops into the diencephalon. UBERON:cjm Wikipedia:Diencephalon presumptive diencephalon TAO:0000574 EHDAA2:0000431 EHDAA:8483 EMAPA:17710 uberon UBERON:0006224 elbow joint primordium consider obsoleting, the ethmoid is endochondral? EHDAA2:0000456 EHDAA:8363 EMAPA:18023 FMA:312597 uberon UBERON:0006227 ethmoid bone primordium FMA AAO EHDAA2 EHDAA:1477 EMAPA:16660 RETIRED_EHDAA2:0000496 VHOG:0000715 uberon facio-acoustic preganglion complex UBERON:0006232 facio-acoustic VII-VIII preganglion complex EHDAA2 facio-acoustic preganglion complex EMAPA:16660 A differentiated genital tubercle that is part of a female reproductive system. EHDAA:8118 EMAPA:18680 RETIRED_EHDAA2:0000500 VHOG:0000666 genital tubercle of female uberon UBERON:0006233 female genital tubercle true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A differentiated genital tubercle that is part of a female reproductive system. OBOL:automatic genital tubercle of female EMAPA:18680 A femur endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000508 EMAPA:17502 VHOG:0000951 uberon femoral pre-cartilage condensation UBERON:0006234 femur pre-cartilage condensation A femur endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic femoral pre-cartilage condensation EMAPA:17502 An anatomical junctions that overlaps the foregut and midgut. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] EHDAA2:0000569 EHDAA:526 EMAPA:16363 VHOG:0000291 uberon UBERON:0006235 foregut-midgut junction An anatomical junctions that overlaps the foregut and midgut. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] 2012-09-17 VHOG:0000291 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ EHDAA2:0000577 EHDAA:9540 EMAPA:18017 FMA:312589 frontal bone primordium uberon UBERON:0006236 tetrapod frontal bone primordium frontal bone primordium EHDAA2:0000577 The embryonic precursor of the brain. The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 ZFA:0000146 brain rudiment presumptive brain encephalon uberon embryonic brain UBERON:0006238 future brain The embryonic precursor of the brain. NLX:94995 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) http://neurolex.org/wiki/Cumbo_terms brain rudiment TAO:0000146 presumptive brain ZFA:0000146 encephalon NLX:94995 embryonic brain BTO:0004726 A tendon that has the potential to develop into a central tendon. The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. EHDAA2:0000593 EHDAA:4118 EMAPA:25035 uberon cranial derivative of septum transversum cranial part of septum transversum UBERON:0006239 future central tendon EHDAA2 mesenchyme cranial part Wikipedia A tendon that has the potential to develop into a central tendon. OBOL:automatic cranial derivative of septum transversum http://orcid.org/0000-0002-6601-2165 cranial part of septum transversum http://orcid.org/0000-0002-6601-2165 A presumptive structure that has the potential to develop into a forebrain. TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate) BAMS:Pros EFO:0003423 EHDAA2:0000661 EHDAA:2643 EMAPA:16640 TAO:0000062 Wikipedia:Prosencephalon ZFA:0000062 future prosencephalon presumptive forebrain presumptive prosencephalon uberon prosencephalon UBERON:0006240 future forebrain A presumptive structure that has the potential to develop into a forebrain. OBOL:automatic presumptive forebrain ZFA:0000062 presumptive prosencephalon TAO:0000062 prosencephalon EHDAA2:0000661 EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16755 TAO:0000417 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon UBERON:0006241 future spinal cord EHDAA2 presumptive spinal cord ZFA:0000417 presumptive spinal cord neural keel TAO:0000417 presumptive spinal cord neural plate TAO:0000417 presumptive spinal cord neural rod TAO:0000417 A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. EHDAA2:0000700 EHDAA:3047 EMAPA:16713 XAO:0004205 gall bladder primordium uberon UBERON:0006242 gallbladder primordium EMAPA EHDAA2 A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. ISBN:0815318960 XAO:0004205 EHDAA2:0000785 EHDAA:8462 EMAPA:17739 uberon UBERON:0006244 hip joint primordium A humerus endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000787 EHDAA:6240 EMAPA:17713 VHOG:0001120 uberon humeral cartilage condensation UBERON:0006245 humerus cartilage element EHDAA2 EHDAA2 A humerus endochondral element that is composed primarily of cartilage tissue. OBOL:automatic humeral cartilage condensation EMAPA:17713 A humerus endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000788 EHDAA:4192 EMAPA:17427 VHOG:0000950 uberon humeral pre-cartilage condensation UBERON:0006246 humerus pre-cartilage condensation EHDAA2 A humerus endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic humeral pre-cartilage condensation EMAPA:17427 An iliac endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000809 EHDAA:9568 EMAPA:18029 VHOG:0000964 uberon UBERON:0006247 iliac pre-cartilage condensation EHDAA2 An iliac endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic An ischial endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000890 EHDAA:9570 EMAPA:26930 uberon ischial cartilage condensation UBERON:0006254 ischial cartilage element EHDAA2 EHDAA2 An ischial endochondral element that is composed primarily of cartilage tissue. OBOL:automatic ischial cartilage condensation EMAPA:26930 An ischial endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000891 EHDAA:7153 EMAPA:18348 VHOG:0000962 uberon UBERON:0006255 ischial pre-cartilage condensation EHDAA2 An ischial endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic EHDAA2:0000897 EHDAA:8467 EMAPA:17740 uberon UBERON:0006256 knee joint primordium Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] EHDAA2:0000996 EMAPA:17186 VHOG:0000449 uberon lingual swelling UBERON:0006260 the collection consisting of the two lateral swellings and the medial swelling lingual swellings EHDAA2 EHDAA2 Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] 2012-09-17 VHOG:0000449 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/lingual+swellings Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000449 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) http://bgee.unil.ch/ lingual swelling EHDAA2:0000996 A differentiated genital tubercle that is part of a male reproductive system. EHDAA:8138 EMAPA:17969 RETIRED_EHDAA2:0001048 VHOG:0000667 genital tubercle of male uberon penis anlage UBERON:0006261 male genital tubercle true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A differentiated genital tubercle that is part of a male reproductive system. OBOL:automatic genital tubercle of male EMAPA:17969 penis anlage EMAPA:17969 An anatomical junctions that overlaps the mouth and foregut. EHDAA:534 EMAPA:16258 RETIRED_EHDAA2:0001205 VHOG:0000592 uberon UBERON:0006264 mouth-foregut junction An anatomical junctions that overlaps the mouth and foregut. OBOL:automatic Groove between maxillary prominence and lateral nasal process. EHDAA2:0001238 EHDAA:4770 EMAPA:16679 FMA:300055 NCIT:C34218 UMLS:C1513875 VHOG:0001307 Wikipedia:Lacrimal_groove naso-lacrimal groove uberon s. lacrimalis maxillae UBERON:0006266 On the nasal surface of the body of the maxilla, in front of the opening of the sinus is a deep groove, the lacrimal groove (or lacrimal sulcus), which is converted into the nasolacrimal canal, by the lacrimal bone and inferior nasal concha; this canal opens into the inferior meatus of the nose and transmits the nasolacrimal duct[WP] See also: oblique facial cleft nasolacrimal groove http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png EHDAA2 EHDAA2 EHDAA2 Groove between maxillary prominence and lateral nasal process. Wikipedia:Lacrimal_groove http://www.indiana.edu/~anat550/hnanim/face/face.html UMLS:C1513875 ncithesaurus:Nasolacrimal_Groove naso-lacrimal groove EMAPA:16679 s. lacrimalis maxillae Wikipedia:Lacrimal_groove The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 NCIT:C34231 UMLS:C1518429 VHOG:0001212 uberon UBERON:0006267 notochordal plate EHDAA2 EHDAA2 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] 2012-09-17 VHOG:0001212 VHOG http://bgee.unil.ch/ UMLS:C1518429 ncithesaurus:Notochordal_Plate A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 NCIT:C34232 UMLS:C1518430 VHOG:0001213 uberon chordamesoderm presumptive notochord UBERON:0006268 The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process EHDAA2 A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm UMLS:C1518430 ncithesaurus:Notochordal_Process Either of two openings transmitting nerves and blood vessels to or from the orbit. EHDAA2:0001328 EHDAA:10648 EMAPA:18717 SCTID:280546005 uberon UBERON:0006271 orbital fissure Either of two openings transmitting nerves and blood vessels to or from the orbit. http://www.merriam-webster.com/medical/orbital%20fissure In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity EHDAA2:0001331 EHDAA:5882 EMAPA:17200 VHOG:0001352 uberon UBERON:0006272 oronasal cavity In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter24/custom3/deluxe-content.html The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles. A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] UBERON:0009123 EHDAA2:0001336 EHDAA:929 EMAPA:16536 FMA:302911 NCIT:C34238 VHOG:0001147 Wikipedia:Otic_pit otic cup uberon UBERON:0006273 otic pit EHDAA2 The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles. ISBN:0-683-40008-8 MP:0011172 A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] 2012-09-17 VHOG:0001147 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Otic+pit otic cup NCBIBook:NBK53175 Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] EHDAA2:0001481 EHDAA:4128 EMAPA:17704 EMAPA:17707 SCTID:361413002 VHOG:0001505 uberon pleuroperitoneal channel UBERON:0006279 pleuroperitoneal canal EHDAA2 EHDAA2 Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. ISBN:0124020607 VHOG:0001505 Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0001505 VHOG http://bgee.unil.ch/ pleuroperitoneal channel VHOG:0001505 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. UBERON:0010226 embryonic ventricle EHDAA2:0001531 EMAPA:16350 FMA:71006 NCIT:C34160 SCTID:361524003 TAO:0002231 Wikipedia:Embryonic_ventricle ZFA:0001719 early heart ventricle embryonic heart ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon UBERON:0006283 The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle ZFA EMAPA Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. ZFA:0001719 presumptive cardiac ventricle heart tube ZFA:0001719 primitive ventricle EHDAA2:0001531 primitive ventricle of heart EMAPA:16350 primordial cardiac ventricle FMA:71006 primordial ventricle FMA:71006 Future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle. The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] DHBA:10595 EHDAA2:0001571 EHDAA:1356 EMAPA:16521 SCTID:361480006 TAO:0001259 VHOG:0000644 ZFA:0001259 prosencephalic vesicle preevaginated forebrain vesicle uberon forebrain ventricle forebrain vesicle prosencephalic ventricle UBERON:0006284 early prosencephalic vesicle EHDAA2 Future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle. https://orcid.org/0000-0002-6601-2165 The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000644 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ prosencephalic vesicle EHDAA2:0001571 forebrain ventricle VHOG:0000644 forebrain vesicle VHOG:0000644 prosencephalic ventricle VHOG:0000644 A pubic endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0001574 EHDAA:9572 EMAPA:18349 VHOG:0000965 uberon UBERON:0006285 pubic pre-cartilage condensation EHDAA2 A pubic endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A rib endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001716 EHDAA:8347 EMAPA:17678 VHOG:0001122 uberon UBERON:0006288 rib cartilage element EHDAA2 EHDAA2 A rib endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A rib endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0001717 EHDAA:6026 EMAPA:17397 VHOG:0000681 uberon UBERON:0006289 rib pre-cartilage condensation EHDAA2 EHDAA2-abduced ZFA A rib endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A scapula endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001777 EHDAA:8368 EMAPA:18343 VHOG:0001125 uberon UBERON:0006290 scapula cartilage element EHDAA2 A scapula endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A scapula endochondral element that is composed primarily of a pre-cartilage condensation. the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005). EHDAA2:0001778 EHDAA:6041 EMAPA:18027 VHOG:0000960 uberon UBERON:0006291 scapula pre-cartilage condensation EHDAA2 A scapula endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005). PMID:21455939 this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness EHDAA2:0001836 EHDAA:8493 EMAPA:17712 uberon UBERON:0006292 shoulder joint primordium EHDAA2 EHDAA2 this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness EHDAA2 A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme UBERON:0009750 EHDAA2:0001904 EHDAA:3003 EMAPA:18535 XAO:0000326 spleen mesenchyme splenic mesenchyme splenic primordium left spleen primordium uberon UBERON:0006293 spleen primordium XAO EHDAA2-modified XAO A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. ISBN:0123747295 MP:0011263 check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme EMAPA spleen mesenchyme MP:0011263 splenic mesenchyme https://orcid.org/0000-0002-6601-2165 splenic primordium EHDAA2:0001904 left spleen primordium XAO:0000326 A primordium that has the potential to develop into a submandibular gland. EHDAA2:0001939 EHDAA:9255 EMAPA:17755 uberon submaxillary gland primordium UBERON:0006298 submandibular gland primordium A primordium that has the potential to develop into a submandibular gland. OBOL:automatic submaxillary gland primordium EMAPA:17755 EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 trigeminal V preganglion uberon trigeminal preganglion UBERON:0006304 See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion EHDAA2 trigeminal V preganglion EMAPA:16663 trigeminal preganglion EMAPA:16663 A segment of the eyeball that is filled with refractive media. BTO:0002085 EMAPA:37529 FMA:58071 MA:0002459 NCIT:C32301 SCTID:280540004 UMLS:C0459556 eye chamber eyeball chamber uberon chamber of eye UBERON:0006311 chamber of eyeball A segment of the eyeball that is filled with refractive media. http://orcid.org/0000-0002-6601-2165 EMAPA:37529 MA:th UMLS:C0459556 ncithesaurus:Chamber_of_the_Eye eye chamber MA:0002459 eyeball chamber FMA:58071 chamber of eye BTO:0002085 Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. ocular refraction MA:0001911 uberon UBERON:0006312 ocular refractive media Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. http://orcid.org/0000-0002-6601-2165 Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 Wikipedia:Body_fluid galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. MESH:A12.207 Wikipedia:Body_fluid EMAPA:37441 MA:th body fluid GAID:266 A nucleus of brain that is part of a brainstem. EMAPA:32790 MA:0000821 uberon brain stem nucleus UBERON:0006331 brainstem nucleus A nucleus of brain that is part of a brainstem. OBOL:automatic brain stem nucleus EMAPA:32790 An embryonic cartilaginous frame, the nasal capsule, an evolutionary-conserved structure composed of ventral and dorsal components: the mesethmoid and ectethmoid cartilages, respectively.[PMID]. consider splitting this class. Developing cartilage in mammals? Multi-tissue structure that is the connective tissue sheath that surrounds, except for external opening(s) in adult, the olfactory epithelium.[TAO] Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium.[AAO] Development information from Brian Hall, Bones and Cartilage: Developmental Skeletal Biology.[TAO] In Aves: The nasal capsule is dorsoventrally divided into two parts: the upper part, the ectethmoid, serves olfaction and is composed of the lamina cribosa, the crista galli apophysis and the conchae. The lower part, the mesethmoid, is a thick cartilage bar extending from the corpus sphenoidalis to the rostral extremity of the nose (Fig. 1A-B). In the avian embryo, the mesethmoid constitutes the cartilage primordium of the upper beak. In avians, the mesethmoid supports upper beak formation, whereas the ectethmoid comprises elements of the olfactory system, including the lamina cribosa, the crista galli apophysis and the conchae. In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates by the process of folding of the cartilaginous nasal capsule during fetal development, outpouchings of the main nasal chamber become enlarged (primary pneumatization) (Witmer, 1999; Macrini, 2014). The resulting paranasal recesses may or may not expand farther into the bodies of facial and basicranial bones (secondary pneumatization). Histori- cally, the result of these processes, paranasal recesses and sinuses, respectively, have not always been distin- guished (see further discussion in Rossie, 2006). Yet, in either case the nasal fossa becomes subdivided into a central nasal chamber and more peripheral paranasal chambers (Smith et al., 2014; Curtis and Van Valken- burgh, 2014)[PMID:25312359] Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase] AAO:0000313 EMAPA:17852 FMA:320527 MA:0000283 TAO:0002035 ZFA:0005507 cartilaginous nasal capsule tripartite nasal capsule uberon UBERON:0006332 nasal capsule An embryonic cartilaginous frame, the nasal capsule, an evolutionary-conserved structure composed of ventral and dorsal components: the mesethmoid and ectethmoid cartilages, respectively.[PMID]. PMID:21270050 consider splitting this class. Developing cartilage in mammals? ZFA Multi-tissue structure that is the connective tissue sheath that surrounds, except for external opening(s) in adult, the olfactory epithelium.[TAO] 2012-08-14 TAO:0002035 TAO TAO:wd Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium.[AAO] 2012-06-20 AAO:0000313 AAO AAO:LAP Development information from Brian Hall, Bones and Cartilage: Developmental Skeletal Biology.[TAO] 2012-09-06 TAO:0002035 TAO Curator In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates ISBN:0073040584 Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase] TAO tripartite nasal capsule PMID:25312359 A choroid plexus stroma that is part of a lateral ventricle. definitions should be fixed to use generic stroma class MA:0000963 uberon UBERON:0006338 lateral ventricle choroid plexus stroma A choroid plexus stroma that is part of a lateral ventricle. OBOL:automatic A choroid plexus stroma that is part of a fourth ventricle. MA:0000985 uberon UBERON:0006340 fourth ventricle choroid plexus stroma A choroid plexus stroma that is part of a fourth ventricle. OBOL:automatic 2 An artery that connects two larger arteries. EMAPA:18598 MA:0001938 NCIT:C52851 UMLS:C1707451 uberon UBERON:0006347 Grouping for anterior and posterior communicating artery An artery that connects two larger arteries. ncithesaurus:Communicating_Artery UMLS:C1707451 ncithesaurus:Communicating_Artery inferred from artery EMAPA:18646 MA:0002227 uberon UBERON:0006355 superior vesical vein true MA The unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species. found in most mammals, with the exception of humans EMAPA:29769 MA:0000406 SCTID:27962002 Wikipedia:Baculum baculum os baculum penile bone penis bone uberon UBERON:0006435 os penis Wikipedia The unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species. MGI:anna MP:0009103 baculum Wikipedia:Baculum penile bone MP:0009104 Wikipedia:Baculum penis bone Wikipedia:Baculum The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals. EMAPA:30823 MA:0000387 baubellum clitoral bone clitoris bone os clitoridis uberon UBERON:0006440 os clitoris Wikipedia The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals. MP:0011849 baubellum Wikipedia:Baculum clitoral bone MP:0011849 os clitoridis Wikipedia:Baculum A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart). anulus BTO:0003627 EMAPA:32670 FMA:76704 MESH:D000070616 anulus fibrosus fibrocartilaginous ring uberon fibrous ring UBERON:0006444 annulus fibrosus A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart). BTO:0003627 anulus BTO:0003627 MESH:D000070616 https://github.com/biopragmatics/biomappings anulus fibrosus FMA:76704 fibrocartilaginous ring http://orcid.org/0000-0002-6601-2165 fibrous ring BTO:0003627 A lobe of lung that is part of a right lung. 4 in mice, divided into 3 in human by two interlobal fissures EMAPA:35155 MA:0001791 NCIT:C48944 SCTID:272654004 UMLS:C1285106 lobe of right lung lobe of the right lung uberon UBERON:0006518 right lung lobe A lobe of lung that is part of a right lung. OBOL:automatic 4 in mice, divided into 3 in human by two interlobal fissures ISBN:0123813611 UMLS:C1285106 ncithesaurus:Lobe_of_the_Right_Lung lobe of the right lung ncithesaurus:Lobe_of_the_Right_Lung System pertaining to a bronchus and alveoli. BTO:0000136 CALOHA:TS-1296 EMAPA:32692 MA:0000416 pulmonary alveolar system uberon bronchoalveolar system UBERON:0006524 alveolar system System pertaining to a bronchus and alveoli. BTO:0000136 pulmonary alveolar system MP:0010899 bronchoalveolar system BTO:0000136 A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted) we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation seminal fluid may have a role in sperm capacitation, sperm motility BTO:0001232 CALOHA:TS-0918 EMAPA:36543 FMA:62967 MA:0002523 MAT:0000057 MIAA:0000057 seminal plasma milt uberon male genital fluid male genital secretion seminal fluid UBERON:0006530 seminal fluid A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. http://orcid.org/0000-0002-6601-2165 This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation DOI:10.1046/j.1365-2540.2001.00961.x seminal plasma BTO:0001232 milt PMID:31287811 PMID:35203131 CURATOR NOTE A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs. seminal fluid BTO:0001232 A portion of organism substance that secreted_by a zone of skin. MA:0002537 skin fluid/secretion uberon skin fluid skin substance UBERON:0006535 skin secretion A portion of organism substance that secreted_by a zone of skin. OBOL:automatic skin fluid/secretion MA:0002537 A portion of organism substance that is secreted by a male reproductive gland. EMAPA:36541 MA:0002521 male reproductive system fluid/secretion uberon male reproductive system fluid male reproductive system secretion UBERON:0006536 male reproductive gland secretion A portion of organism substance that is secreted by a male reproductive gland. UBERON:cjm male reproductive system fluid/secretion MA:0002521 A portion of organism substance that is secreted by a female reproductive gland. MA:0002510 female reproductive system fluid/secretion uberon female reproductive system fluid female reproductive system secretion UBERON:0006537 female reproductive gland secretion A portion of organism substance that is secreted by a female reproductive gland. UBERON:cjm female reproductive system fluid/secretion MA:0002510 A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 uberon respiratory system fluid respiratory system secretion UBERON:0006538 respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. OBOL:automatic UMLS:C1514899 ncithesaurus:Respiratory_System_Fluid_or_Secretion A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. EMAPA:36538 MA:0002505 uberon lactiferous gland fluid lactiferous gland secretion mammary gland fluid mammary gland secreted fluid mammary gland secretion secretion of mammary gland UBERON:0006539 mammary gland fluid/secretion A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. http://orcid.org/0000-0002-6601-2165 A vasculature that is part of a kidney. EMAPA:28457 TAO:0005305 ZFA:0005305 uberon UBERON:0006544 kidney vasculature A vasculature that is part of a kidney. OBOL:automatic A tube in the kidney that collect and transport urine. in ZFA this is defined as part of mesonephros TAO:0005289 ZFA:0005289 uberon UBERON:0006553 renal duct A tube in the kidney that collect and transport urine. ZFIN:ZDB-PUB-071029-9 in ZFA this is defined as part of mesonephros ZFA A tube that is part of a excretory system. uberon UBERON:0006555 excretory tube A tube that is part of a excretory system. OBOL:automatic An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. consider merging with lymph vasculature Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] lymporeticular in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system AAO:0010522 CALOHA:TS-2024 EFO:0000870 EMAPA:18248 FMA:7162 MA:0002961 MESH:D008208 SCTID:362597000 VHOG:0001761 Wikipedia:Lymphatic_system lymphatic system lymphatic tree system uberon lymporeticular system UBERON:0006558 lymphatic part of lymphoid system AAO FMA MA An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. http://orcid.org/0000-0002-6601-2165 Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] 2012-06-20 AAO:0010522 AAO AAO:BJB in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system FMA lymphatic system FMA:7162 MA:0002435 lymphatic tree system FMA:7162 lymporeticular system VHOG:0001761 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. currently this is an extremely generic class, encompassing both protostomes and deuterostomes. 2023-04-20 branchial pharyngeal MAT:0000049 MESH:D010614 MIAA:0000049 uberon anterior part of foregut pharyngeal tube UBERON:0006562 pharynx The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. GO:0060465 Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]. FMA:85030 uberon UBERON:0006563 tunica media of pulmonary trunk Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]. FMA:85030 FMA:FMA A urethral meatus that is part of a female urethra[Automatically generated definition]. The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. EMAPA:36453 FMA:85266 MA:0002639 SCTID:279479008 Wikipedia:External_urethral_orifice_(female) external orifice of female urethra external urethral orifice (female) female urethral meatus ostium urethrae externum (urethra feminina) urethral meatus of clitoral urethra uberon distal urethral opening of female urethral opening of clitoral urethra UBERON:0006565 female urethral meatus A urethral meatus that is part of a female urethra[Automatically generated definition]. OBOL:automatic Wikipedia:External_urethral_orifice_(female) The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. Wikipedia:External_urethral_orifice_(female) external orifice of female urethra FMA:85266 external urethral orifice (female) FMA:85266 female urethral meatus FMA:85266 ostium urethrae externum (urethra feminina) FMA:85266 FMA:TA urethral meatus of clitoral urethra EMAPA:36453 distal urethral opening of female EMAPA:36453 urethral opening of clitoral urethra EMAPA:36453 A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. EMAPA:17339 FMA:9558 MA:0002983 SCTID:362021000 left ventricular myocardium myocardium of left ventricle uberon UBERON:0006566 left ventricle myocardium A myocardium that is part of a left ventricle of a heart. http://orcid.org/0000-0002-6601-2165 Myocardium of ventricle which is continuous with the tunica media of aorta. FMA:9558 left ventricular myocardium FMA:9558 myocardium of left ventricle FMA:9558 A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. EMAPA:17342 FMA:9535 MA:0002984 SCTID:362020004 myocardium of right ventricle right ventricular myocardium uberon UBERON:0006567 right ventricle myocardium A myocardium that is part of a right ventricle of a heart. http://orcid.org/0000-0002-6601-2165 Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. FMA:9535 myocardium of right ventricle FMA:9535 right ventricular myocardium FMA:9535 A nucleus of brain that is part of a hypothalamus. BTO:0002449 EMAPA:35417 FMA:258762 MA:0002426 SCTID:279304003 nucleus of hypothalamus uberon UBERON:0006568 hypothalamic nucleus A nucleus of brain that is part of a hypothalamus. OBOL:automatic nucleus of hypothalamus FMA:258762 A nucleus of brain that is part of a diencephalon. TAO:0002191 ZFA:0001659 uberon UBERON:0006569 diencephalic nucleus A nucleus of brain that is part of a diencephalon. OBOL:automatic The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:. FMA also has FMA:29321 but it's not clear how this differs EMAPA:19159 FMA:75383 NCIT:C34245 SCTID:245445008 UMLS:C0821671 Wikipedia:Pectinate_line linea pectinata canalis analis pectinate line of anal canal uberon Hilton's 'white line' dentate line linea anocutanea recto-anal junction site of anal membrane UBERON:0006574 pectinate line http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:. Wikipedia:Pectinate_line FMA also has FMA:29321 but it's not clear how this differs FMA UMLS:C0821671 ncithesaurus:Pectinate_Line linea pectinata canalis analis FMA:75383 FMA:TA pectinate line of anal canal FMA:75383 Hilton's 'white line' EMAPA:19159 dentate line Wikipedia:Pectinate_line linea anocutanea Wikipedia:Pectinate_line recto-anal junction Wikipedia:Pectinate_line site of anal membrane EMAPA:19159 An organ that is part of a vestibular system. BIRNLEX:2519 UMLS:C0682674 balance organ uberon UBERON:0006585 vestibular organ NIFSTD An organ that is part of a vestibular system. OBOL:automatic UMLS:C0682674 BIRNLEX:2519 balance organ https://orcid.org/0000-0002-6601-2165 Presumptive structure of the blastula that will develop into endoderm. AAO:0000471 EFO:0003437 TAO:0000416 ZFA:0000416 uberon UBERON:0006595 presumptive endoderm Presumptive structure of the blastula that will develop into endoderm. http://orcid.org/0000-0002-6601-2165 AAO:0000468 EFO:0003439 TAO:0000568 ZFA:0000568 future blood uberon UBERON:0006596 presumptive blood Portion of embryonic tissue determined by fate mapping to become a structure. Consider merging with anlage AAO:0000479 TAO:0001116 ZFA:0001116 future structure presumptive structures uberon UBERON:0006598 presumptive structure Portion of embryonic tissue determined by fate mapping to become a structure. GOC:CVS GOC:YMB ZFA:0001116 presumptive structures ZFA:0001116 Presumptive structure of the blastula that will develop into ectoderm. AAO:0000470 EFO:0003466 TAO:0001376 XAO:0004132 ZFA:0001376 uberon presumptive epidermis UBERON:0006601 presumptive ectoderm Presumptive structure of the blastula that will develop into ectoderm. http://orcid.org/0000-0002-6601-2165 presumptive epidermis ZFA:0001376 Presumptive structure of the blastula that will develop into mesoderm. AAO:0000476 EFO:0003467 TAO:0001377 ZFA:0001377 uberon UBERON:0006603 presumptive mesoderm Presumptive structure of the blastula that will develop into mesoderm. http://orcid.org/0000-0002-6601-2165 2 A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]. this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO] in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible AAO:0000277 FMA:75779 MA:0001490 TAO:0001851 Wikipedia:Symphysis_menti ZFA:0005488 dentary symphysis inter-dentary joint inter-mandibular joint symphysis menti uberon mental symphysis symphysis mandibulae UBERON:0006606 mandibular symphysis http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png FMA connects adjacent mandibles A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]. TAO:wd Wikipedia:Symphysis_menti ZFA:0005488 Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO] 2012-08-14 TAO:0001851 TAO TAO:wd in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible ISBN:0073040584 dentary symphysis TAO:0001851 inter-dentary joint TAO:0001851 inter-mandibular joint TAO:0001851 symphysis menti MA:0001490 mental symphysis Wikipedia:Symphysis_menti symphysis mandibulae Wikipedia:Symphysis_menti Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans. not to be confused with dermal skeleton exoskeletal BTO:0004659 Wikipedia:Exoskeleton lorica uberon shell UBERON:0006611 exoskeleton Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans. Wikipedia:Exoskeleton lorica Wikipedia:Lorica_(biology) shell BTO:0004659 A large vein or channel for the circulation of venous blood. check if it is valid to group ZFA class here. MA:0000070 NCIT:C12877 SCTID:341586007 UMLS:C0226504 ZFA:0007072 uberon blood sinus UBERON:0006615 venous sinus A large vein or channel for the circulation of venous blood. http://medical-dictionary.thefreedictionary.com/venous+sinus UMLS:C0226504 ncithesaurus:Venous_Sinus blood sinus ZFA:0007072 An external ear that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right auricular region EMAPA:37361 FMA:53643 SCTID:368567003 uberon UBERON:0006616 right external ear An external ear that is in the right side of a multicellular organism. OBOL:automatic right auricular region FMA:53643 EMAPA:37361 MA:th An external ear that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left auricular region EMAPA:37360 FMA:53644 SCTID:368589004 uberon UBERON:0006617 left external ear An external ear that is in the left side of a multicellular organism. OBOL:automatic left auricular region FMA:53644 EMAPA:37360 MA:th An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic. EMAPA:19215 FMA:10645 SCTID:244242003 Wikipedia:Musculophrenic_artery musculophrenic artery uberon UBERON:0006632 musculo-phrenic artery An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic. http://medical-dictionary.thefreedictionary.com/musculophrenic+artery musculophrenic artery FMA:10645 A muscle layer that is part of a fallopian tube. EMAPA:29046 FMA:18318 SCTID:259488000 muscle layer of fallopian tube muscle layer of oviduct muscle layer of uterine tube muscular coat of uterine tube muscular layer of uterine tube muscularis of uterine tube tunica muscularis (Tuba uterina) tunica muscularis tubae uterinae uterine tubal muscularis uberon UBERON:0006642 muscle layer of oviduct A muscle layer that is part of a fallopian tube. OBOL:automatic muscle layer of fallopian tube FMA:18318 muscle layer of oviduct FMA:18318 muscle layer of uterine tube FMA:18318 muscular coat of uterine tube FMA:18318 muscular layer of uterine tube FMA:18318 muscularis of uterine tube FMA:18318 tunica muscularis (Tuba uterina) FMA:18318 tunica muscularis tubae uterinae FMA:18318 FMA:TA uterine tubal muscularis FMA:18318 An adventitia that is part of a epididymis. EMAPA:30443 FMA:19136 epididymis adventitia uberon UBERON:0006645 adventitia of epididymis An adventitia that is part of a epididymis. OBOL:automatic epididymis adventitia FMA:19136 A muscle layer that is part of a epididymis. EMAPA:30747 FMA:19149 uberon UBERON:0006646 muscle layer of epididymis A muscle layer that is part of a epididymis. OBOL:automatic An adventitia that is part of a vas deferens. EMAPA:29767 FMA:19238 SCTID:299803005 adventitia of deferent duct adventitia of ductus deferens adventitia of vas deferens deferent ductal adventitia tunica adventitia (ductus deferens) tunica adventitia ductus deferentis uberon UBERON:0006647 adventitia of ductus deferens An adventitia that is part of a vas deferens. OBOL:automatic adventitia of deferent duct FMA:19238 adventitia of ductus deferens FMA:19238 adventitia of vas deferens FMA:19238 deferent ductal adventitia FMA:19238 tunica adventitia (ductus deferens) FMA:19238 tunica adventitia ductus deferentis FMA:19238 FMA:TA An adventitia that is part of a seminal vesicle. EMAPA:29775 FMA:19403 SCTID:252406002 adventitia of seminal gland seminal vesicle adventitia tunica adventitia (vesicula seminalis) tunica adventitia glandulae vesiculosae uberon UBERON:0006648 adventitia of seminal vesicle An adventitia that is part of a seminal vesicle. OBOL:automatic adventitia of seminal gland FMA:19403 seminal vesicle adventitia FMA:19403 tunica adventitia (vesicula seminalis) FMA:19403 tunica adventitia glandulae vesiculosae FMA:19403 FMA:TA EMAPA:30997 FMA:19976 SCTID:253069005 muscular coat of vagina tunica muscularis vaginae vaginal muscularis uberon UBERON:0006652 muscular layer of vagina muscular coat of vagina FMA:19976 tunica muscularis vaginae FMA:19976 FMA:TA Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]. BTO:0003117 EMAPA:19170 EMAPA:30829 FMA:19999 NCIT:C32681 SCTID:362241002 UMLS:C0227769 Wikipedia:Clitoral_glans clitoris glans glans of clitoris uberon glans clitoridis glans clitoris UBERON:0006653 glans clitoris http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif cjm Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]. BTO:0003117 Wikipedia:Clitoral_glans UMLS:C0227769 ncithesaurus:Glans_Clitoris clitoris glans FMA:19999 glans of clitoris FMA:19999 glans clitoridis Wikipedia:Clitoral_glans glans clitoris Wikipedia:Clitoral_glans Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure. Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO] relationship loss: part_of scapular area (AAO:0000935)[AAO] The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself AAO:0000749 EMAPA:25122 FMA:23275 MESH:D061165 NCIT:C32682 SCTID:181914008 UMLS:C1261046 Wikipedia:Glenoid_cavity cavitas glenoidalis scapulae cavitus glenoidalis glenoid cavity glenoid cavity of scapula glenoid facet uberon cavitas glenoidalis glenoid cavity UBERON:0006657 glenoid fossa http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png to be revised after scapulocoracoid fixes Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure. PHENOSCAPE:ad Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO] 2012-06-20 AAO:0000749 AAO AAO:LAP relationship loss: part_of scapular area (AAO:0000935)[AAO] 2012-06-20 AAO:0000749 AAO The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans ad FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself FMA MESH:D061165 https://github.com/biopragmatics/biomappings UMLS:C1261046 ncithesaurus:Glenoid_Fossa cavitas glenoidalis scapulae FMA:23275 FMA:TA cavitus glenoidalis FMA:23275 glenoid cavity FMA:23275 glenoid cavity of scapula FMA:23275 cavitas glenoidalis Wikipedia:Glenoid_cavity glenoid cavity AAO:0000749 2 A joint that connects one phalanx to another along a proximodistal axis. Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]. EMAPA:37884 FMA:42765 NCIT:C101527 galen:InterphalangealJoint inter-phalangeal joint inter-phalanx joint uberon UBERON:0006658 interphalangeal joint cjm two phalanges in series A joint that connects one phalanx to another along a proximodistal axis. http://orcid.org/0000-0002-6601-2165 Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]. ncithesaurus:Interphalangeal_Joint EMAPA:37884 MA:th inter-phalangeal joint FMA:42765 A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies) An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle. BTO:0004838 SCTID:86915006 UMLS:C0225358 Wikipedia:Muscular_layer muscular layer muscularis layer tunica muscularis uberon muscular coat muscularis muscularis externa muscularis propria transverse muscular fibers tunica externa tunica muscularis UBERON:0006660 muscular coat A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. Wikipedia:Muscular_layer An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. BTO:0004838 UMLS:C0225358 ncithesaurus:Muscle_Layer muscular layer OBOL:automatic muscularis layer FMA:45634 tunica muscularis BTO:0004838 muscular coat Wikipedia:Muscularis_externa muscularis externa BTO:0004838 muscularis propria Wikipedia:Muscularis_externa transverse muscular fibers Wikipedia:Muscularis_externa tunica externa BTO:0004838 tunica muscularis Wikipedia:Muscularis_externa On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. EMAPA:18707 FMA:55805 Wikipedia:Carotid_canal uberon canalis caroticus UBERON:0006668 carotid canal http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. Wikipedia:Carotid_canal canalis caroticus Wikipedia:Carotid_canal The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] EMAPA:17702 FMA:58279 NCIT:C34119 SCTID:244943002 UMLS:C0230162 VHOG:0001399 Wikipedia:Central_tendon_of_diaphragm central tendon centrum tendineum centrum tendineum diaphragmatis uberon UBERON:0006670 central tendon of diaphragm VHOG definitional The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers. MGI:csmith MP:0012061 In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] 2012-09-17 VHOG:0001399 VHOG DOI:10.1016/j.resp.2006.06.003 http://bgee.unil.ch/ UMLS:C0230162 ncithesaurus:Central_Tendon_of_the_Diaphragm central tendon FMA:58279 centrum tendineum FMA:58279 centrum tendineum diaphragmatis FMA:58279 FMA:TA A valve that is part of a vein. FMA:68095 MESH:D055422 valve of vein uberon UBERON:0006675 venous valve A valve that is part of a vein. OBOL:automatic MESH:D055422 https://github.com/biopragmatics/biomappings valve of vein FMA:68095 An anatomical boundary that adjacent_to a epithelium. FMA:70997 epithelium surface uberon UBERON:0006677 surface of epithelium An anatomical boundary that adjacent_to a epithelium. OBOL:automatic epithelium surface FMA:70997 The hypoglossal canal is a bony canal in the occipital bone of the skull. EMAPA:19012 FMA:75370 SCTID:139380001 Wikipedia:Hypoglossal_canal uberon anterior condylar canal canalis nervi hypoglossi hyperglossal canal UBERON:0006682 hypoglossal canal The hypoglossal canal is a bony canal in the occipital bone of the skull. Wikipedia:Hypoglossal_canal anterior condylar canal EMAPA:19012 canalis nervi hypoglossi Wikipedia:Hypoglossal_canal hyperglossal canal Wikipedia:Hypoglossal_canal A vein that is part of a vertebral column. EMAPA:18255 FMA:76735 MA:0002108 SCTID:181376008 Wikipedia:Spinal_veins vena spinalis uberon spinal branch UBERON:0006686 spinal vein A vein that is part of a vertebral column. OBOL:automatic vena spinalis FMA:76735 FMA:TA spinal branch FMA:76735 A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. TODO - check neural vs vertebral canal; embryonic vs adult? Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] AAO:0000693 FMA:9680 GAID:242 MESH:D013115 NCIT:C33869 NCIT:C34221 SCTID:361746009 UMLS:C0037922 UMLS:C1522467 Wikipedia:Spinal_canal uberon c. vertebralis foramen vertebrale neural canal spinal canal spinal cavity vertebral canal UBERON:0006692 vertebral canal http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. Wikipedia:Spinal_canal http://orcid.org/0000-0002-6601-2165 Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] 2012-06-20 AAO:0000693 AAO AAO:LAP MESH:D013115 https://github.com/biopragmatics/biomappings UMLS:C0037922 ncithesaurus:Vertebral_Canal UMLS:C1522467 ncithesaurus:Neural_Canal c. vertebralis Wikipedia:Spinal_canal foramen vertebrale AAO:0000693 neural canal AAO:0000693 spinal canal AAO:0000693 spinal cavity Wikipedia:Spinal_canal vertebral canal Wikipedia:Spinal_canal A vasculature that is part of a cerebellum. FMA:268519 uberon UBERON:0006694 cerebellum vasculature A vasculature that is part of a cerebellum. OBOL:automatic The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus). Naming conventions for pod terms under discussion within phenoscape group Wikipedia:Carpus_and_tarsus_of_land_vertebrates carpus/tarsus mesopodial limb segment mesopodial segment uberon mesopod UBERON:0006716 mesopodium region MA:th The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus). MA:th Wikipedia:Carpus_and_tarsus_of_land_vertebrates https://orcid.org/0000-0002-6601-2165 mesopodial limb segment MA:th The collection of all skeletal elements in an autopodium region. Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO] Naming conventions for pod terms under discussion within phenoscape group VSAO:0005019 autopod skeleton autopodial skeleton skeletal parts of autopod skeleton of autopod uberon autopodium UBERON:0006717 autopodial skeleton The collection of all skeletal elements in an autopodium region. https://orcid.org/0000-0002-6601-2165 Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO] 2012-08-14 VSAO:0005019 VSAO VSAO:NI autopod skeleton https://orcid.org/0000-0002-6601-2165 autopodial skeleton VSAO:0005019 skeletal parts of autopod https://orcid.org/0000-0002-6601-2165 skeleton of autopod https://orcid.org/0000-0002-6601-2165 autopodium VSAO:0005019 VSAO:NI During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] EHDAA2:0001081 EMAPA:17187 FMA:312476 SCTID:308821003 VHOG:0000730 Wikipedia:Tuberculum_impar median lingual swelling median tongue bud tuberculum impar tuberculum linguale mediale uberon UBERON:0006756 The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview] median lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png EHDAA2 During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. Wikipedia:Tuberculum_impar Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000730 VHOG DOI:10.1046/j.1469-7580.2002.00073.x http://bgee.unil.ch/ median lingual swelling EHDAA2:0001081 median tongue bud http://emedicine.medscape.com/article/845125-overview tuberculum linguale mediale Wikipedia:Tuberculum_impar During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] paired EHDAA2:0000911 EMAPA:17189 FMA:313628 VHOG:0000731 Wikipedia:Lateral_lingual_swelling uberon lateral lingual prominence lateral swellings tuberculum laterale tuberculum linguale laterale UBERON:0006757 lateral lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. Wikipedia:Lateral_lingual_swelling Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000731 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) http://bgee.unil.ch/ lateral swellings Wikipedia:Lateral_lingual_swelling tuberculum laterale Wikipedia:Lateral_lingual_swelling tuberculum linguale laterale Wikipedia:Lateral_lingual_swelling The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm. EFO:0001403 EMAPA:37835 FMA:58342 GAID:896 MESH:D016850 SCTID:63716004 Wikipedia:Corneal_limbus ZFA:0005570 cornea limbus corneal limbus corneal-scleral limbus corneoscleral junction limbus corneae sclerocorneal junction sclerocorneal limbus uberon limbus corneae UBERON:0006761 This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 corneo-scleral junction http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm. MP:0013477 EMAPA:37835 MA:th corneal limbus FMA:58342 GAID:896 corneal-scleral limbus PMID:17051547 corneoscleral junction GAID:896 limbus corneae Wikipedia:Corneal_limbus sclerocorneal junction FMA:58342 sclerocorneal limbus GAID:896 limbus corneae Wikipedia:Corneal_limbus The hemispheric articular surface at the upper extremity of the thigh bone[Stedman, 26th ed]. The femur head is the highest part of the thigh bone. It is supported by the neck of the femur. The head is globular and forms rather more than a hemisphere, is directed upward, medialward, and a little forward, the greater part of its convexity being above and in front. Its surface is smooth, coated with cartilage in the fresh state, except over an ovoid depression, the fovea capitis femoris, which is situated a little below and behind the center of the head, and gives attachment to the ligament of head of femur. If there is a fracture of the neck of the femur, the blood supply through the ligament becomes crucial. In orthopedic surgery, the head of the femur is important because it can undergo avascular necrosis and consequent osteochondritis dissecans. The head is removed in total hip replacement surgery [WP]. Proximal head of the femur, which articulates with the acetabulum.[AAO] AAO:0000892 EMAPA:37541 FMA:32851 MA:0003050 MESH:D005270 NCIT:C32718 SCTID:361791000 UMLS:C0015813 Wikipedia:Femur_head galen:FemoralHead acetabular head femoral head kopf des Schenkelbeins uberon capital femoral epiphysis caput femoris femur head UBERON:0006767 head of femur http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png The hemispheric articular surface at the upper extremity of the thigh bone[Stedman, 26th ed]. The femur head is the highest part of the thigh bone. It is supported by the neck of the femur. The head is globular and forms rather more than a hemisphere, is directed upward, medialward, and a little forward, the greater part of its convexity being above and in front. Its surface is smooth, coated with cartilage in the fresh state, except over an ovoid depression, the fovea capitis femoris, which is situated a little below and behind the center of the head, and gives attachment to the ligament of head of femur. If there is a fracture of the neck of the femur, the blood supply through the ligament becomes crucial. In orthopedic surgery, the head of the femur is important because it can undergo avascular necrosis and consequent osteochondritis dissecans. The head is removed in total hip replacement surgery [WP]. MESH:A02.835.232.500.247.343 Wikipedia:Femur_head Proximal head of the femur, which articulates with the acetabulum.[AAO] 2012-06-20 AAO:0000892 AAO AAO:LAP EMAPA:37541 MA:th UMLS:C0015813 ncithesaurus:Head_of_the_Femur acetabular head AAO:0000892 femoral head FMA:32851 kopf des Schenkelbeins FMA:32851 FMA:TA capital femoral epiphysis http://medical-dictionary.thefreedictionary.com/capital+femoral+epiphysis caput femoris AAO:0000892 Wikipedia:Femur_head femur head MESH:A02.835.232.500.247.343 An epithelium that is composed primarily of secretory cells. consider splitting epithelium from epithelial tissue BTO:0002991 NCIT:C43370 NCIT:C45715 UMLS:C0682578 UMLS:C1708242 uberon UBERON:0006799 glandular epithelium An epithelium that is composed primarily of secretory cells. http://orcid.org/0000-0002-6601-2165 UMLS:C0682578 ncithesaurus:Glandular_Epithelium UMLS:C1708242 ncithesaurus:Glandular_Epithelial_Tissue Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 FMA:60116 SCTID:281486007 skeleton of nose uberon UBERON:0006813 nasal skeleton FMA FMA facial series Kardong-abduced Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 skeleton of nose FMA:60116 Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] cushions body organs AAO:0000027 FMA:63897 SCTID:68477002 loose areolar connective tissue uberon areolar tissue loose connective tissue UBERON:0006815 areolar connective tissue FMA FMA Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. FMA:63897 Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] 2012-06-20 AAO:0000027 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000027 AAO cushions body organs AAO loose areolar connective tissue FMA:63897 loose connective tissue AAO:0000027 An anatomical space that surrounded_by a trachea. FMA:7469 SCTID:197486000 lumen of cartilaginous trachea tracheal lumen uberon UBERON:0006833 lumen of trachea An anatomical space that surrounded_by a trachea. OBOL:automatic lumen of cartilaginous trachea OBOL:automatic tracheal lumen FMA:7469 A subdivision of a the reproductive tract in a female organism that is the site of embryo development. uterus FBbt:00004924 TADS:0000421 WBbt:0006760 uberon UBERON:0006834 uterus or analog A subdivision of a the reproductive tract in a female organism that is the site of embryo development. http://orcid.org/0000-0002-6601-2165 uterus FBbt:00004924 FBbt:00004924 Vein that is central to a lobule in the liver. central vein FMA:17544 NCIT:C32281 SCTID:272023004 TAO:0005168 Wikipedia:Central_veins_of_liver ZFA:0005168 terminal branch of hepatic vein terminal hepatic venule vena centralis (hepar) uberon UBERON:0006841 central vein of liver Vein that is central to a lobule in the liver. ZFA:0005168 central vein ZFA:0005168 terminal branch of hepatic vein FMA:17544 terminal hepatic venule FMA:17544 vena centralis (hepar) FMA:17544 A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 uberon groove UBERON:0006846 Surface groove is modelled as immaterial - see https://github.com/obophenotype/uberon/issues/2667 for discussion surface groove https://github.com/obophenotype/uberon/issues/2667 A furrow or an incomplete tube. AEO:0000161 AEO:JB https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/4 groove AEO:0000161 Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage. Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583]. Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO] relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO] relationship loss: part_of scapular area (AAO:0000935)[AAO] scapular present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals. chick scapula is of dual origin and segmentally organized UBERON:0001124 UBERON:0010904 AAO:0000751 BTO:0001218 CALOHA:TS-0897 EFO:0001400 EMAPA:18722 FMA:13394 GAID:186 MA:0001330 MESH:D012540 NCIT:C12783 SCTID:302517007 TAO:0000583 UMLS:C0036277 VHOG:0001398 VSAO:0000157 Wikipedia:Scapula ZFA:0000583 galen:Scapula scapulae shoulder blade uberon scapula bone scapulas UBERON:0006849 scapula https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg ZFA definitional Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage. VSAO:0000157 https://github.com/obophenotype/uberon/issues/204 https://github.com/obophenotype/uberon/issues/339 Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583]. TAO:0000583 Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO] 2012-06-20 AAO:0000751 AAO AAO:LAP relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO] 2012-06-20 AAO:0000751 AAO relationship loss: part_of scapular area (AAO:0000935)[AAO] 2012-06-20 AAO:0000751 AAO present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals. ISBN:978-0-12-319060-4 UMLS:C0036277 ncithesaurus:Scapula scapulae ZFA:0000583 scapula bone BTO:0001218 scapulas TAO:0000583 A muscular coat that is part of a ureter. EMAPA:28811 FMA:15893 MA:0002654 SCTID:3563003 muscular coat of ureter muscular layer of ureter muscularis of ureter tunica muscularis (ureter) tunica muscularis ureteris uberon ureteral smooth muscle layer UBERON:0006855 muscular coat of ureter FMA A muscular coat that is part of a ureter. OBOL:automatic muscular coat of ureter FMA:15893 muscular layer of ureter FMA:15893 muscularis of ureter FMA:15893 tunica muscularis (ureter) FMA:TA tunica muscularis ureteris FMA:TA ureteral smooth muscle layer EMAPA:28567 This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]. keep this grouping class so long as it is required for GO All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] VHOG:0001141 adrenal gland - interrenal gland adrenal gland/interrenal tissue uberon adrenal - interrenal gland suprarenal gland - interrenal gland UBERON:0006858 adrenal/interrenal gland This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]. GO:0030325 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 http://bgee.unil.ch/ adrenal gland - interrenal gland VHOG:0001141 adrenal - interrenal gland VHOG:0001141 suprarenal gland - interrenal gland VHOG:0001141 Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these. The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate FMA:32688 MA:0002803 body proper of long bone shaft proper of long bone uberon long bone diaphysis UBERON:0006861 diaphysis proper Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these. https://orcid.org/0000-0002-6601-2165 The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate MA body proper of long bone FMA:32688 shaft proper of long bone FMA:32688 long bone diaphysis MA:0002803 A diaphysis that is part of a femur[Automatically generated definition]. The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur]. EMAPA:37538 FMA:32847 MA:0003055 NCIT:C96209 SCTID:182048009 Wikipedia:Body_of_femur body of femur corpus femoris femoral diaphysis femoral shaft shaft of femur uberon UBERON:0006862 diaphysis of femur http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png A diaphysis that is part of a femur[Automatically generated definition]. OBOL:automatic Wikipedia:Body_of_femur The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur]. Wikipedia:Body_of_femur EMAPA:37538 MA:th body of femur FMA:32847 corpus femoris FMA:32847 FMA:TA femoral diaphysis FMA:32847 shaft of femur FMA:32847 A proximal metaphysis that is part of a femur. FMA:32878 uberon UBERON:0006863 proximal metaphysis of femur A proximal metaphysis that is part of a femur. OBOL:automatic A metaphysis that is part of a femur. EMAPA:37540 FMA:32875 MA:0003052 femoral metaphysis uberon UBERON:0006865 metaphysis of femur true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A metaphysis that is part of a femur. OBOL:automatic EMAPA:37540 MA:th femoral metaphysis FMA:32875 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. FBbt:00005756 WBbt:0005773 rectum uberon rectal part of digestive tract terminal section of digestive tract UBERON:0006866 terminal part of digestive tract The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. http://orcid.org/0000-0002-6601-2165 FBbt:00005756 rectum FBbt:00005756 A gland that secretes a seminal fluid. FBbt:00004958 WBbt:0006870 uberon UBERON:0006868 seminal fluid secreting gland A gland that secretes a seminal fluid. OBOL:automatic FBbt:00004958 The distal elements of the developing limb of vertebrates that will give rise to the pes (foot). EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER UBERON:0004343 foot plate footplate EHDAA:5143 EHDAA:6096 EMAPA:17249 FMA:296800 NCIT:C34177 UMLS:C1517291 uberon distal part of hindlimb bud foot disk UBERON:0006871 embryonic footplate The distal elements of the developing limb of vertebrates that will give rise to the pes (foot). MGI:csmith MP:0004576 UBERON:cjm https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2218 EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER EHDAA2 UMLS:C1517291 ncithesaurus:Foot_Plate distal part of hindlimb bud EMAPA:17249 An apical ectodermal ridge that is part of a handplate. EHDAA2:0000729 EMAPA:17247 uberon UBERON:0006872 handplate apical ectodermal ridge An apical ectodermal ridge that is part of a handplate. OBOL:automatic The distal elements of the developing limb of vertebrates that will give rise to the manus (hand). EHDAA:4194 EHDAA:6242 EMAPA:17245 FMA:296794 NCIT:C34185 UMLS:C1512334 hand plate handplate uberon distal part of forelimb bud UBERON:0006875 embryonic handplate The distal elements of the developing limb of vertebrates that will give rise to the manus (hand). MGI:csmith MP:0004576 UBERON:cjm UMLS:C1512334 ncithesaurus:Hand_Plate distal part of forelimb bud EMAPA:17245 A vasculature that is part of a organ. FMA:74612 organ vasculature set of blood vessels of organ uberon UBERON:0006876 vasculature of organ A vasculature that is part of a organ. OBOL:automatic organ vasculature FMA:74612 set of blood vessels of organ FMA:74612 A vasculature that is part of a liver. the EHDAA2 term and the FMA term may not be exact equivalents - check EHDAA2:0003454 EMAPA:35501 FMA:73748 hepatic vasculature uberon hepatic vascular element liver vascular element liver vascular system UBERON:0006877 vasculature of liver A vasculature that is part of a liver. OBOL:automatic the EHDAA2 term and the FMA term may not be exact equivalents - check EHDAA2 hepatic vasculature FMA:73748 hepatic vascular element EMAPA:35501 liver vascular element EMAPA:35501 liver vascular system EHDAA2:0003454 A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 EFO:0003337 EFO:0003603 EHDAA2:0001118 EHDAA:655 EMAPA:16099 EMAPA_RETIRED:16270 FMA:293859 TAO:0000998 VHOG:0000185 XAO:0000053 ZFA:0000998 head mesenchyme derived from mesoderm head mesenchyme from head mesoderm head mesenchyme from mesoderm mesenchyme derived from head mesoderm mesenchyme from head mesoderm uberon cranial mesoderm head mesoderm UBERON:0006904 head mesenchyme from mesoderm ZFA EHDAA2 XAO A head mesenchyme that develops_from a mesoderm. OBOL:automatic head mesenchyme from head mesoderm EHDAA2:0001118 mesenchyme derived from head mesoderm EHDAA:1057 cranial mesoderm UBERON:0005280 head mesoderm AAO:0011051 UBERON:0005280 Mesenchyme that is part of a mandibular prominence. EHDAA2:0001062 EHDAA:5861 EHDAA:5873 EMAPA:17357 mesenchyme of mandibular process mesenchyme of mandibular prominence uberon UBERON:0006905 mandibular process mesenchyme Mesenchyme that is part of a mandibular prominence. OBOL:automatic mesenchyme of mandibular process EMAPA:17357 mesenchyme of mandibular prominence https://orcid.org/0000-0002-6601-2165 The lateral surface parts of the external nose, inferiorly, surrounding the naris[EoM]. FMA:59519 SCTID:361345006 Wikipedia:Ala_of_nose nasal ala uberon ala nasi ala of the nose wing of nose wing of the nose wings of the nose UBERON:0006906 ala of nose http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png FMA-abduced-lr The lateral surface parts of the external nose, inferiorly, surrounding the naris[EoM]. DOI:10.1002/ajmg.a.32600 Wikipedia:Ala_of_nose nasal ala FMA:59519 ala nasi Wikipedia:Ala_of_nose ala of the nose Wikipedia:Ala_of_nose wing of nose Wikipedia:Ala_of_nose wing of the nose Wikipedia:Ala_of_nose wings of the nose Wikipedia:Ala_of_nose An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon UBERON:0006909 lumen of digestive tract An anatomical space that surrounded_by a digestive tract. OBOL:automatic digestive tract lumen https://orcid.org/0000-0002-6601-2165 gut cavity BTO:0000349 gut lumen FMA:45677 lumen of alimentary tract https://orcid.org/0000-0002-6601-2165 lumen of digestive tract https://orcid.org/0000-0002-6601-2165 lumen of gut FMA:45677 An epithelium that is part of a lip. The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] BTO:0004468 TAO:0005334 ZFA:0005334 uberon UBERON:0006913 lip epithelium An epithelium that is part of a lip. OBOL:automatic The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] 2012-08-14 TAO:0005334 TAO ZFIN:ZDB-PUB-060921-12 An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 UMLS:C0221909 Wikipedia:Squamous_epithelium uberon UBERON:0006914 squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium FBbt UMLS:C0221909 ncithesaurus:Squamous_Epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]. FMA:45563 NCIT:C13180 UMLS:C0836131 Wikipedia:Stratified_squamous_epithelium epithelium stratificatum squamosum uberon UBERON:0006915 stratified squamous epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]. FMA:45563 Wikipedia:Stratified_squamous_epithelium UMLS:C0836131 ncithesaurus:Stratified_Squamous_Epithelium epithelium stratificatum squamosum FMA:45563 A non-keratinized stratified squamous epithelium that is part of a tongue. FMA:62130 uberon UBERON:0006916 non-keratinized epithelium of tongue A non-keratinized stratified squamous epithelium that is part of a tongue. OBOL:automatic A squamous epithelium that is part of a tongue. this is a singleton subclass of tongue epithelium in MA MA:0002786 squamous epithelium of tongue uberon UBERON:0006919 tongue squamous epithelium A squamous epithelium that is part of a tongue. OBOL:automatic this is a singleton subclass of tongue epithelium in MA MA squamous epithelium of tongue OBOL:automatic A squamous epithelium that is part of a esophagus. MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass BTO:0003635 CALOHA:TS-1250 EMAPA:35324 MA:0001567 NCIT:C49222 UMLS:C1707950 uberon esophageal squamous epithelium squamous epithelium of esophagus squamous oesophageal epithelium UBERON:0006920 esophagus squamous epithelium A squamous epithelium that is part of a esophagus. OBOL:automatic MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass MA UMLS:C1707950 ncithesaurus:Esophageal_Squamous_Epithelium esophageal squamous epithelium OBOL:automatic squamous epithelium of esophagus OBOL:automatic squamous oesophageal epithelium MA:0001567 A squamous epithelium that is part of a stomach. EMAPA:35824 MA:0001611 uberon UBERON:0006921 stomach squamous epithelium A squamous epithelium that is part of a stomach. OBOL:automatic The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. MA:0001725 NCIT:C49219 UMLS:C1707351 cervical squamous epithelium uberon UBERON:0006922 cervix squamous epithelium The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx UMLS:C1707351 ncithesaurus:Cervix_Squamous_Epithelium A squamous epithelium that is part of a vagina. EMAPA:37794 MA:0001731 NCIT:C49314 UMLS:C1711259 vaginal squamous epithelium uberon UBERON:0006923 vagina squamous epithelium A squamous epithelium that is part of a vagina. OBOL:automatic EMAPA:37794 MA:th UMLS:C1711259 ncithesaurus:Vaginal_Squamous_Epithelium A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 epithelium of gastric gland uberon gastric gland epithelium UBERON:0006924 stomach glandular epithelium FMA A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. ISBN:0073040584 epithelium of gastric gland FMA:63458 gastric gland epithelium FMA:63458 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 uberon digestive gland UBERON:0006925 digestive system gland Any gland that is part of the digestive system. UBERON:cjm digestive gland BTO:0000345 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]. FMA:64800 NCIT:C13182 UMLS:C0225337 uberon UBERON:0006929 glandular columnar epithelium Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]. FMA:64800 UMLS:C0225337 ncithesaurus:Columnar_Epithelium FMA:66809 uberon UBERON:0006930 glandular cuboidal epithelium Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. EMAPA:27167 MA:0001614 stomach glandular region glandular mucous membrane uberon UBERON:0006931 stomach glandular region mucosa Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. http://orcid.org/0000-0002-6601-2165 stomach glandular region glandular mucous membrane EMAPA:27167 Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical CALOHA:TS-0682 FMA:62410 SCTID:309045006 uberon neuroepithelium UBERON:0006934 sensory epithelium Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. BTO:0000314 note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical FMA neuroepithelium BTO:0000314 The epithelial cells lining the capsule and trabeculae of the thymus. TODO - check whether this is part of the thymus or borders it MA:0000769 uberon UBERON:0006936 thymus subcapsular epithelium The epithelial cells lining the capsule and trabeculae of the thymus. ISBN:0-8153-1691-7 MGI:cwg MP:0002369 The epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals. EMAPA:32883 MA:0001189 uberon UBERON:0006937 inner ear epithelium The epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals. MGI:csmith MP:0003308 An epithelium that is part of a pinna. EHDAA2:0001470 EHDAA:8983 EMAPA:17592 VHOG:0000632 uberon UBERON:0006938 pinna surface epithelium An epithelium that is part of a pinna. OBOL:automatic The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis. Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO] There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis Check EMAPA AAO:0010532 EMAPA:18993 FMA:19081 MA:0000398 NCIT:C32492 UMLS:C0228013 Wikipedia:Efferent_ducts efferent ductule seminal duct uberon ductuli efferentes testis vasa efferentia UBERON:0006946 efferent duct http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg FMA The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis. Wikipedia:Efferent_ducts Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO] 2012-06-20 AAO:0010532 AAO AAO:BJB Check EMAPA EMAPA UMLS:C0228013 ncithesaurus:Efferent_Ductule efferent ductule FMA:19081 Wikipedia:Efferent_ducts ductuli efferentes testis Wikipedia:Efferent_ducts vasa efferentia AAO:0010532 Wikipedia:Efferent_ducts A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra. we use this as a generic grouping class for a number of taxa in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct UBERON:0010140 FMA:55678 TAO:0001268 ZFA:0001268 sperm duct sperm ducts uberon UBERON:0006947 male genital duct https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb FMA-abduced-lr A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra. https://orcid.org/0000-0002-6601-2165 in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct FMA sperm duct ZFA:0001268 sperm ducts TAO:0001268 An epithelium that is part of a efferent duct. EMAPA:29747 FMA:19195 MA:0001734 epithelium of efferent ductule of testis uberon UBERON:0006948 efferent duct epithelium An epithelium that is part of a efferent duct. OBOL:automatic epithelium of efferent ductule of testis FMA:19195 The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands. TODO - split off insect classes BTO:0002618 EMAPA:29786 uberon UBERON:0006953 ejaculatory duct epithelium The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands. PMID:1238970 An epithelium that is part of a uterus. BTO:0003082 uberon uterus epithelium UBERON:0006955 uterine epithelium An epithelium that is part of a uterus. OBOL:automatic uterus epithelium BTO:0003082 The inner lining of the cheeks and lips. BTO:0003833 CALOHA:TS-2349 FMA:59785 NCIT:C12505 SCTID:16811007 UMLS:C1578559 uberon UBERON:0006956 buccal mucosa The inner lining of the cheeks and lips. http://www.medterms.com/ UMLS:C1578559 ncithesaurus:Buccal_Mucosa An epithelium that is part of a submandibular gland primordium. EHDAA2:0001940 EHDAA:9257 EMAPA:17756 uberon submaxillary gland primordium epithelium UBERON:0006957 submandibular gland primordium epithelium An epithelium that is part of a submandibular gland primordium. OBOL:automatic submaxillary gland primordium epithelium EMAPA:17756 The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. CALOHA:TS-1246 EMAPA:28880 FMA:18626 MA:0002991 NCIT:C33638 SCTID:259306002 UMLS:C0737271 Wikipedia:Stroma_of_ovary interstitial tissue of ovary ovarian stroma ovary stroma stroma of the ovary stroma ovarica uberon stroma ovarii UBERON:0006960 ovary stroma FMA The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. Wikipedia:Stroma_of_ovary UMLS:C0737271 ncithesaurus:Stroma_of_the_Ovarian_Cortex interstitial tissue of ovary FMA:18626 ovarian stroma FMA:18626 ovary stroma MA:0002991 stroma of the ovary Wikipedia:Stroma_of_ovary stroma ovarica FMA:18626 stroma ovarii Wikipedia:Stroma_of_ovary The distal part of adenohypophysis: the part that makes up the main body of the gland. Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO] The anterior part of the adenohypophysis. [TFD][VHOG] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] DHP pars anterior AAO:0010542 BAMS:DHP BIRNLEX:1022 BTO:0001787 EHDAA2:0001416 EHDAA:7532 EMAPA:17515 FMA:74630 MA:0000854 TAO:0001195 UMLS:C0175322 VHOG:0000244 Wikipedia:Pars_distalis ZFA:0001195 neuronames:410 distal part of hypophysis pars anterior of adenohypophysis pars distalis (glandula pituitaria) pars distalis adenohypophysis pars distalis of anterior lobe of pituitary gland pars glandularis of adenohypophysis uberon anterior lobe distal part of the hypophysis pars distalis pars distalis (hypophysis) pars distalis adenohypophyseos pars distalis lobi anterioris hypophyseos pars glandularis UBERON:0006964 pars distalis of adenohypophysis EHDAA2 MA The distal part of adenohypophysis: the part that makes up the main body of the gland. Dorlands_Medical_Dictionary:MerckSource Wikipedia:Pars_distalis Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO] 2012-06-20 AAO:0010542 AAO AAO:BJB The anterior part of the adenohypophysis. [TFD][VHOG] 2012-09-17 VHOG:0000244 VHOG http://bgee.unil.ch/ http://www.thefreedictionary.com/pars+anterior It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000244 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 http://bgee.unil.ch/ DHP BIRNLEX:1022 NIFSTD:NeuroNames_abbrevSource pars anterior EHDAA2:0001416 MA:0000854 ZFA:0001195 UMLS:C0175322 BIRNLEX:1022 neuronames:410 BIRNLEX:1022 distal part of hypophysis BIRNLEX:1022 pars anterior of adenohypophysis FMA:74630 pars distalis (glandula pituitaria) FMA:74630 FMA:TA pars distalis adenohypophysis FMA:74630 FMA:TA pars distalis of anterior lobe of pituitary gland FMA:74630 pars glandularis of adenohypophysis FMA:74630 anterior lobe MA:0000854 distal part of the hypophysis NeuroNames:410 pars distalis MA:0000854 pars distalis (hypophysis) NeuroNames:410 pars distalis adenohypophyseos BTO:0001787 pars distalis lobi anterioris hypophyseos BTO:0001787 pars glandularis MA:0000854 The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. EFO:0003709 TAO:0005077 ZFA:0005077 uberon UBERON:0006965 vascular cord The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. GO:0072360 ZFA:0005077 A capillary that is part of the coronary system. ZFA:0005813 heart capillary uberon UBERON:0006966 coronary capillary A capillary that is part of the coronary system. http://orcid.org/0000-0002-6601-2165 heart capillary GO:0003248 Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface. AAO:0010266 AEO:0000009 BILA:0000009 CARO:0000009 EHDAA2:0003009 FMA:9658 TAO:0001839 uberon UBERON:0006983 anatomical point Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface. FMA:9658 http://orcid.org/0000-0001-9114-8737 A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n. BILA:0000010 CARO:0001002 EHDAA2_RETIRED:0003192 FMA:24137 NCIT:C34022 UMLS:C1515977 uberon UBERON:0006984 Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface via morphological boundary in CARO A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n. CARO:0001002 UMLS:C1515977 ncithesaurus:Anatomic_Surface The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 SCTID:360387000 VHOG:0001641 XAO:0000235 cardiogenic splanchnopleure uberon cardiac mesoderm cardiogenic mesoderm cardiogenic region heart primordia UBERON:0007005 cardiogenic splanchnic mesoderm The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. XAO:0000235 http://www.drugs.com/dict/cardiogenic-mesoderm.html https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7 cardiogenic splanchnopleure EHDAA2:0000214 cardiac mesoderm XAO:0000235 cardiogenic mesoderm http://www.drugs.com/dict/cardiogenic-mesoderm.html cardiogenic region http://orcid.org/0000-0002-6601-2165 heart primordia XAO:0000235 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo Organism at the cleavage stage. OBOL:automatic A multicellular organism that is at the juvenile stage. Whole organism that is not fully grown or sexually mature.[TAO] juvenile BILA:0000076 TAO:0002047 http://neurolex.org/wiki/Category:Juvenile_organism juvenile organism juveniles uberon UBERON:0007021 sexually immature organism A multicellular organism that is at the juvenile stage. OBOL:automatic Whole organism that is not fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002047 TAO TAO:wd juvenile organism BILA:0000076 juveniles TAO:0002047 A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. Whole organism that is fully grown or sexually mature.[TAO] adult BILA:0000078 FBbt:00003004 HAO:0000087 NCIT:C17600 TAO:0002046 UMLS:C0001675 galen:Adult http://neurolex.org/wiki/Category:Adult_organism adults uberon UBERON:0007023 adult organism A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. OBOL:automatic Whole organism that is fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002046 TAO TAO:wd FBbt:00003004 UMLS:C0001675 ncithesaurus:Adult adults TAO:0002046 The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 UMLS:C1514442 future digestive tract future digestive tube future gut primitive gut uberon embryonic digestive tube primordial digestive tube primordial gut UBERON:0007026 presumptive gut The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis NCBIBook:NBK10107 UMLS:C1514442 ncithesaurus:Primordial_Gut BILA:0000142 uberon UBERON:0007037 mechanosensory system Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 ZFA:0007064 uberon UBERON:0007098 mandibular neural crest ZFA ZFA Cranial neural crest that migrates into the mandibular arch. ZFA:0007064 Cranial neural crest that migrates into the hyoid arch. TAO:0007065 XAO:0000025 ZFA:0007065 hyoid crest uberon UBERON:0007099 hyoid neural crest ZFA ZFA Cranial neural crest that migrates into the hyoid arch. ZFA:0007065 hyoid crest XAO:0000025 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ GO uses blood circulation generically to include the haemolymphatic fluid of arthropods A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. GO:0007507 dorsal tube Wikipedia:Heart heart GO:0007507 adult heart FBbt:00003154 One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present. BTO:0001161 EHDAA2:0004717 MESH:D002824 NCIT:C34125 SCTID:360403003 UMLS:C0008508 Wikipedia:Chorionic_villi uberon chorionic villi chorionic villous chorionic villus embryonic part of placenta embryonic placenta fetal part of placenta fetal placenta placental villi placental villous placental villus villous chorion villous of placenta UBERON:0007106 chorionic villus http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png BTO MP-def One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. BTO:0001161 Wikipedia:Chorionic_villi UMLS:C0008508 ncithesaurus:Chorionic_Villus chorionic villi MESH:A16.254.403.473.200 chorionic villous Wikipedia:Chorionic_villi chorionic villus GAID:1300 embryonic part of placenta http://orcid.org/0000-0002-6601-2165 embryonic placenta http://orcid.org/0000-0002-6601-2165 fetal part of placenta http://orcid.org/0000-0002-6601-2165 fetal placenta http://orcid.org/0000-0002-6601-2165 placental villi GAID:1300 placental villus GAID:1300 The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward. FMA:42385 GAID:201 MESH:D005272 NCIT:C61563 SCTID:361792007 UMLS:C0015815 Wikipedia:Femur_neck galen:NeckOfFemur femoral neck uberon collum femoris femur neck neck of the femur UBERON:0007119 neck of femur http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward. Wikipedia:Femur_neck UMLS:C0015815 ncithesaurus:Femoral_Neck femoral neck FMA:42385 collum femoris Wikipedia:Femur_neck femur neck Wikipedia:Femur_neck neck of the femur Wikipedia:Femur_neck A pharyngeal pouch that is between pharyngeal arches 1 and 2. . [][VHOG] In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery we use adjacency relations rather than part_of, as in EHDAA2. UBERON:0005718 AAO:0011114 EFO:0003631 EHDAA2:0000016 EMAPA:16124 EMAPA:16125 FMA:295668 NCIT:C34176 SCTID:345248006 TAO:0001128 UMLS:C0231068 VHOG:0000555 VHOG:0000970 Wikipedia:Pharyngeal_pouch_(embryology)#First_pouch XAO:0000102 ZFA:0001128 1st arch branchial pouch 1st arch branchial pouch endoderm 1st arch pouch endoderm 1st branchial pouch 1st pharyngeal pouch endoderm first arch pharyngeal pouch first visceral pouch hyomandibular pouch pharyngeal pouches 1 visceral pouch 1 uberon first pharyngeal pouch UBERON:0007122 pharyngeal pouch 1 A pharyngeal pouch that is between pharyngeal arches 1 and 2. ISBN:0124020607 PMID:16313389 VHOG:0000970 . [][VHOG] 2012-09-17 VHOG:0000970 VHOG http://bgee.unil.ch/ In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] 2012-09-17 VHOG:0000970 VHOG DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010) http://bgee.unil.ch/ The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery WP we use adjacency relations rather than part_of, as in EHDAA2. EHDAA2 UMLS:C0231068 ncithesaurus:First_Pharyngeal_Pouch 1st arch branchial pouch EHDAA2:0000013 1st arch branchial pouch endoderm EHDAA2:0000016 1st arch pouch endoderm EHDAA2:0000016 1st pharyngeal pouch endoderm VHOG:0000555 first arch pharyngeal pouch OBOL:automatic first visceral pouch XAO:0000102 pharyngeal pouches 1 ZFA:0001128 visceral pouch 1 XAO:0000102 first pharyngeal pouch VHOG:0000970 A pharyngeal puch that is between the pharyngeal arches 2 and 3. A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG] Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract. Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve UBERON:0005715 AAO:0011115 EFO:0003633 EHDAA2:0000058 EMAPA:16275 EMAPA:16276 FMA:295676 NCIT:C34289 RETIRED_EHDAA2:0000060 SCTID:345349000 TAO:0001130 UMLS:C0231069 VHOG:0000561 VHOG:0000967 Wikipedia:Pharyngeal_pouch_(embryology)#Second_pouch XAO:0000247 ZFA:0001130 2nd arch branchial pouch 2nd arch branchial pouch endoderm 2nd arch pouch endoderm 2nd branchial pouch 2nd pharyngeal pouch endoderm pharyngeal pouches 2 second arch pharyngeal pouch second visceral pouch visceral pouch 2 uberon second pharyngeal pouch UBERON:0007123 pharyngeal pouch 2 A pharyngeal puch that is between the pharyngeal arches 2 and 3. ISBN:0124020607 PMID:16313389 A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000967 VHOG http://bgee.unil.ch/ Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011115 AAO ISBN:0-226-55763-4 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000967 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve WP UMLS:C0231069 ncithesaurus:Second_Pharyngeal_Pouch 2nd arch branchial pouch RETIRED_EHDAA2:0000060 2nd arch branchial pouch endoderm EHDAA2:0000061 2nd arch pouch endoderm EHDAA2:0000058 2nd pharyngeal pouch endoderm VHOG:0000561 pharyngeal pouches 2 ZFA:0001130 second arch pharyngeal pouch OBOL:automatic second visceral pouch XAO:0000247 visceral pouch 2 XAO:0000247 second pharyngeal pouch VHOG:0000967 A pharyngeal pouch that between pharyngeal arches 3 and 4. A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG] Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve UBERON:0005716 AAO:0011116 EFO:0003634 EHDAA2:0000077 EMAPA:16586 FMA:295682 NCIT:C34311 RETIRED_EHDAA2:0000076 SCTID:345450001 TAO:0001131 UMLS:C0231070 VHOG:0000966 VHOG:0001030 Wikipedia:Pharyngeal_pouch_(embryology)#Third_pouch XAO:0000251 ZFA:0001131 3rd arch branchial pouch 3rd arch branchial pouch endoderm 3rd branchial pouch 3rd pharyngeal pouch endoderm pharyngeal pouches 3 third arch pharyngeal pouch third visceral pouch visceral pouch 3 uberon third pharyngeal pouch UBERON:0007124 pharyngeal pouch 3 A pharyngeal pouch that between pharyngeal arches 3 and 4. ISBN:0124020607 PMID:16313389 Wikipedia:Pharyngeal_pouch_(embryology)#Third_pouch A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000966 VHOG http://bgee.unil.ch/ Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011116 AAO ISBN:0-226-55763-4 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000966 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve WP UMLS:C0231070 ncithesaurus:Third_Pharyngeal_Pouch 3rd arch branchial pouch RETIRED_EHDAA2:0000076 3rd arch branchial pouch endoderm EHDAA2:0000077 3rd pharyngeal pouch endoderm VHOG:0001030 pharyngeal pouches 3 ZFA:0001131 third arch pharyngeal pouch OBOL:automatic third visceral pouch XAO:0000251 visceral pouch 3 XAO:0000251 third pharyngeal pouch VHOG:0000966 A pharyngeal pouch between pharyngeal arch 4 and arch 5 or 6 (a fifth arch never establishes in amniotes). A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN:0124020607][VHOG] Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands. AAO:0011117 EFO:0003637 EHDAA2:0000091 EMAPA:16766 FMA:295688 NCIT:C34181 RETIRED_EHDAA2:0000090 SCTID:362858001 TAO:0001134 UMLS:C0231071 VHOG:0000578 VHOG:0000971 Wikipedia:Pharyngeal_pouch_(embryology)#Fourth_pouch XAO:0000254 ZFA:0001134 4th arch branchial pouch 4th arch branchial pouch endoderm 4th branchial pouch 4th pharyngeal pouch endoderm fourth arch pharyngeal pouch fourth branchial pouch fourth visceral pouch pharyngeal pouches 4 visceral pouch 4 uberon fourth pharyngeal pouch UBERON:0007125 pharyngeal pouch 4 A pharyngeal pouch between pharyngeal arch 4 and arch 5 or 6 (a fifth arch never establishes in amniotes). ISBN:0124020607 PMID:16313389 Wikipedia:Pharyngeal_pouch_(embryology)#Fourth_pouch A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000971 VHOG http://bgee.unil.ch/ Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011117 AAO ISBN:0-226-55763-4 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000971 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands. MP UMLS:C0231071 ncithesaurus:Fourth_Pharyngeal_Pouch 4th arch branchial pouch RETIRED_EHDAA2:0000090 4th arch branchial pouch endoderm EHDAA2:0000091 4th pharyngeal pouch endoderm VHOG:0000578 fourth arch pharyngeal pouch OBOL:automatic fourth visceral pouch XAO:0000254 pharyngeal pouches 4 ZFA:0001134 visceral pouch 4 XAO:0000254 fourth pharyngeal pouch VHOG:0000971 Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm. XAO:0000110 uberon corpuscle glomerulus UBERON:0007128 glomeral mesenchyme Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm. ISBN:0815318960 corpuscle XAO:0000110 glomerulus XAO:0000110 Ganglion which is located in the trunk. EFO:0000901 MAT:0000344 MIAA:0000344 TAO:0001573 ZFA:0001573 body ganglion trunk ganglia uberon UBERON:0007134 trunk ganglion Ganglion which is located in the trunk. ZFIN:curator body ganglion MAT:0000344 trunk ganglia ZFA:0001573 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 uberon presumptive central nervous system UBERON:0007135 neural keel An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000131 TAO ZFIN:curator presumptive central nervous system ZFA:0000131 An internal carotid artery that branching_part_of a left common carotid artery plus branches. EMAPA:16329 FMA:4062 SCTID:161452006 arteria caritis interna sinistra uberon UBERON:0007142 left internal carotid artery An internal carotid artery that branching_part_of a left common carotid artery plus branches. OBOL:automatic arteria caritis interna sinistra FMA:4062 An internal carotid artery that branching_part_of a right common carotid artery plus branches. EMAPA:16330 FMA:3949 SCTID:161251001 arteria carotis interna dextra uberon UBERON:0007143 right internal carotid artery An internal carotid artery that branching_part_of a right common carotid artery plus branches. OBOL:automatic arteria carotis interna dextra FMA:3949 An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx). EMAPA:16748 FMA:85540 embryo tail tail of embryo uberon embryonic tail UBERON:0007144 embryonic post-anal tail An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. http://orcid.org/0000-0002-6601-2165 embryo tail FMA:85540 tail of embryo FMA:85540 embryonic tail FMA:85540 An anatomical cavity that surrounded_by a midgut. EMAPA:18377 FMA:54366 midgut lumen uberon UBERON:0007147 lumen of midgut An anatomical cavity that surrounded_by a midgut. OBOL:automatic midgut lumen FMA:54366 An anatomical cavity that surrounded_by a hindgut. EMAPA:18396 FMA:54367 hindgut lumen uberon UBERON:0007148 lumen of hindgut An anatomical cavity that surrounded_by a hindgut. OBOL:automatic hindgut lumen FMA:54367 A valve leafleft that is part of a mitral valve. Leaf of cardiac valve which has as its parts the anterior, and posterior leaflets that is attached to the chorda tendinea of left ventricle and to the frbrous ring of mitral valve. The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG] EMAPA:18628 FMA:7241 SCTID:244353007 VHOG:0000822 leaflet of mitral valve mitral valve leaflet mitral valvular leaflet uberon mitral valve leaflets UBERON:0007151 mitral valve leaflet FMA-abduced A valve leafleft that is part of a mitral valve. http://orcid.org/0000-0002-6601-2165 Leaf of cardiac valve which has as its parts the anterior, and posterior leaflets that is attached to the chorda tendinea of left ventricle and to the frbrous ring of mitral valve. FMA:7241 The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG] 2012-09-17 VHOG:0000822 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ leaflet of mitral valve FMA:7241 mitral valve leaflet FMA:7241 mitral valvular leaflet FMA:7241 mitral valve leaflets VHOG:0000822 An anatomical cavity that surrounded_by a anal canal. EMAPA:18836 FMA:17357 anal canal lumen uberon UBERON:0007158 lumen of anal canal An anatomical cavity that surrounded_by a anal canal. OBOL:automatic anal canal lumen FMA:17357 An anatomical cavity that surrounded_by a colon. EMAPA:18945 FMA:18374 SCTID:362156004 colon lumen uberon colonic lumen UBERON:0007159 lumen of colon An anatomical cavity that surrounded_by a colon. OBOL:automatic colon lumen FMA:18374 colonic lumen FMA:18374 The inferior petrosal sinus, within the human head, is an area beneath the brain, which allows blood veins to span the area, from the center of the head downward. It drains from the cavernous sinus (beneath the brain) to the sigmoid sinuses above the internal jugular vein. EMAPA:19234 FMA:50770 SCTID:279263009 Wikipedia:Inferior_petrosal_sinus sinus petrosal inferior uberon UBERON:0007160 inferior petrosal sinus FMA The inferior petrosal sinus, within the human head, is an area beneath the brain, which allows blood veins to span the area, from the center of the head downward. It drains from the cavernous sinus (beneath the brain) to the sigmoid sinuses above the internal jugular vein. Wikipedia:Inferior_petrosal_sinus sinus petrosal inferior FMA:50770 EMAPA:25124 FMA:23797 scapular border uberon UBERON:0007171 border of scapula scapular border FMA:23797 EMAPA:25125 FMA:23800 scapular angle uberon UBERON:0007172 angle of scapula https://github.com/obophenotype/uberon/issues/58 scapular angle FMA:23800 The lateral border (or axillary border, or margin) is the thickest of the three borders of the scapula. It begins above at the lower margin of the glenoid cavity, and inclines obliquely downward and backward to the inferior angle. Immediately below the glenoid cavity is a rough impression, the infraglenoid tuberosity, about 2.5 cm. in length, which gives origin to the long head of the Triceps brachii; in front of this is a longitudinal groove, which extends as far as the lower third of this border, and affords origin to part of the Subscapularis. The inferior third is thin and sharp, and serves for the attachment of a few fibers of the Teres major behind, and of the Subscapularis in front. EMAPA:25126 FMA:23239 Wikipedia:Lateral_border_of_the_scapula axillary border of scapula lateral border of scapula margo lateralis (scapula) margo lateralis scapulae uberon lateral part of scapula UBERON:0007173 lateral border of scapula EMAPA-modified lexical The lateral border (or axillary border, or margin) is the thickest of the three borders of the scapula. It begins above at the lower margin of the glenoid cavity, and inclines obliquely downward and backward to the inferior angle. Immediately below the glenoid cavity is a rough impression, the infraglenoid tuberosity, about 2.5 cm. in length, which gives origin to the long head of the Triceps brachii; in front of this is a longitudinal groove, which extends as far as the lower third of this border, and affords origin to part of the Subscapularis. The inferior third is thin and sharp, and serves for the attachment of a few fibers of the Teres major behind, and of the Subscapularis in front. Wikipedia:Lateral_border_of_the_scapula axillary border of scapula FMA:23239 lateral border of scapula FMA:23239 margo lateralis (scapula) FMA:23239 margo lateralis scapulae FMA:23239 FMA:TA lateral part of scapula FMA:23239 The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border. consider merging with UBERON:1500000 scapular blade, depending on https://github.com/obophenotype/uberon/issues/339. See also http://www.ncbi.nlm.nih.gov/pubmed/20136669 EMAPA:25127 FMA:23242 SCTID:368187009 Wikipedia:Medial_border_of_scapula margo medialis (scapula) margo medialis scapulae medial part of scapula vertebral border of scapula uberon medial border of the scapula medial margin of the scapula vertebral border vertebral border of the scapula UBERON:0007174 medial border of scapula EMAPA-modified PMID:20136669 The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border. Wikipedia:Medial_border_of_scapula margo medialis (scapula) FMA:23242 margo medialis scapulae FMA:23242 FMA:TA medial part of scapula FMA:23242 vertebral border of scapula FMA:23242 medial border of the scapula Wikipedia:Medial_border_of_scapula medial margin of the scapula Wikipedia:Medial_border_of_scapula vertebral border Wikipedia:Medial_border_of_scapula vertebral border of the scapula Wikipedia:Medial_border_of_scapula An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted]. EMAPA:25128 FMA:13315 Wikipedia:Inferior_angle_of_scapula angulus inferior (scapula) angulus inferior scapulae uberon UBERON:0007175 inferior angle of scapula EMAPA-modified An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted]. Wikipedia:Inferior_angle_of_scapula angulus inferior (scapula) FMA:13315 angulus inferior scapulae Wikipedia:Inferior_angle_of_scapula A lamina propria that is part of a colonic mucosa. EMAPA:27395 FMA:15657 MA:0003196 SCTID:113284008 colonic lamina propria lamina propria mucosae of colon lamina propria of colonic mucosa lamina propria of colonic mucous membrane uberon UBERON:0007177 lamina propria of mucosa of colon A lamina propria that is part of a colonic mucosa. OBOL:automatic colonic lamina propria FMA:15657 lamina propria mucosae of colon FMA:15657 lamina propria of colonic mucosa FMA:15657 lamina propria of colonic mucous membrane FMA:15657 A serous membrane that is part of a uterine tube infundibulum. EMAPA:29903 FMA:18324 serosa of infundibulum of fallopian tube serosa of infundibulum of oviduct uberon UBERON:0007181 serosa of infundibulum of uterine tube A serous membrane that is part of a uterine tube infundibulum. OBOL:automatic serosa of infundibulum of fallopian tube FMA:18324 serosa of infundibulum of oviduct FMA:18324 A muscle layer that is part of a uterine tube infundibulum. EMAPA:31264 FMA:18336 muscle layer of infundibulum of fallopian tube muscle layer of infundibulum of oviduct muscularis of infundibulum of uterine tube uberon UBERON:0007182 muscle layer of infundibulum of uterine tube A muscle layer that is part of a uterine tube infundibulum. OBOL:automatic muscle layer of infundibulum of fallopian tube FMA:18336 muscle layer of infundibulum of oviduct FMA:18336 muscularis of infundibulum of uterine tube FMA:18336 A mesothelium that is part of a serous pericardium. BTO:0003157 EMAPA:16133 FMA:18149 SCTID:67300002 mesothelium of pericardium pericardial mesothelium serous pericardium mesothelium uberon UBERON:0007188 mesothelium of serous pericardium A mesothelium that is part of a serous pericardium. OBOL:automatic mesothelium of pericardium FMA:18149 pericardial mesothelium FMA:18149 serous pericardium mesothelium FMA:18149 The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. CALOHA:TS-0085 FMA:21426 Wikipedia:Bone_marrow#Stroma bone marrow stroma uberon UBERON:0007195 stroma of bone marrow The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. Wikipedia:Bone_marrow#Stroma bone marrow stroma FMA:21426 The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. UBERON:0004102 FMA:7393 NCIT:C117875 SCTID:361384001 Wikipedia:Tracheobronchial_tree arbor tracheobronchialis uberon tracheobronchial system UBERON:0007196 tracheobronchial tree Wikipedia The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. Wikipedia:Tracheobronchial_tree arbor tracheobronchialis FMA:7393 FMA:TA tracheobronchial system HP:0005607 Multicellular organism that can produce both male and female gametes. AAO:0010035 BILA:0000029 CARO:0000029 HAO:0000029 TADS:0000601 WBbt:0007849 uberon dioecious organism hermaphrodite UBERON:0007197 hermaphroditic organism Multicellular organism that can produce both male and female gametes. http://orcid.org/0000-0001-9114-8737 dioecious organism BILA:0000029 hermaphrodite WBbt:0007849 The vasculature consisting of brachiocephalic arteries and veins. uberon UBERON:0007204 brachiocephalic vasculature The vasculature consisting of brachiocephalic arteries and veins. http://orcid.org/0000-0002-6601-2165 Mesenchyme that develops_from a cranial neural crest. EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 TAO:0000787 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon UBERON:0007213 mesenchyme derived from head neural crest ZFA Mesenchyme that develops_from a cranial neural crest. OBOL:automatic head mesenchyme from neural crest EHDAA2:0000735 Mesenchyme that develops_from a trunk neural crest. EHDAA2:0002093 EMAPA:16182 TAO:0000999 ZFA:0000999 trunk mesenchyme from neural crest trunk neural crest derived mesenchyme uberon UBERON:0007214 mesenchyme derived from trunk neural crest Mesenchyme that develops_from a trunk neural crest. OBOL:automatic trunk mesenchyme from neural crest EHDAA2:0002093 An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. EV:0300011 EVM:2990031 FBdv:00005333 FMA:63631 MIAA:0000399 MmusDv:0000031 OGES:000023 SCTID:367619004 embryo late (growth) stage fetal stage fetus fetus stage uberon embryo late growth stage embryo late stage UBERON:0007220 late embryonic stage https://github.com/obophenotype/uberon/issues/355 https://github.com/obophenotype/uberon/issues/565 An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. https://orcid.org/0000-0003-3308-6245 embryo late (growth) stage MIAA:0000399 fetal stage https://orcid.org/0000-0002-6601-2165 fetus MIAA:0000399 fetus stage https://orcid.org/0000-0002-6601-2165 embryo late growth stage BTO:0000449 embryo late stage BTO:0000449 relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 EHDAA:583 EMAPA:16382 VHOG:0000510 ventral pharyngeal arch 1 uberon ventral mandibular arch ventral visceral arch 1 UBERON:0007237 1st arch mandibular component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000510 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ ventral pharyngeal arch 1 VHOG:0000510 ventral mandibular arch VHOG:0000510 ventral visceral arch 1 VHOG:0000510 relationship to palatoquadrate to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000038 EHDAA:595 EMAPA:16388 VHOG:0000511 uberon UBERON:0007238 1st arch maxillary component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000511 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ A tunica media that is part of a artery. EMAPA:36294 EV:0100029 FMA:14273 NCIT:C49321 SCTID:84300001 UMLS:C1710627 arterial media tunica media (arteriae) uberon UBERON:0007239 tunica media of artery A tunica media that is part of a artery. OBOL:automatic UMLS:C1710627 ncithesaurus:Venous_System_Smooth_Muscle_Tissue arterial media EV:0100029 tunica media (arteriae) FMA:14273 A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 FMA:14274 SCTID:113261001 arterial adventitia tunica externa (adventitia)(arteriae) uberon UBERON:0007240 tunica adventitia of artery FMA A tunica adventitia that is part of a artery. OBOL:automatic arterial adventitia EV:0100030 tunica externa (adventitia)(arteriae) FMA:14274 A tunica adventitia that is part of a vein. EMAPA:36310 EV:0100034 FMA:14355 SCTID:13202006 tunica externa (adventitia)(venae) venous adventitia uberon UBERON:0007241 tunica adventitia of vein A tunica adventitia that is part of a vein. OBOL:automatic tunica externa (adventitia)(venae) FMA:14355 venous adventitia EV:0100034 A tunica intima that is part of a vein. EMAPA:36308 EV:0100032 FMA:14353 SCTID:2436009 tunica interna (intima)(venae) venous intima uberon UBERON:0007242 tunica intima of vein A tunica intima that is part of a vein. OBOL:automatic tunica interna (intima)(venae) FMA:14353 venous intima EV:0100032 A tunica media that is part of a vein. EMAPA:36309 EV:0100033 FMA:14354 SCTID:42049001 tunica media (venae) venous media uberon UBERON:0007243 tunica media of vein A tunica media that is part of a vein. OBOL:automatic tunica media (venae) FMA:14354 venous media EV:0100033 Gray matter of the central nervous system which is a collection of clustered nuclei. FMA:256381 FMA:84059 uberon cluster of neural nuclei neural nuclei nuclear complex UBERON:0007245 nuclear complex of neuraxis Gray matter of the central nervous system which is a collection of clustered nuclei. http://orcid.org/0000-0002-6601-2165 Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future. FMA:72246 SCTID:369024009 superior olivary complex nucleus uberon UBERON:0007247 nucleus of superior olivary complex Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. http://orcid.org/0000-0002-6601-2165 superior olivary complex nucleus FMA:72246 An intervertebral disk that is part of a cervical region of vertebral column. A cervical intervertebral disk connects at least one cervical vertebra, either to another cervical vertebra, or at one point on the vertebral colummn, to a thoracic vertebra. EMAPA:19415 FMA:13895 SCTID:68818006 cervical intervertebral disc intervertebral disc of cervical region uberon UBERON:0007252 intervertebral disk of cervical vertebra An intervertebral disk that is part of a cervical region of vertebral column. A cervical intervertebral disk connects at least one cervical vertebra, either to another cervical vertebra, or at one point on the vertebral colummn, to a thoracic vertebra. http://orcid.org/0000-0002-6601-2165 cervical intervertebral disc FMA:13895 intervertebral disc of cervical region EMAPA:19415 An intervertebral disk that is part of a thoracic region of vertebral column. A thoracic intervertebral disk connects at least one thoracic vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a lumbar vertebra. EMAPA:19489 FMA:10455 intervertebral disc of thoracic region uberon UBERON:0007254 intervertebral disk of thoracic vertebra An intervertebral disk that is part of a thoracic region of vertebral column. A thoracic intervertebral disk connects at least one thoracic vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a lumbar vertebra. http://orcid.org/0000-0002-6601-2165 intervertebral disc of thoracic region EMAPA:19489 An intervertebral disk that is part of a lumbar region of vertebral column. A lumbar intervertebral disk connects at least one lumbar vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra. EMAPA:19468 FMA:13894 intervertebral disc of lumbar region uberon UBERON:0007255 intervertebral disk of lumbar vertebra An intervertebral disk that is part of a lumbar region of vertebral column. A lumbar intervertebral disk connects at least one lumbar vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra. http://orcid.org/0000-0002-6601-2165 intervertebral disc of lumbar region EMAPA:19468 An intervertebral disk that is part of a sacral region of vertebral column. A sacral intervertebral disk connects at least one sacral vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra. EMAPA:19575 FMA:268676 intervertebral disc of sacral region uberon UBERON:0007257 intervertebral disk of sacral vertebra An intervertebral disk that is part of a sacral region of vertebral column. A sacral intervertebral disk connects at least one sacral vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra. http://orcid.org/0000-0002-6601-2165 intervertebral disc of sacral region EMAPA:19575 An intervertebral disk that connects a mammalian cervical vertebra 3 and connects a mammalian cervical vertebra 4. EMAPA:19422 FMA:13896 C3 intervertebral disk intervertebral disk, C3-C4 uberon UBERON:0007260 intervertebral disk of third cervical vertebra An intervertebral disk that connects a mammalian cervical vertebra 3 and connects a mammalian cervical vertebra 4. OBOL:automatic C3 intervertebral disk FMA:13896 intervertebral disk, C3-C4 FMA:13896 An intervertebral disk that connects a mammalian cervical vertebra 4 and connects a mammalian cervical vertebra 5. EMAPA:19425 FMA:13897 SCTID:361748005 intervertebral disc of fourth cervical vertebra intervertebral disk, C4-C5 uberon UBERON:0007261 intervertebral disk of fourth cervical vertebra An intervertebral disk that connects a mammalian cervical vertebra 4 and connects a mammalian cervical vertebra 5. OBOL:automatic intervertebral disc of fourth cervical vertebra FMA:13897 intervertebral disk, C4-C5 FMA:13897 An intervertebral disk that connects a mammalian cervical vertebra 5 and connects a mammalian cervical vertebra 6. EMAPA:19428 FMA:13898 SCTID:361749002 intervertebral disc of fifth cervical vertebra intervertebral disk, C5-C6 uberon UBERON:0007262 intervertebral disk of fifth cervical vertebra An intervertebral disk that connects a mammalian cervical vertebra 5 and connects a mammalian cervical vertebra 6. OBOL:automatic intervertebral disc of fifth cervical vertebra FMA:13898 intervertebral disk, C5-C6 FMA:13898 An intervertebral disk that connects a mammalian cervical vertebra 6 and connects a mammalian cervical vertebra 7. EMAPA:19460 FMA:13899 intervertebral disk, C6-C7 uberon UBERON:0007263 intervertebral disk of sixth cervical vertebra An intervertebral disk that connects a mammalian cervical vertebra 6 and connects a mammalian cervical vertebra 7. OBOL:automatic intervertebral disk, C6-C7 FMA:13899 An intervertebral disk that connects a thoracic vertebra and connects a mammalian cervical vertebra 7. EMAPA:19463 FMA:13900 intervertebral disk, C7-T1 uberon UBERON:0007264 intervertebral disk of seventh cervical vertebra An intervertebral disk that connects a thoracic vertebra and connects a mammalian cervical vertebra 7. OBOL:automatic intervertebral disk, C7-T1 FMA:13900 An intervertebral disk that connects a vertebral bone 2 and connects a mammalian cervical vertebra 3. EMAPA:19419 FMA:25058 C2 disk C2 intervertebral disk intervertebral disc of cervical vertebra 2 intervertebral disc of second cervical vertebra intervertebral disk of cervical vertebra 2 intervertebral disk of second cervical vertebra intervertebral disk, C2-C3 second cervical intervertebral disk uberon UBERON:0007265 intervertebral disk of axis An intervertebral disk that connects a vertebral bone 2 and connects a mammalian cervical vertebra 3. OBOL:automatic C2 disk FMA:25058 C2 intervertebral disk FMA:25058 intervertebral disc of cervical vertebra 2 FMA:25058 intervertebral disc of second cervical vertebra FMA:25058 intervertebral disk of cervical vertebra 2 FMA:25058 intervertebral disk of second cervical vertebra FMA:25058 intervertebral disk, C2-C3 FMA:25058 second cervical intervertebral disk FMA:25058 An intervertebral disk that connects a vertebral bone 1 and connects a vertebral bone 2. EMAPA:19416 C1 disk C1 intervertebral disk first cervical intervertebral disk intervertebral disc of cervical vertebra 1 intervertebral disc of first cervical vertebra intervertebral disk of cervical vertebra 1 intervertebral disk of first cervical vertebra intervertebral disk, C1-C2 uberon UBERON:0007266 intervertebral disk of atlas An intervertebral disk that connects a vertebral bone 1 and connects a vertebral bone 2. OBOL:automatic A pre-cartilage condensation that is part of a trachea. EHDAA2:0002070 EHDAA:7082 uberon UBERON:0007267 trachea pre-cartilage rings EHDAA2 A pre-cartilage condensation that is part of a trachea. OBOL:automatic Any collection of muscles that is part of a pectoral appendage. currently defined by location rather than attachment EFO:0003540 TAO:0000563 ZFA:0000563 pectoral fin muscle pectoral fin musculature uberon UBERON:0007269 pectoral appendage musculature Any collection of muscles that is part of a pectoral appendage. OBOL:automatic pectoral fin muscle ZFA:0000563 pectoral fin musculature ZFA:0000563 Any collection of muscles that is part of a pelvic appendage. currently defined by location rather than attachment Musculature that is part of the pelvic fin.[TAO] TAO:0000258 ZFA:0000258 pelvic fin musculature uberon UBERON:0007270 pelvic appendage musculature Any collection of muscles that is part of a pelvic appendage. OBOL:automatic Musculature that is part of the pelvic fin.[TAO] 2012-08-14 TAO:0000258 TAO TAO:curator pelvic fin musculature ZFA:0000258 Any collection of muscles that is part of an appendage. currently defined by location rather than attachment TAO:0000207 ZFA:0000207 fin musculature uberon UBERON:0007271 appendage musculature Any collection of muscles that is part of an appendage. OBOL:automatic fin musculature ZFA:0000207 Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 uberon cheiropterygium UBERON:0007272 pectoral appendage skeleton VSAO Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 VSAO:NI cheiropterygium VSAO:0005000 VSAO:NI The collection of all skeletal elements in a pelvic appendage region. uberon UBERON:0007273 pelvic appendage skeleton VSAO The collection of all skeletal elements in a pelvic appendage region. https://orcid.org/0000-0002-6601-2165 The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 Wikipedia:Rhombencephalon ZFA:0000569 presumptive rhombencephalon uberon embryonic rhombencephalon future hindbrain rhombencephalon UBERON:0007277 presumptive hindbrain XAO-abduced cjm The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. Wikipedia:Rhombencephalon The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. NPX:PDR presumptive rhombencephalon ZFA:0000569 embryonic rhombencephalon CALOHA:TS-2118 future hindbrain https://orcid.org/0000-0002-6601-2165 rhombencephalon EHDAA2:0001630 Portion of tissue that is part of the heart tube and will become the sinus venosus. TAO:0002234 ZFA:0001722 uberon UBERON:0007278 presumptive sinus venosus ZFA Portion of tissue that is part of the heart tube and will become the sinus venosus. ZFA:0001722 A presumptive structure that has the potential to develop into a endocardium. Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] TAO:0002233 ZFA:0001724 uberon UBERON:0007280 presumptive endocardium A presumptive structure that has the potential to develop into a endocardium. OBOL:automatic Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] 2012-08-14 TAO:0002233 TAO ZFIN:curator Embryonic structure that gives rise to the midbrain hindbrain boundary. EFO:0003446 TAO:0001187 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon UBERON:0007281 presumptive midbrain hindbrain boundary ZFA Embryonic structure that gives rise to the midbrain hindbrain boundary. ZFA:0001187 presumptive MHB https://orcid.org/0000-0002-6601-2165 presumptive midbrain-hindbrain boundary ZFA:0001187 A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 ZFA:0000053 uberon presumptive segmental plates UBERON:0007282 presumptive segmental plate https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 A presumptive structure that has the potential to develop into a presomitic mesoderm. OBOL:automatic presumptive segmental plates ZFA:0000053 A presumptive structure that has the potential to develop into a neural plate. consider merging Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 prospective neuroectoderm prospective vegetal ectoderm uberon UBERON:0007284 presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic Region of the gastrula which gives rise to the neural plate.[TAO] 2012-08-14 TAO:0000063 TAO ZFIN:curator prospective neuroectoderm ZFA:0000063 prospective vegetal ectoderm ZFA:0000063 The part of the blastula that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 XAO:0004134 ZFA:0000591 future paraxial mesenchyme future paraxial mesoderm uberon UBERON:0007285 presumptive paraxial mesoderm https://github.com/obophenotype/uberon/issues/1277 The part of the blastula that has the potential to develop into a paraxial mesoderm. UBERON:cjm https://github.com/obophenotype/uberon/issues/1277 future paraxial mesenchyme UBERON:cjm A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. EFO:0003463 TAO:0001368 ZFA:0001368 uberon UBERON:0007288 presumptive forebrain midbrain boundary A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. OBOL:automatic A presumptive structure that has the potential to develop into a pronephric mesoderm. EFO:0003619 TAO:0001070 ZFA:0001070 nephron primordium uberon UBERON:0007297 presumptive pronephric mesoderm A presumptive structure that has the potential to develop into a pronephric mesoderm. OBOL:automatic nephron primordium ZFA:0001070 A blood vessel that is part of a pectoral appendage. TAO:0005301 ZFA:0005301 pectoral fin blood vessel uberon UBERON:0007300 pectoral appendage blood vessel A blood vessel that is part of a pectoral appendage. OBOL:automatic pectoral fin blood vessel ZFA:0005301 A blood vessel that is part of a limb/fin. TAO:0005299 ZFA:0005299 fin blood vessel limb blood vessel uberon UBERON:0007301 appendage blood vessel A blood vessel that is part of a limb/fin. OBOL:automatic fin blood vessel ZFA:0005299 limb blood vessel A vasculature that is part of a pectoral appendage. TAO:0005096 ZFA:0005096 pectoral fin vasculature uberon UBERON:0007302 pectoral appendage vasculature A vasculature that is part of a pectoral appendage. OBOL:automatic pectoral fin vasculature ZFA:0005096 A vasculature that is part of a chordate pharynx. TAO:0005003 ZFA:0005003 branchial vasculature uberon UBERON:0007303 pharyngeal vasculature A vasculature that is part of a chordate pharynx. OBOL:automatic branchial vasculature ZFA:0005003 A vasculature that is part of a limb/fin. TAO:0005095 ZFA:0005095 fin vasculature uberon UBERON:0007304 appendage vasculature A vasculature that is part of a limb/fin. OBOL:automatic fin vasculature ZFA:0005095 A glomerular capillary that is part of a pronephros. TAO:0005309 ZFA:0005309 uberon UBERON:0007306 pronephric glomerular capillary true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A glomerular capillary that is part of a pronephros. OBOL:automatic A glomerular basement membrane that is part of a pronephros. TAO:0005313 ZFA:0005313 pronephric glomerular filtration membrane uberon UBERON:0007307 pronephric glomerular basement membrane true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A glomerular basement membrane that is part of a pronephros. OBOL:automatic pronephric glomerular filtration membrane ZFA:0005313 Matter ejected from the lungs, bronchi, and trachea, through the mouth. BTO:0001297 CALOHA:TS-0963 EMAPA:36553 FMA:312401 GAID:1171 MA:0002536 MESH:D013183 NCIT:C13278 UMLS:C0038056 uberon expectoration UBERON:0007311 sputum Matter ejected from the lungs, bronchi, and trachea, through the mouth. Dorlands_Medical_Dictionary:MerckSource UMLS:C0038056 ncithesaurus:Sputum expectoration BTO:0001297 Either of two main superficial veins of the leg, one larger than the other, that begin at the foot. BTO:0001808 CALOHA:TS-0893 EMAPA:37186 MA:0002215 MESH:D012501 NCIT:C33511 UMLS:C0036186 uberon UBERON:0007318 saphenous vein Either of two main superficial veins of the leg, one larger than the other, that begin at the foot. BTO:0001808 EMAPA:37186 MA:th UMLS:C0036186 ncithesaurus:Saphenous_Vein A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. TODO - check In mice many lobules lack islets, in contrast to other mammals including humans EMAPA:37710 FMA:16012 MA:0000721 lobulus pancreaticus pancreas lobe pancreatic lobule uberon UBERON:0007324 pancreatic lobule A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. ISBN:0123813611 EMAPA:37710 MA:th lobulus pancreaticus FMA:16012 pancreas lobe MA:0000721 pancreatic lobule FMA:16012 A duct that collects and carries secretions of the exocrine pancreas to the intestine. this class groups together accessory (dorsal) and main (ventral) pancreatic ducts Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA:9194 EMAPA:32952 FMA:10419 MA:0000124 MESH:D010183 SCTID:181278006 TAO:0001372 VHOG:0000254 Wikipedia:Pancreatic_duct ZFA:0001372 duct of pancreas pancreas duct uberon ductus pancreaticus UBERON:0007329 pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png ZFA MA A duct that collects and carries secretions of the exocrine pancreas to the intestine. GOC:cvs GOC:ymb Wikipedia:Pancreatic_duct https://github.com/obophenotype/uberon/issues/1250 https://orcid.org/0000-0002-2244-7917 https://orcid.org/0000-0002-6601-2165 https://orcid.org/0000-0002-9900-7880 Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000254 VHOG http://bgee.unil.ch/ These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] 2012-09-17 VHOG:0000254 VHOG DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005) http://bgee.unil.ch/ in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA2 MESH:D010183 https://github.com/biopragmatics/biomappings duct of pancreas OBOL:accepted pancreas duct OBOL:accepted ductus pancreaticus Wikipedia:Pancreatic_duct An anatomical surface that is part of a tongue. FMA:54647 SCTID:314870004 tongue surface uberon UBERON:0007367 surface of tongue An anatomical surface that is part of a tongue. OBOL:automatic tongue surface FMA:54647 The upper (superior) side of the tongue. check superior/dorsal FMA:54646 dorsal surface of tongue uberon UBERON:0007371 superior surface of tongue The upper (superior) side of the tongue. http://orcid.org/0000-0002-6601-2165 dorsal surface of tongue FMA:54646 A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton CALOHA:TS-2212 Wikipedia:Palate roof of buccal cavity roof of oral cavity uberon palate palatum primary or secondary palate UBERON:0007375 roof of mouth A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones. https://orcid.org/0000-0002-6601-2165 palatum The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. this grouping class exists primarily to align with GO - see GO:0008544. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 Wikipedia:Epidermis_(zoology) epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium Wikipedia:Epidermis_(zoology) The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. GO:0008544 FBbt:00004993 epidermis GO:0008544 hypoderm BTO:0000313 hypodermis GO:0008544 WBbt:0005733 The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. BSA:0000081 BTO:0000369 Wikipedia:Egg_(biology) uberon egg UBERON:0007379 shelled egg The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. BTO:0000369 Wikipedia:Egg_(biology) egg BTO:0000369 Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. EFO:0003425 TAO:0000086 ZFA:0000086 EVL enveloping layer uberon UBERON:0007383 enveloping layer of ectoderm Outermost layer of cells surrounding the embryo. http://orcid.org/0000-0002-6601-2165 Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000086 TAO ZFIN:curator relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] 2012-08-14 TAO:0000086 TAO EVL ZFA:0000086 enveloping layer ZFIN:ZDB-PUB-961014-576 A lymphatic vessel that is part of a limb/fin. TAO:0005300 ZFA:0005300 uberon UBERON:0007384 appendage lymph vessel A lymphatic vessel that is part of a limb/fin. OBOL:automatic A lymphatic vessel that is part of a pectoral appendage. TAO:0005302 ZFA:0005302 uberon UBERON:0007385 pectoral appendage lymph vessel A lymphatic vessel that is part of a pectoral appendage. OBOL:automatic A lymphatic vessel that is part of a pelvic appendage. uberon UBERON:0007386 pelvic appendage lymph vessel A lymphatic vessel that is part of a pelvic appendage. OBOL:automatic A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] TAO:0001543 ZFA:0001543 uberon UBERON:0007389 paired limb/fin cartilage A cartilage tissue that is part of a paired limb or fin. http://orcid.org/0000-0002-6601-2165 Cartilage which is part of one of the paired fins.[TAO] 2012-08-14 TAO:0001543 TAO ZFIN:curator A cartilage tissue that is part of a pectoral appendage. Cartilage which is part of the pectoral fin.[TAO] TAO:0000257 ZFA:0000257 uberon pectoral fin cartilage UBERON:0007390 pectoral appendage cartilage tissue A cartilage tissue that is part of a pectoral appendage. OBOL:automatic Cartilage which is part of the pectoral fin.[TAO] 2012-08-14 TAO:0000257 TAO ZFIN:curator pectoral fin cartilage TAO:0000257 A cartilage tissue that is part of a pelvic appendage. Cartilage which is part of the pelvic fin.[TAO] TAO:0001459 ZFA:0001459 uberon pelvic fin cartilage UBERON:0007391 pelvic appendage cartilage tissue A cartilage tissue that is part of a pelvic appendage. OBOL:automatic Cartilage which is part of the pelvic fin.[TAO] 2012-08-14 TAO:0001459 TAO ZFIN:curator pelvic fin cartilage TAO:0001459 A nucleus of brain that spans a midbrain tegmentum. this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species UBERON:0012277 FMA:258768 ZFA:0005577 tegmental nuclei tegmental nucleus uberon UBERON:0007414 nucleus of midbrain tegmentum A nucleus of brain that spans a midbrain tegmentum. OBOL:automatic tegmental nuclei tegmental nucleus ZFA:0005577 The space within an epithelial sphere. AEO:0000079 cavity of vesicle uberon UBERON:0007473 lumen of epithelial sac The space within an epithelial sphere. AEO:JB cavity of vesicle AEO:0000079 A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. AEO:0000081 EHDAA2:0003081 uberon UBERON:0007475 matrix-based tissue A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. AEO:JB Acellular anatomical structure whose predominant constituent is keratin. should all structures composed primarily of keratin be classified here? At what stage of cornification are keratin-filled cells no longer considered cells AEO:0000099 EHDAA2:0003099 uberon keratin-based structure UBERON:0007490 keratin-based acellular structure Acellular anatomical structure whose predominant constituent is keratin. AEO:JB keratin-based structure EHDAA2:0003099 An epithelial tube that is open at one end only. AEO:0000115 EHDAA2:0003115 uberon UBERON:0007499 epithelial sac AEO An epithelial tube that is open at one end only. AEO:JB UBERONREF:0000001 An epithelial tube open at both ends that allows fluid flow. AEO_RETIRED:0000116 RETIRED_EHDAA2:0003116 uberon UBERON:0007500 epithelial tube open at both ends AEO An epithelial tube open at both ends that allows fluid flow. AEO:JB UBERONREF:0000001 A collection of connected epithelial tubes with a single portal. AEO:0000117 EHDAA2:0003117 arborising epithelial duct system uberon UBERON:0007501 arborizing epithelial duct system AEO AEO A collection of connected epithelial tubes with a single portal. AEO:JB UBERONREF:0000001 arborising epithelial duct system AEO:0000117 A closed epithelium with a lumen. AEO:0000119 EHDAA2:0003119 uberon UBERON:0007503 epithelial vesicle AEO A closed epithelium with a lumen. AEO:JB A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:0000143 EHDAA2:0003143 SCTID:362915001 uberon UBERON:0007521 smooth muscle sphincter A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:JB A ring of striated muscle cells whose contraction closes the opening of the ring. AEO:0000144 EHDAA2:0003144 uberon UBERON:0007522 striated muscle sphincter A ring of striated muscle cells whose contraction closes the opening of the ring. AEO:JB Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue AEO AEO Mesenchyme with little extracellular matrix. AEO:JB Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix. AEO:0000151 EHDAA2:0003151 uberon UBERON:0007529 loose mesenchyme tissue AEO AEO AEO Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix. AEO:JB Mesenchymal cells that are migrating. this class will be an important part of the NC reorganization AEO:0000152 EHDAA2:0003152 uberon UBERON:0007530 migrating mesenchyme population Mesenchymal cells that are migrating. AEO:JB An anatomical structure that is undergoing regeneration. we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure. A portion of tissue that is regrowing after damage or amputation.[TAO] AEO:0000200 EHDAA2:0003233 TAO:0005147 XAO:0004059 ZFA:0005147 uberon regenerating tissue regenerating tissues regenerative tissue UBERON:0007567 regenerating anatomical structure An anatomical structure that is undergoing regeneration. http://orcid.org/0000-0002-6601-2165 A portion of tissue that is regrowing after damage or amputation.[TAO] 2012-08-14 TAO:0005147 TAO ZFIN:curator regenerating tissue ZFA:0005147 regenerating tissues ZFA:0005147 A ciliated columnar epithelium that is part of a oviduct. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA:62016 MA:0001719 uberon epithelium of uterine tube uterine tube epithelium UBERON:0007589 ciliated columnar oviduct epithelium MA FMA A ciliated columnar epithelium that is part of a oviduct. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelium of uterine tube FMA:62016 uterine tube epithelium FMA:62016 A cuboidal epithelium that is part of a oviduct. MA:0001720 uberon UBERON:0007590 cuboidal oviduct epithelium MA A cuboidal epithelium that is part of a oviduct. OBOL:automatic Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 uberon UBERON:0007592 ciliated columnar epithelium FMA Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]. FMA:64798 Epithelium bearing vibratile cilia on the free surface. uberon UBERON:0007601 ciliated epithelium Epithelium bearing vibratile cilia on the free surface. http://medical-dictionary.thefreedictionary.com/ciliated+epithelium Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP]. FMA:45564 NCIT:C33620 UMLS:C0836132 Wikipedia:Stratified_columnar_epithelia epithelium stratificatum columnare uberon UBERON:0007602 stratified columnar epithelium FMA Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP]. Wikipedia:Stratified_columnar_epithelia UMLS:C0836132 ncithesaurus:Stratified_Columnar_Epithelium epithelium stratificatum columnare FMA:45564 FMA:67521 uberon UBERON:0007606 ciliated stratified columnar epithelium FMA A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 CALOHA:TS-0998 FMA:66762 synovium stratum synoviale synovial layer synovial membrane uberon synovial tissue UBERON:0007616 layer of synovial tissue BTO A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 http://www.britannica.com/EBchecked/topic/578563/synovial-tissue synovium CALOHA:TS-0998 stratum synoviale FMA:TA synovial layer FMA:66762 synovial membrane FMA:66762 synovial tissue BTO:0001338 An anatomical cavity that surrounded_by a synovial joint. FMA:11356 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint uberon joint cavity synovial cavity UBERON:0007617 synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. OBOL:automatic articular cavity (synovial joint) FMA:11356 cavitas articularis (junctura synovialis) FMA:11356 cavity of synovial joint FMA:11356 joint cavity FMA:11356 synovial cavity FMA:11356 A synovial cavity of joint that is part of a hip joint. EMAPA:19021 FMA:9701 uberon UBERON:0007618 synovial cavity of hip joint FMA A synovial cavity of joint that is part of a hip joint. OBOL:automatic Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. GAID:907 MESH:D010857 uberon eye pigment epithelium UBERON:0007625 pigment epithelium of eye Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. MP:0005200 eye pigment epithelium MESH:A09.371.670 A neural nucleus that is part of a medulla oblongata. FMA:258772 SCTID:304943004 uberon UBERON:0007635 nucleus of medulla oblongata A neural nucleus that is part of a medulla oblongata. OBOL:automatic The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. BIRNLEX:4096 BM:V CALOHA:TS-2077 DHBA:266441713 FMA:71248 HBA:9203 MESH:D014278 UMLS:C0040999 Wikipedia:Trigeminal_nerve_nuclei neuronames:2021 trigeminal nuclei uberon nuclei trigemini UBERON:0007641 trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png FMA FMA The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. Wikipedia:Trigeminal_nerve_nuclei in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. MA MESH:D014278 https://github.com/biopragmatics/biomappings UMLS:C0040999 BIRNLEX:4096 trigeminal nuclei FMA:71248 nuclei trigemini Wikipedia:Trigeminal_nerve_nuclei A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes. FMA:12772 NCIT:C33769 SCTID:196374005 UMLS:C0229745 Wikipedia:Lymph_node#Lymph_nodes_of_the_thorax lymph node of thorax uberon deep thoracic lymph node UBERON:0007644 thoracic lymph node A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes. OBOL:automatic Wikipedia:Lymph_node#Lymph_nodes_of_the_thorax UMLS:C0229745 ncithesaurus:Thoracic_Lymph_Node lymph node of thorax FMA:12772 deep thoracic lymph node FMA:12772 A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d UBERON:0004065 EHDAA2:0004453 primary meninx uberon meninx primitiva primitive meninx primordial meninx UBERON:0007645 future meninx EHDAA2 ISBN:0073040584 A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. http://orcid.org/0000-0002-6601-2165 the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d MP:0009726 primary meninx EHDAA2:0004453 meninx primitiva MP:0009726 The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx. future leptomeninges future leptomeninx uberon UBERON:0007646 endomeninx ISBN:9781607950325 The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx. ISBN:9781607950325 The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer). UBERON:0010115 EHDAA2:0004317 future dura mater uberon UBERON:0007647 ectomeninx ISBN:9781607950325 The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer). ISBN:9781607950325 future dura mater EHDAA2:0004317 2 An anatomical structure that connects two structures. junction FMA:5898 SCTID:91833003 anatomical junction uberon UBERON:0007651 anatomical junction FMA An anatomical structure that connects two structures. http://code.google.com/p/caro2/issues/detail?id=15 A sphincter that is part of an esophagus. check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here SCTID:277765007 uberon UBERON:0007652 esophageal sphincter A sphincter that is part of an esophagus. http://orcid.org/0000-0002-6601-2165 Functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. FMA:17691 uberon UBERON:0007684 uriniferous tubule Functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. ISBN:0073040584 Region of the embryo into the area in which the kidney rudiment will develop. uberon kidney anlage UBERON:0007687 kidney field Region of the embryo into the area in which the kidney rudiment will develop. DOI:10.1371/journal.pone.0099864 GO:0072004 GOC:mtg_kidney_jan10 kidney anlage GOC:mtg_kidney_jan10 Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. field AEO:0000170 EFO:0001649 EHDAA2:0003170 FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon future organ organ field UBERON:0007688 anlage FBbt AEO FBbt Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. FBbt:00005426 http://flybase.org/reports/FBrf0178740.html FBbt:00005426 Endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. Wikipedia:Thyroid_diverticulum uberon diverticulum thyroideum saccus thyroideus UBERON:0007689 thyroid diverticulum VHOG Endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. MP:0004662 Wikipedia:Thyroid_diverticulum diverticulum thyroideum Wikipedia:Thyroid_diverticulum saccus thyroideus Wikipedia:Thyroid_diverticulum EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 ZFA:0001104 early pharyngeal arch endoderm uberon pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm UBERON:0007690 relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm http://dev.biologists.org/content/128/22/4573.full cjm early pharyngeal arch endoderm EHDAA2:0001457 pharyngeal endoderm ZFA:0001104 pharyngeal region endoderm EHDAA2:0001456 The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. FMA:63589 NCIT:C33738 SCTID:368724008 UMLS:C0226971 porus gustatorius taste pore uberon UBERON:0007691 gustatory pore https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg FMA FMA The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. http://www.mondofacto.com/facts/dictionary?gustatory+pore UMLS:C0226971 ncithesaurus:Taste_Pore porus gustatorius http://www.mondofacto.com/facts/dictionary?gustatory+pore taste pore FMA:63589 A nucleus of brain that is part of a thalamus. TODO - consider splitting nucleus and complex BTO:0002452 EMAPA:35859 FMA:256693 MA:0002992 SCTID:279115000 Wikipedia:List_of_thalamic_nuclei thalamic nucleus uberon nuclear complex of thalamus UBERON:0007692 nucleus of thalamus A nucleus of brain that is part of a thalamus. OBOL:automatic thalamic nucleus MA:0002992 nuclear complex of thalamus FMA:256693 A bone that is part of a reproductive organ. baculum uberon os penis/os clitoris UBERON:0007719 bone of reproductive organ A bone that is part of a reproductive organ. OBOL:automatic https://github.com/obophenotype/uberon/issues/1158 Wikipedia 2 The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments. EMAPA:36337 FMA:35225 MESH:D014033 NCIT:C32867 NCIT:C33789 SCTID:182225005 UMLS:C0040356 Wikipedia:Interphalangeal_articulations_of_the_foot foot interphalangeal joint hindlimb digit inter-phalangeal joint interphalangeal joint of foot interphalangeal joint of toe uberon toe joint UBERON:0007721 interphalangeal joint of pes two in series The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments. Wikipedia:Interphalangeal_articulations_of_the_foot UMLS:C0040356 ncithesaurus:Interphalangeal_Joint_of_the_Foot foot interphalangeal joint MESH:A02.835.583.378.900 hindlimb digit inter-phalangeal joint EMAPA:36337 interphalangeal joint of foot FMA:35225 interphalangeal joint of toe FMA:35225 NCBITaxon:9606 toe joint MESH:A02.835.583.378.900 2 The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes. consider renaming: 'finger' is ambiguous as the term in some usages excludes the thumb (we include it) EMAPA:36336 FMA:35285 NCIT:C32868 SCTID:303280009 UMLS:C0016125 Wikipedia:Interphalangeal_articulations_of_the_hand articulationes digitorum manus articulationes interphalangeae manus interphalangeal joint of hand interphalangeal joint of finger uberon IP joint articulations of the digits interphalangeal articulations of hand interphalangeal joints of hand UBERON:0007722 interphalangeal joint of manus two in series The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes. Wikipedia:Interphalangeal_articulations_of_the_hand UMLS:C0016125 ncithesaurus:Interphalangeal_Joint_of_the_Hand articulationes digitorum manus Wikipedia:Interphalangeal_articulations_of_the_hand articulationes interphalangeae manus Wikipedia:Interphalangeal_articulations_of_the_hand interphalangeal joint of hand FMA:35285 interphalangeal joint of finger FMA:35285 NCBITaxon:9606 IP joint FMA:35285 articulations of the digits Wikipedia:Interphalangeal_articulations_of_the_hand interphalangeal articulations of hand Wikipedia:Interphalangeal_articulations_of_the_hand interphalangeal joints of hand Wikipedia:Interphalangeal_articulations_of_the_hand 2 An interphalangeal joint of manus that is part of a manual digit 1. in humans, this connects proximal and distal phalanges of the thumb, so there is only a single inter-phalangeal joint - i.e. there is no distinct proximal and distal joints EMAPA:25058 FMA:35312 NCIT:C102306 SCTID:182192008 interphalangeal joint of first digit of hand interphalangeal joint of hand digit 1 interphalangeal joint of manual digit 1 interphalangeal joint of manual digit I interphalangeal joint of pollex interphalangeal joint of thumb uberon UBERON:0007723 interphalangeal joint of manual digit 1 An interphalangeal joint of manus that is part of a manual digit 1. OBOL:automatic interphalangeal joint of first digit of hand FMA:35312 interphalangeal joint of manual digit I https://github.com/obophenotype/uberon/issues/458 interphalangeal joint of thumb FMA:35312 NCBITaxon:9606 2 An interphalangeal joint of pes that is part of a pedal digit 1. EMAPA:26430 FMA:35353 SCTID:363671008 interphalangeal joint of first digit of foot interphalangeal joint of first digit of pes interphalangeal joint of foot digit 1 interphalangeal joint of great toe interphalangeal joint of hallux interphalangeal joint of pedal digit 1 interphalangeal joint of pedal digit I interphalangeal joint of big toe uberon interphalangeal joint of first toe UBERON:0007724 interphalangeal joint of pedal digit 1 An interphalangeal joint of pes that is part of a pedal digit 1. OBOL:automatic interphalangeal joint of first digit of foot FMA:35353 interphalangeal joint of first digit of pes FMA:35353 interphalangeal joint of great toe FMA:35353 interphalangeal joint of pedal digit I https://github.com/obophenotype/uberon/issues/458 interphalangeal joint of big toe FMA:35353 NCBITaxon:9606 interphalangeal joint of first toe FMA:35353 2 An interphalangeal joint of pes that is part of a pedal digit 5. EMAPA:26478 FMA:35365 interphalangeal joint of fifth digit of foot interphalangeal joint of fifth toe interphalangeal joint of pedal digit V interphalangeal joint of little toe uberon UBERON:0007728 interphalangeal joint of pedal digit 5 An interphalangeal joint of pes that is part of a pedal digit 5. OBOL:automatic interphalangeal joint of fifth digit of foot FMA:35365 interphalangeal joint of fifth toe FMA:35365 interphalangeal joint of pedal digit V https://github.com/obophenotype/uberon/issues/458 interphalangeal joint of little toe FMA:35365 NCBITaxon:9606 2 An interphalangeal joint of manus that is part of a manual digit 5. EMAPA:25070 FMA:35407 interphalangeal joint of fifth digit of hand interphalangeal joint of fifth finger interphalangeal joint of manual digit V interphalangeal joint of little finger uberon UBERON:0007732 interphalangeal joint of manual digit 5 An interphalangeal joint of manus that is part of a manual digit 5. OBOL:automatic interphalangeal joint of fifth digit of hand FMA:35407 interphalangeal joint of fifth finger FMA:35407 interphalangeal joint of manual digit V https://github.com/obophenotype/uberon/issues/458 interphalangeal joint of little finger FMA:35407 NCBITaxon:9606 A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 1. EMAPA:25057 FMA:35249 SCTID:361844001 metacarpophalangeal joint of digit 1 metacarpophalangeal joint of first digit of hand metacarpophalangeal joint of manual digit I metacarpo-phalangeal joint of digit 1 of fore-paw metacarpophalangeal joint of thumb uberon UBERON:0007735 metacarpophalangeal joint of manual digit 1 FMA A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 1. OBOL:automatic metacarpophalangeal joint of first digit of hand FMA:35249 metacarpophalangeal joint of manual digit I https://github.com/obophenotype/uberon/issues/458 metacarpo-phalangeal joint of digit 1 of fore-paw EMAPA:25057 metacarpophalangeal joint of thumb FMA:35249 NCBITaxon:9606 A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 5. EMAPA:25069 FMA:35261 SCTID:361848003 metacarpophalangeal joint of digit 5 metacarpophalangeal joint of fifth digit of hand metacarpophalangeal joint of fifth finger metacarpophalangeal joint of manual digit V metacarpo-phalangeal joint of digit 5 of fore-paw metacarpophalangeal joint of little finger uberon UBERON:0007747 metacarpophalangeal joint of manual digit 5 FMA A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 5. OBOL:automatic metacarpophalangeal joint of fifth digit of hand FMA:35261 metacarpophalangeal joint of fifth finger FMA:35261 metacarpophalangeal joint of manual digit V https://github.com/obophenotype/uberon/issues/458 metacarpo-phalangeal joint of digit 5 of fore-paw EMAPA:25069 metacarpophalangeal joint of little finger FMA:35261 NCBITaxon:9606 A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 1. the name of the structure in EMAPA is incorrect EMAPA:26436 FMA:35228 NCIT:C102321 SCTID:182223003 first metatarsophalangeal joint metatarsophalangeal joint of first digit of foot metatarsophalangeal joint of great toe metatarsophalangeal joint of pedal digit I metatarsophalangeal joint of big toe uberon metatarsophalangeal joint of first toe UBERON:0007750 metatarsophalangeal joint of pedal digit 1 FMA A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 1. OBOL:automatic the name of the structure in EMAPA is incorrect EMAPA metatarsophalangeal joint of first digit of foot FMA:35228 metatarsophalangeal joint of great toe FMA:35228 metatarsophalangeal joint of pedal digit I https://github.com/obophenotype/uberon/issues/458 metatarsophalangeal joint of big toe FMA:35228 NCBITaxon:9606 metatarsophalangeal joint of first toe FMA:35228 A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 5. the name of the structure in EMAPA is incorrect EMAPA:26484 FMA:35240 SCTID:361872008 metatarsophalangeal joint of fifth digit of foot metatarsophalangeal joint of fifth toe metatarsophalangeal joint of pedal digit V metatarsophalangeal joint of little toe uberon UBERON:0007762 metatarsophalangeal joint of pedal digit 5 FMA A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 5. OBOL:automatic the name of the structure in EMAPA is incorrect EMAPA metatarsophalangeal joint of fifth digit of foot FMA:35240 metatarsophalangeal joint of fifth toe FMA:35240 metatarsophalangeal joint of pedal digit V https://github.com/obophenotype/uberon/issues/458 metatarsophalangeal joint of little toe FMA:35240 NCBITaxon:9606 A gland that is part of a epidermis. FMA:59153 epidermal gland gland of epidermis uberon UBERON:0007771 epidermis gland A gland that is part of a epidermis. OBOL:automatic gland of epidermis FMA:59153 Any portion of sweat that is produced by a sweat gland of the scrotum. FMA:73266 scrotum sweat sweat of scrotal sac sweat of scrotum uberon UBERON:0007772 scrotal sweat Any portion of sweat that is produced by a sweat gland of the scrotum. OBOL:automatic scrotum sweat OBOL:automatic sweat of scrotal sac OBOL:automatic sweat of scrotum FMA:73266 Any sweat gland that is part of a scrotum. EMAPA:29743 uberon UBERON:0007773 scrotal sweat gland Any sweat gland that is part of a scrotum. OBOL:automatic An endothelium that is part of a umbilical artery. BTO:0000857 uberon UBERON:0007778 umbilical artery endothelium BTO An endothelium that is part of a umbilical artery. OBOL:automatic Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. transudative characteristically low in protein and cellular content (unless there has been secondary concentration) FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate uberon plasma ultrafiltrate UBERON:0007779 transudate Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces. http://medical-dictionary.thefreedictionary.com/transudate Any fluid produced by a serous gland. serous fluid Wikipedia:Serous_fluid serosal fluid serous gland fluid uberon UBERON:0007794 secretion of serous gland Any fluid produced by a serous gland. UBERON:cjm serosal fluid Wikipedia:Serous_fluid Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 MA:0002718 NCIT:C33854 UMLS:C0489903 uberon UBERON:0007798 vascular system MA Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. ncithesaurus:Vascular_System in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system MA UMLS:C0489903 ncithesaurus:Vascular_System A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels BTO:0004705 NCIT:C34132 UMLS:C1516792 uberon UBERON:0007806 connecting stalk EHDAA2 EHDAA2 A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. http://medical-dictionary.thefreedictionary.com/ UMLS:C1516792 ncithesaurus:Connecting_Stalk A vasculature that is part of a connecting stalk. EHDAA2:0000313 connecting stalk blood vessels uberon connecting stalk blood vessel vasculature of connecting stalk UBERON:0007807 connecting stalk vasculature EHDAA2 A vasculature that is part of a connecting stalk. OBOL:automatic connecting stalk blood vessels EHDAA2:0000313 Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:TS-0002 EFO:0003771 uberon abdominal adipose tissue abdominal fat intra-abdominal fat UBERON:0007808 adipose tissue of abdominal region Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 abdominal adipose tissue BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 NCIT:C12418 SCTID:361355005 UMLS:C0460004 WikipediaCategory:Head_and_neck galen:HeadAndNeck uberon cephalic area cephalic part of animal cephalic region head and neck head or neck UBERON:0007811 craniocervical region MA The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. https://orcid.org/0000-0002-6601-2165 UMLS:C0460004 ncithesaurus:Head_and_Neck cephalic area https://github.com/obophenotype/uberon/issues/379 cephalic part of animal Wikipedia:Head cephalic region https://github.com/obophenotype/uberon/issues/379 head and neck FMA:280881 A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species) AAO:0010338 EMAPA:16748 MA:0000008 NCIT:C77663 TAO:0001117 UMLS:C0039259 XAO:0003026 ZFA:0001117 muscular postanal tail postanal tail post-anal fin tail uberon post-vent region UBERON:0007812 post-anal tail possible exception in hemichordates cjm A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. https://orcid.org/0000-0002-6601-2165 Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] 2012-06-20 AAO:0010338 AAO AAO:EJS Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] 2012-08-14 TAO:0001117 TAO ZFIN:curator UMLS:C0039259 ncithesaurus:Tail post-anal fin tail http://purl.oboibrary.org/obo/uberon/tracker/185 post-vent region TAO:0001117 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). this encompasses non-skeletal tissue An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region EMAPA:37854 FMA:24874 VSAO:0000303 uberon fin girdle fin girdle region limb girdle limb girdle region UBERON:0007823 appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] 2012-08-14 VSAO:0000303 VSAO https://orcid.org/0000-0002-6601-2165 EMAPA:37854 MA:th fin girdle fin girdle region limb girdle limb girdle region Mesentery that is located in the peritoneum. FMA:20570 TAO:0005129 XAO:0000138 ZFA:0005129 uberon UBERON:0007826 peritoneal mesentery FMA Mesentery that is located in the peritoneum. UBERON:cjm External part of the nose containing the external nares. Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515]. EMAPA:37831 FMA:59515 NCIT:C32566 SCTID:265785009 UMLS:C0458561 uberon nose UBERON:0007827 external nose External part of the nose containing the external nares. http://orcid.org/0000-0002-6601-2165 Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515]. FMA:59515 EMAPA:37831 MA:th UMLS:C0458561 ncithesaurus:External_Nose A bone that is part of a appendage girdle region. EMAPA:35379 MA:0000291 girdle bone uberon UBERON:0007828 girdle bone/zone A bone that is part of a appendage girdle region. OBOL:automatic girdle bone MA:0000291 A bone that is part of a pectoral girdle region. EMAPA:35669 MA:0000292 bone of pectoral girdle uberon UBERON:0007829 pectoral girdle bone MA A bone that is part of a pectoral girdle region. OBOL:automatic A bone element or fused bone that is part of pelvic girdle. check sacrum, coccyx (MA does NOT include these) typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone EMAPA:18028 MA:0000293 NCIT:C33287 SCTID:426214007 UMLS:C0030786 bone of pelvic girdle pelvic girdle bone uberon UBERON:0007830 pelvic girdle bone/zone MA A bone element or fused bone that is part of pelvic girdle. https://orcid.org/0000-0002-6601-2165 UMLS:C0030786 ncithesaurus:Pelvic_Bone pelvic girdle bone MA:0000293 A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. AAO:0000422 AAO:0000754 EFO:0000946 EHDAA2:0001420 FMA:24141 MAT:0000181 MIAA:0000181 NCIT:C33547 TAO:0000407 UMLS:C0427245 VHOG:0001156 VSAO:0000156 Wikipedia:Pectoral_girdle XAO:0003063 ZFA:0000407 skeletal parts of pectoral girdle skeleton of pectoral girdle uberon cingulum pectorale pectoral girdle scapular girdle UBERON:0007831 pectoral girdle skeleton http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Wikipedia:Pectoral_girdle Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] 2012-08-14 TAO:0000407 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000156 VSAO https://orcid.org/0000-0002-6601-2165 Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] 2012-06-20 AAO:0000422 AAO AAO:LAP The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] 2012-09-17 VHOG:0001156 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18 http://bgee.unil.ch/ Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. VSAO UMLS:C0427245 ncithesaurus:Shoulder_Girdle skeletal parts of pectoral girdle https://orcid.org/0000-0002-6601-2165 skeleton of pectoral girdle https://orcid.org/0000-0002-6601-2165 cingulum pectorale Wikipedia:Pectoral_girdle pectoral girdle VSAO:0000156 scapular girdle TAO:0000407 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 MAT:0000182 MIAA:0000182 TAO:0000565 VHOG:0000305 VSAO:0000155 Wikipedia:Pelvis XAO:0003064 ZFA:0000565 galen:PelvicGirdle http://people.eku.edu/ritchisong/pectoralgirdles.gif pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon pelvic girdle UBERON:0007832 pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png PMID:21455939 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. VSAO:0000155 Wikipedia:Pelvis Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] 2012-06-20 AAO:0000426 AAO AAO:LAP Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] 2012-08-14 TAO:0000565 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000155 VSAO https://orcid.org/0000-0002-6601-2165 The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000305 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 http://bgee.unil.ch/ Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts VSAO pelvic girdle skeleton VSAO:0000155 skeletal parts of pelvic girdle https://orcid.org/0000-0002-6601-2165 skeleton of pelvic girdle https://orcid.org/0000-0002-6601-2165 pelvic girdle VSAO:0000155 Bone element that arises as a result of intramembranous ossification. Bone element that arises as a result of intramembranous ossification.[VSAO] Intramembranous bone that forms deep in the organism.[TAO] AEO:0000085 EHDAA2:0003085 TAO:0001645 VSAO:0000023 XAO:0004014 ZFA:0001636 uberon membrane bones UBERON:0007842 membrane bone VSAO Bone element that arises as a result of intramembranous ossification. GO_REF:0000034 VSAO:0000023 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Bone element that arises as a result of intramembranous ossification.[VSAO] 2012-08-14 VSAO:0000023 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Intramembranous bone that forms deep in the organism.[TAO] 2012-08-14 TAO:0001645 TAO TAO:wd membrane bones ZFA:0001636 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage organ cartilaginous element chondrogenic element uberon cartilage UBERON:0007844 cartilage element VSAO VSAO VSAO Skeletal element that is composed of cartilage tissue and may be permanent or transient. GO_REF:0000034 PSPUB:0000170 VSAO:0000000 http://dx.plos.org/10.1371/journal.pone.0051070 TAO still mixes tissue and element TAO cartilage organ FMA:55107 cartilaginous element https://orcid.org/0000-0002-6601-2165 chondrogenic element VSAO:0000000 cartilage VSAO:0000000 Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). FMA:20103 uberon UBERON:0007845 regular connective tissue FMA Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. FMA:20103 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 SCTID:22560007 UMLS:C0225333 VSAO:0000050 Wikipedia:Dense_regular_connective_tissue XAO:0004030 dense fibrous connective tissue dense regular collagenous connective tissue dense regular collagenous tissue regular dense connective tissue typus regularis (textus connectivus collagenosus compactus) uberon UBERON:0007846 dense regular connective tissue FMA ncithesaurus Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). GO_REF:0000034 PSPUB:0000170 VSAO:0000050 http://dx.plos.org/10.1371/journal.pone.0051070 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] 2012-08-14 VSAO:0000050 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] 2012-08-29 FMA:64781 FMA UMLS:C0225333 ncithesaurus:Regular_Dense_Connective_Tissue dense fibrous connective tissue FMA:64781 dense regular collagenous connective tissue FMA:64781 dense regular collagenous tissue FMA:64781 typus regularis (textus connectivus collagenosus compactus) FMA:64781 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone uberon cranial bone UBERON:0007914 bone of craniocervical region MA MA A bone that is part of a craniocervical region. OBOL:automatic EMAPA:37245 MA:th head or neck bone MA:0000569 A sesamoid bone that is part of a manus. FMA:42353 SCTID:368448000 sesamoid bone of hand uberon UBERON:0007997 sesamoid bone of manus FMA A sesamoid bone that is part of a manus. OBOL:automatic sesamoid bone of hand FMA:42353 A sesamoid bone that is part of a pes. FMA:45096 SCTID:244675002 sesamoid bone of foot uberon UBERON:0008000 sesamoid bone of pes FMA A sesamoid bone that is part of a pes. OBOL:automatic sesamoid bone of foot FMA:45096 The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. FMA:7477 NCIT:C32881 SCTID:421560006 UMLS:C0502414 Wikipedia:Irregular_bone os irregulare uberon os irregulare UBERON:0008001 irregular bone FMA The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. Wikipedia:Irregular_bone UMLS:C0502414 ncithesaurus:Irregular_Bone os irregulare Wikipedia:Irregular_bone A skeletal joint that is part of a appendage girdle region. MA:0001505 girdle joint uberon UBERON:0008114 joint of girdle MA A skeletal joint that is part of a appendage girdle region. OBOL:automatic girdle joint OBOL:automatic An anatomical surface that is part of a cartilage element. FMA:76668 cartilage surface uberon UBERON:0008115 surface of cartilage An anatomical surface that is part of a cartilage element. OBOL:automatic cartilage surface FMA:76668 A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. subclasses of this should be checked for taxonomic consistency Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity] FMA:7478 SCTID:333008005 Wikipedia:Skeletal_pneumaticity galen:PneumaticBone os pneumaticum pneumatic bone uberon hollow bone UBERON:0008193 pneumatized bone A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. http://www.medilexicon.com/medicaldictionary.php?t=11303 os pneumaticum FMA:7478 pneumatic bone FMA:7478 Any muscle organ that is part of a pectoral girdle region. EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA:17748 FMA:37347 muscle of shoulder girdle pectoral girdle muscle uberon UBERON:0008196 muscle of pectoral girdle Any muscle organ that is part of a pectoral girdle region. OBOL:automatic EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA muscle of shoulder girdle FMA:37347 pectoral girdle muscle FMA:37347 The part of the face above the eyes[MESH]. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond[WP]. EMAPA:37869 FMA:63864 GAID:74 MESH:D005546 NCIT:C89803 SCTID:362614004 UMLS:C0016540 Wikipedia:Forehead galen:Forehead uberon fore head sinciput UBERON:0008200 forehead http://upload.wikimedia.org/wikipedia/commons/8/83/Forhead_01_ies.jpg FMA The part of the face above the eyes[MESH]. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond[WP]. MESH:A01.456.505.580 Wikipedia:Forehead EMAPA:37869 MA:th UMLS:C0016540 ncithesaurus:Forehead fore head Wikipedia:Forehead sinciput Wikipedia:Forehead todo - consider obsoletion in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone EMAPA:37308 FMA:42854 MA:0000655 SCTID:304907005 uberon UBERON:0008202 bone of hip region MA in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone MA EMAPA:37308 MA:th The part of the ventral body cavity that is within the pelvis. EMAPA:37235 FMA:9738 MA:0003089 SCTID:281903009 Wikipedia:Pelvic_cavity space of pelvic compartment uberon cavitas pelvis UBERON:0008203 pelvic cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the pelvis. UBERON:cjm EMAPA:37235 MA:th space of pelvic compartment FMA:9738 cavitas pelvis Wikipedia:Pelvic_cavity Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 MA:0000571 TAO:0000328 ZFA:0000328 head or neck muscle uberon head muscles head or neck muscle UBERON:0008229 craniocervical region musculature MA MA Musculature system of the pharyngeal and head regions. ZFA:0000328 ZFA:curator in MA this is restricted to skeletal muscles MA EMAPA:37259 MA:th head or neck muscle MA:0000571 head muscles ZFA:0000328 head or neck muscle MA:0000571 Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. EMAPA:37234 FMA:24217 MA:0000028 SCTID:362666008 dorsum of thorax posterior part of thorax thoracic back thoracic part of back upper back uberon back of thorax UBERON:0008231 dorsal thoracic segment of trunk FMA MA FMA Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. FMA:24217 EMAPA:37234 MA:th dorsum of thorax FMA:24217 posterior part of thorax FMA:24217 thoracic back FMA:24217 thoracic part of back FMA:24217 upper back MA:0000028 back of thorax FMA:24217 A muscle of back that is part of a lower back. EMAPA:37262 MA:0000502 SCTID:317178000 uberon UBERON:0008242 lower back muscle MA MA A muscle of back that is part of a lower back. OBOL:automatic EMAPA:37262 MA:th A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 SCTID:305071003 uberon UBERON:0008243 upper back muscle MA MA A muscle of back that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37261 MA:th A clavicle that is in the right side of a entire appendicular skeleton. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:13322 uberon UBERON:0008255 right clavicle FMA A clavicle that is in the right side of a entire appendicular skeleton. OBOL:automatic A clavicle that is in the left side of a entire appendicular skeleton. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:13323 uberon UBERON:0008256 left clavicle FMA A clavicle that is in the left side of a entire appendicular skeleton. OBOL:automatic The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html]. The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21]. FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA BTO:0001020 CALOHA:TS-0763 EMAPA:35679 FMA:56665 GAID:1259 MA:0002467 MESH:D010513 SCTID:245775004 Wikipedia:Periodontal_fiber fibra periodontalis periodontal fiber periodontal fibre uberon PDL alveolar periosteum alveolodental ligament alveolodental membrane desmodontium odontoperiosteum paradentium peridental membrane peridontal fiber peridontal fibre peridontal ligament peridontal ligament fiber peridontal ligament fibre peridontal membrane peridontium periodontium UBERON:0008266 periodontal ligament https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg FMA-moved BTO PMID:19767574 Wikipedia:Dental_follicle The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. BTO:0001020 Wikipedia:Periodontal_fiber https://github.com/obophenotype/uberon/issues/1233 https://github.com/obophenotype/uberon/issues/21 The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html]. http://www.drugs.com/dict/desmodentium.html The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21]. Wikipedia:Periodontal_fiber FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA FMA MESH:D010513 https://github.com/biopragmatics/biomappings fibra periodontalis Wikipedia:Periodontal_ligament periodontal fiber Wikipedia:Periodontal_ligament periodontal fibre Wikipedia:Periodontal_ligament PDL Wikipedia:Periodontal_ligament alveolar periosteum BTO:0001020 alveolodental ligament BTO:0001020 alveolodental membrane BTO:0001020 desmodontium BTO:0001020 http://www.drugs.com/dict/desmodentium.html odontoperiosteum BTO:0001020 paradentium BTO:0001020 peridental membrane BTO:0001020 peridontal fiber http://www.drugs.com/dict/desmodentium.html peridontal fibre http://www.drugs.com/dict/desmodentium.html peridontal ligament fiber http://www.drugs.com/dict/desmodentium.html peridontal ligament fibre http://www.drugs.com/dict/desmodentium.html peridontal membrane BTO:0001020 peridontium BTO:0001020 periodontium FMA:56665 A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them. BTO:0001838 FMA:306006 MESH:D014083 NCIT:C34313 SCTID:53301001 UMLS:C0040442 dental bud dental germ tooth germ uberon UBERON:0008281 tooth bud A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them. UBERON:cjm http://medical-dictionary.thefreedictionary.com/tooth+germ UMLS:C0040442 ncithesaurus:Tooth_Bud dental bud FMA:306006 dental germ http://medical-dictionary.thefreedictionary.com/tooth+germ tooth germ Wikipedia:Tooth_development An endothelium that is part of a heart [Automatically generated definition]. this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class. BTO:0004293 uberon cardiac endothelium UBERON:0008307 heart endothelium An endothelium that is part of a heart [Automatically generated definition]. OBOL:automatic cardiac endothelium BTO:0004293 A gland that is part of a nasopharynx. FMA:55076 SCTID:178973008 uberon UBERON:0008310 nasopharyngeal gland A gland that is part of a nasopharynx. OBOL:automatic With numerous vascular spaces that may become engorged with blood. Wikipedia:Erectile_tissue uberon UBERON:0008324 Examples: corpus cavernosum or penis or clitoris erectile tissue With numerous vascular spaces that may become engorged with blood. Wikipedia:Erectile_tissue A smooth muscle tissue that is part of a clitoris. BTO:0005000 uberon clitoris smooth muscle UBERON:0008331 clitoral smooth muscle A smooth muscle tissue that is part of a clitoris. OBOL:automatic clitoris smooth muscle BTO:0005000 BTO:0003122 uberon UBERON:0008339 microvascular endothelium https://github.com/obophenotype/uberon/issues/2186 An intestinal villus in the duodenum. FMA:63300 uberon UBERON:0008342 intestinal villus of duodenum An intestinal villus in the duodenum. OBOL:automatic An intestinal villus in the jejunum. FMA:63301 uberon UBERON:0008343 intestinal villus of jejunum An intestinal villus in the jejunum. OBOL:automatic An intestinal villus in the ileum. FMA:63302 uberon UBERON:0008344 intestinal villus of ileum An intestinal villus in the ileum. OBOL:automatic An epithelium that is part of a ileum. EMAPA:35423 FMA:17233 MA:0003217 SCTID:47046000 epithelium of ileum uberon UBERON:0008345 ileal epithelium FMA An epithelium that is part of a ileum. OBOL:automatic epithelium of ileum FMA:17233 An epithelium that is part of a duodenum. CALOHA:TS-2087 EMAPA:19078 FMA:17231 MA:0003208 SCTID:66036002 epithelium of duodenum uberon UBERON:0008346 duodenal epithelium FMA An epithelium that is part of a duodenum. OBOL:automatic epithelium of duodenum FMA:17231 An epithelium that is part of a breast. BTO:0001428 uberon UBERON:0008367 breast epithelium An epithelium that is part of a breast. OBOL:automatic Epithelium pertaining to the trachea and bronchi. BTO:0002925 CALOHA:TS-1063 uberon bronchotracheal epithelium UBERON:0008397 tracheobronchial epithelium Epithelium pertaining to the trachea and bronchi. Dorlands_Medical_Dictionary:MerckMedicus bronchotracheal epithelium BTO:0002925 An epithelium that is part of a buccal mucosa. BTO:0004803 uberon UBERON:0008420 buccal epithelium BTO An epithelium that is part of a buccal mucosa. OBOL:automatic A ridge of epidermal cells that will form the mammary placodes. consider splitting ridge (precursor) and milk line These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission. in mouse, mammary gland development begins shortly after mid-gestation (about E10.5); epidermal cells within the milk line become columnar and multilayered, defining a ridge that protrudes above and below the plane of the single-layered primitive epidermis or periderm; by E11.5, five pairs of lens-shaped placodes form along the mammary line at the site of each future nipple.[MP] EMAPA:18541 Wikipedia:Milk_line mammary fold mammary gland ridge uberon mammary line milk line UBERON:0008425 mammary ridge A ridge of epidermal cells that will form the mammary placodes. GOC:dph mammary fold http://dictionary.reference.com/browse/mammary+ridge mammary gland ridge EMAPA:18541 mammary line Wikipedia:Milk_line milk line Wikipedia:Milk_line A vertebral foramen that is part of a cervical vertebra. FMA:13480 SCTID:280833008 uberon UBERON:0008429 cervical vertebral foramen A vertebral foramen that is part of a cervical vertebra. OBOL:automatic A vertebral foramen that is part of a lumbar vertebra. FMA:24826 SCTID:280835001 uberon UBERON:0008430 lumbar vertebral foramen A vertebral foramen that is part of a lumbar vertebra. OBOL:automatic A vertebral foramen that is part of a sacral vertebra. FMA:31749 uberon UBERON:0008431 sacral foramen A vertebral foramen that is part of a sacral vertebra. OBOL:automatic A vertebral foramen that is part of a thoracic vertebra. FMA:9143 SCTID:280834002 uberon UBERON:0008432 thoracic vertebral foramen A vertebral foramen that is part of a thoracic vertebra. OBOL:automatic A neural arch that is part of a lumbar vertebra. FMA:16076 SCTID:312766000 arch of lumbar vertebra uberon UBERON:0008433 lumbar vertebral arch A neural arch that is part of a lumbar vertebra. OBOL:automatic arch of lumbar vertebra FMA:16076 A neural arch that is part of a cervical vertebra. FMA:23893 SCTID:165269004 arch of cervical vertebra uberon UBERON:0008434 cervical vertebral arch A neural arch that is part of a cervical vertebra. OBOL:automatic arch of cervical vertebra FMA:23893 A neural arch that is part of a sacral vertebra. FMA:32401 uberon UBERON:0008435 vertebral arch of sacral segment A neural arch that is part of a sacral vertebra. OBOL:automatic A neural arch that is part of a thoracic vertebra. FMA:9151 SCTID:312764002 arch of thoracic vertebra uberon UBERON:0008436 thoracic vertebral arch A neural arch that is part of a thoracic vertebra. OBOL:automatic arch of thoracic vertebra FMA:9151 2 Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation. EMAPA:37762 FMA:44281 GAID:259 MA:0003112 MESH:D013640 NCIT:C33735 SCTID:182221001 SCTID:361283005 UMLS:C1527245 Wikipedia:Intertarsal_articulations uberon articulationes intertarsale articulationes intertarsales articulationes intertarseae intermetatarsal joint intertarsal intertarsal articulation intertarsal joint tarsal joint tarsal joints UBERON:0008447 intertarsal joint http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png two adjacent tarsals Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation. Wikipedia:Intertarsal_articulations EMAPA:37762 MA:th UMLS:C1527245 ncithesaurus:Tarsal_Joint articulationes intertarsale MESH:A02.835.583.378.831 articulationes intertarsales Wikipedia:Intertarsal_articulations articulationes intertarseae MESH:A02.835.583.378.831 intermetatarsal joint MESH:A02.835.583.378.831 intertarsal Wikipedia:Intertarsal_articulations intertarsal articulation Wikipedia:Intertarsal_articulations intertarsal joint MESH:A02.835.583.378.831 tarsal joint MESH:A02.835.583.378.831 tarsal joints Wikipedia:Intertarsal_articulations Any muscle organ that is part of an nose. FMA:73758 NCIT:C33158 SCTID:244730009 UMLS:C0224219 muscle of nose uberon UBERON:0008522 nasal muscle FMA Any muscle organ that is part of an nose. OBOL:automatic UMLS:C0224219 ncithesaurus:Nasal_Muscle muscle of nose OBOL:automatic EHDAA2:0001421 EMAPA:17748 RETIRED_EHDAA2:0001422 uberon UBERON:0008713 pectoral girdle and thoracic body wall skeletal muscle A muscle tissue that is part of a prostate gland. NCIT:C13100 SCTID:251498008 UMLS:C1183911 prostate gland muscle tissue prostate muscle tissue prostatic muscle prostatic musclular tissue uberon UBERON:0008715 muscle tissue of prostate A muscle tissue that is part of a prostate gland. OBOL:automatic UMLS:C1183911 ncithesaurus:Prostatic_Muscular_Tissue prostate gland muscle tissue OBOL:automatic prostate muscle tissue OBOL:automatic A proximal epiphysis that is part of a tibia. FMA:33113 NCIT:C32722 SCTID:302526005 UMLS:C0932431 Wikipedia:Upper_extremity_of_tibia head of tibia proximal end of tibia proximal tibial epiphysis upper end of tibia uberon UBERON:0008772 proximal epiphysis of tibia A proximal epiphysis that is part of a tibia. OBOL:automatic UMLS:C0932431 ncithesaurus:Head_of_the_Tibia head of tibia FMA:33113 proximal end of tibia FMA:33113 upper end of tibia FMA:33113 A proximal epiphysis that is part of a fibula. The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula]. EMAPA:37890 FMA:33729 NCIT:C32719 SCTID:182080006 UMLS:C0223908 Wikipedia:Head_of_fibula galen:HeadOfFibula caput fibulae head of fibula proximal end of fibula upper end of fibula uberon fibular head UBERON:0008775 proximal epiphysis of fibula A proximal epiphysis that is part of a fibula. OBOL:automatic The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula]. Wikipedia:Head_of_fibula EMAPA:37890 MA:th UMLS:C0223908 ncithesaurus:Head_of_the_Fibula caput fibulae Wikipedia:Head_of_fibula head of fibula FMA:33729 proximal end of fibula FMA:33729 upper end of fibula FMA:33729 fibular head FMA:33729 An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers. EHDAA2:0000444 EHDAA:42 EHDAA:75 EMAPA:16050 NCIT:C34164 UMLS:C1516906 uberon embryonic epiblast UBERON:0008780 The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5. inner cell mass derived epiblast Wikipedia An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers. MP:0003886 UMLS:C1516906 ncithesaurus:Epiblast embryonic epiblast MP:0003886 The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein. EMAPA:37521 FMA:44356 MA:0002110 SCTID:231189006 Wikipedia:Dorsal_venous_arch_of_the_foot arcus venosus dorsalis pedis dorsal venous arch of foot uberon arcus venosus dorsalis pedis UBERON:0008783 dorsal venous arch http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png MA The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein. Wikipedia:Dorsal_venous_arch_of_the_foot EMAPA:37521 MA:th arcus venosus dorsalis pedis Wikipedia:Dorsal_venous_arch_of_the_foot dorsal venous arch of foot FMA:44356 arcus venosus dorsalis pedis Wikipedia:Dorsal_venous_arch_of_the_foot A limb segment that is part of a hindlimb. FMA:24877 free lower limb segment free lower limb subdivision segment of free lower limb subdivision of free lower limb uberon UBERON:0008784 lower limb segment A limb segment that is part of a hindlimb. OBOL:automatic free lower limb segment FMA:24877 free lower limb subdivision FMA:24877 segment of free lower limb FMA:24877 subdivision of free lower limb FMA:24877 A limb segment that is part of a forelimb. FMA:24876 free upper limb segment free upper limb subdivision segment of free upper limb subdivision of free upper limb uberon UBERON:0008785 upper limb segment A limb segment that is part of a forelimb. OBOL:automatic free upper limb segment FMA:24876 free upper limb subdivision FMA:24876 segment of free upper limb FMA:24876 subdivision of free upper limb FMA:24876 Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity. todo - review the relationships for this and its subclasses; the relation should be bounded rather than part of, and contains should be used for the brain parts contained by the fossae FMA:321144 uberon UBERON:0008789 cranial fossa true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity. http://mw1.merriam-webster.com/medical/cranial%20fossa A zone of skin that is part of a cheek. FMA:24759 SCTID:181472009 cheek skin uberon UBERON:0008803 skin of cheek A zone of skin that is part of a cheek. OBOL:automatic cheek skin FMA:24759 An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] AAO:0010255 FBbt:00004850 HAO:0000091 TAO:0002036 TGMA:0000585 Wikipedia:Intromittent_organ aedeagus penis uberon copulatory organ UBERON:0008811 intromittent organ An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. Wikipedia:Intromittent_organ Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] 2012-08-14 TAO:0002036 TAO TAO:wd FBbt:00004850 aedeagus FBbt:00004850 A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 NCIT:C34248 UMLS:C1519038 embryonic pharyngeal complex pharyngeal apparatus pharyngeal system uberon pharyngeal arch complex pharyngeal arch region pharyngeal arches and clefts pharyngeal complex UBERON:0008814 pharyngeal arch system A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. GO:0060037 GOC:dph UMLS:C1519038 ncithesaurus:Pharyngeal_Apparatus pharyngeal system GO:0060037 pharyngeal arch region EHDAA2:0000187 A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 uberon UBERON:0008816 embryonic head A head that is part of a embryo. OBOL:automatic FBbt:00000155 An endoderm that is part of a thymus primordium. uberon UBERON:0008817 thymus primordium endoderm PMID:16313389 An endoderm that is part of a thymus primordium. OBOL:automatic A brain that develops_from a neural tube. a reasoner should automatically classify all the vertebrate ontology brain classes here vertebrate brain uberon UBERON:0008823 neural tube derived brain https://github.com/obophenotype/uberon/issues/338 ZFA FMA A brain that develops_from a neural tube. OBOL:automatic https://github.com/obophenotype/uberon/issues/338 Any duct branching of of the main epididymis duct. EMAPA:36525 FMA:18297 MA:0001735 NCIT:C32484 SCTID:279623004 UMLS:C0458632 epididymal duct epididymis duct uberon UBERON:0008824 duct of epididymis FMA Any duct branching of of the main epididymis duct. http://orcid.org/0000-0002-6601-2165 UMLS:C0458632 ncithesaurus:Duct_of_the_Epididymis epididymal duct MA:0001735 epididymis duct FMA:18297 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. AAO:0011057 EHDAA2:0000740 EHDAA:1530 NCIT:C34187 UMLS:C1512407 Wikipedia:Hepatic_diverticulum XAO:0000101 liver diverticulum uberon diverticulum hepaticum UBERON:0008835 hepatic diverticulum http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png EHDAA2 caudal part EHDAA2 EHDAA2 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. MP:MP http://www.stembook.org/node/512 UMLS:C1512407 ncithesaurus:Hepatic_Diverticulum liver diverticulum XAO:0000101 diverticulum hepaticum Wikipedia:Hepatic_diverticulum BTO:0001642 uberon UBERON:0008836 liver bud cjm http://www.stembook.org/node/512 A ligament that does not connect two skeletal elements. Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]. this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus. FMA:25625 MA:0003004 SCTID:410746001 non-skeletal ligament uberon fibrous ligament UBERON:0008845 nonskeletal ligament cjm A ligament that does not connect two skeletal elements. http://orcid.org/0000-0002-6601-2165 Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]. FMA:25625 this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus. FMA fibrous ligament Wikipedia:Ligament Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]. logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO] Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]. ligament AAO:0010444 AEO:0000090 CALOHA:TS-2146 EHDAA2:0003232 EV:0100144 FMA:25624 GAID:118 MA:0003005 SCTID:410744003 VSAO:0000072 Wikipedia:Ligament#Articular_ligaments articular larua articular ligament true ligament uberon UBERON:0008846 skeletal ligament https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg AEO AEO bones or cartilage organs VSAO Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]. GO_REF:0000034 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO] 2012-08-14 VSAO:0000072 VSAO PSPUB:0000170 Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]. FMA:25624 ligament VSAO:0000072 ZFA:0001675 articular larua Wikipedia:Ligament articular ligament Wikipedia:Ligament true ligament Wikipedia:Ligament Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals. EMAPA:16080 epamniotic cavity uberon epamniotic cavity UBERON:0008851 ectoplacental cavity Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals. MP:0011207 http://www.medilexicon.com/medicaldictionary.php?s=epamniotic+cavity epamniotic cavity http://www.medilexicon.com/medicaldictionary.php?s=epamniotic+cavity epamniotic cavity MP:0011207 The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines. the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two FMA:14909 SCTID:362132003 gastric muscularis muscle layer of stomach muscularis externa of stomach tunica muscularis (gaster) tunica muscularis gastris uberon UBERON:0008856 stomach muscularis externa MA-abduced The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines. MP:0010779 the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two WP gastric muscularis FMA:14909 muscle layer of stomach FMA:14909 muscularis externa of stomach FMA:14909 tunica muscularis (gaster) FMA:14909 The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter. EMAPA:37944 FMA:14580 SCTID:245417002 Wikipedia:Pyloric_canal canalis pyloricus uberon canalis pyloricus UBERON:0008858 pyloric canal https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg FMA Wikipedia The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter. MP:0010791 Wikipedia:Pyloric_canal EMAPA:37944 MA:th canalis pyloricus Wikipedia:Pyloric_canal canalis pyloricus Wikipedia:Pyloric_canal A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP]. The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]. Kardong places this in the glandular epithelium, FMA more generally in the mucosa EMAPA:37459 FMA:14920 SCTID:8894005 Wikipedia:Cardiac_glands gardiac gland gastric cardiac gland gastric cardiac mucuous gland gastric gland of cardia glandula cardiaca (gaster) uberon cardiac gland UBERON:0008859 cardiac gastric gland MP FMA A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP]. MP:0010795 Wikipedia:Cardiac_glands The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]. Wikipedia:Cardiac_glands Kardong places this in the glandular epithelium, FMA more generally in the mucosa FMA EMAPA:37459 MA:th gardiac gland ISBN:0073040584 gastric cardiac gland FMA:14920 gastric gland of cardia FMA:14920 glandula cardiaca (gaster) FMA:14920 cardiac gland FMA:14920 The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. check relationship to pylorus vs antrum EMAPA:27211 FMA:14922 NCIT:C33431 SCTID:70710007 UMLS:C0227239 Wikipedia:Pyloric_gland glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon UBERON:0008861 pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png MP Wikipedia:Tubular_gland The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. MP:0010797 Wikipedia:Pyloric_gland UMLS:C0227239 ncithesaurus:Pyloric_Gland glandula pylorica FMA:14922 pyloric antrum gland OBOL:automatic pyloric gland FMA:14922 Any skeletal muscle organ in the hypodermis / superficial fascia. We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this UBERON:0010934 EMAPA:18188 MA:0003140 hypodermal muscle layer hypodermis muscle layer superficial fascia muscular layer panniculus carnosus uberon UBERON:0008876 hypodermis skeletal muscle layer MP-def Any skeletal muscle organ in the hypodermis / superficial fascia. ISBN:0123813611 MP:0011157 hypodermal muscle layer MP:0011157 hypodermis muscle layer MP:0011157 panniculus carnosus MP:0011157 Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue. Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO] Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. EMAPA:37923 FMA:66830 NCIT:C33228 SCTID:39365008 UMLS:C0682561 VSAO:0000046 Wikipedia:Osteoid XAO:0004035 galen:Osteoid osteoid tissue pre-bone prebone prebone tissue uberon UBERON:0008883 osteoid https://upload.wikimedia.org/wikipedia/commons/9/9c/Active_osteoblasts.jpg VSAO Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue. GO_REF:0000034 VSAO:0000046 http://dx.plos.org/10.1371/journal.pone.0051070 Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO] 2012-08-14 VSAO:0000046 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n ISBN:0-683-40008-8 MP:0010924 Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. VSAO EMAPA:37923 MA:th UMLS:C0682561 ncithesaurus:Osteoid osteoid tissue http://orcid.org/0000-0002-6601-2165 pre-bone PSPUB:0000170 prebone VSAO:curator prebone tissue FMA:66830 MP:0002113 The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA:45621 Wikipedia:Pulmonary_circulation pulmonary circulatory system pulmonary system uberon UBERON:0008886 pulmonary vascular system Obol The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. ISBN:0073040584 Wikipedia:Pulmonary_circulation Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA FMA:45621 pulmonary circulatory system FMA:45621 pulmonary system ISBN:0073040584 The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus. FMA:18933 NCIT:C32728 SCTID:303051005 UMLS:C0226766 Wikipedia:Rectal_venous_plexus uberon haemorrhoidal plexus hemorrhoidal plexus plexus haemorrhoidalis plexus venosus rectalis UBERON:0008887 rectal venous plexus http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png FMA The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus. Wikipedia:Rectal_venous_plexus UMLS:C0226766 ncithesaurus:Hemorrhoidal_Plexus haemorrhoidal plexus Wikipedia:Rectal_venous_plexus hemorrhoidal plexus Wikipedia:Rectal_venous_plexus plexus haemorrhoidalis Wikipedia:Rectal_venous_plexus plexus venosus rectalis Wikipedia:Rectal_venous_plexus Subdivision of endoskeleton derived from pharyngeal arches. Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both AAO:0010157 TAO:0001216 VHOG:0000315 VSAO:0000149 Wikipedia:Facial_skeleton XAO:0003176 ZFA:0001216 pharyngeal endoskeleton viscerocranium uberon branchial arch skeleton gill arch skeleton pharyngeal arch pharyngeal arch skeleton pharyngeal skeleton visceral cranium visceral skeletal system visceral skeleton UBERON:0008895 splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg https://github.com/obophenotype/uberon/issues/83 redundant Grays PMID:11237469 Subdivision of endoskeleton derived from pharyngeal arches. ISBN:0073040584 Wikipedia:Facial_skeleton https://orcid.org/0000-0002-6601-2165 Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] 2012-08-14 TAO:0001216 TAO ZFIN:curator Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] 2012-06-20 AAO:0010157 AAO AAO:EJS The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] 2012-09-17 VHOG:0000315 VHOG http://bgee.unil.ch/ The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000315 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235 http://bgee.unil.ch/ VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO pharyngeal endoskeleton http://orcid.org/0000-0002-6601-2165 viscerocranium VHOG:0000315 Wikipedia:Viscerocranium ZFA:0001216 pharyngeal arch VSAO:0000149 pharyngeal arch skeleton ZFA:0001216 pharyngeal skeleton ZFA:0001216 visceral cranium http://orcid.org/0000-0002-6601-2165 visceral skeletal system http://orcid.org/0000-0002-6601-2165 visceral skeleton UBERONREF:0000007 A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] AAO:0010362 BTO:0002152 EFO:0003694 SCTID:308766004 TAO:0001597 XAO:0000099 ZFA:0001613 branchial arch branchial arches branchial bar branchial bars gill arch gill arches 1-5 pharyngeal arch 3-7 visceral arches 3-7 uberon gill bar UBERON:0008896 post-hyoid pharyngeal arch A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. https://orcid.org/0000-0002-6601-2165 Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] 2012-06-20 AAO:0010362 AAO AAO:EJS branchial arch ZFA:0001613 branchial arches ZFA:0001613 branchial bar ZFA:0001613 branchial bars ZFA:0001613 gill arch ZFA:0001613 gill arches 1-5 ZFA:0001613 pharyngeal arch 3-7 ZFA:0001613 visceral arches 3-7 ZFA:0001613 gill bar https://orcid.org/0000-0002-6601-2165 Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification AAO:0010769 TAO:0001590 VSAO:0000130 Wikipedia:Dermal_bone XAO:0004015 ZFA:0001590 uberon dermal bones UBERON:0008907 dermal bone wd VSAO VSAO Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. GO_REF:0000034 VSAO:0000130 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Intramembranous bone that forms superficially in the organism.[TAO] 2012-08-14 TAO:0001590 TAO TAO:wd dermal bones ZFA:0001590 Bone element that is adjacent to the notochord. We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] AAO:0010777 TAO:0001639 VSAO:0000307 ZFA:0001629 perichordal bones uberon perichordal bone UBERON:0008909 perichordal bone not in VSAO ZFA Bone element that is adjacent to the notochord. GO_REF:0000034 VSAO:0000307 http://dx.plos.org/10.1371/journal.pone.0051070 Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] 2012-08-14 TAO:0001639 TAO TAO:wd perichordal bones ZFA:0001629 perichordal bone ZFA:0001629 A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 MA:0003168 SCTID:201712001 respiratory portion of lung uberon parenchyma of lung pulmonary parenchyma UBERON:0008946 lung parenchyma FMA FMA A parenchyma that is part of a lung. OBOL:automatic respiratory portion of lung FMA:27360 parenchyma of lung BTO:0000763 pulmonary parenchyma EMAPA:35522 EHDAA2:0004069 NCIT:C34283 UMLS:C1514898 uberon UBERON:0008947 respiratory primordium Obol UMLS:C1514898 ncithesaurus:Respiratory_Primordium A lobe of lung that is part of a left lung. 1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure EHDAA:2981 NCIT:C48945 SCTID:272655003 UMLS:C1285107 lobe of left lung lobe of the left lung uberon UBERON:0008951 left lung lobe A lobe of lung that is part of a left lung. OBOL:automatic 1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure ISBN:0123813611 UMLS:C1285107 ncithesaurus:Lobe_of_the_Left_Lung A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder. GAID:178 MESH:D001133 NCIT:C12983 SCTID:368532003 UMLS:C0003793 free forelimb bone wing bone uberon UBERON:0008962 forelimb bone A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder. https://orcid.org/0000-0002-6601-2165 UMLS:C0003793 ncithesaurus:Bone_of_the_Upper_Extremity free forelimb bone UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 wing bone Geisha:syn NCBITaxon:8782 OBOL:automatic A sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively. BTO:0000337 EMAPA:35275 MA:0003121 MESH:D003795 NCIT:C34138 SCTID:110975002 Wikipedia:Dental_follicle uberon dental sac tooth follicle UBERON:0008969 dental follicle A sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively. Wikipedia:Dental_follicle MESH:D003795 https://github.com/biopragmatics/biomappings dental sac MA:0003121 Wikipedia:Dental_follicle tooth follicle BTO:0000337 Any exocrine gland whose cells bud their secretions off through the plasma membrane producing membrane-bound vesicles in the lumen; the apical portion of the secretory cell of the gland pinches off and enters the lumen; it loses part of its cytoplasm in their secretions; apocrine secretion is functional during hormonal stress or puberty; an example of true apocrine glands are mammary glands, responsible for secreting breast milk. apocrine Mammary glands are modified apocrine glands present in both humans and mice; unlike humans, mice do not have axillary apocrine sweat glands[MGI:anna] BTO:0001162 EMAPA:35141 MA:0003040 MESH:D001050 SCTID:361698000 Wikipedia:Apocrine true apocrine gland uberon UBERON:0008974 apocrine gland Any exocrine gland whose cells bud their secretions off through the plasma membrane producing membrane-bound vesicles in the lumen; the apical portion of the secretory cell of the gland pinches off and enters the lumen; it loses part of its cytoplasm in their secretions; apocrine secretion is functional during hormonal stress or puberty; an example of true apocrine glands are mammary glands, responsible for secreting breast milk. MGI:anna MESH:D001050 https://github.com/biopragmatics/biomappings The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 SCTID:29704000 parenchyma of kidney uberon kidney parenchyma UBERON:0008987 renal parenchyma FMA FMA The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 parenchyma of kidney FMA:15574 kidney parenchyma BTO:0003604 One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed. BTO:0003634 FMA:9404 NCIT:C32536 SCTID:322749003 UMLS:C0227178 Wikipedia:Esophageal_glands esophageal gland glandulae oesophageae mucous gland of submucosa of esophagus uberon submocosal esophageal gland UBERON:0008989 submucosal esophageal gland http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed. BTO:0003634 Wikipedia:Esophageal_glands UMLS:C0227178 ncithesaurus:Esophageal_Gland esophageal gland FMA:9404 glandulae oesophageae Wikipedia:Esophageal_glands mucous gland of submucosa of esophagus FMA:9404 System pertaining to blood vessels in the brain. UBERON:0005284 BTO:0003840 EFO:0003491 EMAPA:35186 FMA:242007 FMA:61935 SCTID:362029003 TAO:0000099 ZFA:0000099 brain vasculature cerebrovascular system intracerebral vasculature uberon UBERON:0008998 vasculature of brain System pertaining to blood vessels in the brain. BTO:0003840 cerebrovascular system BTO:0003840 intracerebral vasculature FMA:61935 Any portion of tissue that surrounds a urethra. BTO:0005081 SCTID:256880003 uberon UBERON:0009010 periurethral tissue Any portion of tissue that surrounds a urethra. UBERON:cjm A zone of skin that is part of a lower back. EMAPA:37281 MA:0000504 SCTID:286601005 uberon UBERON:0009014 lower back skin MA A zone of skin that is part of a lower back. OBOL:automatic EMAPA:37281 MA:th A zone of skin that is part of a dorsal thoracic segment of trunk. EMAPA:37280 MA:0000510 SCTID:304890003 uberon UBERON:0009015 upper back skin MA A zone of skin that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37280 MA:th An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:0002078 SCTID:244307000 arteria vesicali vesical arteries uberon UBERON:0009027 vesical artery An artery that supplies blood to the urinary bladder. http://orcid.org/0000-0002-6601-2165 EMAPA:37131 MA:th arteria vesicali vesical arteries Either the internal or external pudendal vein, running from the genital-vulvar area and abdomen and down the leg. EMAPA:37184 MA:0002202 SCTID:395225000 vena pudendae vena pudendales uberon pudic vein UBERON:0009029 pudendal vein MA Either the internal or external pudendal vein, running from the genital-vulvar area and abdomen and down the leg. http://orcid.org/0000-0002-6601-2165 https://veintreatmentcenter.com/vein-information/pudendal-veins/ EMAPA:37184 MA:th vena pudendae doi:10.1002/ca.23705 vena pudendales doi:10.1002/ca.23705 Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. EMAPA:37165 MA:0002207 NCIT:C48946 SCTID:304057004 UMLS:C0226670 uberon UBERON:0009030 left pulmonary vein Vein that drains left lung and returns blood to the heart. http://orcid.org/0000-0002-6601-2165 A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. ncithesaurus:Left_Pulmonary_Vein EMAPA:37165 MA:th UMLS:C0226670 ncithesaurus:Left_Pulmonary_Vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. EMAPA:37379 MA:0002208 NCIT:C48947 SCTID:304056008 UMLS:C0226669 uberon UBERON:0009032 right pulmonary vein Vein that drains right lung and returns blood to the heart. http://orcid.org/0000-0002-6601-2165 A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. ncithesaurus:Right_Pulmonary_Vein EMAPA:37379 MA:th UMLS:C0226669 ncithesaurus:Right_Pulmonary_Vein The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses. FMA:29711 SCTID:303052003 Wikipedia:Prostatic_venous_plexus uberon plexus venosus prostaticus pudendal venous plexus UBERON:0009042 prostatic venous plexus http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses. Wikipedia:Prostatic_venous_plexus plexus venosus prostaticus Wikipedia:Prostatic_venous_plexus pudendal venous plexus FMA:29711 An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 IDOMAL:0000443 uberon gravid pregnant adult pregnant adult stage pregnant organism pregnant stage UBERON:0009097 gravid organism An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 IDOMAL:0000443 https://github.com/biopragmatics/biomappings gravid BTO:0004733 pregnant adult BTO:0004733 pregnant adult stage BTO:0004733 pregnant stage BTO:0004733 The uterus in pregnancy. NCIT:C12406 SCTID:362253003 UMLS:C1514389 ncithesaurus:Gravid_Uterus uberon womb UBERON:0009098 gravid uterus The uterus in pregnancy. http://medical-dictionary.thefreedictionary.com/gravid+uterus UMLS:C1514389 ncithesaurus:Pregnant_Uterus A mature thymus that is entirely part of the cervical region. A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125] uberon UBERON:0009114 cervical thymus A mature thymus that is entirely part of the cervical region. https://orcid.org/0000-0002-6601-2165 A mature thymus that is entirely part of thoracic region. uberon UBERON:0009115 thoracic thymus A mature thymus that is entirely part of thoracic region. https://orcid.org/0000-0002-6601-2165 A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 NCIT:C34192 UMLS:C1512703 uberon gonad rudiment UBERON:0009117 typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. http://www.medterms.com/script/main/art.asp?articlekey=8981 UMLS:C1512703 ncithesaurus:Indifferent_Gonad The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary. consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009) EFO:0000229 TAO:0001198 XAO:0004208 ZFA:0001198 uberon pituitary placode UBERON:0009122 adenohypophyseal placode NCBIBook:NBK53175 ZFA The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary. http://www.ncbi.nlm.nih.gov/books/NBK53175/ pituitary placode ZFA:0001198 Rostralmost epibranchial placode. Associated with 1st branchial cleft. EHDAA2:0004206 TAO:0001295 XAO:0004211 ZFA:0001295 epibranchial placode 1 facial epibranchial placode facial placode uberon facial VII placode hyoid VII placode hyoid placode UBERON:0009124 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion geniculate placode ZFA Rostralmost epibranchial placode. Associated with 1st branchial cleft. NCBIBook:NBK53175 epibranchial placode 1 EHDAA2:0004206 facial epibranchial placode XAO:0004211 facial placode ZFA:0001295 hyoid VII placode ISBN:0471888893 hyoid placode ISBN:0471888893 Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. EHDAA2:0004207 TAO:0001296 XAO:0004212 ZFA:0001296 epibranchial placode 2 glossopharyngeal IX placode glossopharyngeal epibranchial placode glossopharyngeal placode uberon UBERON:0009125 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode ZFA Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. NCBIBook:NBK53175 epibranchial placode 2 EHDAA2:0004207 glossopharyngeal IX placode ISBN:0471888893 glossopharyngeal epibranchial placode XAO:0004212 glossopharyngeal placode ISBN:0471888893 ZFA:0001296 Cranial ganglion which develops from an epibranchial placode. BTO:0006250 TAO:0001555 ZFA:0001555 epibranchial ganglia uberon UBERON:0009127 Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion ZFA NCBIBook:NBK53175 Cranial ganglion which develops from an epibranchial placode. PMID:20133851 ZFIN:curator BTO:0006250 https://github.com/biopragmatics/biomappings epibranchial ganglia ZFA:0001555 Endocardium that is part of the right atrium. EHDAA2:0000274 FMA:7281 NCIT:C102339 SCTID:3194006 VHOG:0001228 endocardium of right atrium right atrial endocardium uberon right atrium endocardial tissue UBERON:0009129 right atrium endocardium EHDAA2 EHDAA2 Endocardium that is part of the right atrium. http://orcid.org/0000-0002-6601-2165 endocardium of right atrium FMA:7281 right atrial endocardium FMA:7281 right atrium endocardial tissue VHOG:0001228 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] UBERON:0009146 EHDAA2:0001483 EMAPA:17709 NCIT:C34256 SCTID:361429005 UMLS:C1283968 VHOG:0000757 Wikipedia:Pleuroperitoneal pleuroperitoneal fold pleuroperitoneal membranes uberon UBERON:0009133 pleuroperitoneal membrane EHDAA2 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. Wikipedia:Pleuroperitoneal http://medical-dictionary.thefreedictionary.com/pleuroperitoneal+membrane In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000757 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ UMLS:C1283968 ncithesaurus:Pleuroperitoneal_Membrane pleuroperitoneal fold VHOG:0000757 pleuroperitoneal membranes EHDAA2:0001483 A vein that is part of a craniocervical region. EHDAA2:0004542 SCTID:32945007 craniocervical vein head and neck veins vein of head and neck uberon UBERON:0009141 craniocervical region vein A vein that is part of a craniocervical region. OBOL:automatic head and neck veins EHDAA2:0004542 Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 uberon UBERON:0009142 entire embryonic mesenchyme EHDAA2 Sum total of mesenchyme in the embryo. https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7 EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region uberon UBERON:0009145 pharyngeal region of foregut EHDAA2 pharyngeal region EMAPA:16549 A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0003446 EMAPA:18015 uberon UBERON:0009191 sphenoid bone pre-cartilage condensation EHDAA2 EHDAA2 EHDAA2 EHDAA2 A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A sphenoid endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001888 sphenoid bone cartilage condensation uberon UBERON:0009193 sphenoid cartilage element EHDAA2 A sphenoid endochondral element that is composed primarily of cartilage tissue. OBOL:automatic sphenoid bone cartilage condensation EHDAA2:0001888 EHDAA2:0004021 uberon UBERON:0009196 indifferent external genitalia cjm 2 Any suture between cranial and/or facial bones. we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA joint of the skull bones uberon articulation of skull bones UBERON:0009198 craniofacial suture Any suture between cranial and/or facial bones. GO:0097094 joint of the skull bones OBOL:automatic articulation of skull bones OBOL:automatic 2 Any suture between facial bones. uberon UBERON:0009199 facial suture between two adjacent facial bones Any suture between facial bones. GO:0097096 The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. EMAPA:32728 uberon UBERON:0009200 limb epidermis The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. GOC:dph GOC:sdb_2009 GOC:tb A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:16577 Wikipedia:Wolffian_duct uberon UBERON:0009201 pronephric duct or mesonephric duct nephric duct EHDAA2 A nephric duct is a tube that drains a primitive kidney[GO]. GO:0072176 Mesenchyme that is part of a medial nasal prominence. EHDAA2:0001077 EMAPA:16810 FMA:312659 uberon UBERON:0009204 medial nasal process mesenchyme EHDAA2 lexical Mesenchyme that is part of a medial nasal prominence. OBOL:automatic Mesenchyme that is part of a lateral nasal prominence. EHDAA2:0000917 EMAPA:16807 FMA:312665 mesenchyme of latero-nasal process uberon UBERON:0009205 lateral nasal process mesenchyme Mesenchyme that is part of a lateral nasal prominence. OBOL:automatic mesenchyme of latero-nasal process EMAPA:16807 An ectoderm that is part of a lateral nasal prominence. EHDAA2:0000918 EMAPA:16806 ectoderm of latero-nasal process uberon UBERON:0009206 lateral nasal process surface ectoderm EHDAA2 An ectoderm that is part of a lateral nasal prominence. OBOL:automatic ectoderm of latero-nasal process EMAPA:16806 A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo. In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG] EMAPA:32749 FMA:295758 NCIT:C34251 UMLS:C1519040 branchial arch membrane branchial membrane pharyngeal membrane uberon UBERON:0009210 each membrane is initially composed of an inner layer formed by the endodermal lining of a branchial pouch and an outer layer formed by the ectodermal lining of the branchial groove; later, these two layers become separated by a thin layer of mesoderm; only the first branchial membrane contributes to the formation of an adult structure, i.e. the tympanic membrane (aka eardrum); the second, third, and fourth membranes are obliterated[MP] pharyngeal membrane EMAPA A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo. http://musom.marshall.edu/anatomy/grosshom/z_devbranc.html In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG] 2012-09-17 VHOG:0001427 VHOG ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72 http://bgee.unil.ch/ UMLS:C1519040 ncithesaurus:Pharyngeal_Membrane branchial arch membrane EMAPA:32749 A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch. check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches EHDAA:3788 EMAPA:16121 EMAPA:16992 EMAPA:17281 VHOG:0001427 1st branchial membrane 1st pharyngeal membrane future tympanic membrane tympanic membrane primordium uberon UBERON:0009213 pharyngeal membrane of 1st arch EMAPA A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch. http://orcid.org/0000-0002-6601-2165 1st branchial membrane EMAPA:16992 1st pharyngeal membrane VHOG:0001427 future tympanic membrane EMAPA:17281 tympanic membrane primordium ISBN:1416037055 Cartilaginous form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. SCTID:317278007 cartilaginous centrum of vertebra postcaudal cartilaginous centrum uberon UBERON:0009291 cartilaginous centrum of vertebra[PMID:11746457] cartilaginous vertebral centrum Cartilaginous form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. VSAO:0000183 VSAO:curator http://orcid.org/0000-0002-6601-2165 postcaudal cartilaginous centrum PMID:11746457 medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2:0000581 EHDAA:4776 EMAPA:16680 FMA:293971 SCTID:308881001 uberon nasal placode UBERON:0009292 embryonic nasal process medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2 The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis). FMA:54651 NCIT:C32482 SCTID:66938003 UMLS:C0226952 dorsal tongue dorsum linguae tongue dorsum uberon UBERON:0009471 dorsum of tongue FMA The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis). http://www.drugs.com/dict/dorsum-of-tongue.html UMLS:C0226952 ncithesaurus:Dorsum_of_the_Tongue dorsal tongue FMA:54651 dorsum linguae http://www.drugs.com/dict/dorsum-of-tongue.html tongue dorsum FMA:54651 The axilla is the area directly under the joint where the forelimb connects to the shoulder. axillary CALOHA:TS-2208 EFO:0001395 FMA:24864 MESH:D001365 NCIT:C12674 SCTID:362732006 UMLS:C0004454 Wikipedia:Axilla galen:Axilla arm pit armpit axillary region regio axillaris uberon armpits axilla axillae axillary region oxter underarm UBERON:0009472 axilla http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png FMA The axilla is the area directly under the joint where the forelimb connects to the shoulder. Wikipedia:Axilla UMLS:C0004454 ncithesaurus:Axilla arm pit Wikipedia:Axilla armpit Wikipedia:Axilla axillary region FMA:24864 regio axillaris FMA:TA armpits Wikipedia:Axilla axilla Wikipedia:Axilla axillae Wikipedia:Axilla axillary region Wikipedia:Axilla oxter Wikipedia:Axilla underarm Wikipedia:Axilla Mesenchyme that is part of a otic placode. EHDAA2:0001340 EMAPA:16196 uberon UBERON:0009477 associated mesenchyme of otic placode Mesenchyme that is part of a otic placode. OBOL:automatic An ectoderm that is part of a buccopharyngeal membrane. EHDAA2:0000190 EMAPA:16260 uberon UBERON:0009479 ectoderm of buccopharyngeal membrane An ectoderm that is part of a buccopharyngeal membrane. OBOL:automatic An endoderm that is part of a buccopharyngeal membrane. EHDAA2:0000191 EMAPA:16261 uberon UBERON:0009480 endoderm of buccopharyngeal membrane An endoderm that is part of a buccopharyngeal membrane. OBOL:automatic Mesenchyme that is part of a foregut-midgut junction. EHDAA2:0000570 EMAPA:16364 uberon UBERON:0009482 associated mesenchyme of foregut-midgut junction Mesenchyme that is part of a foregut-midgut junction. OBOL:automatic A mesentery that is part of a foregut-midgut junction. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0000575 EMAPA:16365 VHOG:0000430 foregut-midgut junction mesentery uberon UBERON:0009483 mesentery of foregut-midgut junction A mesentery that is part of a foregut-midgut junction. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000430 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ foregut-midgut junction mesentery VHOG:0000430 A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 FMA:295694 branchial arch mesenchyme pharyngeal arch mesenchyme uberon UBERON:0009494 pharyngeal arch mesenchymal region EHDAA2 cjm A portion of mesenchymal tissue associated with an individual pharyngeal arch. https://orcid.org/0000-0002-6601-2165 this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. MP:0011262 branchial arch mesenchyme MP:0011262 pharyngeal arch mesenchyme https://orcid.org/0000-0002-6601-2165 An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 uberon UBERON:0009497 epithelium of foregut-midgut junction EHDAA2 EHDAA2 An epithelium that is part of a foregut-midgut junction. OBOL:automatic Anatomical region that surrounds the otic vesicle. EHDAA2:0001343 EMAPA:16670 XAO:0004474 otocyst associated mesenchyme otocyst mesenchyme uberon periotic region UBERON:0009500 periotic mesenchyme XAO EHDAA2 Anatomical region that surrounds the otic vesicle. PMID:3794595 XAO:0004474 XAO:curators otocyst associated mesenchyme EHDAA2:0001343 otocyst mesenchyme EMAPA:16670 periotic region XAO:0004474 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head. EHDAA2:0004109 EMAPA:16683 FMA:295821 frontonasal mesenchyme naso-frontal mesenchyme uberon UBERON:0009501 mesenchyme of fronto-nasal process The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head. MP:0011266 frontonasal mesenchyme MP:0011266 naso-frontal mesenchyme MP:0011266 Mesenchyme that is part of a developing hindgut. EHDAA2:0000780 EMAPA:16716 hindgut associated mesenchyme uberon UBERON:0009503 mesenchyme of hindgut Mesenchyme that is part of a developing hindgut. OBOL:automatic hindgut associated mesenchyme EHDAA2:0000780 Mesenchyme that is part of a developing trachea. EHDAA2:0002067 EMAPA:16854 trachea associated mesenchyme uberon UBERON:0009505 mesenchyme of trachea EHDAA2 Mesenchyme that is part of a developing trachea. OBOL:automatic trachea associated mesenchyme EHDAA2:0002067 Mesenchyme that is part of a developing middle ear. Also 1st arch maxillary mesenchyme in EHDAA2 otic mesenchyme EHDAA2:0001182 EMAPA:17001 middle ear associated mesenchyme uberon UBERON:0009506 mesenchyme of middle ear EHDAA2 EHDAA2 EHDAA2 Mesenchyme that is part of a developing middle ear. OBOL:automatic Also 1st arch maxillary mesenchyme in EHDAA2 EHDAA2 middle ear associated mesenchyme EHDAA2:0001182 An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 uberon UBERON:0009521 anal membrane endodermal component An endoderm that is part of a anal region. OBOL:automatic An epithelium that is part of a lateral lingual swelling. EHDAA2:0000913 EMAPA:17190 FMA:313717 uberon UBERON:0009522 lateral lingual swelling epithelium An epithelium that is part of a lateral lingual swelling. OBOL:automatic Mesenchyme that is part of a handplate. We group two EMAPA classes here but these may need to be separated EHDAA2:0000731 EMAPA:17248 EMAPA:17457 hand plate mesenchyme handplate mesenchyme uberon UBERON:0009523 mesenchyme of handplate EHDAA2 Mesenchyme that is part of a handplate. OBOL:automatic We group two EMAPA classes here but these may need to be separated EMAPA handplate mesenchyme EHDAA2:0000731 Mesenchyme that is part of a maxillary prominence. EHDAA2:0001071 EMAPA:17361 FMA:312691 mesenchyme of maxillary process mesenchyme of maxillary prominence uberon UBERON:0009526 maxillary process mesenchyme Mesenchyme that is part of a maxillary prominence. OBOL:automatic mesenchyme of maxillary process EMAPA:17361 mesenchyme of maxillary prominence https://orcid.org/0000-0002-6601-2165 A vascular plexus that is part of a left lung. EHDAA2:0000963 EMAPA:17660 uberon UBERON:0009536 vascular element of left lung A vascular plexus that is part of a left lung. OBOL:automatic A vascular plexus that is part of a right lung. EHDAA2:0001757 EMAPA:17668 uberon UBERON:0009537 vascular element of right lung A vascular plexus that is part of a right lung. OBOL:automatic Mesenchyme that is part of a submandibular gland primordium. EHDAA2:0001941 EMAPA:17757 uberon submaxillary gland primordium mesenchyme UBERON:0009539 mesenchyme of submandibular gland primordium Mesenchyme that is part of a submandibular gland primordium. OBOL:automatic submaxillary gland primordium mesenchyme EMAPA:17757 A hepatic sinusoid that is part of a left lobe of liver. EHDAA2:0001001 EMAPA:18309 VHOG:0000709 left lobe hepatic sinusoids uberon UBERON:0009548 hepatic sinusoid of left of lobe of liver A hepatic sinusoid that is part of a left lobe of liver. OBOL:automatic left lobe hepatic sinusoids VHOG:0000709 A hepatic sinusoid that is part of a right lobe of liver. EHDAA2:0001009 EMAPA:18316 VHOG:0000710 right lobe hepatic sinusoids uberon UBERON:0009549 hepatic sinusoid of right of lobe of liver A hepatic sinusoid that is part of a right lobe of liver. OBOL:automatic right lobe hepatic sinusoids VHOG:0000710 An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 uberon UBERON:0009550 endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. OBOL:automatic A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults digit tip distal digit segment tip of digit uberon UBERON:0009551 distal segment of digit cjm A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). DOI:10.1038/nature10346 digit tip https://orcid.org/0000-0002-6601-2165 distal digit segment https://orcid.org/0000-0002-6601-2165 tip of digit https://orcid.org/0000-0002-6601-2165 A segment of the manual digit containing the distal phalanx. UBERON:0004093 SCTID:312543003 finger digit tip finger distal segment finger tip fingertip forelimb digit tip tip of finger uberon UBERON:0009552 distal segment of manual digit A segment of the manual digit containing the distal phalanx. http://orcid.org/0000-0002-6601-2165 finger digit tip DOI:10.1038/nature10346 finger distal segment https://orcid.org/0000-0002-6601-2165 finger tip https://orcid.org/0000-0002-6601-2165 fingertip HP:0001211 forelimb digit tip DOI:10.1038/nature10346 A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone. hindlimb digit tip tip of toe toe digit tip toe distal segment uberon P3 segment of pedal digit distalmost part of toe UBERON:0009553 distal segment of pedal digit A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone. http://orcid.org/0000-0002-6601-2165 hindlimb digit tip DOI:10.1038/nature10346 tip of toe https://orcid.org/0000-0002-6601-2165 toe digit tip DOI:10.1038/nature10346 toe distal segment https://orcid.org/0000-0002-6601-2165 P3 segment of pedal digit https://orcid.org/0000-0002-6601-2165 distalmost part of toe https://orcid.org/0000-0002-6601-2165 A skeletal joint that connects a mesopodium bone and connects a proximal phalanx. We include these joints as being part of the digits; this is consistent with the FMA, and makes classification easier. Note that digit and metapodial regions are part-disjoint metacarpo-tarsophalangeal joint metapodial-phalangeal joint metapodium-phalanx joint fetlock uberon UBERON:0009559 metacarpal/tarsal-phalangeal joint A skeletal joint that connects a mesopodium bone and connects a proximal phalanx. OBOL:automatic metacarpo-tarsophalangeal joint https://orcid.org/0000-0002-6601-2165 metapodial-phalangeal joint https://orcid.org/0000-0002-6601-2165 metapodium-phalanx joint https://orcid.org/0000-0002-6601-2165 fetlock NCBITaxon:9788 Wikipedia:Fetlock https://orcid.org/0000-0002-6601-2165 A submucosa that is part of a intestine. FMA:15696 submucosa of intestine uberon UBERON:0009566 intestinal submucosa FMA A submucosa that is part of a intestine. OBOL:automatic submucosa of intestine FMA:15696 Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 FMA:72066 NCIT:C92597 SCTID:281699004 thoracolumbar column thoracolumbar region of vertebral column thoracolumbar vertebrae set thoracolumbar vertebral column trunk vertebrae series trunk vertebral column uberon presacral region thoracolumbar region trunk region trunk skeleton trunk spine UBERON:0009568 trunk region of vertebral column Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. UBERONREF:0000006 Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 thoracolumbar vertebrae set FMA:72066 presacral region AAO:0000612 thoracolumbar region AAO:0000612 trunk region AAO:0000612 FMA:25054 SCTID:22943007 region of trunk trunk subdivision uberon UBERON:0009569 subdivision of trunk region of trunk FMA:25054 trunk subdivision FMA:25054 A sulcus limitans of neural tube that is part of a future spinal cord. EHDAA2:0001265 EMAPA:17584 VHOG:0001548 spinal cord lateral wall sulcus limitans uberon UBERON:0009570 spinal cord sulcus limitans A sulcus limitans of neural tube that is part of a future spinal cord. OBOL:automatic spinal cord lateral wall sulcus limitans EHDAA2:0001265 A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 uberon UBERON:0009576 medulla oblongata sulcus limitans EHDAA2 A sulcus limitans of neural tube that is part of a future medulla oblongata. OBOL:automatic A sulcus limitans of neural tube that is part of a future metencephalon. EHDAA2:0001161 EMAPA:17567 uberon UBERON:0009577 metencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future metencephalon. OBOL:automatic A sulcus limitans of neural tube that is part of a future myelencephalon. EHDAA2:0001945 uberon UBERON:0009578 myelencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future myelencephalon. OBOL:automatic EHDAA2:0000397 EMAPA:16906 VHOG:0000912 diencephalon lateral wall mantle layer mantle layer lateral wall diencephalon uberon UBERON:0009580 diencephalon mantle layer mantle layer lateral wall diencephalon VHOG:0000912 EHDAA2:0001172 EMAPA:16977 VHOG:0000910 mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon mantle layer lateral wall mesencephalon UBERON:0009581 midbrain mantle layer mantle layer lateral wall midbrain VHOG:0000910 mantle layer lateral wall mesencephalon VHOG:0000910 EMAPA:17580 VHOG:0000911 mantle layer lateral wall spinal cord spinal cord lateral wall mantle layer uberon UBERON:0009583 spinal cord mantle layer mantle layer lateral wall spinal cord VHOG:0000911 Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 EMAPA:16385 mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component uberon mandibular component mesenchyme mandibular mesenchyme UBERON:0009584 1st arch mandibular mesenchyme EMAPA Mesenchyme that is part of a 1st arch mandibular component. OBOL:automatic mesenchymal region of mandibular component of first pharyngeal arch https://orcid.org/0000-0002-6601-2165 mesenchyme of mandibular component EMAPA:16385 Mesenchyme that is part of a developing left lung. EHDAA2:0000944 EMAPA:16730 EMAPA:17654 left lung mesenchyme uberon UBERON:0009602 left lung associated mesenchyme Mesenchyme that is part of a developing left lung. OBOL:automatic left lung mesenchyme EMAPA:17654 Mesenchyme that is part of a developing right lung. EHDAA2:0001739 EMAPA:17662 right lung mesenchyme uberon UBERON:0009603 right lung associated mesenchyme Mesenchyme that is part of a developing right lung. OBOL:automatic right lung mesenchyme EMAPA:17662 A neural plate that develops_from a future forebrain. TAO:0007018 ZFA:0007018 uberon UBERON:0009610 forebrain neural plate ZFA ZFA A neural plate that develops_from a future forebrain. OBOL:automatic A neural plate that develops_from a presumptive midbrain. TAO:0007019 ZFA:0007019 uberon UBERON:0009611 midbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive midbrain. OBOL:automatic A neural plate that develops_from a presumptive hindbrain. TAO:0007022 ZFA:0007022 uberon UBERON:0009614 hindbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive hindbrain. OBOL:automatic TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 MHB neural plate midbrain-hindbrain boundary neural plate uberon UBERON:0009615 midbrain hindbrain boundary neural plate ZFA https://github.com/obophenotype/uberon/issues/438 Bgee:AN MHB neural plate https://orcid.org/0000-0002-6601-2165 midbrain-hindbrain boundary neural plate ZFA:0007044 A presumptive structure that has the potential to develop into a midbrain. TODO - unify naming conventions BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 TAO:0000148 Wikipedia:Mesencephalon ZFA:0000148 presumptive mesencephalon uberon early midbrain future midbrain mesencephalon UBERON:0009616 presumptive midbrain ZFA ZFA A presumptive structure that has the potential to develop into a midbrain. OBOL:automatic presumptive mesencephalon ZFA:0000148 early midbrain https://orcid.org/0000-0002-6601-2165 future midbrain https://orcid.org/0000-0002-6601-2165 mesencephalon EHDAA2:0000615 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 EHDAA:364 EMAPA:16171 cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme uberon somitomere somitomeric mesoderm UBERON:0009617 head paraxial mesoderm EHDAA2 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. PMID:21610022 cephalic paraxial mesenchyme https://orcid.org/0000-0002-6601-2165 cephalic paraxial mesoderm https://orcid.org/0000-0002-6601-2165 cranial paraxial mesenchyme https://orcid.org/0000-0002-6601-2165 cranial paraxial mesoderm https://orcid.org/0000-0002-6601-2165 head paraxial mesenchyme EHDAA2:0000736 https://github.com/obophenotype/uberon/issues/30 EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm EHDAA2 trunk and cervical paraxial mesenchyme EHDAA2:0002094 trunk paraxial mesenchyme https://github.com/obophenotype/uberon/issues/30 A somite that is part of a tail. AAO:0010383 EMAPA:16860 XAO:0003143 uberon UBERON:0009621 tail somite A somite that is part of a tail. OBOL:automatic The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions. FMA:5861 NCIT:C33015 SCTID:361600002 UMLS:C0228897 Wikipedia:Lumbar_nerves neuronames:1730 lumbar spinal nerve nervus lumbalis uberon nervi lumbales UBERON:0009624 lumbar nerve http://upload.wikimedia.org/wikipedia/commons/d/d1/Gray802.png The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions. Wikipedia:Lumbar_nerves UMLS:C0228897 ncithesaurus:Lumbar_Nerve lumbar spinal nerve FMA:5861 nervus lumbalis FMA:5861 FMA:TA nervi lumbales Wikipedia:Lumbar_nerves The five sacral nerves emerge from the sacrum. Although the vertebral components of the sacrum are fused into a single bone, the sacral vertebrae are still used to number the sacral nerves. Posteriorly, they emerge from the posterior sacral foramina, and form the posterior branches of sacral nerves. Anteriorly, they emerge from the anterior sacral foramina, and contribute to the sacral plexus (S1-S4) and coccygeal plexus. FMA:5862 NCIT:C33505 SCTID:361601003 UMLS:C0228922 Wikipedia:Sacral_nerves neuronames:1720 nervus sacralis sacral spinal nerve uberon nervi sacrales UBERON:0009625 sacral nerve http://upload.wikimedia.org/wikipedia/commons/d/d1/Gray802.png The five sacral nerves emerge from the sacrum. Although the vertebral components of the sacrum are fused into a single bone, the sacral vertebrae are still used to number the sacral nerves. Posteriorly, they emerge from the posterior sacral foramina, and form the posterior branches of sacral nerves. Anteriorly, they emerge from the anterior sacral foramina, and contribute to the sacral plexus (S1-S4) and coccygeal plexus. Wikipedia:Sacral_nerves UMLS:C0228922 ncithesaurus:Sacral_Nerve nervus sacralis FMA:5862 FMA:TA sacral spinal nerve FMA:5862 nervi sacrales Wikipedia:Sacral_nerves EMAPA:35878 MA:0001859 uberon UBERON:0009644 trachea non-cartilage connective tissue MA A sympathetic nerve trunk that is part of a lower back. EMAPA:37655 FMA:6263 MA:0001163 NCIT:C52828 SCTID:280534006 UMLS:C1708762 lumbar sympathetic trunk uberon lumbar part of sympathetic trunk lumbar sympathetic chain UBERON:0009646 lumbar sympathetic nerve trunk A sympathetic nerve trunk that is part of a lower back. OBOL:automatic EMAPA:37655 MA:th UMLS:C1708762 ncithesaurus:Lumbar_Sympathetic_Nerve_Trunk lumbar sympathetic trunk FMA:6263 lumbar part of sympathetic trunk FMA:6263 lumbar sympathetic chain FMA:6263 One of the two epithelia which make up the tympanic membrane (along with the fibrous layer). EMAPA:19064 MA:0001224 NCIT:C49308 SCTID:70839004 UMLS:C1711401 tympanic epithelium tympanic membrane epithelial layer uberon UBERON:0009647 tympanic membrane epithelium One of the two epithelia which make up the tympanic membrane (along with the fibrous layer). PMID:11237469 https://orcid.org/0000-0002-6601-2165 UMLS:C1711401 ncithesaurus:Tympanic_Epithelium tympanic epithelium MA:0001224 A basement membrane that is part of a nephron tubule. EMAPA:37490 MA:0001680 NCIT:C49273 SCTID:245251000 UMLS:C1709901 kidney tubule basement membrane renal tubular basement membrane renal tubule basement membrane uberon UBERON:0009651 nephron tubule basement membrane true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A basement membrane that is part of a nephron tubule. OBOL:automatic EMAPA:37490 MA:th UMLS:C1709901 ncithesaurus:Renal_Tubule_Basement_Membrane kidney tubule basement membrane MA:0001680 renal tubule basement membrane MA:0001680 A basement membrane that is part of a bronchus. MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 EMAPA:37809 MA:0001832 NCIT:C49208 UMLS:C1707051 bronchial basement membrane uberon UBERON:0009652 bronchus basement membrane true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A basement membrane that is part of a bronchus. OBOL:automatic MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 MA EMAPA:37809 MA:th UMLS:C1707051 ncithesaurus:Bronchus_Basement_Membrane bronchial basement membrane http://orcid.org/0000-0002-6601-2165 A basement membrane that is part of a trachea. EMAPA:37552 MA:0001854 NCIT:C49302 UMLS:C1710455 uberon UBERON:0009653 trachea basement membrane true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships MA-modified A basement membrane that is part of a trachea. OBOL:automatic EMAPA:37552 MA:th UMLS:C1710455 ncithesaurus:Trachea_Basement_Membrane An artery that supplies oxygenated blood to the ear. add child terms EMAPA:37072 MA:0001918 NCIT:C52849 UMLS:C1706858 uberon UBERON:0009655 auricular artery An artery that supplies oxygenated blood to the ear. ncithesaurus:Auricular_Artery EMAPA:37072 MA:th UMLS:C1706858 ncithesaurus:Auricular_Artery labial artery EMAPA:37092 MA:0001987 NCIT:C52947 UMLS:C1708633 uberon UBERON:0009657 artery of lip labial artery MA:0001987 EMAPA:37092 MA:th UMLS:C1708633 ncithesaurus:Labial_Artery Nucleus located in the midbrain. SCTID:279285003 TAO:0002209 ZFA:0001665 uberon UBERON:0009661 midbrain nucleus Nucleus located in the midbrain. ZFIN:curator Nucleus located within the hindbrain. TAO:0002177 ZFA:0001658 uberon UBERON:0009662 hindbrain nucleus Nucleus located within the hindbrain. ZFIN:curator A nucleus of brain that is part of a telencephalon. TAO:0002178 ZFA:0001660 uberon UBERON:0009663 telencephalic nucleus A nucleus of brain that is part of a telencephalon. OBOL:automatic EHDAA2:0004566 EMAPA:32911 MA:0003203 uberon peritoneal cavity mesentary peritoneal mesentary UBERON:0009664 gut mesentery https://github.com/obophenotype/uberon/issues/509 EHDAA2 peritoneal cavity mesentary http://orcid.org/0000-0002-6601-2165 peritoneal mesentary http://orcid.org/0000-0002-6601-2165 Ventral mesentery is the part of the peritoneum closest to the navel. degenerates during development except foregut portion EHDAA2:0004569 SCTID:361430000 Wikipedia:Ventral_mesentery uberon UBERON:0009668 ventral mesentery EHDAA2 Ventral mesentery is the part of the peritoneum closest to the navel. Wikipedia:Ventral_mesentery An anatomical space that surrounded_by a embryonic cloaca. EHDAA2:0004586 uberon UBERON:0009669 embryonic cloacal lumen An anatomical space that surrounded_by a embryonic cloaca. OBOL:automatic An anatomical space that surrounded_by a rectum. EHDAA2:0004587 EMAPA:18388 FMA:14598 SCTID:259740004 lumen of rectum uberon UBERON:0009670 rectal lumen cjm EHDAA2 An anatomical space that surrounded_by a rectum. OBOL:automatic lumen of rectum FMA:14598 The nasal fin is an epithelial seam that develops by fusion between the epithelial linings of the medial and lateral nasal swellings. Shortly after its formation the nasal fin regresses and is replaced by mesenchyme, with exception of its most posterior portion which remains as the bucconasal membrane. EHDAA2:0004548 FMA:295940 uberon UBERON:0009671 nasal fin EHDAA2 EHDAA2 The nasal fin is an epithelial seam that develops by fusion between the epithelial linings of the medial and lateral nasal swellings. Shortly after its formation the nasal fin regresses and is replaced by mesenchyme, with exception of its most posterior portion which remains as the bucconasal membrane. DOI:10.1002/aja.1001500308 The oronasal membrane separates the oral cavity and nasal cavity. split into two? In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity EHDAA2:0000188 EHDAA:7840 EHDAA:7984 FMA:295942 bucconasal membrane uberon UBERON:0009672 oronasal membrane EHDAA2 EHDAA2 EHDAA2 posterior portion EHDAA2 The oronasal membrane separates the oral cavity and nasal cavity. http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter24/custom3/deluxe-content.html bucconasal membrane EHDAA:7840 EFO:0003562 EHDAA2:0001981 EHDAA:1993 EHDAA:2671 EMAPA:16914 early telencephalic vesicle uberon early telencephalic ventricle UBERON:0009676 early telencephalic vesicle EHDAA2 EHDAA2 early telencephalic vesicle EHDAA2:0001981 Anatomical cluster consisting of adjacent teeth constituting a row. FMA:59415 TAO:0001667 ZFA:0001642 dental arcade row of teeth tooth rows uberon UBERON:0009678 tooth row Anatomical cluster consisting of adjacent teeth constituting a row. ZFIN:curator dental arcade FMA:59415 row of teeth https://orcid.org/0000-0002-6601-2165 tooth rows ZFA:0001642 A tooth row that is part of a skeleton of lower jaw. EHDAA2:0001029 FMA:55635 arcus dentalis inferior lower dental arcade lower jaw teeth set of all lower teeth uberon mandibular dental arcade UBERON:0009679 set of lower jaw teeth A tooth row that is part of a skeleton of lower jaw. OBOL:automatic arcus dentalis inferior FMA:TA lower dental arcade FMA:55635 lower jaw teeth EHDAA2:0001029 set of all lower teeth FMA:55635 mandibular dental arcade FMA:55635 A tooth row that is part of a skeleton of upper jaw. EHDAA2:0002129 FMA:55634 arcus dentalis superior set of all upper teeth upper dental arcade upper jaw teeth uberon maxillary dental arcade UBERON:0009680 set of upper jaw teeth A tooth row that is part of a skeleton of upper jaw. OBOL:automatic arcus dentalis superior FMA:TA set of all upper teeth FMA:55634 upper dental arcade FMA:55634 upper jaw teeth EHDAA2:0002129 maxillary dental arcade FMA:55634 An epithelium that is part of a hypopharynx. EHDAA2:0004575 FMA:62454 epithelium of laryngeal pharynx laryngopharynx epithelium uberon UBERON:0009695 epithelium of laryngopharynx EHDAA2 EHDAA2 An epithelium that is part of a hypopharynx. OBOL:automatic epithelium of laryngeal pharynx FMA:62454 laryngopharynx epithelium FMA:62454 An epithelium that is part of a vermiform appendix. CALOHA:TS-2062 EHDAA2:0004561 FMA:63581 appendix epithelium epithelium of vermiform appendix uberon UBERON:0009697 epithelium of appendix EHDAA2 EHDAA2 An epithelium that is part of a vermiform appendix. OBOL:automatic appendix epithelium FMA:63581 epithelium of vermiform appendix FMA:63581 EHDAA2:0001371 uberon pancreatis dorsalis UBERON:0009708 dorsal pancreas EHDAA2 EHDAA2 EHDAA2 cjm EHDAA2:0001393 uberon pancreatis ventralis UBERON:0009709 ventral pancreas EHDAA2 EHDAA2 EHDAA2 cjm Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 EMAPA:17341 FMA:9536 NCIT:C102343 SCTID:8911002 VHOG:0001235 right ventricle endocardium right ventricular endocardium uberon endocardial lining of right ventricle right ventricle endocardial tissue UBERON:0009712 endocardium of right ventricle EHDAA2 FMA Any endocardium that is part of the right ventricle of the heart. http://orcid.org/0000-0002-6601-2165 Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. FMA:9536 right ventricle endocardium VHOG:0001235 right ventricular endocardium FMA:9536 endocardial lining of right ventricle EMAPA:17341 right ventricle endocardial tissue VHOG:0001235 Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 EMAPA:17338 FMA:9559 SCTID:191004004 VHOG:0001233 left ventricle endocardium left ventricular endocardium uberon endocardial lining of left ventricle left ventricle endocardial tissue UBERON:0009713 endocardium of left ventricle FMA Any endocardium that is part of the left ventricle of the heart. http://orcid.org/0000-0002-6601-2165 Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. FMA:9559 left ventricle endocardium VHOG:0001233 left ventricular endocardium FMA:9559 endocardial lining of left ventricle EMAPA:17338 left ventricle endocardial tissue VHOG:0001233 The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate. requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip EHDAA2:0000868 EHDAA:7856 FMA:295872 Wikipedia:Intermaxillary_segment uberon globular process globular processes of his intermaxillary segment UBERON:0009714 intermaxillary process EHDAA2-modified inconsistent EHDAA2 EHDAA2 The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate. http://www.medilexicon.com/medicaldictionary.php?s=intermaxillary+segment globular process Wikipedia:Intermaxillary_segment globular processes of his Wikipedia:Intermaxillary_segment intermaxillary segment Wikipedia:Intermaxillary_segment An anatomical cavity that surrounded_by a stomodeum. lumen of stomatodaeum lumen of stomodeum stomatodeal cavity uberon UBERON:0009715 stomodeal lumen An anatomical cavity that surrounded_by a stomodeum. OBOL:automatic EHDAA2:0004621 EMAPA:32754 FMA:293087 uberon pharyngeal arch endoderm UBERON:0009722 entire pharyngeal arch endoderm EHDAA2 pharyngeal arch endoderm EHDAA2:0004621 The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels. medullary sinus EMAPA:37898 FMA:312359 uberon lymph node medullary sinusoid UBERON:0009744 Lymph flows into the medullary sinuses from cortical sinuses, and into efferent lymphatic vessels. Medullary sinuses contain histiocytes (immobile macrophages) and reticular cells.[WP] lymph node medullary sinus The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels. MP:0011222 EMAPA:37898 MA:th The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node. medullary cord EMAPA:37897 uberon UBERON:0009745 lymph node medullary cord The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node. MP:0011224 EMAPA:37897 MA:th The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. EMAPA mapping from TH EMAPA:32705 uberon limb mesoderm UBERON:0009749 limb mesenchyme The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. MP:0011261 EMAPA mapping from TH EMAPA limb mesoderm Geisha:syn NCBITaxon:8782 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures. decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts EHDAA2:0004162 EMAPA:36438 heart mesenchyme uberon UBERON:0009751 cardiac mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures. MP:0011264 heart mesenchyme EMAPA:36438 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas. EFO:0002557 EMAPA:26220 uberon UBERON:0009752 pancreas mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas. MP:0011265 A ganglion that is part of a abdominal segment of trunk. SCTID:280508003 uberon UBERON:0009758 abdominal ganglion A ganglion that is part of a abdominal segment of trunk. OBOL:automatic An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx. FMA:65022 NCIT:C101528 PIJ joint PIP joint uberon UBERON:0009767 proximal interphalangeal joint An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx. http://orcid.org/0000-0002-6601-2165 PIJ joint Wikipedia:Interphalangeal_articulations_of_the_hand PIP joint Wikipedia:Interphalangeal_articulations_of_the_hand An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx. FMA:65024 NCIT:C101529 DIJ joint DIP joint uberon UBERON:0009768 distal interphalangeal joint An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx. http://orcid.org/0000-0002-6601-2165 DIJ joint Wikipedia:Interphalangeal_articulations_of_the_hand DIP joint Wikipedia:Interphalangeal_articulations_of_the_hand A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule (generic) tubule of excretory system uberon UBERON:0009773 renal tubule A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. DOI:10.1371/journal.pone.0099864 GO:0061333 GOC:dph GOC:mtg_kidney_jan10 renal tubule (generic) https://orcid.org/0000-0002-6601-2165 tubule of excretory system OBOL:automatic https://orcid.org/0000-0002-6601-2165 A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2:0004737 FMA:9690 SCTID:361996004 uberon UBERON:0009778 pleural sac FMA FMA-abduced-lr A serous sac that has the pleura and the pleural cavity as parts. https://github.com/obophenotype/uberon/issues/86 despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2 The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinar acinus FMA:55588 Wikipedia:Acinus uberon acini UBERON:0009842 glandular acinus http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. Wikipedia:Acinus acinus FMA:55588 acini Wikipedia:Acinus A solid cord of prostate epithelium. cord of prostate epithelium epithelial cord of prostate uberon UBERON:0009843 Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204] prostate epithelial cord A solid cord of prostate epithelium. GO:0060527 OBOL:automatic PMID:18977204 cord of prostate epithelium PMID:18977204 An anatomical space that surrounded_by a primitive urogenital sinus. EHDAA2:0002142 uberon UBERON:0009844 urogenital sinus lumen EHDAA2 An anatomical space that surrounded_by a primitive urogenital sinus. OBOL:automatic Mesenchyme that surrounds primitive urogenital sinus. Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth EMAPA:31500 UGM uberon UBERON:0009845 urogenital sinus mesenchyme PMID:18977204 Mesenchyme that surrounds primitive urogenital sinus. OBOL:automatic UGM PMID:18977204 An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 uberon UBERON:0009846 embryonic cloacal epithelium EHDAA2 EHDAA2 An epithelium that is part of a embryonic cloaca. OBOL:automatic cloacal epithelium EHDAA2:0004585 A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. uberon prostate primordium UBERON:0009847 prostate field PMID:18977204 PMID:18977204 A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. GO:0060515 GOC:dph PMID:18977204 The part of the uterus above the isthmus and below the orifices of the uterine tubes. CALOHA:TS-1265 EFO:0000382 FMA:17739 NCIT:C12316 SCTID:279878007 UMLS:C0227813 corpus uteri uterine body uterine corpus uberon UBERON:0009853 body of uterus https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb FMA The part of the uterus above the isthmus and below the orifices of the uterine tubes. http://medical-dictionary.thefreedictionary.com/corpus+uteri UMLS:C0227813 ncithesaurus:Corpus_Uteri corpus uteri https://orcid.org/0000-0002-6601-2165 uterine body FMA:17739 uterine corpus FMA:17739 Branch or outpocketing of the digestive tract. FBbt:00100316 uberon diverticulum of gut intestinal pouch UBERON:0009854 digestive tract diverticulum Branch or outpocketing of the digestive tract. https://orcid.org/0000-0002-6601-2165 FBbt:00100316 diverticulum of gut FBbt:00100316 galen:Diverticulum pouch uberon diverticulum UBERON:0009856 sac A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach UBERON:0009034 EMAPA:35821 FMA:14558 MA:0002561 SCTID:245415005 Wikipedia:Stomach#Sections gastric zone region of stomach section of stomach uberon UBERON:0009870 zone of stomach http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. ISBN:0073040584 Wikipedia:Stomach#Sections gastric zone FMA:14558 Outer portion of the renal cortex. Site of formation of medullary and cortical elements. see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish. EMAPA:27721 MA:0002996 http://www.gudmap.org/Images/Organ_Summaries/Metanephros/NZ.png cortical nephrogenic niche cortical nephrogenic zone uberon nephrogenic tissue UBERON:0009871 nephrogenic zone Outer portion of the renal cortex. Site of formation of medullary and cortical elements. http://orcid.org/0000-0002-6601-2165 cortical nephrogenic niche PMID:29449449 cortical nephrogenic zone PMID:29449449 Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region. considering adding 'acropodial region' Naming conventions for pod terms under discussion within phenoscape group SCTID:370640001 metacarpal or metatarsal part of limb metacarpus/metatarsus region metapodial segment cannon region equine cannon region uberon metacarpus/metatarsus metapodium UBERON:0009877 metapodium region PHENOSCAPE:ni Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region. MA:th https://orcid.org/0000-0002-6601-2165 cannon region NCBITaxon:9788 http://orcid.org/0000-0002-6601-2165 equine cannon region NCBITaxon:9788 http://orcid.org/0000-0002-6601-2165 The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton. Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] VSAO:0005022 basipodium skeleton carpal/tarsal skeleton mesopodial skeleton mesopodium skeleton skeletal parts of mesopodium uberon basipodium mesopodium UBERON:0009878 mesopodial skeleton The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton. https://orcid.org/0000-0002-6601-2165 Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO] 2012-08-14 VSAO:0005022 VSAO VSAO:NI relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0005022 VSAO basipodium skeleton VSAO:0005022 VSAO:NI mesopodial skeleton VSAO:0005022 mesopodium skeleton https://orcid.org/0000-0002-6601-2165 skeletal parts of mesopodium https://orcid.org/0000-0002-6601-2165 basipodium VSAO:0005022 VSAO:NI mesopodium VSAO:0005022 VSAO:NI Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad]. Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO] The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. AAO:0000220 EMAPA:19133 FMA:71339 GAID:1223 MA:0000050 SCTID:264228001 SCTID:361796005 VHOG:0001160 VSAO:0005024 Wikipedia:Tarsus_(skeleton) XAO:0003211 hind mesopodial skeleton hind mesopodium hind mesopodium skeleton set of tarsal bones skeletal parts of hind mesopodium tarsal bones set tarsalia uberon basipodium mesopodium tarsal bones tarsus UBERON:0009879 tarsal skeleton Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad]. PHENOSCAPE:ad VSAO:0005024 https://github.com/obophenotype/uberon/issues/94 Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO] 2012-06-20 AAO:0000220 AAO AAO:LAP The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] 2012-09-17 VHOG:0001160 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) http://bgee.unil.ch/ Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present PHENOSCAPE:ad we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. MA set of tarsal bones FMA:71339 tarsal bones set FMA:71339 tarsalia XAO:0003211 basipodium VSAO:0005024 mesopodium VSAO:0005024 tarsus XAO:0003211 Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad]. Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO] The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]. The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. AAO:0000201 FMA:71335 MA:0000040 VHOG:0001161 VSAO:0005023 Wikipedia:Carpus XAO:0003207 http://palaeos.com/vertebrates/glossary/images/382x366xUnciform1.jpg.pagespeed.ic.NirdxtwNVu.jpg carpal bones carpal bones set fore mesopodial skeleton fore mesopodium skeleton ossa carpi skeletal parts of fore mesopodium skeleton of carpus uberon carpus fore mesopodium ossa carpi set of carpal bones UBERON:0009880 carpal skeleton http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad]. PHENOSCAPE:ad https://github.com/obophenotype/uberon/issues/93 Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO] 2012-06-20 AAO:0000201 AAO AAO:LAP The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] 2012-09-17 VHOG:0001161 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) http://bgee.unil.ch/ Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]. Wikipedia:Carpus#Evolutionary_variations we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. MA carpal bones EMAPA:25056 FMA:71335 carpal bones set FMA:71335 carpus MA:0000040 XAO:0003207 fore mesopodium AAO:0000201 ossa carpi Wikipedia:Carpus set of carpal bones FMA:71335 EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm ZFA ALPM ZFA:0005041 A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla. FMA says parenchyma, MP says cortex Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla BTO:0001155 EMAPA:37906 FMA:74299 Wikipedia:Bone_marrow_of_ovaryry_ray_(anatomy) Ferrein's pyramid kidney medullary ray renal medullary ray uberon UBERON:0009883 medullary ray FMA MP A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla. MP:0011347 Wikipedia:Bone_marrow_of_ovaryry_ray_(anatomy) FMA says parenchyma, MP says cortex FMA EMAPA:37906 MA:th Ferrein's pyramid MP:0011347 kidney medullary ray MP:0011347 renal medullary ray MP:0011347 An artery that supplies a renal lobe. FMA only has the set term EMAPA:37091 FMA:71637 SCTID:62802007 Wikipedia:Interlobar_arteries arteriae interlobares renis interlobar artery of kidney kidney interlobar artery renal interlobar artery uberon arteriae interlobares renis interlobar arteries of kidney set of interlobar arteries of kidney UBERON:0009885 interlobar artery https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png An artery that supplies a renal lobe. Wikipedia:Interlobar_arteries http://orcid.org/0000-0002-6601-2165 FMA only has the set term FMA EMAPA:37091 MA:th arteriae interlobares renis FMA:TA interlobar artery of kidney FMA:71637 renal interlobar artery MP:0011355 arteriae interlobares renis Wikipedia:Interlobar_arteries interlobar arteries of kidney FMA:71637 set of interlobar arteries of kidney FMA:71637 The interlobar veins are veins of the renal circulation which drain the renal lobes. FMA only has the set term FMA:71631 Wikipedia:Interlobar_veins interlobar vein of kidney venae interlobares renis uberon interlobar veins of kidney set of interlobar veins of kidney venae interlobares renis UBERON:0009887 interlobar vein https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png The interlobar veins are veins of the renal circulation which drain the renal lobes. Wikipedia:Interlobar_veins FMA only has the set term FMA interlobar vein of kidney FMA:71631 venae interlobares renis FMA:TA interlobar veins of kidney FMA:71631 set of interlobar veins of kidney FMA:71631 venae interlobares renis Wikipedia:Interlobar_veins A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested in mouse has left ventricular identity[PMID:22855565] XAO:0004186 anterior heart field anterior/second heart field second heart field uberon SHF UBERON:0009889 secondary heart field GO:0003129 PMID:17276708 PMID:17276708 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). GO:0003139 GOC:mtg_heart GOC:rl extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. PMID:17276708 In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested PMID:17276708 anterior heart field PMID:17276708 anterior/second heart field Geisha:syn NCBITaxon:8782 second heart field XAO:0004186 SHF XAO:0004186 Mesenchyme that is part of a developing face. EMAPA:35337 FMA:302884 face mesenchyme mesenchyme of face uberon UBERON:0009891 facial mesenchyme Mesenchyme that is part of a developing face. OBOL:automatic todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) FMA:45737 NCIT:C12990 UMLS:C0921005 lobulus uberon UBERON:0009911 lobule cjm UMLS:C0921005 ncithesaurus:Lobule lobulus FMA:45737 FMA:TA A portion of an organ, such as the liver, lung, breast, or brain. FMA:45728 NCIT:C13393 UMLS:C0796494 lobus uberon UBERON:0009912 anatomical lobe cjm A portion of an organ, such as the liver, lung, breast, or brain. ncithesaurus:Lobe lobus FMA:45728 FMA:TA The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. todo - add has_part relationships. human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys FMA:17881 NCIT:C32894 UMLS:C0736382 Wikipedia:Renal_lobe kidney lobe lobi renalis lobus renalis uberon lobi renales UBERON:0009913 renal lobe https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. MP:0011381 Wikipedia:Renal_lobe human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys MP UMLS:C0736382 ncithesaurus:Kidney_Lower_Lobe kidney lobe MP:0011381 lobi renalis Wikipedia:Renal_lobe lobus renalis http://www.mondofacto.com/facts/dictionary?lobus+renalis lobi renales Wikipedia:Renal_lobe The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys. FMA:17670 SCTID:361330004 Wikipedia:Cortical_lobule kidney lobule lobulus renalis uberon cortical lobule cortical lobule of kidney lobuli corticales renis lobulus corticalis renalis renal cortical lobule renculus reniculus renunculus UBERON:0009914 Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis renal lobule FMA The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys. MP:0011382 Wikipedia:Cortical_lobule kidney lobule MP:0011382 cortical lobule MP:0011382 Wikipedia:Cortical_lobule cortical lobule of kidney http://www.mondofacto.com/facts/dictionary?lobus+renalis lobuli corticales renis Wikipedia:Cortical_lobule lobulus corticalis renalis http://www.mondofacto.com/facts/dictionary?lobus+renalis renal cortical lobule http://www.mondofacto.com/facts/dictionary?lobus+renalis renculus http://www.mondofacto.com/facts/dictionary?lobus+renalis reniculus http://www.mondofacto.com/facts/dictionary?lobus+renalis renunculus http://www.mondofacto.com/facts/dictionary?lobus+renalis An anatomical wall that is part of a ureter. FMA:15888 SCTID:279397004 ureteral wall uberon UBERON:0009916 wall of ureter An anatomical wall that is part of a ureter. OBOL:automatic ureteral wall FMA:15888 The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary. EMAPA:37886 uberon UBERON:0009917 kidney corticomedullary boundary MP The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary. MP:0011376 EMAPA:37886 MA:th The smooth muscle tissue surrounding the epithelium of the ureter. EMAPA:28811 ureteral smooth muscle ureteral smooth muscle layer uberon UBERON:0009919 ureter smooth muscle The smooth muscle tissue surrounding the epithelium of the ureter. MP:0011426 ureteral smooth muscle MP:0011426 ureteral smooth muscle layer EMAPA:28844 EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest EHDAA2 EHDAA2 A multicellular organism that existence_starts_with a post-embryonic stage. MA:0002405 postnatal organism TS28 mouse post-hatching organism post-natal organism postnatal mouse uberon UBERON:0009953 post-embryonic organism https://github.com/obophenotype/uberon/issues/667 A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism https://orcid.org/0000-0002-6601-2165 post-natal organism https://orcid.org/0000-0002-6601-2165 postnatal mouse MA:0002405 Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. Includes: trigeminal, otic, lateral line and epibranchial placodes. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) EFO:0003460 TAO:0001309 Wikipedia:Neurogenic_placodes XAO:0004620 ZFA:0001309 neurogenic placodes uberon placodae neurogenicae UBERON:0009955 neurogenic placode cjm Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. PMID:11523831 http://orcid.org/0000-0002-6601-2165 While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) NCBIBook:NBK53171 neurogenic placodes ZFA:0001309 placodae neurogenicae Wikipedia:Neurogenic_placodes An anatomical space that is enclosed by a urinary bladder. EHDAA2:0004058 FMA:15924 SCTID:279405003 galen:UrinaryBladderCavity bladder cavity cavity of urinary bladder lumen of urinary bladder urinary bladder lumen uberon UBERON:0009958 bladder lumen FMA FMA EHDAA2 An anatomical space that is enclosed by a urinary bladder. OBOL:automatic bladder cavity FMA:15924 cavity of urinary bladder FMA:15924 lumen of urinary bladder FMA:15924 urinary bladder lumen FMA:15924 An anatomical space that is enclosed by a oropharynx. EHDAA2:0004556 FMA:55095 oropharyngeal cavity oropharynx lumen uberon UBERON:0009959 lumen of oropharynx EHDAA2 An anatomical space that is enclosed by a oropharynx. OBOL:automatic oropharyngeal cavity EHDAA2:0004556 oropharynx lumen FMA:55095 An epithelium that is part of a pancreatic duct. in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this EFO:0002556 FMA:67681 pancreatic duct epithelium pancreatic ductal epithelium uberon UBERON:0009970 epithelium of pancreatic duct An epithelium that is part of a pancreatic duct. OBOL:automatic pancreatic duct epithelium FMA:67681 pancreatic ductal epithelium FMA:67681 The junction between the ureter and the renal pelvis of the kidney. EMAPA:37782 FMA:15898 MA:0003021 NCIT:C106203 SCTID:264130006 pelviureteric junction pelvoureteric junction uberon UBERON:0009972 ureteropelvic junction MP The junction between the ureter and the renal pelvis of the kidney. MP:0011487 EMAPA:37782 MA:th pelviureteric junction FMA:15898 The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney. EMAPA:37783 FMA:15899 MA:0003020 NCIT:C106202 SCTID:261187001 vesico-ureteral junction vesico-ureteric junction vesicoureteric junction uberon UBERON:0009973 ureterovesical junction MP The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney. MP:0011488 EMAPA:37783 MA:th vesico-ureteral junction MA:0003020 An anatomical cavity that surrounded_by a Rathke's pouch. EHDAA2:0004138 EMAPA:25037 Rathkes pouch invagination uberon UBERON:0009974 lumen of Rathke's pouch EHDAA2 EHDAA2-modified An anatomical cavity that surrounded_by a Rathke's pouch. OBOL:automatic Rathkes pouch invagination EHDAA2:0004138 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure FBbt:00100313 A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]. May be obsoleted. FMA:256381 NLXANAT:20090509 uberon set of nuclei of neuraxis UBERON:0010009 aggregate regional part of brain A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]. NLXANAT:20090509 set of nuclei of neuraxis FMA:256381 The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity. The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG] EHDAA2:0004115 EHDAA:6772 EMAPA:17002 MA:0001218 NCIT:C34318 SCTID:361516008 UMLS:C1284046 VHOG:0001297 uberon tubotympanic recess UBERON:0010020 tubotympanic recess epithelium EHDAA2 EHDAA2 ISBN:0073040584 PMID:11237469 The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity. ISBN:0124020607 VHOG:0001297 The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG] 2012-09-17 VHOG:0001297 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417 http://bgee.unil.ch/ UMLS:C1284046 ncithesaurus:Tubotympanic_Recess tubotympanic recess VHOG:0001297 in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN:1607950324]. the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract dorsal 2nd branchial pouch dorsal pharyngeal pouch 2 uberon dorsal branchial pouch 2 endoderm dorsal elongation of second pouch endoderm dorsal pharyngeal pouch 2 endoderm UBERON:0010023 dorsal part of pharyngeal pouch 2 in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN:1607950324]. the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract MP Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III) EHDAA2:0000409 EMAPA:16758 dorsal 3rd arch pharyngeal pouch endoderm dorsal 3rd branchial pouch dorsal pharyngeal pouch 3 dorsal wing of pharyngeal pouch 3 uberon cranial dorsal aspect of third dorsal pharyngeal pouch dorsal branchial pouch 3 endoderm dorsal pharyngeal pouch 3 endoderm UBERON:0010025 dorsal part of pharyngeal pouch 3 EHDAA2 EHDAA2 Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III) MP dorsal 3rd arch pharyngeal pouch endoderm EHDAA2:0000409 dorsal wing of pharyngeal pouch 3 http://orcid.org/0000-0002-6601-2165 The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium EHDAA2:0002173 EMAPA:16759 ventral 3rd arch pharyngeal pouch endoderm ventral 3rd branchial pouch ventral pharyngeal pouch 3 ventral wing of pharyngeal pouch 3 uberon caudal ventral aspect of third dorsal pharyngeal pouch ventral branchial pouch 3 endoderm ventral pharyngeal pouch 3 endoderm UBERON:0010026 ventral part of pharyngeal pouch 3 EHDAA2 EHDAA2 The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium MP ventral 3rd arch pharyngeal pouch endoderm EHDAA2:0002173 ventral wing of pharyngeal pouch 3 http://orcid.org/0000-0002-6601-2165 dorsal 4th branchial pouch dorsal pharyngeal pouch 4 uberon dorsal branchial pouch 4 endoderm dorsal pharyngeal pouch 4 endoderm UBERON:0010027 dorsal part of pharyngeal pouch 4 ventral 4th branchial pouch ventral pharyngeal pouch 4 uberon ventral branchial pouch 4 endoderm ventral pharyngeal pouch 4 endoderm UBERON:0010028 ventral part of pharyngeal pouch 4 Mesenchyme that is part of a pharyngeal arch 6. EHDAA2:0004076 EMAPA:32765 FMA:318209 6th pharyngeal arch mesenchyme uberon 6th branchial arch mesenchyme pharyngeal arch 6 mesenchyme UBERON:0010031 6th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 6. OBOL:automatic The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch. The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue check NCIT EMAPA:37437 FMA:229084 NCIT:C32130 UMLS:C0226946 Wikipedia:Anterior_tongue uberon anterior 2/3 of the tongue anterior 2/3 of tongue anterior two thirds of the tongue apex linguae apex of the tongue buccal part of the tongue front of the tongue oral part of the tongue pars anterior dorsi linguae UBERON:0010032 anterior part of tongue https://upload.wikimedia.org/wikipedia/commons/4/4c/Illu04_tongue.jpg ISBN:1607950324 The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch. Wikipedia:Anterior_tongue check NCIT NCIT EMAPA:37437 MA:th UMLS:C0226946 ncithesaurus:Apex_of_the_Tongue anterior 2/3 of the tongue Wikipedia:Anterior_tongue anterior 2/3 of tongue Wikipedia:Anterior_tongue anterior two thirds of the tongue Wikipedia:Anterior_tongue apex linguae Wikipedia:Anterior_tongue apex of the tongue Wikipedia:Anterior_tongue buccal part of the tongue Wikipedia:Anterior_tongue front of the tongue Wikipedia:Anterior_tongue oral part of the tongue Wikipedia:Anterior_tongue pars anterior dorsi linguae Wikipedia:Anterior_tongue An organ of the digestive tract that is capable of retaining and storing food. This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates BSA:0000123 TADS:0000172 TGMA:0001041 uberon UBERON:0010039 food storage organ An organ of the digestive tract that is capable of retaining and storing food. https://orcid.org/0000-0002-6601-2165 Mesenchyme that is part of a pharyngeal arch 1. EMAPA:16128 mesenchyme of 1st arch uberon UBERON:0010042 1st arch mesenchyme Mesenchyme that is part of a pharyngeal arch 1. OBOL:automatic mesenchyme of 1st arch EMAPA:16128 Mesenchyme that is part of a 1st arch maxillary component. EHDAA2:0000041 EMAPA:16391 mesenchyme of maxillary component uberon maxillary component mesenchyme maxillary mesenchyme UBERON:0010045 1st arch maxillary mesenchyme Mesenchyme that is part of a 1st arch maxillary component. OBOL:automatic mesenchyme of maxillary component EMAPA:16391 The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 XAO:0004524 associated mesenchyme of pharyngeal region entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme uberon UBERON:0010046 entire pharyngeal arch associated mesenchyme EHDAA2 EHDAA2 cjm The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. XAO:0004524 https://orcid.org/0000-0002-6601-2165 associated mesenchyme of pharyngeal region EMAPA:16550 entire branchial arch associated mesenchyme https://orcid.org/0000-0002-6601-2165 pharyngeal arch associated mesenchyme EHDAA2:0001459 Gland of the epithelium lining the oral cavity. The most common are the salivary glands. Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa UBERON:0003293 EHDAA2:0001327 EHDAA:2181 EMAPA:16572 EMAPA:16723 VHOG:0000652 buccal gland uberon gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland UBERON:0010047 oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. ISBN:0073040584 Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa EHDAA2 A mucosa that is part of a dorsum of tongue. check surface terms develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324 FMA:74871 SCTID:245835003 mucosa of dorsal surface of tongue uberon UBERON:0010052 mucosa of dorsum of tongue A mucosa that is part of a dorsum of tongue. OBOL:automatic A compound organ that has the potential to develop into a tongue. EHDAA2:0000696 EHDAA:2951 uberon UBERON:0010056 future tongue EHDAA2 A compound organ that has the potential to develop into a tongue. OBOL:automatic EHDAA2:0004610 uberon UBERON:0010059 hypoglossal cord EHDAA2 EHDAA2 EHDAA2:0004116 uberon UBERON:0010063 tympanic cavity epithelium EHDAA2 EHDAA2 An anatomical space with at least one opening to another space or the exterior. AEO:0000221 EHDAA2:0004616 uberon UBERON:0010064 open anatomical space cjm An anatomical space with at least one opening to another space or the exterior. AEO:0000221 EHDAA2:0004114 uberon UBERON:0010065 auditory meatus epithelium EHDAA2 EHDAA2 PMID:16313389 A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane. FMA:56819 SCTID:39725007 cuticular layer of tympanic membrane cuticular stratum of tympanic membrane outer cuticular layer of tympanic membrane outer layer of tympanic membrane tympanic membrane external acoustic meatus epithelial component uberon UBERON:0010069 outer epithelial layer of tympanic membrane A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane. PMID:11237469 https://orcid.org/0000-0002-6601-2165 cuticular layer of tympanic membrane FMA:56819 cuticular stratum of tympanic membrane FMA:56819 outer cuticular layer of tympanic membrane FMA:56819 tympanic membrane external acoustic meatus epithelial component https://orcid.org/0000-0002-6601-2165 The intermediate fibrous layer of the tympanic membrane. check MA EMAPA:19063 FMA:56830 MA:0001223 SCTID:44692008 connective tissue layer of tympanic membrane fibrous layer of tympanic membrane fibrous stratum of tympanic membrane intermediate fibrous layer of tympanic membrane tympanic endothelium uberon UBERON:0010070 intermediate layer of tympanic membrane FMA The intermediate fibrous layer of the tympanic membrane. PMID:11237469 https://sourceforge.net/tracker/?func=detail&aid=3468783&group_id=76834&atid=1205376 check MA MA connective tissue layer of tympanic membrane FMA:56830 fibrous layer of tympanic membrane FMA:56830 fibrous stratum of tympanic membrane FMA:56830 intermediate fibrous layer of tympanic membrane FMA:56830 tympanic endothelium MA:0001223 In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer FMA:56732 tympanic membrane layer uberon UBERON:0010071 layer of tympanic membrane tympanic membrane layer FMA:56732 Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies FMA:79645 MESH:D002838 uberon argentaffin system chromaffin tissue UBERON:0010074 chromaffin system cjm Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. http://orcid.org/0000-0002-6601-2165 argentaffin system MESH:A06.224 One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia. XAO:0004192 uberon UBERON:0010075 sacral neural crest One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia. XB:curator http://www.ncbi.nlm.nih.gov/books/NBK10065/ An epithelium consisting of cuboidal epithelial cells. TODO - coordinate with CL, add cuboidal cell in NCIT this is glandular NCIT:C32415 UMLS:C0682577 Wikipedia:Cuboidal_epithelium uberon UBERON:0010077 cuboidal epithelium An epithelium consisting of cuboidal epithelial cells. Wikipedia:Cuboidal_epithelium in NCIT this is glandular NCIT UMLS:C0682577 ncithesaurus:Cuboidal_Epithelium An extrahepatic bile duct that has the potential to develop into a common hepatic duct. EHDAA2:0000595 uberon UBERON:0010081 future common hepatic duct An extrahepatic bile duct that has the potential to develop into a common hepatic duct. OBOL:automatic Mesenchyme that has the potential to develop into a dermis. check development EHDAA2:0000598 uberon UBERON:0010083 future dermis EHDAA2 EHDAA2 XAO Mesenchyme that has the potential to develop into a dermis. OBOL:automatic A structure that will develop into a diaphragm. EHDAA2:0000599 uberon UBERON:0010084 future diaphragm EHDAA2 PMID:23586979 PMID:23586979 A structure that will develop into a diaphragm. http://orcid.org/0000-0002-6601-2165 A multi-tissue structure that has the potential to develop into a meninx of hindbrain. EHDAA2:0000610 future hindbrain meninges uberon UBERON:0010091 future hindbrain meninx A multi-tissue structure that has the potential to develop into a meninx of hindbrain. OBOL:automatic future hindbrain meninges EHDAA2:0000610 A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 uberon UBERON:0010092 future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. OBOL:automatic A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 uberon UBERON:0010096 future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. OBOL:automatic A gray matter that has the potential to develop into a facial nucleus. EHDAA2:0004639 uberon UBERON:0010123 future facial nucleus A gray matter that has the potential to develop into a facial nucleus. OBOL:automatic A gray matter that has the potential to develop into a superior salivatory nucleus. EHDAA2:0004644 uberon UBERON:0010125 future superior salivatory nucleus A gray matter that has the potential to develop into a superior salivatory nucleus. OBOL:automatic A femur endochondral element that is composed primarily of cartilage tissue. TODO - request EHDAA2 EMAPA:17742 femoral cartilage condensation uberon UBERON:0010129 femur cartilage element EMAPA A femur endochondral element that is composed primarily of cartilage tissue. OBOL:automatic femoral cartilage condensation EMAPA:17742 The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw). autopod plate limb plate uberon UBERON:0010130 embryonic autopod plate The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw). MP:0004576 UBERON:cjm https://github.com/obophenotype/mammalian-phenotype-ontology/issues/1151 Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 specialized conducting tissue of heart specialized muscle tissue of heart uberon UBERON:0010131 conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. http://orcid.org/0000-0002-6601-2165 specialized conducting tissue of heart FMA:83378 specialized muscle tissue of heart FMA:83378 Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli. MA:0000720 neuroendocrine system gland uberon UBERON:0010133 neuroendocrine gland Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli. ISBN:0-683-40008-8 MP:0000631 A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid. EMAPA:35759 MA:0002943 neuronames:2857 uberon UBERON:0010134 secretory circumventricular organ MA MA A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid. http://orcid.org/0000-0002-6601-2165 A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid. EMAPA:37741 MA:0002944 neuronames:2856 uberon humerosensory circumventricular organ humerosensory system humerosensory system organ sensitive circumventricular organs sensitive organs sensory CVOs sensory circumventricular organs UBERON:0010135 sensory circumventricular organ A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid. http://orcid.org/0000-0002-6601-2165 EMAPA:37741 MA:th humerosensory system NeuroNames:2856 sensitive circumventricular organs NeuroNames:2856 sensitive organs NeuroNames:2856 sensory CVOs NeuroNames:2856 sensory circumventricular organs NeuroNames:2856 A sex cord that is part of a indifferent gonad. note that this represents the indifferent structure. EHDAA2:0004051 indifferent sex cord primitive sex cords uberon UBERON:0010141 primitive sex cord of indifferent gonad EHDAA2 EHDAA2 A sex cord that is part of a indifferent gonad. OBOL:automatic primitive sex cords EHDAA2:0004051 A bodily secretion that is produced by a seminal vesicle. constitutes 60-70 % of the ejaculate in humans[MP] important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP] in ncit, seminal fluid is a subtype of seminal vesicle secretion vesicular fluid BTO:0002053 FMA:62969 MA:0002526 NCIT:C33529 NCIT:C52552 UMLS:C0036614 UMLS:C0227987 secretion of seminal vesicle seminal vesicle secretion uberon seminal fluid UBERON:0010143 seminal vesicle fluid FMA A bodily secretion that is produced by a seminal vesicle. http://orcid.org/0000-0002-6601-2165 in ncit, seminal fluid is a subtype of seminal vesicle secretion ncit UMLS:C0036614 ncithesaurus:Seminal_Fluid UMLS:C0227987 ncithesaurus:Seminal_Vesicle_Secretion secretion of seminal vesicle FMA:62969 seminal vesicle secretion FMA:62969 seminal fluid Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 uberon male accessory gland male accessory reproductive gland UBERON:0010147 male accessory sex gland BTO Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 male accessory gland BTO:0004798 A mucous secretion that is produced by glands in the epidermis. uberon epidermal mucus skin mucous UBERON:0010152 skin mucus A mucous secretion that is produced by glands in the epidermis. http://orcid.org/0000-0002-6601-2165 epidermal mucus BTO:0005082 The Sphenofrontal suture is the cranial suture between the sphenoid bone and the frontal bone. FMA:52938 SCTID:136349005 Wikipedia:Sphenofrontal_suture frontosphenoid suture sphenofrontal suture of skull uberon spheno-frontal suture sphenofrontal sutura sphenofrontalis UBERON:0010156 sphenofrontal suture http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png The Sphenofrontal suture is the cranial suture between the sphenoid bone and the frontal bone. Wikipedia:Sphenofrontal_suture frontosphenoid suture FMA:52938 sphenofrontal suture of skull FMA:52938 sphenofrontal Wikipedia:Sphenofrontal_suture sutura sphenofrontalis Wikipedia:Sphenofrontal_suture An anatomical cavity that surrounded_by a lymphatic vessel. FMA:59681 lumen of lymphatic duct lymphatic vessel lumen uberon UBERON:0010160 lumen of lymphatic vessel An anatomical cavity that surrounded_by a lymphatic vessel. OBOL:automatic lumen of lymphatic duct FMA:59681 lymphatic vessel lumen FMA:59681 An anatomical cavity that surrounded_by a blood vessel. FMA:312610 SCTID:91747007 blood vessel lumen uberon UBERON:0010161 lumen of blood vessel An anatomical cavity that surrounded_by a blood vessel. OBOL:automatic The distal end of the tail. EMAPA:37760 MA:0002848 XAO:0004057 tail tip uberon end of tail UBERON:0010162 post-anal tail tip MA The distal end of the tail. http://orcid.org/0000-0002-6601-2165 EMAPA:37760 MA:th tail tip MA:0002848 end of tail MA:0002848 An anatomical cluster that composed_primarily_of a strand of hair. FMA:70752 hairs hairs set pili set of hairs uberon UBERON:0010164 collection of hairs An anatomical cluster that composed_primarily_of a strand of hair. OBOL:automatic hairs FMA:70752 hairs set FMA:70752 pili FMA:TA set of hairs FMA:70752 A collection of hairs that is part of a face. FMA:70741 facial hairs set set of facial hairs uberon facial hair UBERON:0010165 collection of hair on face A collection of hairs that is part of a face. OBOL:automatic facial hairs set FMA:70741 set of facial hairs FMA:70741 A strand of hair that is part of a face. FMA:54360 SCTID:368910000 face hair face hair strand hair of face uberon facial hair UBERON:0010171 strand of hair of face A strand of hair that is part of a face. OBOL:automatic face hair FMA:54360 hair of face FMA:54360 facial hair FMA:54360 A trabecula that is part of a liver. liver trabeculae uberon hepatic trabecula UBERON:0010183 liver trabecula A trabecula that is part of a liver. GO:0060344 OBOL:automatic liver trabeculae Any of the numerous small mucous-secreting glands located in the wall of the penile urethra. EMAPA:29645 FMA:21443 NCIT:C49311 SCTID:303562001 UMLS:C1314737 Wikipedia:Urethral_gland Littre's gland gland of Littre gland of male urethra male urethra gland urethral gland (male) uberon glandulae urethrales urethrae masculinae UBERON:0010186 male urethral gland Any of the numerous small mucous-secreting glands located in the wall of the penile urethra. MGI:anna MP:0011794 UMLS:C1314737 ncithesaurus:Urethral_Gland Littre's gland FMA:21443 urethral gland (male) FMA:21443 glandulae urethrales urethrae masculinae Wikipedia:Urethral_gland An urethral gland that is part of a female urethra. EMAPA:29653 FMA:21444 SCTID:279476001 female urethra gland gland of female urethra urethral gland (female) uberon UBERON:0010187 female urethral gland An urethral gland that is part of a female urethra. OBOL:automatic urethral gland (female) FMA:21444 A roughly circular bulge in a surface. requires review AEO:0000205 EHDAA2:0003250 FMA:82506 uberon UBERON:0010188 protuberance FMA A roughly circular bulge in a surface. EHDAA2:0003250 part_of in EHDAA2. Only child in MA. EHDAA2:0001762 EMAPA:17010 EMAPA:17328 MA:0001872 uberon right venous valve UBERON:0010189 right atrium venous valve part_of in EHDAA2. Only child in MA. EHDAA2 right venous valve EHDAA2:0001762 The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation. EHDAA2:0000410 EMAPA:18606 MA:0000476 paired dorsal aortae uberon UBERON:0010190 pair of dorsal aortae EHDAA2 EHDAA2 The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation. ISBN:0-914294-08-3 MP:0004787 paired dorsal aortae EHDAA2:0000410 EHDAA2:0004512 uberon UBERON:0010191 aortic system Wikipedia One of the laterally paired arteries that supply the gonads. Wikipedia:Gonadal_artery gonadal artery uberon UBERON:0010192 genital artery One of the laterally paired arteries that supply the gonads. ISBN:0073040584 Wikipedia:Gonadal_artery A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver. Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO] AAO:0010225 hepatic-portal system portal system of liver uberon UBERON:0010194 hepatic portal system A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver. ISBN:0073040584 Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO] 2012-06-20 AAO:0010225 AAO AAO:BJB hepatic-portal system AAO:0010225 An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 uberon UBERON:0010199 One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) bona-fide anatomical boundary CARO An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 A vasculature that is part of a post-anal tail. isa blood vessel in XAO TAO:0005037 XAO:0004151 ZFA:0005037 post-vent vasculature uberon tail vasculature UBERON:0010204 tail vasculature A vasculature that is part of a post-anal tail. OBOL:automatic isa blood vessel in XAO XAO post-vent vasculature ZFA:0005037 tail vasculature ZFA:0005037 A semisolid gelatinous mass of coagulated blood that consists of red blood cells, white blood cells, and platelets entrapped in a fibrin network. BTO:0000102 Wikipedia:Thrombus galen:BloodClot coagulated blood fibrin clot hemostatic plug thrombus clot uberon UBERON:0010210 blood clot BTO A semisolid gelatinous mass of coagulated blood that consists of red blood cells, white blood cells, and platelets entrapped in a fibrin network. BTO:0000102 Wikipedia:Thrombus hemostatic plug Wikipedia:Thrombus thrombus BTO:0000102 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton AAO:0000267 EHDAA2:0000904 laryngeal cartilage system uberon UBERON:0010212 laryngeal apparatus EHDAA2 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. AAO:0000267 laryngeal cartilage system EHDAA2:0000904 uberon UBERON:0010213 laryngeal pre-cartilage condensation EHDAA2-abstracted EHDAA2-abstracted EHDAA2:0004085 uberon UBERON:0010221 Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme EHDAA2 EHDAA2 Wikipedia Wikipedia Wikipedia A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. EHDAA2:0004469 FMA:258745 uberon UBERON:0010225 thalamic complex A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. Wikipedia:Thalamus#Thalamic_nuclei Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. FMA:71005 TAO:0002228 ZFA:0001718 presumptive atrium heart tube primordial atrium primordial cardiac atrium uberon UBERON:0010227 future cardiac atrium ZFA Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. ZFA:0001718 presumptive atrium heart tube ZFA:0001718 primordial atrium FMA:71005 primordial cardiac atrium FMA:71005 The core globe-shaped component of the camera-type eye. See notes for camera-type eye FMA:12513 MIAA:0000283 SCTID:244486005 VHOG:0001616 Wikipedia:Globe_(human_eye) bulbus oculi eye globe eyeball uberon eye globe UBERON:0010230 eyeball of camera-type eye FMA The core globe-shaped component of the camera-type eye. UBERON:cjm eye globe VHOG:0001616 eyeball FMA:12513 eye globe HP:0100886 MIAA:0000283 The connective tissue that supports the lobules and follicles of the thyroid gland. FMA:86304 SCTID:157862000 thyroid gland stroma thyroid stroma uberon UBERON:0010233 stroma of thyroid gland The connective tissue that supports the lobules and follicles of the thyroid gland. http://www.drugs.com/dict/stroma-of-thyroid-gland.html thyroid gland stroma FMA:86304 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000037 uberon UBERON:0010252 1st arch mandibular mesenchyme from neural crest inferred EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000044 uberon UBERON:0010253 1st arch maxillary mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. EHDAA2:0000068 EMAPA:16281 neural crest derived arch 2 mesenchyme pharyngeal arch 2 mesenchyme from neural crest uberon branchial arch 2 mesenchyme from neural crest UBERON:0010254 2nd arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000083 EMAPA:16404 VHOG:0000571 3rd pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 3rd arch neural crest derived arch 3 mesenchyme pharyngeal arch 3 mesenchyme from neural crest uberon branchial arch 3 mesenchyme from neural crest UBERON:0010255 3rd arch mesenchyme from neural crest EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000571 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch mesenchyme derived from neural crest VHOG:0000571 mesenchyme derived from neural crest of mesenchyme of 3rd arch EMAPA:16404 Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 EMAPA:16772 VHOG:0000580 4th pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 4th arch neural crest derived arch 4 mesenchyme pharyngeal arch 4 mesenchyme from neural crest uberon branchial arch 4 mesenchyme from neural crest UBERON:0010256 4th arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000580 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch mesenchyme derived from neural crest VHOG:0000580 mesenchyme derived from neural crest of mesenchyme of 4th arch EMAPA:16772 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from neural crest uberon branchial arch 6 mesenchyme from neural crest UBERON:0010257 6th arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a rhombencephalon neural crest. EHDAA2:0004423 uberon UBERON:0010258 mesenchyme from rhombencephalic neural crest EHDAA2 Mesenchyme that develops_from a rhombencephalon neural crest. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. EMAPA:16129 mesenchyme derived from neural crest of mesenchyme of 1st arch neural crest derived arch 1 mesenchyme pharyngeal arch 1 mesenchyme from neural crest uberon branchial arch 1 mesenchyme from neural crest UBERON:0010259 1st arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from neural crest of mesenchyme of 1st arch EMAPA:16129 One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta. EMAPA:36493 SCTID:408728001 allantoic vessel umbilical cord blood vessel umbilical vessel uberon umbilical cord blood vessels umbilical vasculature UBERON:0010260 umbilical blood vessel One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta. MP:0003230 allantoic vessel Hymans:Hymans umbilical cord blood vessels A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage. Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO] relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO] In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process). AAO:0000225 AAO:0000682 EMAPA:37600 MA:0003037 SCTID:410035009 http://palaeos.com/vertebrates/bones/gill_arches/images/ReptileHyoids.gif uberon apparatus hyobranchialis apparatus hyoideus hyobranchial apparatus hyolingual system UBERON:0010272 hyoid apparatus AAO A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage. http://www.biology-online.org/dictionary/Hyoid_apparatus Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO] 2012-06-20 AAO:0000225 AAO AAO:LAP relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO] 2012-06-20 AAO:0000225 AAO EMAPA:37600 MA:th apparatus hyobranchialis apparatus hyoideus http://www.biology-online.org/dictionary/Hyoid_apparatus hyobranchial apparatus AAO:0000225 hyolingual system AAO:0000225 A zone of bone organ that is part of a hyoid bone. FMA:59494 SCTID:119534005 hyoid bone zone uberon UBERON:0010273 zone of hyoid bone A zone of bone organ that is part of a hyoid bone. OBOL:automatic hyoid bone zone FMA:59494 Any anatomical space that is part of a vertebral column. AAO:0000700 vertebral column opening vertebral conduit uberon UBERON:0010276 space in vertebral column Any anatomical space that is part of a vertebral column. OBOL:automatic vertebral column opening AAO:0000700 A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi. collect tears produced by the lacrimal glands FMA:59365 SCTID:263344003 Wikipedia:Lacrimal_punctum uberon lacrimal point lacrimal puncta puncta lacrimalia UBERON:0010284 lacrimal punctum http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png FMA A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi. Wikipedia:Lacrimal_punctum lacrimal point Wikipedia:Lacrimal_punctum lacrimal puncta Wikipedia:Lacrimal_punctum puncta lacrimalia Wikipedia:Lacrimal_punctum Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 EHDAA2:0004375 TAO:0000761 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon UBERON:0010285 midbrain basal plate EHDAA2 EHDAA2 ZFA Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. ZFA:0000761 basal plate midbrain TAO:0000761 basal plate midbrain region ZFA:0000761 Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 ZFA:0007039 uberon UBERON:0010286 midbrain neural tube ZFA Portion of neural tube that gives rise to the midbrain. ZFA:0007039 Wikipedia:Sclera#Histology uberon UBERON:0010291 layer of sclera cjm An endothelium that is part of a sclera. uberon UBERON:0010294 scleral endothelium Wikipedia An endothelium that is part of a sclera. OBOL:automatic A stroma that is part of a sclera. subsantia propria FMA:58365 NCIT:C33652 SCTID:368851004 UMLS:C1704397 scleral stroma stroma of sclera subsantia propria sclerae substantia propria sclerae uberon UBERON:0010295 substantia propria of sclera Wikipedia A stroma that is part of a sclera. OBOL:automatic UMLS:C1704397 ncithesaurus:Substantia_Propria scleral stroma FMA:58365 stroma of sclera FMA:58365 subsantia propria sclerae FMA:58365 substantia propria sclerae FMA:58365 FMA:TA Mesenchyme surrounding the developing optic cup which develops into the sclera. The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288 uberon UBERON:0010299 scleral mesenchyme Mesenchyme surrounding the developing optic cup which develops into the sclera. PMID:16496288 https://orcid.org/0000-0002-6601-2165 An epithelium that is part of a extraembryonic structure. extra-embryonic epithelium uberon UBERON:0010303 extraembryonic epithelium An epithelium that is part of a extraembryonic structure. OBOL:automatic Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 Wikipedia:Stratified_squamous_epithelium#Nonkeratinized epithelium stratificatum squamosum noncornificatum nonkeratinizing stratified squamous epithelium stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium uberon UBERON:0010304 non-keratinized stratified squamous epithelium FMA Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 Wikipedia:Stratified_squamous_epithelium#Nonkeratinized epithelium stratificatum squamosum noncornificatum FMA:45569 nonkeratinizing stratified squamous epithelium FMA:45569 stratified squamous non-keratinized epithelium http://orcid.org/0000-0002-6601-2165 stratified squamous nonkeratinizing epithelium http://orcid.org/0000-0002-6601-2165 Developing anatomical structure that develops into the eyeball and associated structures. Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye uberon UBERON:0010312 immature eye definitional Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] 2012-08-14 TAO:0002201 TAO ZFIN:curator An anatomical structure that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 uberon UBERON:0010316 germ layer / neural crest A skeletal element that is part of a orbital region. uberon eye skeleton ocular skeleton skeletal element of orbital region UBERON:0010321 skeletal element of eye region A skeletal element that is part of a orbital region. OBOL:automatic Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints) that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] AAO:0000109 AAO:0000971 AAO:0010185 TAO:0000737 VSAO:0000049 XAO:0003075 ZFA:0000737 cranial skeleton osteocranium uberon cranium UBERON:0010323 cranial skeletal system Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. GO_REF:0000034 PSPUB:0000170 VSAO:0000049 http://dx.plos.org/10.1371/journal.pone.0051070 Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] 2012-06-20 AAO:0000109 AAO AAO:LAP Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] 2012-08-14 TAO:0000737 TAO ZFIN:curator cranium ZFA:0000737 Mesenchyme that is part of a limb bud. uberon UBERON:0010328 limb bud mesenchyme Mesenchyme that is part of a limb bud. OBOL:automatic Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme EHDAA2-abduced Mesenchyme that is part of a limb/fin bud. OBOL:automatic An epithelium that is part of a handplate. EHDAA2:0000730 EMAPA:32630 handplate epithelium uberon UBERON:0010332 epithelium of handplate EHDAA2 EHDAA2 An epithelium that is part of a handplate. OBOL:automatic handplate epithelium EHDAA2:0000730 Mesenchyme that is part of a extraembryonic membrane. uberon UBERON:0010333 extraembryonic membrane mesenchyme EHDAA2-abduced Mesenchyme that is part of a extraembryonic membrane. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. EHDAA2:0004601 uberon UBERON:0010334 maxillary process mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. EHDAA2:0004602 uberon UBERON:0010335 maxillary process mesenchyme from head mesenchyme EHDAA2 EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme EHDAA2 EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000043 uberon UBERON:0010338 1st arch maxillary mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch uberon UBERON:0010341 1st arch mesenchyme from head mesenchyme EMAPA Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 1st arch EMAPA:16130 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. EHDAA2:0000067 EMAPA:16280 head mesenchyme derived arch 2 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 2nd arch pharyngeal arch 2 mesenchyme from head mesenchyme uberon branchial arch 2 mesenchyme from head mesenchyme UBERON:0010343 2nd arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 2nd arch EMAPA:16280 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. EHDAA2:0000082 EMAPA:16403 head mesenchyme derived arch 3 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 3rd arch pharyngeal arch 3 mesenchyme from head mesenchyme uberon branchial arch 3 mesenchyme from head mesenchyme UBERON:0010344 3rd arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 3rd arch EMAPA:16403 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 head mesenchyme derived arch 4 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 4th arch pharyngeal arch 4 mesenchyme from head mesenchyme uberon branchial arch 4 mesenchyme from head mesenchyme UBERON:0010345 4th arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 4th arch EMAPA:16771 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from head mesenchyme uberon branchial arch 6 mesenchyme from head mesenchyme UBERON:0010347 6th arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. OBOL:automatic The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&. currently classified as a zone of a bone organ, but exists prior to bone ossifying FMA:75436 Wikipedia:Ossification_center centrum ossificationis ossification centre uberon center of ossification centrum ossificationis UBERON:0010355 ossification center http://upload.wikimedia.org/wikipedia/commons/f/fd/Gray79.png FMA The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&. Wikipedia:Ossification_center centrum ossificationis FMA:TA ossification centre FMA:75436 center of ossification Wikipedia:Ossification_center centrum ossificationis Wikipedia:Ossification_center An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum. (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] Note that humans do not have hemal arches, so VA=NA for FMA EMAPA:36614 FMA:11946 arch of vertebra arcus vertebrae (vertebralis) vertebra arch vertebral arch uberon UBERON:0010358 arch of centrum of vertebra FMA An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum. http://orcid.org/0000-0002-6601-2165 (...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG] 2012-09-17 VHOG:0001670 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270 http://bgee.unil.ch/ Note that humans do not have hemal arches, so VA=NA for FMA FMA arch of vertebra FMA:11946 arcus vertebrae (vertebralis) FMA:11946 vertebra arch MA:0001453 vertebral arch FMA:11946 Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from neural crest branchial arch mesenchyme from neural crest neural crest derived arch mesenchyme uberon UBERON:0010359 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from head mesenchyme branchial arch mesenchyme from head mesenchyme head mesenchyme derived arch mesenchyme uberon UBERON:0010360 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t VSAO:0000037 Wikipedia:Endoskeleton XAO:0004026 replacement skeleton uberon UBERON:0010362 endoskeleton VSAO Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. GO_REF:0000034 PSPUB:0000170 VSAO:0000037 http://dx.plos.org/10.1371/journal.pone.0051070 An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t Wikipedia:Endoskeleton replacement skeleton VSAO:curator A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element uberon UBERON:0010363 endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern VSAO A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. GO_REF:0000034 PSPUB:0000170 VSAO:0000139 http://dx.plos.org/10.1371/journal.pone.0051070 endochondral replacement element VSAO:0000139 Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. exoskeleton VSAO:0000035 XAO:0004025 uberon dermal skeletal system dermoskeleton desmoskeleton UBERON:0010364 This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton VSAO Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. GO_REF:0000034 PSPUB:0000170 VSAO:0000035 http://dx.plos.org/10.1371/journal.pone.0051070 exoskeleton VSAO:curator dermal skeletal system VSAO:curator dermoskeleton VSAO:curator desmoskeleton VSAO:curator Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla. in many vertebrates, odontoid tissue is not restricted to the teeth Classified as a portion of organism substance in FMA UBERON:0001973 EMAPA:35872 FMA:63001 MA:0002540 NCIT:C33794 UMLS:C1519551 VSAO:0000063 XAO:0004046 ZFA:0005623 odontogenic tissue portion of substance of tooth substance of tooth tooth substance uberon dental tissue tooth hard tissue tooth tissue UBERON:0010365 odontoid tissue Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla. GO_REF:0000034 PSPUB:0000170 VSAO:0000063 http://dx.plos.org/10.1371/journal.pone.0051070 Classified as a portion of organism substance in FMA FMA UMLS:C1519551 ncithesaurus:Tooth_Tissue odontogenic tissue VSAO:curator portion of substance of tooth FMA:63001 substance of tooth FMA:63001 tooth substance MA:0002540 dental tissue VSAO:curator tooth hard tissue VT:0003930 The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. FMA:75739 NCIT:C33428 lobulus pulmonis uberon UBERON:0010368 pulmonary lobule The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. ncithesaurus:Pulmonary_Lobule lobulus pulmonis FMA:75739 FMA:TA One of the veins of the lower leg; empty into the popliteal vein. EMAPA:37199 MA:0002243 NCIT:C33787 UMLS:C0447138 vena tibialis uberon UBERON:0010370 tibial vein MA One of the veins of the lower leg; empty into the popliteal vein. http://www.thefreedictionary.com/tibial+vein EMAPA:37199 MA:th UMLS:C0447138 ncithesaurus:Tibial_Vein Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') EHDAA2:0001384 FMA:79793 uberon dorsal pancreas UBERON:0010375 pancreas dorsal primordium EHDAA2 dorsal pancreas FMA:79793 Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') EHDAA2:0001387 FMA:79794 uberon ventral pancreas UBERON:0010376 pancreas ventral primordium EHDAA2 ventral pancreas FMA:79794 Mesenchyme that develops_from a somatopleure. the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives EHDAA2:0001120 uberon UBERON:0010377 mesenchyme from somatopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a somatopleure. OBOL:automatic Mesenchyme that develops_from a splanchnopleure. EHDAA2:0001122 uberon UBERON:0010378 mesenchyme from splanchnopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a splanchnopleure. OBOL:automatic An anatomical space that is enclosed by a hypopharynx. FMA:55096 laryngopharynx lumen uberon UBERON:0010384 lumen of laryngopharynx FMA An anatomical space that is enclosed by a hypopharynx. OBOL:automatic laryngopharynx lumen FMA:55096 The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID]. EMAPA:37495 MA:0001400 MA:0001414 proximal part of rib proximal rib proximal rib segment uberon costal part of rib vertebral part of rib UBERON:0010388 The proximal rib derives from the caudal half of somite[PMID:15906248] proximal segment of rib MA The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID]. MP:0000152 PMID:15906248 EMAPA:37495 MA:th proximal part of rib PMID:15906248 proximal rib MA:0001400 An organ cavity that is part of a urethra. FMA:19709 SCTID:279432008 urethral lumen uberon UBERON:0010390 lumen of urethra An organ cavity that is part of a urethra. OBOL:automatic urethral lumen FMA:19709 One of the branches of the splenic artery[MP]. When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia] MA:0000759 NCIT:C49775 UMLS:C1710159 Wikipedia:Trabecular_arteries uberon trabecular artery UBERON:0010399 spleen trabecular artery MP One of the branches of the splenic artery[MP]. MP:0002354 Wikipedia:Trabecular_arteries When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia] Wikipedia Wikipedia:Trabecular_arteries UMLS:C1710159 ncithesaurus:Splenic_Trabecular_Artery One of the veins that feed the splenic vein. The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia] MA:0000760 NCIT:C49779 UMLS:C1710160 Wikipedia:Trabecular_veins uberon trabecular vein UBERON:0010400 spleen trabecular vein One of the veins that feed the splenic vein. MP:0002228 Wikipedia:Trabecular_veins The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia] Wikipedia Wikipedia:Trabecular_veins UMLS:C1710160 ncithesaurus:Splenic_Trabecular_Vein trabecular vein Wikipedia:Trabecular_veins The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 eye surface eye surface region ocular surface uberon UBERON:0010409 ocular surface region The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. MP:0013754 eye surface MA:0002486 An orifice that is part of a lower urinary tract. EMAPA:35965 MA:0002867 urethral orifice uberon UBERON:0010418 urethral opening An orifice that is part of a lower urinary tract. OBOL:automatic urethral orifice OBOL:automatic A naris that is located inside the nasal cavity and connects to the pharynx. choanal In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx NCIT:C32856 choana internal choana uberon choanae internal nares internal nostril UBERON:0010425 internal naris A naris that is located inside the nasal cavity and connects to the pharynx. http://orcid.org/0000-0002-6601-2165 choanae internal nares Opening/conduit between the nasal cavity and the oropharynx via the roof of the mouth. todo - check AAO:0000025 apertura nasalis interna Hole on the nasal capsule that connects the nasal and buccal cavites.[AAO] relationship loss: subclass nasal opening (AAO:0000316)[AAO] has function in pressure equalization in birds that fly to high altitudes choana of oropharynx oropharyngeal naris palatal choana uberon apertura nasalis interna cleft palate palatal cleft UBERON:0010426 oropharyngeal choana Opening/conduit between the nasal cavity and the oropharynx via the roof of the mouth. https://orcid.org/0000-0002-6601-2165 Hole on the nasal capsule that connects the nasal and buccal cavites.[AAO] 2012-06-20 AAO:0000025 AAO AAO:LAP relationship loss: subclass nasal opening (AAO:0000316)[AAO] 2012-06-20 AAO:0000025 AAO apertura nasalis interna AAO:0000025 The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. FMA:76551 SCTID:280860001 Wikipedia:Ciliary_processes ciliary processes ciliary processes set processus ciliares set of ciliary processes uberon ciliary process processus ciliares UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. Wikipedia:Ciliary_processes ciliary processes FMA:76551 ciliary processes set FMA:76551 processus ciliares FMA:TA set of ciliary processes FMA:76551 ciliary process Wikipedia:Ciliary_processes processus ciliares Wikipedia:Ciliary_processes A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult mammal, most red blood cells are formed in flat bones Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment FMA:7476 NCIT:C32616 SCTID:332907008 UMLS:C0222649 Wikipedia:Flat_bone galen:FlatBone uberon os planum UBERON:0010428 Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs flat bone FMA A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. Wikipedia:Flat_bone UMLS:C0222649 ncithesaurus:Flat_Bone os planum Wikipedia:Flat_bone A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. glandular in NCIT; we consider the two NCIT terms synonymous FMA:45572 NCIT:C33419 NCIT:C49316 UMLS:C0836138 UMLS:C1514590 Wikipedia:Pseudostratified_columnar_epithelium uberon UBERON:0010498 pseudostratified columnar epithelium FMA A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Wikipedia:Pseudostratified_columnar_epithelium http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium glandular in NCIT; we consider the two NCIT terms synonymous NCIT UMLS:C0836138 ncithesaurus:Pseudostratified_Columnar_Epithelium UMLS:C1514590 ncithesaurus:Pseudostratified_Epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 NCIT:C13181 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon UBERON:0010499 pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. NCIT:NCIT UMLS:C0506992 ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) FMA:13146 Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 ZFA:0005624 uberon UBERON:0010522 replacement element VSAO cjm Skeletal element that forms as a replacement or substitution of another element or tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000135 http://dx.plos.org/10.1371/journal.pone.0051070 A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 ZFA:0005251 uberon microcirculatory vessels UBERON:0010523 microcirculatory vessel ZFA A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 ZFA:0005251 http://orcid.org/0000-0002-6601-2165 microcirculatory vessels TAO:0005251 An organ cavity that surrounded_by a bone. FMA:24021 bone organ cavity uberon UBERON:0010527 cavity of bone organ An organ cavity that surrounded_by a bone. OBOL:automatic bone organ cavity FMA:24021 FMA:24028 air space of bone uberon UBERON:0010528 pneumatic cavity of bone FMA air space of bone FMA:24028 different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic. EHDAA2:0001143 EHDAA:7007 EHDAA:8105 EMAPA:17953 EMAPA:27621 MA:0002998 VHOG:0001241 induced blastemal cells nephrogenic interstitium of nephrogenic zone uberon cap mesenchyme of metanephros of urinary system nephrogenic interstitium peripheral blastema UBERON:0010531 metanephros induced blastemal cells EHDAA2 different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic. EMAPA induced blastemal cells VHOG:0001241 nephrogenic interstitium of nephrogenic zone EMAPA:17953 cap mesenchyme of metanephros of urinary system EMAPA:17645 peripheral blastema EMAPA:17953 An epithelial tube that is fated to become a nephron. EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells developing nephron primitive nephron future nephron presumptive nephron uberon UBERON:0010532 primitive nephron EHDAA2-inferred EHDAA2 An epithelial tube that is fated to become a nephron. http://orcid.org/0000-0002-6601-2165 EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells EHDAA2 The metanephric cortex is the outer region of the metanephros[GO]. VHOG:0000714 uberon UBERON:0010533 metanephros cortex VHOG The metanephric cortex is the outer region of the metanephros[GO]. GO:0072214 Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons. ZFA:0005584 developing mesonephric nephron primitive mesonephric nephron uberon UBERON:0010534 primitive mesonephric nephron Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons. GOC:cvs ZFA:0005584 https://orcid.org/0000-0002-2244-7917 developing mesonephric nephron ZFA:0005584 A primitive nephron that is part of a metanephros. primitive nephron EHDAA2:0001516 developing metanephric nephron primitive metanephric nephron uberon UBERON:0010535 primitive metanephric nephron EHDAA2 A primitive nephron that is part of a metanephros. OBOL:automatic primitive nephron EHDAA2:0001516 uberon UBERON:0010536 nephron progenitor ZFA cjm Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells. ZFA:0005587 uberon UBERON:0010537 mesonephric nephron progenitor Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells. ZFA:0005587 An appendage segment that is part of a limb/fin. limb/fin segment uberon UBERON:0010538 paired limb/fin segment An appendage segment that is part of a limb/fin. OBOL:automatic A pre-cartilage condensation that has the potential to develop into a tarsal bone. EHDAA2:0001978 uberon UBERON:0010540 tarsus pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a tarsal bone. OBOL:automatic A cartilaginous condensation that has the potential to develop into a tarsal bone. EHDAA2:0001977 uberon UBERON:0010541 tarsus cartilage element EHDAA2 EHDAA2 A cartilaginous condensation that has the potential to develop into a tarsal bone. OBOL:automatic The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]. FMA:231315 VSAO:0005028 acropodial skeleton acropodium skeleton set of phalanges skeletal parts of acropodial region uberon acropodium digital skeleton digits skeleton phalangeal skeleton skeletal parts of acropodium skeleton of digits UBERON:0010543 acropodial skeleton PHENOSCAPE:ni The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]. VSAO:0005028 VSAO:NI https://orcid.org/0000-0002-6601-2165 set of phalanges FMA:231315 acropodium VSAO:0005028 VSAO:NI The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted]. Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] AAO:0000946 EMAPA:36158 FMA:71336 MESH:D050279 VSAO:0005026 Wikipedia:Metacarpus XAO:0003208 anterior metapodial skeleton metacarpal bones metacarpal skeleton metacarpals [I-V] metacarpals set ossa metacarpalia [I-V] ossa metacarpi [I-V] set of metacarpal bones set of metacarpals set of metacarpals [I-V] skeleton of metacarpus uberon anterior metapodium fore metapodial skeleton fore metapodium metacarpalia UBERON:0010544 metacarpus skeleton https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg many to one lexical The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted]. Wikipedia:Metacarpus Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] 2012-06-20 AAO:0000946 AAO AAO:LAP metacarpal bones FMA:71336 metacarpals [I-V] FMA:71336 metacarpals set FMA:71336 ossa metacarpalia [I-V] FMA:71336 FMA:TA ossa metacarpi [I-V] FMA:71336 FMA:TA set of metacarpal bones FMA:71336 set of metacarpals FMA:71336 set of metacarpals [I-V] FMA:71336 anterior metapodium VSAO:0005026 VSAO:NI fore metapodium AAO:0000946 MA:th http://en.wiktionary.org/wiki/metapodial metacarpalia Wikipedia:Metacarpus Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus. Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] AAO:0000221 FMA:71340 MESH:D008684 VSAO:0005027 Wikipedia:Metatarsus XAO:0003212 metatarsal bones set metatarsal skeleton metatarsals [I-V] ossa metatarsalia [I-V] ossa metatarsi[I-V] posterior metapodial skeleton set of metatarsal bones set of metatarsals [I-V] skeleton of metatarsus uberon metatarsalia ossa metatarsalia posterior metapodium UBERON:0010545 metatarsus skeleton http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png many to one Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus. Wikipedia:Metatarsus Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] 2012-06-20 AAO:0000221 AAO AAO:LAP metatarsal bones set FMA:71340 metatarsals [I-V] FMA:71340 ossa metatarsalia [I-V] FMA:71340 FMA:TA ossa metatarsi[I-V] FMA:71340 FMA:TA set of metatarsal bones FMA:71340 set of metatarsals [I-V] FMA:71340 ossa metatarsalia Wikipedia:Metatarsus posterior metapodium VSAO:0005027 VSAO:NI Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton. Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] VSAO:0005025 metacarpal/metatarsal skeleton metapodial skeleton metapodium skeleton skeletal parts of metapodium skeleton of metapodium uberon metapodium UBERON:0010546 metapodial skeleton PHENOSCAPE:ni Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton. https://orcid.org/0000-0002-6601-2165 Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO] 2012-08-14 VSAO:0005025 VSAO VSAO:NI relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0005025 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0005025 VSAO metapodial skeleton VSAO:0005025 metapodium skeleton https://orcid.org/0000-0002-6601-2165 skeletal parts of metapodium https://orcid.org/0000-0002-6601-2165 metapodium VSAO:0005025 VSAO:NI A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. EHDAA2:0002040 EMAPA:17725 hind limb digit 1 metatarsal pre-cartilage condensation pedal digit I metatarsal pre-cartilage condensation toe 1 metatarsal pre-cartilage condensation foot digit 1 metatarsal pre-cartilage condensation uberon UBERON:0010547 pedal digit 1 metatarsal pre-cartilage condensation A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 metatarsal pre-cartilage condensation OBOL:accepted pedal digit I metatarsal pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 toe 1 metatarsal pre-cartilage condensation EHDAA2:0002040 foot digit 1 metatarsal pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. EHDAA2:0002060 EMAPA:17733 hind limb digit 5 metatarsal pre-cartilage condensation pedal digit V metatarsal pre-cartilage condensation toe 5 metatarsal pre-cartilage condensation foot digit 5 metatarsal pre-cartilage condensation uberon UBERON:0010551 pedal digit 5 metatarsal pre-cartilage condensation A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 metatarsal pre-cartilage condensation OBOL:accepted pedal digit V metatarsal pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 toe 5 metatarsal pre-cartilage condensation EHDAA2:0002060 foot digit 5 metatarsal pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pedal digit metatarsal cartilage condensation that is part of a pedal digit 1 mesenchyme. EMAPA:18106 hind limb digit 1 metatarsal cartilage condensation pedal digit I metatarsal cartilage element toe 1 metatarsal cartilage condensation foot digit 1 metatarsal cartilage element uberon UBERON:0010557 pedal digit 1 metatarsal cartilage element A pedal digit metatarsal cartilage condensation that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 metatarsal cartilage condensation OBOL:accepted pedal digit I metatarsal cartilage element https://github.com/obophenotype/uberon/issues/458 foot digit 1 metatarsal cartilage element NCBITaxon:9606 OBOL:accepted A pedal digit metatarsal cartilage element that is part of a pedal digit 5 mesenchyme. EMAPA:18126 hind limb digit 5 metatarsal cartilage element pedal digit V metatarsal cartilage element toe 5 metatarsal cartilage element foot digit 5 metatarsal cartilage element uberon UBERON:0010561 pedal digit 5 metatarsal cartilage element A pedal digit metatarsal cartilage element that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 metatarsal cartilage element OBOL:accepted pedal digit V metatarsal cartilage element https://github.com/obophenotype/uberon/issues/458 foot digit 5 metatarsal cartilage element NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a developing pedal digit 1. EHDAA2:0002039 EMAPA:17462 hind limb digit 1 mesenchyme pedal digit I mesenchyme foot digit 1 mesenchyme uberon UBERON:0010562 pedal digit 1 mesenchyme Mesenchyme that is part of a developing pedal digit 1. OBOL:automatic hind limb digit 1 mesenchyme OBOL:accepted pedal digit I mesenchyme https://github.com/obophenotype/uberon/issues/458 foot digit 1 mesenchyme NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a developing manual digit 1. EHDAA2:0000513 EMAPA:17431 fore limb digit 1 mesenchyme manual digit I mesenchyme hand digit 1 mesenchyme uberon UBERON:0010564 manual digit 1 mesenchyme Mesenchyme that is part of a developing manual digit 1. OBOL:automatic fore limb digit 1 mesenchyme OBOL:accepted manual digit I mesenchyme https://github.com/obophenotype/uberon/issues/458 hand digit 1 mesenchyme NCBITaxon:9606 OBOL:accepted A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 1 mesenchyme. EHDAA2:0000515 EMAPA:17714 finger 1 metacarpus pre-cartilage condensation fore limb digit 1 metacarpus pre-cartilage condensation manual digit I metacarpus pre-cartilage condensation metacarpal 1 pre-cartilage condensation hand digit 1 metacarpus pre-cartilage condensation uberon UBERON:0010565 manual digit 1 metacarpus pre-cartilage condensation A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 1 mesenchyme. OBOL:automatic finger 1 metacarpus pre-cartilage condensation EHDAA2:0000515 fore limb digit 1 metacarpus pre-cartilage condensation OBOL:accepted manual digit I metacarpus pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 hand digit 1 metacarpus pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 5 mesenchyme. EHDAA2:0000539 EMAPA:17722 finger 5 metacarpus pre-cartilage condensation fore limb digit 5 metacarpus pre-cartilage condensation manual digit V metacarpus pre-cartilage condensation metacarpal 5 pre-cartilage condensation hand digit 5 metacarpus pre-cartilage condensation uberon UBERON:0010569 manual digit 5 metacarpus pre-cartilage condensation A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 5 mesenchyme. OBOL:automatic finger 5 metacarpus pre-cartilage condensation EHDAA2:0000539 fore limb digit 5 metacarpus pre-cartilage condensation OBOL:accepted manual digit V metacarpus pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 hand digit 5 metacarpus pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A manual digit metacarpus cartilage element that is part of a manual digit 1 mesenchyme. EHDAA2:0000514 EMAPA:18065 finger 1 metacarpus cartilage element fore limb digit 1 metacarpus cartilage element manual digit I metacarpus cartilage element metacarpus 1 cartilage element hand digit 1 metacarpus cartilage element uberon UBERON:0010570 manual digit 1 metacarpus cartilage element A manual digit metacarpus cartilage element that is part of a manual digit 1 mesenchyme. OBOL:automatic finger 1 metacarpus cartilage element EHDAA2:0000514 fore limb digit 1 metacarpus cartilage element OBOL:accepted manual digit I metacarpus cartilage element https://github.com/obophenotype/uberon/issues/458 hand digit 1 metacarpus cartilage element NCBITaxon:9606 OBOL:accepted A manual digit metacarpus cartilage element that is part of a manual digit 5 mesenchyme. EHDAA2:0000538 EMAPA:18085 finger 5 metacarpus cartilage condensation fore limb digit 5 metacarpus cartilage element manual digit V metacarpus cartilage element metacarpus 5 cartilage element hand digit 5 metacarpus cartilage element uberon UBERON:0010574 manual digit 5 metacarpus cartilage element A manual digit metacarpus cartilage element that is part of a manual digit 5 mesenchyme. OBOL:automatic finger 5 metacarpus cartilage condensation EHDAA2:0000538 fore limb digit 5 metacarpus cartilage element OBOL:accepted manual digit V metacarpus cartilage element https://github.com/obophenotype/uberon/issues/458 hand digit 5 metacarpus cartilage element NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a manual digit 1 mesenchyme. EHDAA2:0000516 EMAPA:17715 fore limb digit 1 phalanx pre-cartilage condensation manual digit I phalanx pre-cartilage condensation hand digit 1 phalanx pre-cartilage condensation uberon UBERON:0010575 manual digit 1 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a manual digit 1 mesenchyme. OBOL:automatic fore limb digit 1 phalanx pre-cartilage condensation OBOL:accepted manual digit I phalanx pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 hand digit 1 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a manual digit 5 mesenchyme. EHDAA2:0000540 EMAPA:17723 fore limb digit 5 phalanx pre-cartilage condensation manual digit V phalanx pre-cartilage condensation hand digit 5 phalanx pre-cartilage condensation uberon UBERON:0010579 manual digit 5 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a manual digit 5 mesenchyme. OBOL:automatic fore limb digit 5 phalanx pre-cartilage condensation OBOL:accepted manual digit V phalanx pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 hand digit 5 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. EHDAA2:0002041 EMAPA:17726 hind limb digit 1 phalanx pre-cartilage condensation pedal digit I phalanx pre-cartilage condensation foot digit 1 phalanx pre-cartilage condensation uberon UBERON:0010580 pedal digit 1 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 phalanx pre-cartilage condensation OBOL:accepted pedal digit I phalanx pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 foot digit 1 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. EHDAA2:0002061 EMAPA:17734 hind limb digit 5 phalanx pre-cartilage condensation pedal digit V phalanx pre-cartilage condensation foot digit 5 phalanx pre-cartilage condensation uberon UBERON:0010584 pedal digit 5 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 phalanx pre-cartilage condensation OBOL:accepted pedal digit V phalanx pre-cartilage condensation https://github.com/obophenotype/uberon/issues/458 foot digit 5 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a pedal digit mesenchyme. EMAPA:32950 VHOG:0000952 foot phalanx pre-cartilage condensation hind limb digit phalanx pre-cartilage condensation hindlimb phalanx pre-cartilage condensation pes phalanx pre-cartilage condensation foot digit phalanx pre-cartilage condensation uberon UBERON:0010585 pedal digit phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a pedal digit mesenchyme. OBOL:automatic foot phalanx pre-cartilage condensation VHOG:0000952 hind limb digit phalanx pre-cartilage condensation OBOL:accepted foot digit phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a manual digit mesenchyme. EMAPA:32639 VHOG:0000954 fore limb digit phalanx pre-cartilage condensation forelimb phalanx pre-cartilage condensation hand phalanx pre-cartilage condensation manus phalanx pre-cartilage condensation hand digit phalanx pre-cartilage condensation uberon UBERON:0010586 manual digit phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a manual digit mesenchyme. OBOL:automatic fore limb digit phalanx pre-cartilage condensation OBOL:accepted hand phalanx pre-cartilage condensation VHOG:0000954 hand digit phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a manual digit 1 mesenchyme. EMAPA:18066 fore limb digit 1 phalanx cartilage condensation manual digit I phalanx cartilage element hand digit 1 phalanx cartilage element uberon UBERON:0010675 manual digit 1 phalanx cartilage element A cartilage element that is part of a manual digit 1 mesenchyme. OBOL:automatic fore limb digit 1 phalanx cartilage condensation OBOL:accepted manual digit I phalanx cartilage element https://github.com/obophenotype/uberon/issues/458 hand digit 1 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a manual digit 5 mesenchyme. EMAPA:18086 fore limb digit 5 phalanx cartilage condensation manual digit V phalanx cartilage element hand digit 5 phalanx cartilage element uberon UBERON:0010679 manual digit 5 phalanx cartilage element A cartilage element that is part of a manual digit 5 mesenchyme. OBOL:automatic fore limb digit 5 phalanx cartilage condensation OBOL:accepted manual digit V phalanx cartilage element https://github.com/obophenotype/uberon/issues/458 hand digit 5 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a pedal digit 1 mesenchyme. EMAPA:18107 hind limb digit 1 phalanx cartilage condensation pedal digit I phalanx cartilage element foot digit 1 phalanx cartilage element uberon UBERON:0010680 pedal digit 1 phalanx cartilage element A cartilage element that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 phalanx cartilage condensation OBOL:accepted pedal digit I phalanx cartilage element https://github.com/obophenotype/uberon/issues/458 foot digit 1 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a pedal digit 5 mesenchyme. EMAPA:18127 hind limb digit 5 phalanx cartilage condensation pedal digit V phalanx cartilage element foot digit 5 phalanx cartilage element uberon UBERON:0010684 pedal digit 5 phalanx cartilage element A cartilage element that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 phalanx cartilage condensation OBOL:accepted pedal digit V phalanx cartilage element https://github.com/obophenotype/uberon/issues/458 foot digit 5 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a pedal digit mesenchyme. EMAPA:32948 hind limb digit phalanx cartilage condensation foot digit phalanx cartilage element uberon UBERON:0010685 pedal digit phalanx cartilage element A cartilage element that is part of a pedal digit mesenchyme. OBOL:automatic hind limb digit phalanx cartilage condensation OBOL:accepted foot digit phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a manual digit mesenchyme. EMAPA:32658 fore limb digit phalanx cartilage condensation hand digit phalanx cartilage condensation uberon UBERON:0010686 manual digit phalanx cartilage element A cartilage element that is part of a manual digit mesenchyme. OBOL:automatic fore limb digit phalanx cartilage condensation OBOL:accepted hand digit phalanx cartilage condensation NCBITaxon:9606 OBOL:accepted EMAPA:32956 EMAPA:35568 VHOG:0000948 hind limb digit metatarsal pre-cartilage condensation metatarsal bone pre-cartilage condensation metatarsus pre-cartilage condensation foot digit metatarsal pre-cartilage condensation uberon metatarsal pre-cartilage condensation UBERON:0010687 pedal digit metatarsal pre-cartilage condensation hind limb digit metatarsal pre-cartilage condensation OBOL:accepted metatarsus pre-cartilage condensation VHOG:0000948 foot digit metatarsal pre-cartilage condensation NCBITaxon:9606 OBOL:accepted metatarsal pre-cartilage condensation EMAPA:32956 The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified]. FMA:71337 VSAO:0005029 Wikipedia:Phalanges_of_the_hand all phalanges in forelimb autopod anterior acropodium skeleton fore acropodium skeleton hand digit skeleton manual digit skeleton manual phalanges phalanges of hand phalanges of manus set of manual phalanges set of phalanges of hand set of phalanges of manus uberon anterior acropodium UBERON:0010688 skeleton of manual acropodium PHENOSCAPE:ni lexical The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified]. VSAO:0005029 VSAO:NI https://orcid.org/0000-0002-6601-2165 manual phalanges VSAO:0005029 VSAO:NI phalanges of hand FMA:71337 set of phalanges of hand FMA:71337 anterior acropodium VSAO:0005029 VSAO:NI An epithelium that is part of a manual digit 1. EHDAA2:0000512 EMAPA:17430 fore limb digit 1 epithelium manual digit I epithelium hand digit 1 epithelium uberon UBERON:0010690 manual digit 1 epithelium An epithelium that is part of a manual digit 1. OBOL:automatic fore limb digit 1 epithelium OBOL:accepted manual digit I epithelium https://github.com/obophenotype/uberon/issues/458 hand digit 1 epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a pedal digit 1. EHDAA2:0002038 EMAPA:17461 hind limb digit 1 epithelium pedal digit I epithelium foot digit 1 epithelium uberon UBERON:0010693 pedal digit 1 epithelium An epithelium that is part of a pedal digit 1. OBOL:automatic hind limb digit 1 epithelium OBOL:accepted pedal digit I epithelium https://github.com/obophenotype/uberon/issues/458 foot digit 1 epithelium NCBITaxon:9606 OBOL:accepted Mesenchyme of the carpal region that contributes to the tarsal skeleton. EMAPA:18502 uberon UBERON:0010695 mesenchyme of tarsal region Mesenchyme of the carpal region that contributes to the tarsal skeleton. https://orcid.org/0000-0002-6601-2165 The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm]. FMA:78512 VSAO:0005030 Wikipedia:Phalanges_of_the_foot all phalanges in hindlimb autopod foot digit skeleton hind acropodium skeleton pedal phalanges phalanges of foot phalanges of pes posterior acropodium skeleton set of pedal phalanges set of phalanges of foot set of phalanges of pes uberon posterior acropodium UBERON:0010696 skeleton of pedal acropodium PHENOSCAPE:ni The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm]. https://orcid.org/0000-0002-6601-2165 pedal phalanges VSAO:0005030 VSAO:NI phalanges of foot FMA:78512 set of phalanges of foot FMA:78512 posterior acropodium VSAO:0005030 VSAO:NI EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton EMAPA:32951 hind limb digit metatarsal cartilage condensation foot digit metatarsal cartilage condensation uberon metatarsal cartilage condensation UBERON:0010697 pedal digit metatarsal cartilage element hind limb digit metatarsal cartilage condensation OBOL:accepted foot digit metatarsal cartilage condensation NCBITaxon:9606 OBOL:accepted metatarsal cartilage condensation EMAPA:32951 EMAPA:32850 VHOG:0000953 fore limb digit metacarpus pre-cartilage condensation metacarpal bone pre-cartilage condensation metacarpal pre-cartilage condensation metacarpus pre-cartilage condensation hand digit metacarpus pre-cartilage condensation uberon UBERON:0010698 manual digit metacarpus pre-cartilage condensation fore limb digit metacarpus pre-cartilage condensation OBOL:accepted metacarpal bone pre-cartilage condensation VHOG:0000953 metacarpus pre-cartilage condensation VHOG:0000953 hand digit metacarpus pre-cartilage condensation NCBITaxon:9606 OBOL:accepted EMAPA:32849 finger metacarpus cartilage element fore limb digit metacarpus cartilage element metacarpal cartilage element metacarpus cartilage element hand digit metacarpus cartilage element uberon metacarpal cartilage condensation UBERON:0010699 manual digit metacarpus cartilage element fore limb digit metacarpus cartilage element OBOL:accepted hand digit metacarpus cartilage element NCBITaxon:9606 OBOL:accepted metacarpal cartilage condensation EMAPA:32849 EMAPA:32720 uberon UBERON:0010700 phalanx pre-cartilage condensation EMAPA EMAPA:32721 phalanx cartilage condensation uberon UBERON:0010701 phalanx cartilage element phalanx cartilage condensation EMAPA:32721 Mesenchyme of the digit region. EMAPA:32719 NCIT:C34141 UMLS:C1511959 uberon digital ray UBERON:0010702 digit mesenchyme Mesenchyme of the digit region. http://orcid.org/0000-0002-6601-2165 digital ray NCIT:C34141 The collection of all skeletal elements in an forelimb zeugopod region. adding proxinally_connected_to humerus causes inconsistencies - requires investigation Segment of the forearm corresponding to the radius and ulna.[AAO] AAO:0000200 FMA:71199 VSAO:0005011 antebrachial skeleton antebrachium skeleton anterior zeugopodium skeleton fore epipodium skeleton forearm skeleton skeleton of forearm wing zeugopod skeleton uberon anterior zeugopodium fore epipodium forelimb epipodium forelimb epipodium skeleton mesomere 2 of pectoral appendage radius and ulna UBERON:0010703 forelimb zeugopod skeleton lexical The collection of all skeletal elements in an forelimb zeugopod region. https://orcid.org/0000-0002-6601-2165 Segment of the forearm corresponding to the radius and ulna.[AAO] 2012-06-20 AAO:0000200 AAO AAO:LAP antebrachium skeleton PHENOSCAPE:ni anterior zeugopodium skeleton VSAO:0005011 VSAO:NI forearm skeleton FMA:71199 skeleton of forearm FMA:71199 wing zeugopod skeleton NCBITaxon:8782 OBOL:automatic anterior zeugopodium VSAO:0005011 VSAO:NI fore epipodium AAO:0000200 forelimb epipodium VSAO:0005011 VSAO:NI mesomere 2 of pectoral appendage ISBN:0226313409 An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) 2012-04-23T10:46:51Z EMAPA:37858 FMA:7182 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin uberon limb UBERON:0010707 appendage girdle complex An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton https://orcid.org/0000-0002-6601-2165 Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] 2012-08-14 VSAO:0000214 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] 2012-09-06 VSAO:0000214 VSAO Curator note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37858 MA:th appendage complex https://orcid.org/0000-0002-6601-2165 appendage-girdle complex https://orcid.org/0000-0002-6601-2165 appendage/girdle complex VSAO:0000214 girdle plus limb or fin https://orcid.org/0000-0002-6601-2165 limb FMA:7182 Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) EMAPA:37860 FMA:7183 SCTID:110716002 VSAO:0000213 pectoral appendage/girdle complex pectoral girdle plus anterior limb or fin pectoral girdle plus pectoral limb or fin uberon upper limb upper limb and pectoral girdle upper limb and shoulder UBERON:0010708 pectoral complex Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. VSAO:0000213 Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] 2012-08-14 VSAO:0000213 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37860 MA:th pectoral appendage/girdle complex VSAO:0000213 pectoral girdle plus anterior limb or fin https://orcid.org/0000-0002-6601-2165 pectoral girdle plus pectoral limb or fin https://orcid.org/0000-0002-6601-2165 upper limb FMA:7183 upper limb and pectoral girdle https://orcid.org/0000-0002-6601-2165 upper limb and shoulder https://orcid.org/0000-0002-6601-2165 Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 SCTID:416631005 VSAO:0000215 pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon lower limb lower limb and pelvic girdle lower limb and pelvis UBERON:0010709 pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] 2012-08-14 VSAO:0000215 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here FMA EMAPA:37863 MA:th pelvic appendage/girdle complex VSAO:0000215 pelvic girdle plus pelvic limb or fin https://orcid.org/0000-0002-6601-2165 pelvic girdle plus posterior limb or fin https://orcid.org/0000-0002-6601-2165 lower limb FMA:7184 lower limb and pelvic girdle https://orcid.org/0000-0002-6601-2165 lower limb and pelvis https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is a segment of the limb skeleton. note the distinction between this and skeleton of limb VSAO:0005018 uberon UBERON:0010712 limb skeleton subdivision VSAO Skeletal subdivision that is a segment of the limb skeleton. VSAO:0005018 VSAO:NI An iliac endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000808 EMAPA:18347 VHOG:0001126 uberon iliac cartilage condensation UBERON:0010714 iliac cartilage element EHDAA2 EHDAA2 An iliac endochondral element that is composed primarily of cartilage tissue. OBOL:automatic iliac cartilage condensation EMAPA:18347 A pubic endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001573 EMAPA:26928 uberon pubic cartilage condensation UBERON:0010718 pubic cartilage element EHDAA2 EHDAA2 A pubic endochondral element that is composed primarily of cartilage tissue. OBOL:automatic pubic cartilage condensation EMAPA:26928 The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle uberon UBERON:0010719 girdle skeleton The subdivision of the skeleton of either the pectoral or pelvic girdle. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the appendage girdle region.[VSAO] 2012-08-14 VSAO:0000302 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula. Segment of the leg corresponding to the tibia and fibula.[AAO] AAO:0000216 VSAO:0005014 crural skeleton crus skeleton hindlimb zygopod skeleton posterior zeugopodium skeleton skeleton cruris uberon hind epipodium hindlimb epipodium mesomere 2 of pelvic appendage posterior zeugopodium UBERON:0010720 hindlimb zeugopod skeleton Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula. https://orcid.org/0000-0002-6601-2165 Segment of the leg corresponding to the tibia and fibula.[AAO] 2012-06-20 AAO:0000216 AAO AAO:LAP crural skeleton http://orcid.org/0000-0002-6601-2165 crus skeleton PHENOSCAPE:ni skeleton cruris NominaAnatomicaVeterinaria:2005 hind epipodium AAO:0000216 hindlimb epipodium VSAO:0005014 VSAO:NI mesomere 2 of pelvic appendage ISBN:0226313409 posterior zeugopodium VSAO:0005014 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 uberon bone of extended limb/fin region limb bone UBERON:0010740 bone of appendage girdle complex UBERONREF:0000003 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 bone of extended limb/fin region UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 limb bone MA:0000688 UBERONREF:0000003 A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. considering adding pectoral and pelvic complex skeleton classes note that the MA class includes girdle parts so it belongs here; EMAPA:32623 EMAPA:35933 MA:0000612 wing bone uberon bone of forelimb or pectoral fin or pectoral girdle forelimb bone UBERON:0010741 bone of pectoral complex A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 note that the MA class includes girdle parts so it belongs here; MA wing bone UBERONREF:0000003 bone of forelimb or pectoral fin or pectoral girdle UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 forelimb bone MA:0000612 UBERONREF:0000003 A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle EMAPA:32633 EMAPA:35934 MA:0000660 uberon hindlimb bone UBERON:0010742 bone of pelvic complex MA A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle MA hindlimb bone MA:0000660 UBERONREF:0000003 The collection of all meningeal layers that line a central nervous system. meningeal In some primitive organisms, the meningeal cluster includes only the primitive meninx EHDAA2:0004661 EMAPA:32660 FMA:231572 NCIT:C12349 SCTID:362879001 UMLS:C0228116 Wikipedia:Meninges neuronames:1465 cerebral meninges cluster of meninges meninges uberon UBERON:0010743 meningeal cluster The collection of all meningeal layers that line a central nervous system. https://orcid.org/0000-0002-6601-2165 cluster of meninges FMA:231572 meninges FMA:231572 A sacral vertebra endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0001774 EMAPA:17677 sacral vertebral pre-cartilage condensation group uberon UBERON:0010744 sacral vertebra pre-cartilage condensation A sacral vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic sacral vertebral pre-cartilage condensation group EHDAA2:0001774 A sacral vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001773 EMAPA:18009 sacral vertebral cartilage condensation sacral vertebral cartilage condensation group uberon UBERON:0010745 sacral vertebra cartilage element EHDAA2 A sacral vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic sacral vertebral cartilage condensation group EHDAA2:0001773 A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. FBbt:00007018 appendage segment appendicular segment uberon UBERON:0010758 subdivision of organism along appendicular axis A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. https://orcid.org/0000-0002-6601-2165 FBbt:00007018 appendage segment FBbt:00007018 A cartilaginous condensation that has the potential to develop into a clavicle. In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. EMAPA:18342 uberon UBERON:0010843 clavicle cartilage element A cartilaginous condensation that has the potential to develop into a clavicle. OBOL:automatic In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. ISBN:978-0-12-319060-4 A pre-cartilage condensation that has the potential to develop into a clavicle. In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. EMAPA:18026 uberon UBERON:0010844 clavicle pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a clavicle. OBOL:automatic In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal. ISBN:978-0-12-319060-4 A cartilaginous condensation that has the potential to develop into a tibia. EMAPA:18155 uberon UBERON:0010849 tibia cartilage element EMAPA A cartilaginous condensation that has the potential to develop into a tibia. OBOL:automatic A pre-cartilage condensation that has the potential to develop into a tibia. EHDAA2:0002036 uberon UBERON:0010850 tibia pre-cartilage condensation EHDAA2 A pre-cartilage condensation that has the potential to develop into a tibia. OBOL:automatic A cartilaginous condensation that has the potential to develop into a fibula. EMAPA:18154 fibulal cartilage condensation fibular cartilage condensation uberon fibulra cartilage condensation UBERON:0010851 fibula cartilage element EMAPA A cartilaginous condensation that has the potential to develop into a fibula. OBOL:automatic fibulal cartilage condensation EMAPA:18154 fibular cartilage condensation EMAPA:18154 fibulra cartilage condensation EMAPA:18154 A pre-cartilage condensation that has the potential to develop into a fibula. EHDAA2:0000509 EHDAA:6196 fibulal pre-cartilage condensation fibular pre-cartilage condensation uberon UBERON:0010852 fibula pre-cartilage condensation EHDAA2 A pre-cartilage condensation that has the potential to develop into a fibula. OBOL:automatic A skin of neck that is part of a throat. FMA:23023 SCTID:181482005 skin of anterior neck skin of anterior part of neck skin of anterior portion of neck skin of throat uberon UBERON:0010854 skin of front of neck A skin of neck that is part of a throat. OBOL:automatic skin of anterior neck FMA:23023 skin of anterior part of neck FMA:23023 skin of anterior portion of neck FMA:23023 A zone of skin that is part of a forelimb wing. uberon UBERON:0010855 skin of forelimb wing A zone of skin that is part of a forelimb wing. OBOL:automatic A skeletal element that is part of a limb and composed of cartilage tissue. uberon UBERON:0010881 limb cartilage element A skeletal element that is part of a limb and composed of cartilage tissue. http://orcid.org/0000-0002-6601-2165 A skeletal element that is part of a limb and composed of pre-cartilage tissue. uberon UBERON:0010882 limb bone pre-cartilage condensation A skeletal element that is part of a limb and composed of pre-cartilage tissue. http://orcid.org/0000-0002-6601-2165 A cartilaginous condensation that has the potential to develop into a forelimb bone. EMAPA:32626 forelimb wing cartilaginous condensation wing cartilaginous condensation uberon UBERON:0010883 forelimb cartilage element A cartilaginous condensation that has the potential to develop into a forelimb bone. OBOL:automatic forelimb wing cartilaginous condensation NCBITaxon:8782 OBOL:automatic wing cartilaginous condensation NCBITaxon:8782 OBOL:automatic A pre-cartilage condensation that has the potential to develop into a forelimb bone. EMAPA:32625 wing bone pre-cartilage condensation uberon UBERON:0010884 forelimb bone pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a forelimb bone. OBOL:automatic wing bone pre-cartilage condensation NCBITaxon:8782 OBOL:automatic A cartilaginous condensation that has the potential to develop into a hindlimb bone. EMAPA:32632 hindlimb cartilage condensation uberon UBERON:0010885 hindlimb cartilage element A cartilaginous condensation that has the potential to develop into a hindlimb bone. OBOL:automatic hindlimb cartilage condensation EMAPA:32632 A pre-cartilage condensation that has the potential to develop into a hindlimb bone. EMAPA:32638 hindlimb pre-cartilage condensation uberon UBERON:0010886 hindlimb pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a hindlimb bone. OBOL:automatic hindlimb pre-cartilage condensation EMAPA:32638 Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 EMAPA:32634 FMA:9622 MA:0000663 pelvic girdle and hind limb muscles pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle uberon lower limb muscle muscle of lower limb muscle of pelvic girdle and leg UBERON:0010890 pelvic complex muscle prolog Muscles of the pelvic girdle, hindlimb or pelvic fin. https://orcid.org/0000-0002-6601-2165 Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] 2012-06-20 AAO:0000218 AAO AAO:EJS pelvic girdle and hind limb muscles AAO:0000218 pelvic girdle or hind limb muscle https://orcid.org/0000-0002-6601-2165 pelvic girdle or posterior limb muscle https://orcid.org/0000-0002-6601-2165 lower limb muscle FMA:9622 muscle of lower limb FMA:9622 A muscle of a pectoral girdle, pectoral fin or anterior limb. the MA class belongs here, based on its current child classes Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] AAO:0010687 EMAPA:32624 FMA:9621 MA:0000615 pectoral girdle and fore limb muscles muscle of pectoral girdle and wing muscle of upper limb upper limb muscle uberon muscle of pectoral girdle and limb UBERON:0010891 pectoral complex muscle prolog A muscle of a pectoral girdle, pectoral fin or anterior limb. https://orcid.org/0000-0002-6601-2165 Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] 2012-06-20 AAO:0010687 AAO AAO:EJS pectoral girdle and fore limb muscles AAO:0010687 muscle of pectoral girdle and wing NCBITaxon:8782 muscle of upper limb FMA:9621 upper limb muscle FMA:9621 Am unpaired external naris that lies in the midline of the head. UBERON:0012123 median anterior naris median nostril nasohypophysial opening uberon UBERON:0010893 median external naris Am unpaired external naris that lies in the midline of the head. OBOL:automatic nasohypophysial opening http://tolweb.org/Hyperoartia horny denticle uberon UBERON:0010894 The hagfish's jawless mouth contains two parallel rows of pointed keratinous teeth keratinous tooth horny denticle http://tolweb.org/Hyperoartia Hermaphroditic organism that produces both male and female gametes at the same time. AAO:0010046 BILA:0000046 CARO:0000046 HAO:0000046 TADS:0000609 uberon serially hermaphroditic organism simultaneous hermaphroditic organism UBERON:0010899 synchronous hermaphroditic organism CARO Hermaphroditic organism that produces both male and female gametes at the same time. CARO:0000046 serially hermaphroditic organism CARO:0000046 simultaneous hermaphroditic organism https://orcid.org/0000-0002-6601-2165 A primordium that develops into a clavicle bone. EHDAA2:0000254 clavicle primordium uberon UBERON:0010905 lateral part derives from a fish dermal bone while the medial part comes from a spur off the manubrium endochondral bone[JB] clavicle bone primordium EHDAA2 EHDAA2 mah shown in mouse PMC1352163 A primordium that develops into a clavicle bone. https://github.com/obophenotype/uberon/issues/327 Skeletal element that is often isolated, small, and variable in composition. VSAO:0000132 Wikipedia:Ossicles uberon UBERON:0010911 Ossicles are composed of a combination skeletal tissues, including bone, calcified cartilage, hyaline cartilage, etc, and exhibit variable development across species. Ossicles are not necessarily jointed, and examples include the menisci of synovial joints, 'Panda's thumb' (radial sesamoid), cardiac skeletal elements, sclerotic bones, middle ear ossicles, and sesamoids. ossicle VSAO Skeletal element that is often isolated, small, and variable in composition. PSPUB:0000169 VSAO:0000132 Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 skeletal subdivision uberon subdivision of skeleton (in vivo) UBERON:0010912 subdivision of skeleton cjm UBERONREF:0000003 VSAO Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] 2012-08-14 VSAO:0000042 incorrect VSAO VSAO:curator skeletal subdivision VSAO:0000042 subdivision of skeleton (in vivo) FMA:23879 Skeletal element that forms around the notochord and is part of the vertebral column. we include a distinct subclass for bony vertebra In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] vertebral Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage UBERON:0015005 vertebra skeletal element VHOG:0001143 VSAO:0000184 vertebra element vertebra endochondral element vertebral endochondral element uberon UBERON:0010913 vertebral element VSAO https://github.com/obophenotype/uberon/issues/82 cjm Skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/294 In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001143 VHOG DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011) http://bgee.unil.ch/ vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern vertebra endochondral element https://github.com/obophenotype/uberon/issues/82 vertebral endochondral element https://github.com/obophenotype/uberon/issues/82 A muscle organ that attaches_to a clavicle and attaches_to a occipital bone. EMAPA:37688 MA:0002276 NCIT:C52895 cleido-occipitalis cleido-occipitalis muscle cleidooccipital uberon UBERON:0010948 Some studies have indicated a supernumerary cleido-occipital muscle more or less separate from the sterno-cleido-mastoid muscle; The frequency of cleido-occipital muscle occurrence has been reported up to 33% cleidooccipital muscle A muscle organ that attaches_to a clavicle and attaches_to a occipital bone. OBOL:automatic EMAPA:37688 MA:th cleidooccipital MA:0002276 A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum. EMAPA:37702 MA:0002385 NCIT:C53069 UMLS:C1710196 sternooccipital uberon UBERON:0010949 sternooccipital muscle A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum. OBOL:automatic EMAPA:37702 MA:th UMLS:C1710196 ncithesaurus:Sternooccipital sternooccipital MA:0002385 EHDAA2:0002079 uberon UBERON:0010955 trapezius pre-muscle mass EHDAA2 EHDAA2 EHDAA2 Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 muscle of head or neck uberon muscle of head and neck UBERON:0010959 craniocervical muscle prolog Any muscle organ that is part of either the head or the neck. http://orcid.org/0000-0002-6601-2165 UMLS:C0448281 ncithesaurus:Head_and_Neck_Muscle EHDAA2:0003425 uberon UBERON:0010963 isa row in EHDAA2 trunk and cervical myotome group EHDAA2 EHDAA2:0000933 uberon UBERON:0010982 latissimus dorsi pre-muscle mass EHDAA2 EHDAA2 EHDAA2 EHDAA2:0000993 uberon UBERON:0010983 levator scapulae pre-muscle mass EHDAA2 EHDAA2 EHDAA2 EHDAA2:0001833 EHDAA:5992 serratus anterior pre-muscle mass uberon UBERON:0010986 serratus ventralis pre-muscle mass EHDAA2 EHDAA2 EHDAA2 serratus anterior pre-muscle mass EHDAA2:0001833 A cartilage element that is part of a splanchnocranium. BTO:0006051 EFO:0003689 TAO:0001460 ZFA:0001460 pharyngeal arch cartilages splanchnocranium cartilage uberon UBERON:0011004 pharyngeal arch cartilage ZFA ZFA A cartilage element that is part of a splanchnocranium. OBOL:automatic BTO:0006051 https://github.com/biopragmatics/biomappings pharyngeal arch cartilages ZFA:0001460 splanchnocranium cartilage ZFA:0001460 The eighth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. EMAPA:19549 FMA:9991 MA:0001445 NCIT:C33730 SCTID:181836007 UMLS:C0459953 T8 vertebra eighth dorsal vertebra eighth thoracic vertebra uberon UBERON:0011050 thoracic vertebra 8 MA FMA The eighth thoracic vertebra counting from the top down. Note that members of this class are not necessarily homologous[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:T8_Vertebra UMLS:C0459953 ncithesaurus:T8_Vertebra T8 vertebra FMA:9991 eighth dorsal vertebra FMA:9991 eighth thoracic vertebra FMA:9991 The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG]. Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EFO:0003659 TAO:0001272 VHOG:0000511 ZFA:0001272 dorsal visceral arch 1 upper pharyngeal jaw uberon dorsal mandibular arch dorsal pharyngeal arch 1 dorsal visceral arch 1 palatoquadrate arch upper jaw upper pharyngeal jaw UBERON:0011085 palatoquadrate arch cjm VHOG The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG]. VHOG:0000511 https://github.com/obophenotype/uberon/issues/153 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000511 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ dorsal visceral arch 1 ZFA:0001272 upper pharyngeal jaw ZFA:0001272 dorsal mandibular arch VHOG:0000511 dorsal pharyngeal arch 1 VHOG:0000511 dorsal visceral arch 1 VHOG:0000511 palatoquadrate arch VHOG:0000511 upper jaw VHOG:0000511 upper pharyngeal jaw VHOG:0000511 A ligament that is part of a knee joint. FMA:44580 SCTID:182440009 knee joint ligament uberon UBERON:0011088 ligament of knee joint A ligament that is part of a knee joint. OBOL:automatic knee joint ligament FMA:44580 A skeleton of pelvic girdle that is part of a right pelvic girdle region. FMA:87593 uberon UBERON:0011090 skeleton of right pelvic girdle A skeleton of pelvic girdle that is part of a right pelvic girdle region. OBOL:automatic A skeleton of pelvic girdle that is part of a left pelvic girdle region. FMA:87594 uberon UBERON:0011091 skeleton of left pelvic girdle A skeleton of pelvic girdle that is part of a left pelvic girdle region. OBOL:automatic A pelvic girdle region that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16582 right pelvic girdle uberon UBERON:0011092 right pelvic girdle region A pelvic girdle region that is in the right side of a multicellular organism. OBOL:automatic right pelvic girdle FMA:16582 A pelvic girdle region that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16583 left pelvic girdle uberon UBERON:0011093 left pelvic girdle region A pelvic girdle region that is in the left side of a multicellular organism. OBOL:automatic left pelvic girdle FMA:16583 The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EMAPA:32669 VHOG:0000584 vertebral cartilage condensation uberon UBERON:0011094 vertebra cartilage element The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist PMC3157150 This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EHDAA2 vertebral cartilage condensation VHOG:0000584 The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. EMAPA:32671 VHOG:0000582 vertebral pre-cartilage condensation uberon UBERON:0011095 vertebra pre-cartilage condensation The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 vertebral pre-cartilage condensation VHOG:0000582 The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. FMA:52628 NCIT:C32908 SCTID:280218007 Wikipedia:Lacrimal_nerve nervus lacrimalis uberon UBERON:0011096 lacrimal nerve FMA The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. Wikipedia:Lacrimal_nerve nervus lacrimalis Wikipedia:Lacrimal_nerve An epiphysis that is part of a metacarpal bone of digit 5. FMA:86330 fifth metacarpal bone epiphysis metacarpal 5 epiphysis uberon UBERON:0011104 epiphysis of fifth metacarpal bone An epiphysis that is part of a metacarpal bone of digit 5. OBOL:automatic fifth metacarpal bone epiphysis FMA:86330 A synovial joint that is part of a pelvic girdle region. FMA:35173 NCIT:C32890 UMLS:C0827002 joint of pelvic girdle pelvic girdle joint uberon UBERON:0011107 synovial joint of pelvic girdle A synovial joint that is part of a pelvic girdle region. OBOL:automatic UMLS:C0827002 ncithesaurus:Joint_of_the_Pelvic_Girdle pelvic girdle joint FMA:35173 A synovial joint that is part of a pectoral girdle region. in FMA, these are part of the bony pectoral girdle FMA:35243 SCTID:303080001 joint of shoulder girdle pectoral girdle joint uberon UBERON:0011108 synovial joint of pectoral girdle A synovial joint that is part of a pectoral girdle region. OBOL:automatic in FMA, these are part of the bony pectoral girdle FMA pectoral girdle joint FMA:35243 A joint that connects the tibia and the fibula. we include location as part of the logical definition to prevent accidental classification of ankle joints as tibiofibular joints FMA:35181 SCTID:244554002 Wikipedia:Tibiofibular_joint fibulatibial joint fibulotibial joint tibiafibular joint uberon UBERON:0011112 tibiofibular joint FMA A joint that connects the tibia and the fibula. Wikipedia:Tibiofibular_joint https://orcid.org/0000-0002-6601-2165 The tarsometatarsal articulations are arthrodial joints in the pes. FMA:35216 SCTID:182222008 Wikipedia:Tarsometatarsal_articulations tarso-metatarsal join uberon Lisfranc joint articulationes tarsometatarsales cuboideometatarsal tarsometatarsal tarsometatarsal articulation UBERON:0011118 tarsometatarsal joint http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png The tarsometatarsal articulations are arthrodial joints in the pes. Wikipedia:Tarsometatarsal_articulations Lisfranc joint Wikipedia:Tarsometatarsal_articulations articulationes tarsometatarsales Wikipedia:Tarsometatarsal_articulations cuboideometatarsal Wikipedia:Tarsometatarsal_articulations tarsometatarsal Wikipedia:Tarsometatarsal_articulations tarsometatarsal articulation Wikipedia:Tarsometatarsal_articulations The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones. CMJ carpometacarpal FMA:35287 MESH:D052737 NCIT:C32265 SCTID:361842002 UMLS:C0224620 Wikipedia:Carpometacarpal_joint articulationes carpometacarpeæ uberon carpometacarpal articulation UBERON:0011119 carpometacarpal joint http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones. Wikipedia:Carpometacarpal_joint CMJ Wikipedia:Carpometacarpal_joint carpometacarpal Wikipedia:Carpometacarpal_joint MESH:D052737 https://github.com/biopragmatics/biomappings UMLS:C0224620 ncithesaurus:Carpometacarpal_Joint articulationes carpometacarpeæ Wikipedia:Carpometacarpal_joint carpometacarpal articulation Wikipedia:Carpometacarpal_joint A skeletal joint that connects a laryngeal cartilage. FMA:55100 joint of larynx laryngeal articulation uberon UBERON:0011120 laryngeal joint FMA A skeletal joint that connects a laryngeal cartilage. OBOL:automatic joint of larynx FMA:55100 laryngeal articulation FMA:55100 2 A skeletal joint that connects two adjacent metacarpals[FMA,modified]. FMA:35288 SCTID:303065007 Wikipedia:Intermetacarpal_articulations uberon intermetacarpal intermetacarpal articulation UBERON:0011131 intermetacarpal joint two adjacent metacarpals A skeletal joint that connects two adjacent metacarpals[FMA,modified]. FMA:35288 intermetacarpal Wikipedia:Intermetacarpal_articulations intermetacarpal articulation Wikipedia:Intermetacarpal_articulations 2 A skeletal joint that connects two carpal bones. FMA:35292 MESH:D050824 NCIT:C32264 SCTID:182176003 UMLS:C1262468 Wikipedia:Intercarpal_articulations carpal joint uberon intercarpal intercarpal articulation midcarpal articulation UBERON:0011132 intercarpal joint http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png FMA two adjacent carpals A skeletal joint that connects two carpal bones. http://orcid.org/0000-0002-6601-2165 MESH:D050824 https://github.com/biopragmatics/biomappings UMLS:C1262468 ncithesaurus:Carpal_Joint carpal joint FMA:35292 intercarpal Wikipedia:Intercarpal_articulations intercarpal articulation Wikipedia:Intercarpal_articulations midcarpal articulation Wikipedia:Intercarpal_articulations 2 A joint that connects two adjacent metatarsals. In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb FMA:35219 SCTID:361868009 Wikipedia:Intermetatarsal_articulations uberon UBERON:0011133 intermetatarsal joint http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png two adjacent metatarsals A joint that connects two adjacent metatarsals. Wikipedia:Intermetatarsal_articulations In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb WP Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint uberon UBERON:0011134 nonsynovial joint FMA Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint FMA:7491 2 A cartilage element that lies between two successive vertebral centra. Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO] AAO:0000795 uberon UBERON:0011135 intervertebral cartilage FMA MA between two centra A cartilage element that lies between two successive vertebral centra. ISBN:0073040584 Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO] 2012-06-20 AAO:0000795 AAO AAO:Trueb_1973 Ligament that joins successive centra. Important in controlling the stiffness of the vertebral column when it flexes. intervertebral ligament vertebral centrum ligament FMA:31892 SCTID:244590009 vertebral column ligament uberon UBERON:0011136 ligament of vertebral column Ligament that joins successive centra. Important in controlling the stiffness of the vertebral column when it flexes. ISBN:0073040584 vertebral column ligament FMA:31892 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. FMA:7483 uberon UBERON:0011137 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 post-cranial axial skeletal system uberon UBERON:0011138 postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA cjm Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. https://github.com/obophenotype/uberon/issues/44 https://orcid.org/0000-0002-6601-2165 axial skeletal system https://github.com/obophenotype/uberon/wiki/The-axial-skeleton Any synovial joint that is part of a (free) limb. FMA:258776 synovial joint of free limb segment uberon UBERON:0011139 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. synovial limb joint Any synovial joint that is part of a (free) limb. https://orcid.org/0000-0002-6601-2165 synovial joint of free limb segment FMA:258776 Ossicle that is part of the appendicular skeleton. VSAO:0000131 XAO:0004194 ossicle of appendicular skeleton uberon UBERON:0011141 Examples of appendicular ossicles include the patella and meniscus of the knee joint. appendicular ossicle Ossicle that is part of the appendicular skeleton. PSPUB:0000169 VSAO:0000131 ossicle of appendicular skeleton OBOL:automatic Ossicle that is part of the axial skeleton. VSAO:0000133 ossicle of axial skeleton ossicle of postcranial-axial skeleton uberon vertebral ossicle UBERON:0011142 Examples of axial ossicles include the ossified tendons adjacent to the neural spines of the vertebral column. axial ossicle Ossicle that is part of the axial skeleton. PSPUB:0000169 VSAO:0000133 ossicle of axial skeleton OBOL:automatic ossicle of postcranial-axial skeleton OBOL:automatic vertebral ossicle OBOL:automatic Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 NCIT:C61107 SCTID:181413006 galen:UpperUrinaryTract uberon UBERON:0011143 upper urinary tract FMA FMA-abduced-lr Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 Wikipedia:Submucosal_glands uberon UBERON:0011148 submucosal gland perforates Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 Wikipedia:Submucosal_glands EMAPA:37970 MA:th Surface structure that extends from the chin covering pharynx and larynx. Surface structure that is the region between the chin and the isthmus. (from http://www.briancoad.com/Dictionary/introduction.htm).[TAO] TAO:0002286 uberon UBERON:0011154 gular region TAO Surface structure that extends from the chin covering pharynx and larynx. http://orcid.org/0000-0002-6601-2165 Surface structure that is the region between the chin and the isthmus. (from http://www.briancoad.com/Dictionary/introduction.htm).[TAO] 2012-08-14 TAO:0002286 TAO TAO:wd Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 Wikipedia:Facial_skeleton facial skeleton uberon facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg FMA FMA Subdivision of skull that consists of the facial bones. MP:0005274 Wikipedia:Facial_skeleton http://www.bartleby.com/107/37.html https://orcid.org/0000-0002-6601-2165 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia Wikipedia:Facial_skeleton ossa faciei Wikipedia:Facial_skeleton viscerocranium MA:0000318 The skull can be divided into two: the neurocranium and the facial skeleton. FMA:54964 skull subdivision subdivision of skull uberon UBERON:0011158 primary subdivision of skull FMA The skull can be divided into two: the neurocranium and the facial skeleton. http://orcid.org/0000-0002-6601-2165 skull subdivision FMA:54964 subdivision of skull FMA:54964 uberon UBERON:0011159 primary subdivision of cranial skeletal system FMA A bone that is part of a neurocranium [Automatically generated definition]. EMAPA:35238 MA:0001478 SCTID:120229002 chondrocranium bone uberon UBERON:0011164 neurocranium bone A bone that is part of a neurocranium [Automatically generated definition]. OBOL:automatic chondrocranium bone MA:0001478 Synovial joint that articulates bones of upper and lower jaw. Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long jaw joint NCIT:C32888 craniomandibular joint uberon UBERON:0011171 joint connecting upper and lower jaws abduced Synovial joint that articulates bones of upper and lower jaw. http://evolution.berkeley.edu/evolibrary/article/evograms_05 https://orcid.org/0000-0002-6601-2165 Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long http://evolution.berkeley.edu A sphincter muscle that is part of the gastrointestinal system. NCIT:C32669 UMLS:C1517464 uberon UBERON:0011185 gastrointestinal sphincter A sphincter muscle that is part of the gastrointestinal system. OBOL:automatic UMLS:C1517464 ncithesaurus:Gastrointestinal_Sphincter A lamina propria that is part of a large intestine. FMA:15654 NCIT:C49298 UMLS:C1708644 lamina propria of mucosa of large intestine large intestinal lamina propria large intestine lamina propria uberon UBERON:0011189 lamina propria of large intestine FMA A lamina propria that is part of a large intestine. OBOL:automatic UMLS:C1708644 ncithesaurus:Large_Intestinal_Lamina_Propria lamina propria of mucosa of large intestine FMA:15654 large intestine lamina propria FMA:15654 Ophthalmic veins are veins which drain the eye. More specifically, they can refer to: Superior ophthalmic vein Inferior ophthalmic vein. EHDAA2:0004113 EMAPA:19313 Wikipedia:Ophthalmic_veins XAO:0004169 opthalmic vein uberon vena ophthalmica UBERON:0011191 ophthalmic vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb EHDAA2-modified Ophthalmic veins are veins which drain the eye. More specifically, they can refer to: Superior ophthalmic vein Inferior ophthalmic vein. Wikipedia:Ophthalmic_veins opthalmic vein EHDAA2:0004113 vena ophthalmica Wikipedia:Ophthalmic_veins The superior ophthalmic vein begins at the inner angle of the orbit in a vein named the nasofrontal which communicates anteriorly with the angular vein; it pursues the same course as the ophthalmic artery, and receives tributaries corresponding to the branches of that vessel. Forming a short single trunk, it passes between the two heads of the Rectus lateralis and through the medial part of the superior orbital fissure, and ends in the cavernous sinus. The ethmoidal veins drain into the superior ophthalmic vein. Vorticose veins also drain into the superior ophthalmic vein. FMA:51246 SCTID:149481004 Wikipedia:Superior_ophthalmic_vein uberon anterior ethmoidal vein posterior ethmoidal vein superior ophthalmic superior opthalmic vein UBERON:0011192 superior ophthalmic vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png The superior ophthalmic vein begins at the inner angle of the orbit in a vein named the nasofrontal which communicates anteriorly with the angular vein; it pursues the same course as the ophthalmic artery, and receives tributaries corresponding to the branches of that vessel. Forming a short single trunk, it passes between the two heads of the Rectus lateralis and through the medial part of the superior orbital fissure, and ends in the cavernous sinus. The ethmoidal veins drain into the superior ophthalmic vein. Vorticose veins also drain into the superior ophthalmic vein. Wikipedia:Superior_ophthalmic_vein anterior ethmoidal vein Wikipedia:Superior_ophthalmic_vein posterior ethmoidal vein Wikipedia:Superior_ophthalmic_vein superior ophthalmic Wikipedia:Superior_ophthalmic_vein An epithelium that is part of a parathyroid gland. CALOHA:TS-2141 NCIT:C48258 UMLS:C1709466 uberon UBERON:0011197 parathyroid epithelium EHDAA2-abduced An epithelium that is part of a parathyroid gland. OBOL:automatic UMLS:C1709466 ncithesaurus:Parathyroid_Gland_Epithelial_Tissue A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 UMLS:C0734205 muscular coat of large intestine muscular layer of large intestine muscularis externa of large intestine tunica muscularis intestini crassi uberon UBERON:0011198 muscle layer of large intestine FMA A muscle layer that is part of a large intestine. OBOL:automatic UMLS:C0734205 ncithesaurus:Large_Intestinal_Muscular_Coat muscular coat of large intestine FMA:14971 muscular layer of large intestine FMA:14971 muscularis externa of large intestine FMA:14971 tunica muscularis intestini crassi FMA:TA The sacrococcygeal symphysis (sacrococcygeal articulation, articulation of the sacrum and coccyx) is an amphiarthrodial joint, formed between the oval surface at the apex of the sacrum, and the base of the coccyx. It is a slightly moveable joint which is frequently, partially or completely, obliterated in old age, homologous with the joints between the bodies of the vertebrae. FMA:16210 NCIT:C33506 UMLS:C0224593 Wikipedia:Sacrococcygeal_symphysis sacrococcygeal joint uberon sacrococcygeal joint UBERON:0011200 sacrococcygeal symphysis http://upload.wikimedia.org/wikipedia/commons/7/7f/Gray320.png FMA The sacrococcygeal symphysis (sacrococcygeal articulation, articulation of the sacrum and coccyx) is an amphiarthrodial joint, formed between the oval surface at the apex of the sacrum, and the base of the coccyx. It is a slightly moveable joint which is frequently, partially or completely, obliterated in old age, homologous with the joints between the bodies of the vertebrae. Wikipedia:Sacrococcygeal_symphysis UMLS:C0224593 ncithesaurus:Sacrococcygeal_Joint sacrococcygeal joint FMA:16210 sacrococcygeal joint Wikipedia:Sacrococcygeal_symphysis A muscle layer that is part of a small intestine. FMA:14932 NCIT:C33569 SCTID:362145004 UMLS:C0227269 muscular coat of small intestine muscular layer of small intestine muscularis externa of small intestine small intestine muscularis propria tunica muscularis (intestinum tenue) tunica muscularis intestini tenuis uberon UBERON:0011201 muscle layer of small intestine FMA A muscle layer that is part of a small intestine. OBOL:automatic UMLS:C0227269 ncithesaurus:Small_Intestinal_Muscular_Coat muscular coat of small intestine FMA:14932 muscular layer of small intestine FMA:14932 muscularis externa of small intestine FMA:14932 small intestine muscularis propria FMA:14932 tunica muscularis (intestinum tenue) FMA:14932 tunica muscularis intestini tenuis FMA:TA A multi cell part structure that is part of a central nervous system. FMA:83143 cell part cluster of neuraxis neuraxis layer uberon UBERON:0011215 central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. OBOL:automatic cell part cluster of neuraxis FMA:83143 neuraxis layer FMA:83143 A subdivision of an anatomical system. FBbt:00007330 FMA:67509 SCTID:91690000 uberon UBERON:0011216 organ system subdivision FBbt A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 FBbt:00007330 Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 FMA:49150 intrinsic muscle of eyeball intrinsic ocular muscle uberon UBERON:0011222 intra-ocular muscle EMAPA Muscles within the eye (bulbus oculi).[AAO] 2012-06-20 AAO:0010038 AAO AAO:EJS intrinsic ocular muscle EMAPA:18808 Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. synovium BTO:0001823 FMA:40878 Wikipedia:Synovial_sheath uberon UBERON:0011233 Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath] synovial membrane of synovial tendon sheath Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. FMA:45087 Wikipedia:Synovial_sheath synovium BTO:0001823 FMA:40877 uberon UBERON:0011234 fibrous membrane of synovial tendon sheath The most anterior region of the braincase. Provides structural support for peripheral olfactory organ. currently this is not restricted to skeletal elements, unlike UBERONREF:0000007 AAO:0000986 uberon UBERON:0011241 ethmoid region The most anterior region of the braincase. Provides structural support for peripheral olfactory organ. UBERONREF:0000007 http://palaeos.com/vertebrates/bones/braincase/ethmoid.html Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] 2012-08-14 VSAO:0000306 VSAO https://orcid.org/0000-0002-6601-2165 A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern uberon UBERON:0011250 autopod bone A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones. https://orcid.org/0000-0002-6601-2165 Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal-not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals. Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820]. BTO:0002068 MESH:D012543 Wikipedia:Scent_gland uberon UBERON:0011252 scent gland http://upload.wikimedia.org/wikipedia/commons/8/85/Civetglands.png Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal-not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals. Wikipedia:Scent_gland Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820]. MESH:A13.820 A carpometacarpal joint that connects to metacarpal 1. In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average FMA:35421 SCTID:361843007 Wikipedia:Carpometacarpal_joint#Thumb carpometacarpal joint of digit I carpometacarpal joint of pollex carpometacarpal joint of thumb uberon TMJ carpometacarpal joint of the thumb trapeziometacarpal joint UBERON:0011265 carpometacarpal joint of digit 1 A carpometacarpal joint that connects to metacarpal 1. Wikipedia:Carpometacarpal_joint#Thumb In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average WP carpometacarpal joint of digit I https://github.com/obophenotype/uberon/issues/458 carpometacarpal joint of pollex FMA:35421 carpometacarpal joint of thumb FMA:35421 TMJ Wikipedia:Carpometacarpal_joint#Thumb carpometacarpal joint of the thumb Wikipedia:Carpometacarpal_joint#Thumb trapeziometacarpal joint Wikipedia:Carpometacarpal_joint#Thumb The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 FMA:25056 MA:0000020 Wikipedia:Human_back back of trunk dorsal part of trunk dorsum of trunk trunk back uberon UBERON:0011270 dorsal trunk FMA FMA The part of the trunk that is in the dorsum[cjm]. UBERONREF:0000006 Wikipedia:Human_back back of trunk FMA:25056 dorsum of trunk FMA:25056 trunk back FMA:25056 compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon basal cell layer of skin outer epithelium of body UBERON:0011272 embryonic skin basal layer EHDAA2 EHDAA2 EHDAA2 outer epithelium of body Wikipathways:WP2062 The submucous layer of the wall of the uterine tube. BTO:0002116 SCTID:245489008 submucosa of fallopian tube tela submucosa tubae uterinae uberon submucous layer of uterine tube uterine submucosa UBERON:0011298 submucosa of uterine tube The submucous layer of the wall of the uterine tube. BTO:0002116 tela submucosa tubae uterinae BTO:0002116 submucous layer of uterine tube BTO:0002116 A portion of gray matter that is part of a telencephalon. UBERON:0024186 BIRNLEX:1067 FMA:83911 predominantly gray regional part of telencephalon uberon UBERON:0011300 gray matter of telencephalon A portion of gray matter that is part of a telencephalon. OBOL:automatic predominantly gray regional part of telencephalon BIRNLEX:1067 EMAPA:17884 uberon UBERON:0011332 extrinsic tongue pre-muscle mass A blood vasculature that is part of a head. Blood vessel part of cranial vasculature.[TAO] TAO:0005297 ZFA:0005297 cranial blood vessel set of blood vessels of head uberon cranial blood vessels UBERON:0011362 cranial blood vasculature A blood vasculature that is part of a head. OBOL:automatic Blood vessel part of cranial vasculature.[TAO] 2012-08-14 TAO:0005297 TAO ZFIN:curator cranial blood vessel ZFA:0005297 cranial blood vessels TAO:0005297 A lymph vasculature that is part of a head. FMA:224562 TAO:0005298 ZFA:0005298 cranial lymph vessel cranial lymphatics set of lymphatic vessels of head uberon cranial lymph vessels set of cranial lymphatic vessels UBERON:0011363 cranial lymph vasculature A lymph vasculature that is part of a head. OBOL:automatic cranial lymph vessel ZFA:0005298 cranial lymphatics UBERON:cjm set of lymphatic vessels of head FMA:224562 cranial lymph vessels TAO:0005298 set of cranial lymphatic vessels FMA:224562 A transverse process of vertebra that is part of a vertebral bone 1. FMA:23981 SCTID:181895009 Wikipedia:Transverse_processes uberon UBERON:0011370 transverse process of atlas FMA-abduced-lr A transverse process of vertebra that is part of a vertebral bone 1. OBOL:automatic A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present. this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue preputial NCIT:C12323 uberon UBERON:0011374 prepuce A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present. http://orcid.org/0000-0002-6601-2165 A zone of skin that is part of a prepuce of clitoris. FMA:27886 SCTID:367670008 preputial skin of clitoris uberon UBERON:0011375 skin of prepuce of clitoris A zone of skin that is part of a prepuce of clitoris. OBOL:automatic preputial skin of clitoris FMA:27886 FMA:54364 SCTID:432899004 cavity of digestive tract cavity of gastrointestinal tract gastrointestinal tract lumen lumen of gastrointestinal tract uberon UBERON:0011565 lumen of gastrointestinal system gastrointestinal tract lumen FMA:54364 lumen of gastrointestinal tract FMA:54364 An anatomical cavity that is part of a esophagus. EMAPA:18380 FMA:9398 SCTID:322648002 cavity of eosophagus cavity of esophagus eosophageal cavity eosophageal lumen eosophagus lumen esophageal cavity esophageal lumen esophagus lumen uberon UBERON:0011566 lumen of esophagus FMA An anatomical cavity that is part of a esophagus. OBOL:automatic cavity of esophagus FMA:9398 esophageal cavity FMA:9398 esophageal lumen FMA:9398 esophagus lumen FMA:9398 A tube lumen that is part of a mesonephric duct. EHDAA2:0001244 nephric duct lumen uberon cavity of nephric duct UBERON:0011574 mesonephric duct lumen A tube lumen that is part of a mesonephric duct. OBOL:automatic nephric duct lumen EHDAA2:0001244 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon UBERON:0011582 paired limb/fin skeleton ISBN:9780878932504 The collection of all skeletal elements in an individual limb or fin. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the paired limb/fin.[VSAO] 2012-08-14 VSAO:0000301 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 limb/fin skeleton VSAO:0000301 Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO] propodial stylopodial VSAO:0005007 stylopodium skeleton uberon mesomere 1 propodial skeleton propodium proximal metapterygial mesomere stylopod stylopodium UBERON:0011583 stylopodial skeleton VSAO Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. VSAO:0005007 Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO] 2012-08-14 VSAO:0005007 VSAO VSAO:NI mesomere 1 ISBN:0226313409 propodium VSAO:0005007 proximal metapterygial mesomere ISBN:0226313409 stylopod VSAO:0005007 Section of the forelimb skeleton located between the stylopodium and the autopodium. zeugopodial zygopodial VSAO:0005010 epipodial skeleton skeleton of zeugopod zeugopod skeleton uberon epipodium mesomere 2 mesomere 2 skeleton zygopodium UBERON:0011584 zeugopodial skeleton VSAO Section of the forelimb skeleton located between the stylopodium and the autopodium. VSAO:0005010 skeleton of zeugopod https://orcid.org/0000-0002-6601-2165 zeugopod skeleton https://orcid.org/0000-0002-6601-2165 epipodium VSAO:0005010 mesomere 2 ISBN:0226313409 mesomere 2 skeleton ISBN:0226313409 zygopodium VSAO:0005010 Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). consider obsoleting, coordinate with VSAO VSAO:0000006 XAO:0004021 uberon UBERON:0011585 cell condensation VSAO Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). GO_REF:0000034 PSPUB:0000170 VSAO:0000006 http://dx.plos.org/10.1371/journal.pone.0051070 Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix. EMAPA:36439 VSAO:0000071 XAO:0004052 pre-dentine tissue predentin predentine tissue uberon UBERON:0011587 pre-dentine VSAO text definition Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix. GO_REF:0000034 PSPUB:0000170 VSAO:0000071 http://dx.plos.org/10.1371/journal.pone.0051070 pre-dentine tissue VSAO:curator predentin PMCID:PMC3360947 predentine tissue VSAO:curator Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix. VSAO:0000066 XAO:0004202 pre-enamel tissue preenamel tissue uberon UBERON:0011588 pre-enamel VSAO Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix. GO_REF:0000034 PSPUB:0000170 VSAO:0000066 http://dx.plos.org/10.1371/journal.pone.0051070 pre-enamel tissue VSAO:curator preenamel tissue VSAO:curator Cartilage tissue that is not mineralized. add developmental relationships; add disjointness axiom VSAO:0000089 XAO:0004044 uberon UBERON:0011589 non-mineralized cartilage tissue VSAO Cartilage tissue that is not mineralized. GO_REF:0000034 PSPUB:0000170 VSAO:0000089 http://dx.plos.org/10.1371/journal.pone.0051070 EHDAA2:0002120 upper jaw future lip uberon UBERON:0011592 future upper lip EHDAA2 fusion fusion upper jaw future lip EHDAA2:0002120 Tooth that is attached to a dentary/mandible[TAO,modified]. Note that we treat dentary tooth and mandibular tooth as equivalent Tooth that is attached to the dentary.[TAO] relationship loss: part_of dentary tooth row (TAO:0001952)[TAO] AAO:0000125 AAO:0000641 FMA:321647 SCTID:245547003 TAO:0001628 uberon mandibular teeth mandibular tooth tooth of dentary UBERON:0011594 dentary tooth Tooth that is attached to a dentary/mandible[TAO,modified]. TAO:0001628 Tooth that is attached to the dentary.[TAO] 2012-08-14 TAO:0001628 TAO TAO:wd relationship loss: part_of dentary tooth row (TAO:0001952)[TAO] 2012-08-14 TAO:0001628 TAO mandibular teeth AAO:0000641 A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EMAPA:32905 NCIT:C114916 uberon UBERON:0011595 jaw region http://eol.org/collections/11578 EMAPA FMA-abduced ZFA-abduced A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. http://orcid.org/0000-0002-6601-2165 EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip EHDAA2 Wikipedia:Mandibular_prominence lower jaw future lip EHDAA2:0001020 Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species). Do not manually classify under here - bones are automatically classified upper jaw bone uberon UBERON:0011597 bone of upper jaw Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species). https://orcid.org/0000-0002-6601-2165 A gingiva that is part of a upper jaw region. EMAPA:18970 FMA:59763 NCIT:C54205 SCTID:304703001 UMLS:C0227121 gum of maxilla gum of upper jaw upper gingiva upper jaw gingiva uberon maxillary gum upper gum UBERON:0011601 gingiva of upper jaw A gingiva that is part of a upper jaw region. OBOL:automatic gum of upper jaw EMAPA:18970 upper jaw gingiva FMA:59763 maxillary gum FMA:59763 A gingiva that is part of a lower jaw region. EMAPA:18967 FMA:59764 NCIT:C54204 SCTID:304704007 UMLS:C0227123 gum of lower jaw gum of mandible lower gingiva lower jaw gingiva uberon lower gum lower jaw gum mandibular gum UBERON:0011602 gingiva of lower jaw A gingiva that is part of a lower jaw region. OBOL:automatic gum of lower jaw EMAPA:18967 lower jaw gingiva FMA:59764 lower jaw gum FMA:59764 mandibular gum FMA:59764 An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm EHDAA2 EHDAA2 An epithelium that develops_from a ectoderm and is part of a oral epithelium. OBOL:automatic Limb extensor that runs from ilium to femur. iliofemoralis uberon UBERON:0011645 iliofemoralis muscle Limb extensor that runs from ilium to femur. ISBN:0073040584 AAO:0000247 EFO:0003511 TAO:0000236 XAO:0003269 ZFA:0000236 mandibular muscle mandibular muscles uberon UBERON:0011648 jaw muscle mandibular muscle TAO:0000236 mandibular muscles TAO:0000236 A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem axial subdivision of organism uberon body segment main body segment UBERON:0011676 subdivision of organism along main body axis A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. https://orcid.org/0000-0002-6601-2165 A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. thoracolumbar vertebra uberon presacral vertebra UBERON:0011677 trunk vertebra true A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. UBERONREF:0000006 presacral vertebra http://orcid.org/0000-0002-6601-2165 A tarsal bone that connected_to a hindlimb zeugopod skeleton. uberon UBERON:0011679 proximal tarsal bone A tarsal bone that connected_to a hindlimb zeugopod skeleton. OBOL:automatic VHOG:0001157 extraembryonic umbilical artery uberon UBERON:0011693 extraembryonic portion of umbilical artery EHDAA2-abduced EHDAA2-abduced FMA extraembryonic umbilical artery VHOG:0001157 A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 NCIT:C34148 conceptus cardiovascular system uberon embryonic circulatory system fetal circulatory system UBERON:0011695 embryonic cardiovascular system A cardiovascular system that is part of a conceptus. OBOL:automatic EHDAA2:0000937 extraembryonic umbilical artery left uberon UBERON:0011696 left extraembryonic umbilical artery extraembryonic umbilical artery left EHDAA2:0000937 EHDAA2:0001721 extraembryonic umbilical artery right uberon UBERON:0011697 right extraembryonic umbilical artery extraembryonic umbilical artery right EHDAA2:0001721 EMAPA:35903 MA:0003179 uberon valve leaflet UBERON:0011741 cardiac valve leaflet valve leaflet MA:0003179 A cardiac valve leaflet that is part of a pulmonary valve. Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[uncertain][VHOG] EMAPA:18629 VHOG:0000820 uberon UBERON:0011745 pulmonary valve leaflets A cardiac valve leaflet that is part of a pulmonary valve. OBOL:automatic Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[uncertain][VHOG] 2012-09-17 VHOG:0000820 VHOG DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009) http://bgee.unil.ch/ Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum. todo - add parthood relationships to tubercles EMAPA:30074 EMAPA:35377 VHOG:0000976 Wikipedia:Labioscrotal_swelling labioscrotal swelling uberon tuberculum labioscrotale UBERON:0011754 genital swelling EHDAA2 Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum. Wikipedia:Labioscrotal_swelling tuberculum labioscrotale Wikipedia:Labioscrotal_swelling A genital swelling that is part of a female reproductive system. labial swelling EHDAA2:0000501 EHDAA:9363 EMAPA:18329 EMAPA:30423 labioscrotal swelling of female uberon labial primordium UBERON:0011755 female labial swelling A genital swelling that is part of a female reproductive system. OBOL:automatic labial swelling EMAPA:18329 labioscrotal swelling of female EMAPA:30423 A genital swelling that is part of a male reproductive organ. EHDAA2:0001049 EMAPA:30509 labioscrotal swelling of male scrotal bulge scrotal primordium uberon UBERON:0011756 male genital swelling A genital swelling that is part of a male reproductive organ. OBOL:automatic labioscrotal swelling of male EMAPA:30509 NCIT:C34274 UMLS:C1514448 Wikipedia:Primordial_phallus uberon phallus phallus primordialis primordial phallus UBERON:0011757 differentiated genital tubercle UMLS:C1514448 ncithesaurus:Primordial_Phallus phallus Wikipedia:Primordial_phallus phallus primordialis Wikipedia:Primordial_phallus primordial phallus Wikipedia:Primordial_phallus The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP] EMAPA:25350 FMA:14469 MA:0001107 SCTID:280300006 left recurrent laryngeal branch left recurrent laryngeal nerve vagus X nerve left recurrent laryngeal branch uberon UBERON:0011766 left recurrent laryngeal nerve https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg left recurrent laryngeal branch EMAPA:25350 left recurrent laryngeal nerve FMA:14469 vagus X nerve left recurrent laryngeal branch MA:0001107 EMAPA:17275 FMA:14468 MA:0001108 SCTID:280299003 right recurrent laryngeal branch right recurrent laryngeal nerve vagus X nerve right recurrent laryngeal branch uberon UBERON:0011767 right recurrent laryngeal nerve right recurrent laryngeal branch EMAPA:17275 right recurrent laryngeal nerve FMA:14468 vagus X nerve right recurrent laryngeal branch MA:0001108 Anatomical projection that is composed of cartilage tissue. FMA:284626 cartilage process cartilaginous process uberon UBERON:0011769 cartilaginous projection Anatomical projection that is composed of cartilage tissue. VSAO:wd An anatomical space that is part of a bone of lower jaw. AAO:0000273 uberon UBERON:0011772 lower jaw opening An anatomical space that is part of a bone of lower jaw. OBOL:automatic An anatomical space that is part of a bone of upper jaw. AAO:0000621 uberon UBERON:0011773 upper jaw opening An anatomical space that is part of a bone of upper jaw. OBOL:automatic A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 SCTID:362467005 nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus vagal X nucleus vagal nucleus vagus nucleus uberon nodosal nucleus UBERON:0011775 vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. OBOL:automatic nucleus of vagus nerve FMA:54573 tenth cranial nerve nucleus FMA:54573 vagal X nucleus http://orcid.org/0000-0002-6601-2165 vagal nucleus http://orcid.org/0000-0002-6601-2165 vagus nucleus http://orcid.org/0000-0002-6601-2165 nodosal nucleus http://orcid.org/0000-0002-6601-2165 A neural nucleus that is part of the spinal cord. FMA:77011 spinal cord nucleus uberon UBERON:0011777 nucleus of spinal cord A neural nucleus that is part of the spinal cord. http://orcid.org/0000-0002-6601-2165 spinal cord nucleus FMA:77011 A nerve that is part of a head. uberon cephalic nerve head nerve UBERON:0011779 nerve of head region A nerve that is part of a head. OBOL:automatic Ectodermal placode that does not develop into a component of the nervous system. uberon UBERON:0011814 non-neurogenic ectodermal placode cjm Ectodermal placode that does not develop into a component of the nervous system. PMID:11523831 http://orcid.org/0000-0002-6601-2165 An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). cutaneous appendage follicle placode skin follicle placode uberon UBERON:0011817 skin appendage placode NCBIBook:NBK53175 An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). https://github.com/obophenotype/uberon/issues/1266 An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. EHDAA2:0004149 FMA:85125 uberon AV region AV segment atrial ventricular junction atrioventricular junction atrioventricular segment UBERON:0011820 atrioventricular region An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. http://orcid.org/0000-0002-6601-2165 AV region PMID:21234997 AV segment PMID:21234997 atrial ventricular junction GO:0003294 atrioventricular junction FMA:85125 GO:0003294 atrioventricular segment PMID:21234997 Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 uberon UBERON:0011821 irregular connective tissue FMA Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 Wikipedia:Dense_irregular_connective_tissue irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon UBERON:0011822 dense irregular connective tissue FMA Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20109 Wikipedia:Dense_irregular_connective_tissue Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] 2012-08-29 ncithesaurus:Irregular_Dense_Connective_Tissue NCIT UMLS:C0738366 ncithesaurus:Irregular_Dense_Connective_Tissue typus irregularis (textus connectivus collagenosus compactus) FMA:20109 Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 Wikipedia:Dense_connective_tissue uberon UBERON:0011823 dense connective tissue Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. Wikipedia:Dense_connective_tissue Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] 2012-08-29 ncithesaurus:Dense_Connective_Tissue NCIT UMLS:C1511770 ncithesaurus:Dense_Connective_Tissue FMA:75634 SCTID:363130003 uberon UBERON:0011824 fibrous connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 NCIT:C33007 UMLS:C1253917 Wikipedia:Loose_connective_tissue textus connectivus collagenosus laxus textus connectivus laxus uberon UBERON:0011825 loose connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 UMLS:C1253917 ncithesaurus:Loose_Connective_Tissue textus connectivus collagenosus laxus FMA:19783 FMA:TA textus connectivus laxus FMA:19783 FMA:TA A duct that is part of a sebaceous gland. FMA:70947 NCIT:C33520 sebaceous gland duct uberon UBERON:0011845 duct of sebaceous gland A duct that is part of a sebaceous gland. OBOL:automatic sebaceous gland duct FMA:70947 An acinus that is part of a sebaceous gland. FMA:59657 sebaceous gland acinus uberon UBERON:0011846 acinus of sebaceous gland An acinus that is part of a sebaceous gland. OBOL:automatic sebaceous gland acinus FMA:59657 An acinus that is part of a salivary gland. FMA:59870 salivary gland acinus uberon UBERON:0011850 acinus of salivary gland An acinus that is part of a salivary gland. OBOL:automatic salivary gland acinus FMA:59870 An acinus that is part of a mammary gland. FMA:74438 lactiferous gland acinus uberon UBERON:0011856 acinus of lactiferous gland An acinus that is part of a mammary gland. OBOL:automatic lactiferous gland acinus FMA:74438 An acinus that is part of a lacrimal gland. FMA:85250 lacrimal gland acinus uberon UBERON:0011857 acinus of lacrimal gland An acinus that is part of a lacrimal gland. OBOL:automatic lacrimal gland acinus FMA:85250 An acinus that is part of a exocrine gland. exocrine gland acinus uberon UBERON:0011858 acinus of exocrine gland An acinus that is part of a exocrine gland. OBOL:automatic the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils ZFA the FMA class specifically refers to ureter FMA The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011861 aorta collagen fibril The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011640 The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011862 pulmonary collagen fibril The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011641 The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011863 bone collagen fibril The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011642 The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011864 tendon collagen fibril The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011643 The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity. uberon UBERON:0011865 corneal stroma collagen fibril The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity. MP:0011650 A skeletal ligament that is part of a sternoclavicular joint. FMA:63980 SCTID:182386007 ligamentum sternoclavicularis sternoclavicular joint ligament uberon UBERON:0011875 ligament of sternoclavicular joint A skeletal ligament that is part of a sternoclavicular joint. OBOL:automatic ligamentum sternoclavicularis sternoclavicular joint ligament FMA:63980 A muscle layer that is part of a wall of esophagus. In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle FMA:62998 muscle coat of esophagus muscular coat of oesophagus muscular layer of oesophagus tela muscularis (oesophagus) tunica muscularis esophagi tunica muscularis oesophageae uberon UBERON:0011878 muscle layer of esophagus upper part Wikipedia:Muscular_layer A muscle layer that is part of a wall of esophagus. OBOL:automatic In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle WP muscle coat of esophagus FMA:62998 muscular coat of oesophagus FMA:62998 muscular layer of oesophagus FMA:62998 tela muscularis (oesophagus) FMA:62998 FMA:TA tunica muscularis esophagi tunica muscularis oesophageae FMA:TA Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. EMAPA:37417 SCTID:280656002 Haller tunica vascula anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye tunica vasculosa bulbosa ventral uveal tract uberon ciliary body and iris vasculosa oculi UBERON:0011892 anterior uvea ZFA MP Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. MP:0005194 EMAPA:37417 MA:th Haller tunica vascula MP:0005194 tunica vasculosa bulbosa MP:0005194 vasculosa oculi MP:0005194 An organ cavity that is part of a vagina. FMA:19982 vaginal lumen uberon UBERON:0011894 lumen of vagina An organ cavity that is part of a vagina. OBOL:automatic vaginal lumen FMA:19982 Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 Wikipedia:Epimysium fascia of muscle organ uberon epimysia UBERON:0011899 epimysium FMA FMA Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. Wikipedia:Epimysium UMLS:C0504096 ncithesaurus:Epimysium fascia of muscle organ FMA:9726 epimysia Wikipedia:Epimysium Masses of developing blood cells attached to endothelium in the yolk sac. EHDAA2:0000177 EMAPA:16115 visceral yolk sac blood island yolk sac blood islands uberon UBERON:0011919 yolk sac blood island EHDAA2 Masses of developing blood cells attached to endothelium in the yolk sac. MP:0011204 visceral yolk sac blood island MP:0011204 yolk sac blood islands EHDAA2:0000177 in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels EHDAA2:0003242 blood island of umbilical vesicle insula sanguinea vesiculae umbilicalis uberon UBERON:0011921 connecting stalk blood islands EHDAA2 EHDAA2 EHDAA2 in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels EHDAA2 blood island of umbilical vesicle Wikipedia:Blood_island insula sanguinea vesiculae umbilicalis Wikipedia:Blood_island Hair in the nose. FMA:53670 SCTID:368885003 Wikipedia:Nasal_hair hair of nose hair of vestibular part of nose nose hair uberon UBERON:0011931 nasal hair Hair in the nose. Wikipedia:Nasal_hair hair of nose FMA:53670 hair of vestibular part of nose FMA:53670 nose hair FMA:53670 An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle. EMAPA:36582 FMA:70661 Wikipedia:Pilosebaceous_unit fabrica pilosebacea pilo-sebaceous apparatus pilo-sebaceous unit pilosebaceous apparatus uberon pilosebaceous gland UBERON:0011932 pilosebaceous unit ISBN:0123813611 An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle. ISBN:0123813611 PMCID:PMC3130146 Wikipedia:Pilosebaceous_unit fabrica pilosebacea Wikipedia:Pilosebaceous_unit pilo-sebaceous apparatus FMA:70661 pilosebaceous gland FMA:70661 A region of the stomach that is lined with glandular epithelium. as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus EMAPA:17623 MA:0001613 NCIT:C77661 SCTID:27633001 UMLS:C0227197 uberon glandular stomach UBERON:0011953 stomach glandular region A region of the stomach that is lined with glandular epithelium. http://orcid.org/0000-0002-6601-2165 UMLS:C0227197 ncithesaurus:Glandular_Stomach A hepatic vein that is part of a left lobe of liver. EMAPA:37164 FMA:14339 MA:0003032 SCTID:55188000 uberon UBERON:0011955 left hepatic vein A hepatic vein that is part of a left lobe of liver. OBOL:automatic EMAPA:37164 MA:th A hepatic vein that is part of a right lobe of liver. EMAPA:37377 FMA:14338 MA:0003034 SCTID:18135006 uberon UBERON:0011956 right hepatic vein A hepatic vein that is part of a right lobe of liver. OBOL:automatic EMAPA:37377 MA:th An articular capsule that is part of the glenohumeral joint. FMA:34944 SCTID:361836001 Wikipedia:Articular_capsule_of_the_humerus articular capsule of humerus articular capsule of shoulder joint capsule of shoulder joint fibrous capsule of glenohumeral joint uberon glenohumeral joint capsule UBERON:0011960 articular capsule of glenohumeral joint An articular capsule that is part of the glenohumeral joint. http://orcid.org/0000-0002-6601-2165 articular capsule of humerus Wikipedia:Articular_capsule_of_the_humerus capsule of shoulder joint FMA:34944 fibrous capsule of glenohumeral joint FMA:34944 glenohumeral joint capsule FMA:34944 An articular capsule that is part of the hip joint. FMA:42821 SCTID:263382006 Wikipedia:Capsule_of_hip_joint capsula articularis coxae capsule of hip joint fibrous capsule of hip joint uberon UBERON:0011961 articular capsule of hip joint An articular capsule that is part of the hip joint. http://orcid.org/0000-0002-6601-2165 capsula articularis coxae Wikipedia:Capsule_of_hip_joint capsule of hip joint Wikipedia:Capsule_of_hip_joint fibrous capsule of hip joint FMA:42821 In a saddle joint (sellar joint, articulation by reciprocal reception) the opposing surfaces are reciprocally concave-convex. FMA:75298 SCTID:23059003 Wikipedia:Saddle_joint sellar joint uberon articulation by reciprocal reception UBERON:0011965 saddle joint In a saddle joint (sellar joint, articulation by reciprocal reception) the opposing surfaces are reciprocally concave-convex. Wikipedia:Saddle_joint sellar joint Wikipedia:Saddle_joint articulation by reciprocal reception Wikipedia:Saddle_joint A skeletal ligament that connects a tibia and connects a tarsal skeleton. FMA:44055 SCTID:41159004 deltoid collateral ligament of ankle joint deltoid ligament of ankle joint ligamentum collaterale mediale (articulatio talocruralis) ligamentum collaterale mediale articulationis talocruralis ligamentum deltoideum ligamentum deltoideum (articulatio talocruralis) medial collateral ligament of ankle joint uberon UBERON:0011972 medial ligament of ankle joint A skeletal ligament that connects a tibia and connects a tarsal skeleton. OBOL:automatic deltoid collateral ligament of ankle joint FMA:44055 deltoid ligament of ankle joint FMA:44055 ligamentum collaterale mediale (articulatio talocruralis) FMA:44055 ligamentum collaterale mediale articulationis talocruralis FMA:44055 FMA:TA ligamentum deltoideum FMA:TA ligamentum deltoideum (articulatio talocruralis) FMA:44055 medial collateral ligament of ankle joint FMA:44055 An epiphysis that is part of a phalanx of a pes [Automatically generated definition]. SCTID:314621001 epiphysis of phalanx of toe uberon UBERON:0011973 epiphysis of phalanx of pes An epiphysis that is part of a phalanx of a pes [Automatically generated definition]. OBOL:automatic An epiphysis that is part of a proximal phalanx of pes. SCTID:280047006 epiphysis of proximal phalanx of toe uberon UBERON:0011974 epiphysis of proximal phalanx of pes An epiphysis that is part of a proximal phalanx of pes. OBOL:automatic An epiphysis that is part of a middle phalanx of pes. SCTID:280048001 epiphysis of middle phalanx of toe uberon UBERON:0011975 epiphysis of middle phalanx of pes An epiphysis that is part of a middle phalanx of pes. OBOL:automatic An epiphysis that is part of a distal phalanx of pes. SCTID:280049009 epiphysis of distal phalanx of toe uberon UBERON:0011976 epiphysis of distal phalanx of pes An epiphysis that is part of a distal phalanx of pes. OBOL:automatic An epiphysis that is part of a proximal phalanx of manus. SCTID:280044004 epiphysis of proximal phalanx of finger uberon UBERON:0011977 epiphysis of proximal phalanx of manus An epiphysis that is part of a proximal phalanx of manus. OBOL:automatic An epiphysis that is part of a middle phalanx of manus. SCTID:280045003 epiphysis of middle phalanx of finger uberon UBERON:0011978 epiphysis of middle phalanx of manus An epiphysis that is part of a middle phalanx of manus. OBOL:automatic An epiphysis that is part of a distal phalanx of manus. FMA:321561 SCTID:280046002 epiphysis of distal phalanx of finger uberon UBERON:0011979 epiphysis of distal phalanx of manus An epiphysis that is part of a distal phalanx of manus. OBOL:automatic A joint that connects the bones of the crus to the proximal tarsal bones. an ankle joint that passes between the astragalus and calcaneum[Palaeos]. Wikipedia:Crurotarsal uberon crurotarsal UBERON:0011980 line of flexion between calcaneus and astragalus crurotarsal joint A joint that connects the bones of the crus to the proximal tarsal bones. Wikipedia:Crurotarsal an ankle joint that passes between the astragalus and calcaneum[Palaeos]. http://palaeos.com/vertebrates/glossary/glossaryCr.html#Crurotarsal%20joint The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom haemocoelom schizocoelom uberon coelem coelomic cavity UBERON:0011997 coelom EHDAA2 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:cjm Wikipedia:Body_cavity Wikipedia:Coelom Wikipedia:Acoelomorpha enterocoelom NCBITaxon:33511 coelomic cavity EHDAA2:0004731 The cavity within a myotome. The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] EMAPA:31134 VHOG:0001283 uberon UBERON:0012054 myocoele The cavity within a myotome. http://medical-dictionary.thefreedictionary.com/myocoele The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001283 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6 http://bgee.unil.ch/ FMA:62811 uberon UBERON:0012069 epithelium-associated lymphoid tissue FMA A tooth that is on the roof of the mouth. palatal teeth uberon UBERON:0012070 palatal tooth A tooth that is on the roof of the mouth. http://palaeos.com/vertebrates/therapsida/anteosauria.html palatal teeth Any bone that is part of a palate. this is distinct (but not disjoint) from palatine bone EMAPA:37930 NCIT:C33248 UMLS:C1518857 palatal bone uberon UBERON:0012071 palate bone Any bone that is part of a palate. https://orcid.org/0000-0002-6601-2165 EMAPA:37930 MA:th UMLS:C1518857 ncithesaurus:Palate_Bone uberon dermatocranium, palatal series palatal series UBERON:0012072 palatal part of dermatocranium dermatocranium, palatal series ISBN:0073040584 palatal series ISBN:0073040584 Bone that forms as a replacement of another structural tissue. Bone that forms as a replacement of another structural tissue.[TAO] This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. AAO:0010768 TAO:0001637 ZFA:0001628 replacement bones uberon UBERON:0012075 replacement bone ZFA ZFA Bone that forms as a replacement of another structural tissue. ZFA:0001628 Bone that forms as a replacement of another structural tissue.[TAO] 2012-08-14 TAO:0001637 TAO TAO:wd This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. ZFA replacement bones ZFA:0001628 A cartilaginous condensation that has the potential to develop into a patella. Note some sources have this as intramembranous EMAPA:19140 uberon UBERON:0012080 patella cartilage element A cartilaginous condensation that has the potential to develop into a patella. OBOL:automatic A pre-cartilage condensation that has the potential to develop into a patella. EMAPA:18510 uberon UBERON:0012081 patella pre-cartilage condensation EMAPA A pre-cartilage condensation that has the potential to develop into a patella. OBOL:automatic An anatomical cavity that is part of a bronchus. FMA:62646 SCTID:199401001 bronchial lumen lumen of bronchus uberon UBERON:0012082 bronchial lumen FMA FMA An anatomical cavity that is part of a bronchus. OBOL:automatic bronchial lumen FMA:62646 lumen of bronchus FMA:62646 A salivary gland that is part of a cheek. FMA:59793 NCIT:C32237 uberon UBERON:0012102 buccal salivary gland A salivary gland that is part of a cheek. OBOL:automatic Anatomical system that consists of the integumental system plus all mucosae and submucosae. uberon dermatological system UBERON:0012125 dermatological-muscosal system Anatomical system that consists of the integumental system plus all mucosae and submucosae. https://github.com/obophenotype/uberon/issues/53 dermatological system OBI:MC Outermost point on an external nose or snout. EMAPA:37915 FMA:59518 SCTID:361926005 apex nasi apex of nose nasal tip tip of nose uberon pirula snout tip tip of snout UBERON:0012128 nose tip FMA Outermost point on an external nose or snout. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/109 EMAPA:37915 MA:th apex nasi FMA:TA apex of nose FMA:59518 nasal tip FMA:59518 tip of nose FMA:59518 pirula https://www.abdn.ac.uk/bestiary/translat/84v.hti uberon UBERON:0012139 segment of autopod may be revised A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon acropodium (Wagner) UBERON:0012140 digitopodium region https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region. PHENOSCAPE:ni https://github.com/obophenotype/uberon/issues/131 A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon UBERON:0012141 manual digitopodium region https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region. http://orcid.org/0000-0002-6601-2165 A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon UBERON:0012142 pedal digitopodium region https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region. http://orcid.org/0000-0002-6601-2165 A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon digitopodium skeleton of digits UBERON:0012150 skeleton of digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton. PHENOSCAPE:ni digitopodium PHENOSCAPE:ni skeleton of digits A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon manual digitopodium UBERON:0012151 skeleton of manual digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod FMA A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton. PHENOSCAPE:ni https://orcid.org/0000-0002-6601-2165 A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon pedal digitopodium UBERON:0012152 skeleton of pedal digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton. PHENOSCAPE:ni https://orcid.org/0000-0002-6601-2165 Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. BTO:0004053 CALOHA:TS-1079 EFO:0001942 MESH:D005312 Wikipedia:Cord_blood uberon cord blood fetal blood umbilical cord blood UBERON:0012168 Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP] umbilical cord blood Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. Wikipedia:Cord_blood cord blood BTO:0004053 fetal blood MESH:A12.207.152.200 umbilical cord blood MESH:A12.207.152.200 A primordium that has the potential to develop into a stomach. EFO:0002580 NCIT:C34305 UMLS:C1514976 uberon stomach endoderm UBERON:0012172 stomach primordium A primordium that has the potential to develop into a stomach. OBOL:automatic UMLS:C1514976 ncithesaurus:Stomach_Primordium stomach endoderm EFO:0002580 EHDAA2:0000494 EMAPA:16794 SCTID:361514006 VHOG:0000715 acousticofacial ganglion facio-acoustic ganglion facio-acoustic ganglion complex VII-VIII uberon facio-acoustic VII-VIII ganglion complex facio-acoustic ganglion complex UBERON:0012175 acoustico-facial VII-VIII ganglion complex cjm EHDAA2 cjm facio-acoustic ganglion complex VII-VIII EMAPA:16794 facio-acoustic VII-VIII ganglion complex VHOG:0000715 facio-acoustic ganglion complex EMAPA:16794 An apocrine gland that is part of a skin of body. MA:0000147 uberon UBERON:0012177 Note that 'skin apocrine gland' does not cover 'apocrine sweat gland': in the former, "apocrine" refers to the type of secretion mechanism, while in the latter it refers to a structural feature. skin apocrine gland MA An apocrine gland that is part of a skin of body. OBOL:automatic A zone of skin that is part of a craniocervical region. EMAPA:37276 MA:0000574 NCIT:C12294 UMLS:C1522650 uberon UBERON:0012180 head or neck skin A zone of skin that is part of a craniocervical region. OBOL:automatic EMAPA:37276 MA:th UMLS:C1522650 ncithesaurus:Skin_of_the_Scalp_and_Neck The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. EMAPA:37180 MA:0002194 NCIT:C53062 UMLS:C1709532 uberon UBERON:0012193 phrenic vein The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. ncithesaurus:Phrenic_Vein EMAPA:37180 MA:th UMLS:C1709532 ncithesaurus:Phrenic_Vein Network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP]. EMAPA:28679 bladder vasculature blood vessels of bladder set of urinary bladder blood vessels uberon blood vessel of bladder UBERON:0012239 urinary bladder vasculature EMAPA Network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP]. MP:MP blood vessels of bladder EMAPA:28679 blood vessel of bladder EMAPA:28679 External opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. EMAPA:37977 FMA:19650 SCTID:181424008 Wikipedia:Urinary_meatus external meatus of urethra external urethral orifice external urethral ostium external urinary meatus meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus uberon urinary meatus UBERON:0012240 urethral meatus External opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. MP:MP Wikipedia:Urinary_meatus EMAPA:37977 MA:th external meatus of urethra FMA:19650 external urethral orifice FMA:19650 external urethral ostium FMA:19650 external urinary meatus FMA:19650 meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus FMA:19650 A urethral meatus that is part of a male urethra[Automatically generated definition]. The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis. EMAPA:36434 FMA:85265 MA:0002642 SCTID:279478000 Wikipedia:External_urethral_orifice_(male) external orifice of male urethra external urethral orifice (male) male urethra ostium ostium urethrae externum (urethra masculina) urethral meatus of penile urethra uberon distal urethral opening of male urethral opening of penile urethra UBERON:0012241 male urethral meatus A urethral meatus that is part of a male urethra[Automatically generated definition]. OBOL:automatic Wikipedia:External_urethral_orifice_(male) The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis. Wikipedia:External_urethral_orifice_(male) external orifice of male urethra FMA:85265 external urethral orifice (male) FMA:85265 male urethra ostium MA:0002642 ostium urethrae externum (urethra masculina) FMA:TA urethral meatus of penile urethra EMAPA:36434 distal urethral opening of male EMAPA:36434 urethral opening of penile urethra EMAPA:36434 The usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone. FMA:85263 SCTID:362228001 Wikipedia:Internal_urethral_orifice internal meatus of urethra internal urethral orifice of urinary bladder internal urethral ostium orificium urethrae internum ostium orificium internum ostium urethrae internum vesicourethral orifice uberon internal urethral ostium internal urinary meatus UBERON:0012242 internal urethral orifice The usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone. MGI:anna MP:0011782 internal meatus of urethra FMA:85263 internal urethral orifice of urinary bladder FMA:85263 internal urethral ostium FMA:85263 orificium urethrae internum MP:0011782 ostium orificium internum ostium urethrae internum Wikipedia:Internal_urethral_orifice vesicourethral orifice FMA:85263 internal urethral ostium MP:0011782 internal urinary meatus MP:0011782 Mucus-secreting glands in the mucosa of the uterine cervix. NCIT:C32296 SCTID:280836000 UMLS:C2724437 glandulae cervicales uberon UBERON:0012247 cervical gland Mucus-secreting glands in the mucosa of the uterine cervix. http://www.thefreedictionary.com/cervical+glands UMLS:C2724437 ncithesaurus:Cervical_Gland glandulae cervicales FMA:TA Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 uberon UBERON:0012248 cervical mucosa Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. distinction between two FMA classes not clear - we merge them here UBERON:0010182 BTO:0001850 CALOHA:TS-1098 FMA:77056 FMA:86484 NCIT:C12310 SCTID:264459002 UMLS:C0227829 Wikipedia:Vaginal_portion_of_cervix ectocervix portio vaginalis portio vaginalis cervicis uterine ectocervix vaginal part of cervix uberon exocervix UBERON:0012249 ectocervix BTO The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. BTO:0001850 Wikipedia:Vaginal_portion_of_cervix distinction between two FMA classes not clear - we merge them here FMA UMLS:C0227829 ncithesaurus:Ectocervix ectocervix BTO:0001850 FMA:86484 portio vaginalis Wikipedia:Vaginal_portion_of_cervix portio vaginalis cervicis BTO:0001850 uterine ectocervix CALOHA:TS-1098 vaginal part of cervix FMA:77056 exocervix BTO:0001850 A glandular epithelium that is part of a uterine cervix. The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. NCIT:C54414 UMLS:C1707350 uberon cervix columnar epithelium UBERON:0012250 cervix glandular epithelium A glandular epithelium that is part of a uterine cervix. OBOL:automatic The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx UMLS:C1707350 ncithesaurus:Cervix_Columnar_Epithelium An epithelium that is part of a ectocervix. SCTID:361376000 exocervical epithelium uberon UBERON:0012251 ectocervical epithelium An epithelium that is part of a ectocervix. OBOL:automatic The glandular epithelium that lines the endocervix. NCIT:C96180 SCTID:362256006 endocervical glandular epithelium uberon UBERON:0012252 endocervical epithelium The glandular epithelium that lines the endocervix. ncithesaurus:Endocervical_Glandular_Epithelium Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet. squamocolumnar junction NCIT:C97148 SCTID:280451001 squamo-columnar junction of uterine cervix squamocolumnar junction of uterine cervix uberon UBERON:0012253 Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia. cervical squamo-columnar junction Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet. http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx An artery that originates from the abdominal aorta. SCTID:281470000 abdominal artery artery of abdomen uberon UBERON:0012254 abdominal aorta artery An artery that originates from the abdominal aorta. Wikipedia:Abdominal_aorta#Branches https://orcid.org/0000-0002-6601-2165 An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]. Wikipedia:Columnar_epithelium uberon UBERON:0012274 columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]. Wikipedia:Columnar_epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 mesoderm-derived epithelium mesoepithelium uberon UBERON:0012275 meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. OBOL:automatic EMAPA:35308 FMA:86488 MA:0002732 glandular part of endometrium uterine glands uterine glands set uberon UBERON:0012276 endometrium glandular epithelium glandular part of endometrium FMA:86488 The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. nasal gland EMAPA:37871 FMA:321518 NCIT:C22725 SCTID:368881007 UMLS:C1522269 Wikipedia:Nasal_glands glandula nasalis glandulae nasales uberon UBERON:0012278 gland of nasal mucosa The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. Wikipedia:Nasal_glands EMAPA:37871 MA:th UMLS:C1522269 ncithesaurus:Nose_Nasal_Cavity_Nasal_Gland_MMHCC glandula nasalis glandulae nasales A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus. EMAPA:37936 MESH:D010481 NCIT:C77620 uberon circumanal gland perianal gland UBERON:0012281 perianal sebaceous gland ISBN:0123813611 A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus. ISBN:0123813611 EMAPA:37936 MA:th circumanal gland MESH:A13.734 perianal gland MESH:A13.734 An epithelial sac that is part of a Rathke's pouch. See https://github.com/obophenotype/uberon/issues/1305 EHDAA2:0001473 EMAPA:25036 uberon UBERON:0012287 Rathkes pouch epithelium EHDAA2 An epithelial sac that is part of a Rathke's pouch. OBOL:automatic One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly. cloacal fold EHDAA2:0004009 uberon UBERON:0012292 We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold EHDAA2 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly. MP:0011836 MP:anna cloacal fold EHDAA2:0004009 A mucosa that is part of a urethra. EMAPA:37912 FMA:76904 SCTID:362229009 mucous membrane of urethra tunica mucosa urethrae urethral mucosa uberon UBERON:0012299 mucosa of urethra A mucosa that is part of a urethra. OBOL:automatic EMAPA:37912 MA:th mucous membrane of urethra FMA:76904 tunica mucosa urethrae FMA:TA urethral mucosa FMA:76904 EHDAA2:0000039 EMAPA:16389 ectoderm of maxillary component uberon UBERON:0012313 1st arch maxillary ectoderm EHDAA2 EHDAA2 EHDAA2 EHDAA2 ectoderm of maxillary component EMAPA:16389 One of five swellings formed during the development of the face. FMA:293103 SCTID:89066004 uberon embryonic facial process facial primordium primordium of face UBERON:0012314 embryonic facial prominence One of five swellings formed during the development of the face. http://www.indiana.edu/~anat550/hnanim/face/face.html The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice. introitus EMAPA:37983 FMA:19984 Wikipedia:Vaginal_orifice opening of vagina orifice of vagina ostium vaginae vagina opening vaginal orifice uberon introitus introitus of vagina vaginal introitus UBERON:0012317 vagina orifice The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice. MGI:anna MGI:csmith MP:0001142 introitus FMA:19984 EMAPA:37983 MA:th orifice of vagina FMA:19984 ostium vaginae FMA:TA vagina opening MP:0001142 vaginal orifice FMA:19984 introitus FMA:19984 introitus of vagina MP:0001142 An artery of the neck. EMAPA:37075 NCIT:C52850 UMLS:C1707349 uberon UBERON:0012320 cervical artery An artery of the neck. https://orcid.org/0000-0002-6601-2165 EMAPA:37075 MA:th UMLS:C1707349 ncithesaurus:Cervical_Artery The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 SCTID:244223002 Wikipedia:Deep_cervical_artery uberon profunda cervicalis UBERON:0012321 deep cervical artery FMA The deep cervical artery (Profunda cervicalis) is an artery of the neck. Wikipedia:Deep_cervical_artery profunda cervicalis Wikipedia:Deep_cervical_artery The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery. Unclear if MA class belongs here or in parent FMA:10664 MA:0001936 SCTID:244224008 Wikipedia:Transverse_cervical_artery uberon cervical artery cervical transverse artery descending branch of the transverse cervical transversalis artery colli transversalis colli artery transverse cervical transverse cervical vessels UBERON:0012324 transverse cervical artery The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery. Wikipedia:Transverse_cervical_artery Unclear if MA class belongs here or in parent MA cervical artery MA:0001936 Wikipedia:Transverse_cervical_artery cervical transverse artery Wikipedia:Transverse_cervical_artery descending branch of the transverse cervical Wikipedia:Transverse_cervical_artery transversalis artery colli Wikipedia:Transverse_cervical_artery transversalis colli artery Wikipedia:Transverse_cervical_artery transverse cervical Wikipedia:Transverse_cervical_artery transverse cervical vessels Wikipedia:Transverse_cervical_artery Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin. FMA:45568 Wikipedia:Stratified_squamous_epithelium#Keratinized epithelium stratificatum squamosum cornificatum uberon UBERON:0012329 keratinized stratified squamous epithelium Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin. FMA:45568 Wikipedia:Stratified_squamous_epithelium#Keratinized epithelium stratificatum squamosum cornificatum FMA:45568 The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals. FMA:79771 MA:0003030 NCIT:C77659 UMLS:C2698431 NALT naso-pharyngeal lymphoid tissue uberon UBERON:0012330 nasal-associated lymphoid tissue The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals. ncithesaurus:Nasal-Associated_Lymphoid_Tissue UMLS:C2698431 ncithesaurus:Nasal-Associated_Lymphoid_Tissue NALT Wikipedia:Mucosa-associated_lymphoid_tissue#Categorisation naso-pharyngeal lymphoid tissue FMA:79771 A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis. FMA:16516 MESH:D001956 NCIT:C12318 SCTID:362723009 UMLS:C0006205 Wikipedia:Broad_ligament_of_the_uterus broad uterine ligament uberon broad ligament ligamentum latum uteri UBERON:0012332 broad ligament of uterus MESH A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis. MESH:A02.513.170 Wikipedia:Broad_ligament_of_the_uterus UMLS:C0006205 ncithesaurus:Broad_Ligament broad uterine ligament FMA:16516 broad ligament MESH:A02.513.170 ligamentum latum uteri A zone of skin that is part of the area surrounding the anus. EMAPA:37715 FMA:29350 MA:0003046 SCTID:181522009 skin of perianal area uberon UBERON:0012336 perianal skin MA A zone of skin that is part of the area surrounding the anus. http://orcid.org/0000-0002-6601-2165 EMAPA:37715 MA:th Any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. BTO:0002325 MA:0003042 Wikipedia:Holocrine uberon UBERON:0012344 holocrine gland MA MP Any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. MP:0013543 The segment of the autopod that is distal to the metapodial region and consists of the digits. class refers to an entire limb segment, not just the bones acropodial limb segment acropodial region acropodial segment of autopod set of digits uberon UBERON:0012354 acropodium region The segment of the autopod that is distal to the metapodial region and consists of the digits. https://orcid.org/0000-0002-6601-2165 The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers). class refers to an entire limb segment, not just the bones FMA:75592 acropodial hindlimb segment acropodial region of manus acropodial segment of manus all fingers anterior acropodium region anterior acropodium segment of limb digiti manus digits of hand fingers including thumb fingers set manual acropodium region manual acropodium segment of limb set of digits of hand set of fingers uberon anterior acropodium manual acropodium UBERON:0012355 manual acropodium region The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers). https://orcid.org/0000-0002-6601-2165 digiti manus FMA:TA digits of hand FMA:75592 fingers including thumb FMA:75592 fingers set FMA:75592 set of digits of hand FMA:75592 set of fingers FMA:75592 The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes). class refers to an entire limb segment, not just the bones FMA:70664 SCTID:362835004 acropodial forelimb segment acropodial region of pes acropodial segment of pes all toes digits of foot pedal acropodium region set of toes toes set uberon toes UBERON:0012356 pedal acropodium region The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes). https://orcid.org/0000-0002-6601-2165 digits of foot FMA:70664 set of toes FMA:70664 toes set FMA:70664 toes FMA:70664 A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton. uberon digit bone UBERON:0012357 digitopodium bone A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton. https://orcid.org/0000-0002-6601-2165 digit bone A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton. SCTID:265809008 bone of forelimb digitopodium uberon UBERON:0012358 manual digitopodium bone A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton. https://orcid.org/0000-0002-6601-2165 A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton. bone of hindlimb digitopodium uberon UBERON:0012359 pedal digitopodium bone A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton. https://orcid.org/0000-0002-6601-2165 A bone element that is part of a jaw region. Do not manually classify under here - bones are automatically classified EMAPA:35453 MA:0003130 SCTID:369003004 jaw bone uberon UBERON:0012360 bone of jaw A bone element that is part of a jaw region. OBOL:automatic EHDAA2:0004588 uberon UBERON:0012361 internal anal region EHDAA2 A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria muscularis externa of intestine uberon smooth muscle of intestine UBERON:0012367 muscle layer of intestine FMA A muscle layer that is part of an intestine. OBOL:automatic intestinal muscularis propria FMA:15697 muscularis externa of intestine FMA:15697 A nerve plexus that is part of a sympathetic nervous system. EMAPA:37617 MA:0001160 uberon UBERON:0012373 sympathetic nerve plexus A nerve plexus that is part of a sympathetic nervous system. OBOL:automatic EMAPA:37617 MA:th A layer of tissue between the muscularis and serosa. FMA:45636 NCIT:C94494 SCTID:2255006 UMLS:C0225334 Wikipedia:Subserosa uberon UBERON:0012375 Contains nerves, blood vessels, lymphatics and lymph nodes subserosa A layer of tissue between the muscularis and serosa. Wikipedia:Subserosa UMLS:C0225334 ncithesaurus:Subserosa A muscular coat that is part of a jejunum. FMA:14951 muscularis externa of jejunum uberon jejunal smooth muscle muscularis propria of jejunum smooth muscle of jejunum UBERON:0012377 muscle layer of jejunum A muscular coat that is part of a jejunum. OBOL:automatic muscularis externa of jejunum FMA:14951 jejunal smooth muscle https://orcid.org/0000-0002-6601-2165 muscularis propria of jejunum https://orcid.org/0000-0002-6601-2165 smooth muscle of jejunum https://orcid.org/0000-0002-6601-2165 A muscular coat that is part of a urinary bladder. FMA:15930 NCIT:C32206 UMLS:C1288327 bladder muscular coat muscle layer of urinary bladder muscular coat of bladder muscular coat of urinary bladder muscular layer of bladder muscular layer of urinary bladder tunica musculari vesicae tunica muscularis (vesica urinaria) uberon UBERON:0012378 muscle layer of urinary bladder FMA A muscular coat that is part of a urinary bladder. OBOL:automatic UMLS:C1288327 ncithesaurus:Bladder_Muscular_Coat muscle layer of urinary bladder FMA:15930 muscular coat of bladder FMA:15930 muscular coat of urinary bladder FMA:15930 muscular layer of bladder FMA:15930 muscular layer of urinary bladder FMA:15930 tunica musculari vesicae FMA:TA tunica muscularis (vesica urinaria) FMA:TA EMAPA:37567 MA:0001802 uberon UBERON:0012416 respiratory system arterial smooth muscle EMAPA:37567 MA:th A smooth muscle tissue that is part of a respiratory system venous blood vessel. EMAPA:37586 MA:0001812 uberon UBERON:0012418 respiratory system venous smooth muscle A smooth muscle tissue that is part of a respiratory system venous blood vessel. OBOL:automatic EMAPA:37586 MA:th A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]. a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction increases the surface area of a cell lining whilst minimizing increase in volume FMA class represents an individual microvillus. FMA:67296 MESH:D008871 NCIT:C33112 UMLS:C0026049 Wikipedia:Microvillus uberon microvilli microvillus UBERON:0012423 layer of microvilli A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]. GO:0005902 Wikipedia:Microvillus FMA class represents an individual microvillus. FMA UMLS:C0026049 ncithesaurus:Microvillus microvilli MESH:A11.284.180.565 microvillus FMA:67296 A microvillus layer that is striated and found in the intestine. FMA class represents an individual microvillus FMA:70978 NCIT:C33634 uberon striated border UBERON:0012425 striated border microvillus layer A microvillus layer that is striated and found in the intestine. http://medical-dictionary.thefreedictionary.com/striated+border http://orcid.org/0000-0002-6601-2165 FMA class represents an individual microvillus FMA striated border FMA:70978 Blood-forming tissue, consisting of reticular fibers and cells. Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 UMLS:C0229619 haemopoietic tissue hematopoietic tissue hemopoietic tissue textus haemopoieticus bone marrow tissue uberon UBERON:0012429 hematopoietic tissue FMA defitional Blood-forming tissue, consisting of reticular fibers and cells. http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue UMLS:C0229619 ncithesaurus:Hematopoietic_Tissue haemopoietic tissue FMA:14073 hematopoietic tissue FMA:14073 hemopoietic tissue FMA:14073 textus haemopoieticus FMA:14073 bone marrow tissue NCBITaxon:9606 The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. tunica fibrosa FMA:58102 SCTID:361318005 Wikipedia:Fibrous_tunic_of_eyeball fibrous layer of eyeball uberon corneosclera fibrous tunic UBERON:0012430 tunica fibrosa of eyeball FMA The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. Wikipedia:Fibrous_tunic_of_eyeball DOI:10.1177/0192623311409597 fibrous layer of eyeball FMA:58102 corneosclera Wikipedia:Fibrous_tunic_of_eyeball fibrous tunic Wikipedia:Fibrous_tunic_of_eyeball An anatomical space that is enclosed by a cloaca. the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ TAO:0000330 ZFA:0000330 cloaca lumen cloacal chamber uberon UBERON:0012463 cloacal lumen cjm An anatomical space that is enclosed by a cloaca. OBOL:automatic the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ ZFA cloaca lumen ZFA:0000330 cloacal chamber ZFA:0000330 The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. cloacal opening uberon cloacal orifice vent UBERON:0012464 cloacal vent The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. http://orcid.org/0000-0002-6601-2165 An anatomical space that is enclosed by a terminal part of digestive tract. includes the cloacal lumen, in species where this is present uberon UBERON:0012465 lumen of terminal part of digestive tract An anatomical space that is enclosed by a terminal part of digestive tract. OBOL:automatic EHDAA2:0000472 EMAPA:16054 VHOG:0000767 uberon extraembryonic cavities UBERON:0012466 extraembryonic cavity extraembryonic cavities EHDAA2:0000472 An anatomical space with no opening to another space or to the exterior. AEO:0000222 closed anatomical space uberon UBERON:0012467 enclosed anatomical space An anatomical space with no opening to another space or to the exterior. AEO:0000222 Triangular calcified papillae (often five) placed radially around the anus of some Holothuriidae. anal teeth uberon calcified anal papilla cloacal tooth perianal tooth UBERON:0012468 anal tooth Triangular calcified papillae (often five) placed radially around the anus of some Holothuriidae. http://species-identification.org/species.php?species_group=nasc&selected=definitie&menuentry=woordenlijst&record=Anal%20teeth https://orcid.org/0000-0002-6601-2165 https://www.karger.com/Article/Pdf/142845 anal teeth EHDAA2:0004589 uberon UBERON:0012469 external anal region EHDAA2 The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. FMA:24139 uberon bones of upper limb ossa membri superioris pectoral complex skeleton set of bones of upper limb skeleton of anterior limb/fin and girdle upper limb skeleton UBERON:0012475 skeleton of pectoral complex FMA The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. https://orcid.org/0000-0002-6601-2165 bones of upper limb FMA:24139 ossa membri superioris FMA:TA pectoral complex skeleton https://orcid.org/0000-0002-6601-2165 set of bones of upper limb FMA:24139 skeleton of anterior limb/fin and girdle https://orcid.org/0000-0002-6601-2165 upper limb skeleton FMA:24139 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. FMA:24140 uberon bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle UBERON:0012476 skeleton of pelvic complex FMA The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. https://orcid.org/0000-0002-6601-2165 bones of lower limb FMA:24140 lower limb skeleton FMA:24140 ossa membri inferioris FMA:TA pelvic complex skeleton https://orcid.org/0000-0002-6601-2165 set of bones of lower limb FMA:24140 skeleton of posterior limb/fin and girdle https://orcid.org/0000-0002-6601-2165 The posterior region of the neck, including the suboccipital region. nuchal nape BTO:0000957 FMA:24189 SCTID:182326009 SCTID:304036007 back of neck nape of neck neck back nucha nuchal region posterior cervical region posterior neck region posterior part of neck regio cervicalis posterior uberon hindneck UBERON:0012477 dorsal part of neck FMA FMA FMA The posterior region of the neck, including the suboccipital region. MP:0012723 nape BTO:0000957 back of neck FMA:24189 neck back FMA:24189 nucha FMA:24189 nuchal region FMA:24189 posterior cervical region FMA:24189 posterior neck region FMA:24189 posterior part of neck FMA:24189 regio cervicalis posterior FMA:TA A gland that is part of a cloaca. uberon UBERON:0012478 cloacal gland A gland that is part of a cloaca. OBOL:automatic A mucosa that is part of a cloaca [Automatically generated definition]. UBERON:0003349 cloaca mucosa cloaca mucosa of organ cloaca mucous membrane cloaca organ mucosa cloacal mucous membrane mucosa of cloaca mucosa of organ of cloaca mucous membrane of cloaca organ mucosa of cloaca uberon UBERON:0012480 cloacal mucosa A mucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 EMAPA:36070 ZFA:0005783 uberon cloacal endoderm UBERON:0012481 cloacal epithelium An epithelium that is part of a cloaca. http://orcid.org/0000-0002-6601-2165 cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 cloacal endoderm EMAPA:27577 A submucosa that is part of a cloaca [Automatically generated definition]. cloaca submucosa cloacal submucosa uberon UBERON:0012482 submucosa of cloaca A submucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic A serous membrane that is part of a cloaca [Automatically generated definition]. cloaca serosa cloaca serous membrane cloacal serosa serous membrane of cloaca visceral peritoneum of cloaca uberon UBERON:0012483 serosa of cloaca A serous membrane that is part of a cloaca [Automatically generated definition]. OBOL:automatic cloacal villi uberon UBERON:0012485 cloacal villus cloacal villi A muscular coat that is part of a cloaca. muscularis externa of cloaca uberon smooth muscle of cloaca UBERON:0012486 muscle layer of cloaca A muscular coat that is part of a cloaca. OBOL:automatic A sphincter muscle that is part of a vagina. sphincter of vagina uberon UBERON:0012487 vaginal sphincter A sphincter muscle that is part of a vagina. OBOL:automatic A muscular coat that is part of a duodenum. FMA:14944 SCTID:362147007 duodenal muscularis propria muscularis externa of duodenum uberon muscularis propria of duodenum smooth muscle of duodenum UBERON:0012488 muscle layer of duodenum A muscular coat that is part of a duodenum. OBOL:automatic duodenal muscularis propria FMA:14944 muscularis externa of duodenum FMA:14944 muscularis propria of duodenum https://orcid.org/0000-0002-6601-2165 smooth muscle of duodenum https://orcid.org/0000-0002-6601-2165 A muscular coat that is part of a colon. EMAPA:27383 FMA:14986 MA:0003198 SCTID:362158003 colonic muscularis propria muscular coat of colon muscular layer of colon muscularis externa of colon tunica muscularis coli uberon colon muscularis UBERON:0012489 muscle layer of colon A muscular coat that is part of a colon. OBOL:automatic colonic muscularis propria FMA:14986 muscular coat of colon FMA:14986 muscular layer of colon FMA:14986 muscularis externa of colon FMA:14986 tunica muscularis coli FMA:TA colon muscularis MA:0003198 A muscular coat that is part of a anal canal. FMA:15708 SCTID:362171000 anal canal muscularis propria anal muscularis propria muscular coat of anal canal muscular layer of anal canal muscularis externa of anal canal muscularis propria of anal canal uberon UBERON:0012490 muscle layer of anal canal A muscular coat that is part of a anal canal. OBOL:automatic anal muscularis propria FMA:15708 muscularis propria of anal canal FMA:15708 A serous membrane that is part of a vermiform appendix. FMA:14997 SCTID:22488003 appendiceal serosa appendix serosa serosa of vermiform appendix visceral peritoneum of vermiform appendix uberon UBERON:0012498 serosa of appendix A serous membrane that is part of a vermiform appendix. OBOL:automatic appendiceal serosa FMA:14997 appendix serosa FMA:14997 serosa of vermiform appendix FMA:14997 visceral peritoneum of vermiform appendix FMA:14997 A serous membrane that is part of a fallopian tube. FMA:18316 SCTID:259593000 serosa of fallopian tube serosa of oviduct serous coat of uterine tube tunica serosa (tuba uterina) tunica serosa tubae uterinae uterine tubal serosa uterine tube serosa uberon UBERON:0012499 serosa of uterine tube A serous membrane that is part of a fallopian tube. OBOL:automatic serosa of fallopian tube FMA:18316 serosa of oviduct FMA:18316 serous coat of uterine tube FMA:18316 tunica serosa (tuba uterina) FMA:18316 tunica serosa tubae uterinae FMA:TA uterine tubal serosa FMA:18316 uterine tube serosa FMA:18316 An adventitia that is part of a esophagus. FMA:63006 SCTID:85950006 adventitia of oesophagus adventitious layer of esophagus esophageal adventitia esophagus adventitia tunica adventitia (esophagus) tunica adventitia oesophageae uberon UBERON:0012504 adventitia of esophagus An adventitia that is part of a esophagus. OBOL:automatic adventitia of oesophagus FMA:63006 adventitious layer of esophagus FMA:63006 esophageal adventitia FMA:63006 esophagus adventitia FMA:63006 tunica adventitia (esophagus) FMA:63006 tunica adventitia oesophageae FMA:TA A smooth muscle tissue that is part of a umbilical cord. BTO:0001847 uberon UBERON:0012615 umbilical smooth muscle A smooth muscle tissue that is part of a umbilical cord. OBOL:automatic An anatomical junction that connects a stomach and connects a duodenum. FMA:17046 SCTID:264014000 uberon UBERON:0012650 gastroduodenal junction An anatomical junction that connects a stomach and connects a duodenum. OBOL:automatic A mucosa that is part of a gastroduodenal junction. BTO:0005415 gastroduodenal mucosa uberon UBERON:0012651 mucosa of gastroduodenal junction A mucosa that is part of a gastroduodenal junction. OBOL:automatic gastroduodenal mucosa BTO:0005415 The subdivision of the digestive tract that consists of the colon and the rectum. colorectal BTO:0001613 CALOHA:TS-1298 NCIT:C54189 UMLS:C1711309 uberon UBERON:0012652 colorectum non-canonical cjm The subdivision of the digestive tract that consists of the colon and the rectum. http://orcid.org/0000-0002-6601-2165 UMLS:C1711309 ncithesaurus:Colorectal_Region A mucosa that is part of a colorectum. UBERON:0019041 BTO:0002435 uberon UBERON:0013067 colorectal mucosa A mucosa that is part of a colorectum. OBOL:automatic FMA:32888 basal epiphysis of phalanx of foot base of phalanx of foot basis phalangis (pedis) basis phalangis pedis proximal epiphysis of phalanx of toe uberon UBERON:0013121 proximal epiphysis of phalanx of pes basal epiphysis of phalanx of foot FMA:32888 base of phalanx of foot FMA:32888 basis phalangis (pedis) FMA:32888 basis phalangis pedis FMA:TA proximal epiphysis of phalanx of toe FMA:32888 A vein that is part of a abdomen. TODO mirror representation of abdominal aorta this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein SCTID:281473003 abdominal vein uberon UBERON:0013126 vein of abdomen A vein that is part of a abdomen. OBOL:automatic The part of the venous system that drains the lungs[Kardong]. Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung. Wikipedia:Pulmonary_venous_system pulmonary venous circulatory system uberon UBERON:0013127 pulmonary venous system The part of the venous system that drains the lungs[Kardong]. ISBN:0073040584 Wikipedia:Pulmonary_venous_system Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung. Wikipedia:Pulmonary_circulation A vein that drains a lip. SCTID:367664002 labial vein of face lip vein vena labialis uberon labial vein UBERON:0013136 vein of lip FMA A vein that drains a lip. OBOL:automatic lip vein OBOL:automatic vena labialis A nonskeletal ligament that is part of a liver. FMA:15820 NCIT:C32997 SCTID:48536008 UMLS:C0230238 hepatic ligament liver ligament uberon UBERON:0013139 ligament of liver A nonskeletal ligament that is part of a liver. OBOL:automatic UMLS:C0230238 ncithesaurus:Liver_Ligament hepatic ligament FMA:15820 Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 NCIT:C33719 SCTID:244389004 UMLS:C0447117 systemic venous tree organ part uberon UBERON:0013140 systemic vein Any vein within the general circulation that transports blood back to the right atrium of the heart. ncithesaurus:Systemic_Vein UMLS:C0447117 ncithesaurus:Systemic_Vein systemic venous tree organ part FMA:66644 EHDAA2:0000101 SCTID:361482003 rhombencephalic vesicle uberon UBERON:0013149 gives rise of 4th ventricle hindbrain vesicle EHDAA2 rhombencephalic vesicle EHDAA2:0000101 consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle' NCIT:C34259 SCTID:360409004 neuronames:2499 early brain vesicle primitive brain vesicle primary brain vesicle secondary brain vesicle uberon brain vesicle UBERON:0013150 future brain vesicle EHDAA2 EHDAA2 One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions. NCIT:C32310 SCTID:244210009 UMLS:C0226164 artery of choroid plexus choroid artery uberon UBERON:0013151 choroidal artery One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions. ncithesaurus:Choroidal_Artery UMLS:C0226164 ncithesaurus:Choroidal_Artery EHDAA2:0000033 EMAPA:16384 endoderm of mandibular component uberon UBERON:0013156 1st arch mandibular endoderm EHDAA2 EHDAA2 EHDAA2 endoderm of mandibular component EMAPA:16384 A gland that is part of a foregut-midgut junction. EHDAA2:0000574 EMAPA:17065 gland of foregut-midgut junction uberon UBERON:0013158 foregut-midgut junction gland A gland that is part of a foregut-midgut junction. OBOL:automatic gland of foregut-midgut junction EMAPA:17065 EHDAA2:0000449 EHDAA:5435 EMAPA:17533 VHOG:0000913 mantle layer epithalamus mantle layer of epithalamus uberon UBERON:0013159 epithalamus mantle layer mantle layer epithalamus VHOG:0000913 EHDAA2:0000450 EHDAA:5437 EMAPA:17535 VHOG:0000884 ventricular layer epithalamus ventricular layer of epithalamus uberon UBERON:0013160 epithalamus ventricular layer ventricular layer epithalamus VHOG:0000884 A telencephalic ventricle that is in_the_left_side_of a telencephalon. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:78450 SCTID:368593005 left telencephalic ventricle uberon UBERON:0013161 left lateral ventricle FMA A telencephalic ventricle that is in_the_left_side_of a telencephalon. OBOL:automatic A telencephalic ventricle that is in_the_right_side_of a telencephalon. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:78449 SCTID:368571000 right telencephalic ventricle uberon UBERON:0013162 right lateral ventricle FMA A telencephalic ventricle that is in_the_right_side_of a telencephalon. OBOL:automatic The layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. EMAPA:37927 FMA:18613 NCIT:C33243 UMLS:C0227878 cortex of ovary cortex ovarii (zona parenchymatosa) uberon UBERON:0013191 ovarian cortex The layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. MGI:anna EMAPA:37927 MA:th UMLS:C0227878 ncithesaurus:Ovarian_Cortex cortex of ovary FMA:18613 cortex ovarii (zona parenchymatosa) FMA:18613 Highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. composed of loose connective tissue that contains blood vessels, lymph vessels and nerves EMAPA:37928 FMA:18616 NCIT:C33245 UMLS:C0227879 Wikipedia:Medulla_of_ovary medulla of ovary medulla ovarii (zona vasculosa) uberon zona vasculosa of Waldeyer UBERON:0013192 ovarian medulla Highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. MGI:anna composed of loose connective tissue that contains blood vessels, lymph vessels and nerves NCIT EMAPA:37928 MA:th UMLS:C0227879 ncithesaurus:Ovarian_Medulla medulla of ovary FMA:18616 medulla ovarii (zona vasculosa) FMA:18616 zona vasculosa of Waldeyer Wikipedia:Medulla_of_ovary The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. FMA:86279 acinus of serous gland uberon UBERON:0013232 serous acinus The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm uberon UBERON:0013238 future glans A future glans that is part of a male genital tubercle. EMAPA:29252 glans of male genital tubercle uberon UBERON:0013239 future glans penis EMAPA A future glans that is part of a male genital tubercle. OBOL:automatic A future glans that is part of a female genital tubercle. EMAPA:19170 glans of female genital tubercle uberon UBERON:0013240 future glans clitoris EMAPA A future glans that is part of a female genital tubercle. OBOL:automatic The precursor of the urethra. In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week SCTID:361531004 Wikipedia:Urethral_groove sulcus urethralis primarius urethral groove urethral sulcus uberon UBERON:0013241 embryonic urethral groove Wikipedia The precursor of the urethra. http://orcid.org/0000-0002-6601-2165 In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week Wikipedia:Urethral_groove sulcus urethralis primarius Wikipedia:Urethral_groove An epithelial tube that develops from a Mullerian duct in a male. Later degenerates. consider separating the duct from the degenerating portion, as in EMAPA EHDAA2:0001052 EMAPA:29161 EMAPA:35661 uberon degenerating mesonephric portion of male paramesonephric duct UBERON:0013247 male paramesonephric duct EHDAA2 EHDAA2 An epithelial tube that develops from a Mullerian duct in a male. Later degenerates. http://orcid.org/0000-0002-6601-2165 degenerating mesonephric portion of male paramesonephric duct EMAPA:29161 A diaphysis that is part of a fibula[Automatically generated definition]. The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula]. EMAPA:37892 FMA:33738 SCTID:302528006 Wikipedia:Body_of_fibula body of fibula corpus fibulae fibula diaphysis shaft of fibula uberon UBERON:0013279 diaphysis of fibula A diaphysis that is part of a fibula[Automatically generated definition]. OBOL:automatic Wikipedia:Body_of_fibula The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula]. Wikipedia:Body_of_fibula EMAPA:37892 MA:th body of fibula FMA:33738 corpus fibulae FMA:TA fibula diaphysis FMA:33738 shaft of fibula FMA:33738 A diaphysis that is part of a tibia. The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia]. EMAPA:37770 FMA:33125 MA:0003049 SCTID:302525009 Wikipedia:Body_of_tibia body of tibia corpus tibiae shaft of tibia tibial diaphysis uberon body of the tibia shaft of tibia UBERON:0013280 diaphysis of tibia A diaphysis that is part of a tibia. OBOL:automatic Wikipedia:Body_of_tibia The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia]. Wikipedia:Body_of_tibia EMAPA:37770 MA:th body of tibia FMA:33125 corpus tibiae FMA:TA shaft of tibia FMA:33125 tibial diaphysis FMA:33125 body of the tibia Wikipedia:Body_of_tibia shaft of tibia Wikipedia:Body_of_tibia Anatomical cavity that is the lumen of the skull and contains the brain. EMAPA:37497 FMA:9644 MA:0003061 NCIT:C77638 SCTID:264452006 UMLS:C0230041 Wikipedia:Cranial_cavity neuronames:2806 cavitas cranii uberon intracranial cavity intracranial space UBERON:0013411 cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg Wikipedia Anatomical cavity that is the lumen of the skull and contains the brain. UBERON:cjm EMAPA:37497 MA:th UMLS:C0230041 ncithesaurus:Cranial_Cavity cavitas cranii FMA:9644 FMA:TA intracranial cavity Wikipedia:Cranial_cavity intracranial space Wikipedia:Cranial_cavity The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. NCIT:C12253 SCTID:276801001 UMLS:C0227187 uberon proximal part of esophagus upper third of esophagus UBERON:0013472 upper esophagus The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. ncithesaurus:Upper_Third_of_the_Esophagus UMLS:C0227187 ncithesaurus:Upper_Third_of_the_Esophagus A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus. In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil SCTID:14239003 caecal tonsil uberon cecal GALT UBERON:0013478 cecal tonsil A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus. ISBN:0824754077 A blood vessel endothelium that is part of a lung [Automatically generated definition]. BTO:0004128 CALOHA:TS-0573 uberon respiratory endothelium UBERON:0013479 lung endothelium A blood vessel endothelium that is part of a lung [Automatically generated definition]. OBOL:automatic respiratory endothelium BTO:0004128 The panniculus adiposus is the fatty layer of the subcutaneous tissues, superficial to a deeper vestigial layer of muscle, the panniculus carnosus. An example is the Fascia of Camper. Another example is the superficial cervical fascia[WP]. It includes structures that are considered fascia by some sources but not by others. Consider merging with subcutaneous adipose tissue Wikipedia:Panniculus_adiposus panniculus adiposus group uberon subcutaneous fat UBERON:0013488 panniculus adiposus The panniculus adiposus is the fatty layer of the subcutaneous tissues, superficial to a deeper vestigial layer of muscle, the panniculus carnosus. An example is the Fascia of Camper. Another example is the superficial cervical fascia[WP]. Wikipedia:Panniculus_adiposus subcutaneous fat Wikipedia:Panniculus_adiposus A sphincter muscle that is part of a cloaca. NCIT:C34129 UMLS:C1516658 sphincter cloacae uberon UBERON:0013501 the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938). cloacal sphincter A sphincter muscle that is part of a cloaca. OBOL:automatic UMLS:C1516658 ncithesaurus:Cloacal_Sphincter sphincter cloacae A mesenchyme that is part of a pharyngeal arch 5. 5th pharyngeal arch mesenchyme uberon 5th branchial arch mesenchyme pharyngeal arch 5 mesenchyme UBERON:0013502 5th arch mesenchyme A mesenchyme that is part of a pharyngeal arch 5. OBOL:automatic 5th pharyngeal arch mesenchyme VHOG:0001052 A caudal vertebra endochondral element that is composed primarily of cartilage tissue. UBERON:0013517 EHDAA2:0000260 EMAPA:18044 coccygeal vertebra cartilage element coccygeal vertebral cartilage condensation group tail vertebral cartilage condensation uberon UBERON:0013503 caudal vertebra cartilage element A caudal vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic coccygeal vertebra cartilage element http://orcid.org/0000-0002-6601-2165 coccygeal vertebral cartilage condensation group EHDAA2:0000260 tail vertebral cartilage condensation EMAPA:18044 A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. UBERON:0013518 EMAPA:18045 coccygeal vertebra pre-cartilage condensation tail vertebral pre-cartilage condensation uberon UBERON:0013504 caudal vertebra pre-cartilage condensation A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic coccygeal vertebra pre-cartilage condensation http://orcid.org/0000-0002-6601-2165 tail vertebral pre-cartilage condensation EMAPA:18045 A cervical vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000240 cervical vertebral cartilage condensation group uberon UBERON:0013505 cervical vertebra cartilage element A cervical vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic cervical vertebral cartilage condensation group EHDAA2:0000240 A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013506 cervical vertebra pre-cartilage condensation A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0002014 thoracic vertebral cartilage condensation group uberon UBERON:0013507 thoracic vertebra cartilage element A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic thoracic vertebral cartilage condensation group EHDAA2:0002014 A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013508 thoracic vertebra pre-cartilage condensation A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A lumbar vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001038 lumbar vertebral cartilage condensation group uberon UBERON:0013509 lumbar vertebra cartilage element A lumbar vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic lumbar vertebral cartilage condensation group EHDAA2:0001038 A lumbar vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013510 lumbar vertebra pre-cartilage condensation A lumbar vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic The space that surrounds an organism. external to organism outside of body uberon UBERON:0013514 space surrounding organism The space that surrounds an organism. https://orcid.org/0000-0002-6601-2165 A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA:18302 subdivision of oviduct subdivision of uterine tube uterine tube zone zone of uterine tube subdivision of fallopian tube uberon UBERON:0013515 subdivision of oviduct A section through the tube or network of tubes that connects the ovaries to the outside of the body. http://orcid.org/0000-0002-6601-2165 FMA class may only represent the uterine portion FMA subdivision of oviduct FMA:18302 uterine tube zone FMA:18302 zone of uterine tube FMA:18302 subdivision of fallopian tube FMA:18302 uberon UBERON:0013522 subdivision of tube The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. EMAPA:18395 FMA:14585 cavity of stomach uberon gastric cavity UBERON:0013525 stomach lumen FMA The anatomical space that is enclosed by a stomach. http://orcid.org/0000-0002-6601-2165 Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. FMA:14585 cavity of stomach FMA:14585 gastric cavity FMA:14585 An anatomical cavity that is part of a ear vesicle. EHDAA2:0004121 EMAPA:25363 lumen of otocyst uberon UBERON:0013526 otocyst lumen EHDAA2 EHDAA2 EHDAA2 An anatomical cavity that is part of a ear vesicle. OBOL:automatic lumen of otocyst EMAPA:25363 A metapodium bone that is part of a digit 1 plus metapodial segment. metapodium 1 metapodium I uberon UBERON:0013581 metapodium bone 1 A metapodium bone that is part of a digit 1 plus metapodial segment. OBOL:automatic A metapodium bone that is part of a digit 5 plus metapodial segment. metapodium 5 metapodium V uberon UBERON:0013585 metapodium bone 5 A metapodium bone that is part of a digit 5 plus metapodial segment. OBOL:automatic Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand. TODO - make subclass links FMA:7475 NCIT:C33545 SCTID:332807009 Wikipedia:Short_bone uberon UBERON:0013630 short bone NCIT Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand. Wikipedia:Short_bone Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation. VSAO:0000137 sesamoid uberon UBERON:0013631 Sesamoids are often endochondral replacement elements and in addition to bone tissue, may also be composed of articular cartilage, fibrocartilage, hyaline cartilage, and calcified cartilage. sesamoid element VSAO VSAO Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation. PSPUB:0000169 VSAO:0000137 sesamoid VSAO:0000137 A sesamoid element that is composed primarily of cartilage tissue. FMA:55379 cartilago sesamoidea sesamoid cartilage of cricopharyngeal ligament uberon UBERON:0013632 sesamoid cartilage A sesamoid element that is composed primarily of cartilage tissue. OBOL:automatic cartilago sesamoidea FMA:55379 sesamoid cartilage of cricopharyngeal ligament FMA:55379 An epithelium that is part of a intestinal villus. FMA:63587 intestinal villus epithelium uberon villous epithelium villus epithelium UBERON:0013636 epithelium of intestinal villus FMA An epithelium that is part of a intestinal villus. OBOL:automatic intestinal villus epithelium FMA:63587 The prostate gland lobe that is located on the lateral side of the organ. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:29822 FMA:19577 MA:0003125 NCIT:C13092 lateral lobe of prostate lateral lobe of prostate gland uberon lateral prostate lateral ventral lobe of prostate gland UBERON:0013637 prostate gland lateral lobe The prostate gland lobe that is located on the lateral side of the organ. ncithesaurus:Lateral_Lobe_of_the_Prostate lateral lobe of prostate FMA:19577 lateral lobe of prostate gland FMA:19577 lateral ventral lobe of prostate gland MorphoBank:MorphoBank A gland that is part of the gular region (throat). uberon UBERON:0013645 gular gland A gland that is part of the gular region (throat). http://orcid.org/0000-0002-6601-2165 Anatomical space that is an opening in a bone of the skull. FMA:53165 SCTID:276742007 Wikipedia:Foramina_of_the_skull foramen of skull cranial conduit cranial foramen uberon foramina of the skull UBERON:0013685 foramen of skull Anatomical space that is an opening in a bone of the skull. TAO:curator http://orcid.org/0000-0002-6601-2165 foramen of skull Wikipedia:Foramina_of_the_skull cranial conduit FMA:53165 foramina of the skull Wikipedia:Foramina_of_the_skull 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 foramen space uberon UBERON:0013686 anatomical conduit space FMA An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 http://orcid.org/0000-0002-6601-2165 Lymphoid tissue located in the appendix. CALOHA:TS-1268 lymphatic tissue of appendix lymphatic tissue of vermiform appendix uberon appendix lymphoid UBERON:0013689 appendix lymphoid tissue Lymphoid tissue located in the appendix. CALOHA:TS-1268 lymphatic tissue of appendix OBOL:automatic lymphatic tissue of vermiform appendix OBOL:automatic appendix lymphoid CALOHA:TS-1268 Vascular endothelium found in blood vessels of the blood-brain-barrier. BTO:0001852 BTO:0003248 CALOHA:TS-0092 uberon cerebromicrovascular endothelium UBERON:0013694 brain endothelium Vascular endothelium found in blood vessels of the blood-brain-barrier. CALOHA:TS-0092 cerebromicrovascular endothelium CALOHA:TS-0092 Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 uberon colon endothelial cell colon endothelial cells colonic endothelial cell colonic endothelium colorectal endothelial cell colorectal endothelium UBERON:0013695 colon endothelium Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 colon endothelial cell CALOHA:TS-0162 colon endothelial cells CALOHA:TS-0162 colonic endothelial cell CALOHA:TS-0162 colonic endothelium CALOHA:TS-0162 colorectal endothelial cell CALOHA:TS-0162 colorectal endothelium CALOHA:TS-0162 The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule. CALOHA:TS-2070 uberon epithelium of tonsil tonsil epithelial cell UBERON:0013696 tonsil epithelium The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule. CALOHA:TS-2070 epithelium of tonsil CALOHA:TS-2070 tonsil epithelial cell CALOHA:TS-2070 Epithelium lining the exocrine pancreas. CALOHA:TS-2108 uberon epithelium of exocrine pancreas exocrine pancreas epithelial cell UBERON:0013697 exocrine pancreas epithelium Epithelium lining the exocrine pancreas. CALOHA:TS-2108 epithelium of exocrine pancreas CALOHA:TS-2108 exocrine pancreas epithelial cell CALOHA:TS-2108 A strand of hair that is part of a axilla. FMA:54253 SCTID:280911007 axilla hair axillary hair hair of axilla uberon UBERON:0013699 strand of axillary hair A strand of hair that is part of a axilla. OBOL:automatic axillary hair FMA:54253 hair of axilla FMA:54253 Musculature of the head and neck, spine, and ribs. EHDAA2:0000159 EMAPA:18166 uberon UBERON:0013700 axial musculature Musculature of the head and neck, spine, and ribs. HP:0003327 A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. uberon UBERON:0013701 main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. https://orcid.org/0000-0002-6601-2165 The region of the organism associated with the visceral organs. Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 EMAPA:36031 FMA:231424 uberon body whole body UBERON:0013702 body proper AEO The region of the organism associated with the visceral organs. AEO:0000103 Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. FMA:231424 body AEO:0000103 whole body BTO:0001489 Anatomical projection that is part of the integumentl system. skin projection uberon UBERON:0013703 integumentary projection Anatomical projection that is part of the integumentl system. http://orcid.org/0000-0002-6601-2165 A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. FMA:293127 NCIT:C34230 UMLS:C1518428 uberon chordal canal UBERON:0013704 notochordal canal A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. http://medical-dictionary.thefreedictionary.com/notochordal+canal UMLS:C1518428 ncithesaurus:Notochordal_Canal Fluid contained within the notochordal canal. notochord fluid portion of notochordal fluid uberon UBERON:0013727 Distinct feature of coelocanths notochordal fluid Fluid contained within the notochordal canal. http://animaldiversity.org/accounts/Latimeria_chalumnae/ http://orcid.org/0000-0002-6601-2165 A metaphysis that is part of a metaphysis. FMA:32830 diaphyseal end of humerus humeral metaphysis uberon UBERON:0013749 metaphysis of humerus A metaphysis that is part of a metaphysis. OBOL:automatic diaphyseal end of humerus FMA:32830 humeral metaphysis FMA:32830 A metaphysis that is part of a tibia. EMAPA:37772 FMA:33135 MA:0003106 tibial metaphysis uberon UBERON:0013750 metaphysis of tibia A metaphysis that is part of a tibia. OBOL:automatic EMAPA:37772 MA:th tibial metaphysis FMA:33135 A diaphysis that is part of a metacarpal bone. FMA:33804 body of metacarpal corpus ossis metacarpi metacarpal bone diaphysis shaft of metacarpal shaft of metacarpal bone uberon UBERON:0013752 diaphysis of metacarpal bone A diaphysis that is part of a metacarpal bone. OBOL:automatic body of metacarpal FMA:33804 corpus ossis metacarpi FMA:TA metacarpal bone diaphysis FMA:33804 shaft of metacarpal FMA:33804 shaft of metacarpal bone FMA:33804 An organ component layer that is part of a integumental system. SCTID:314820002 layer of skin skin layer uberon UBERON:0013754 integumentary system layer An organ component layer that is part of a integumental system. OBOL:automatic A blood that is part of a artery. BTO:0006188 FMA:83066 arterial blood blood in artery portion of arterial blood uberon UBERON:0013755 arterial blood A blood that is part of a artery. OBOL:automatic BTO:0006188 https://github.com/biopragmatics/biomappings arterial blood FMA:83066 blood in artery FMA:83066 portion of arterial blood FMA:83066 A blood that is part of a vein. BTO:0006187 FMA:83067 blood in vein portion of venous blood venous blood uberon UBERON:0013756 venous blood A blood that is part of a vein. OBOL:automatic BTO:0006187 https://github.com/biopragmatics/biomappings blood in vein FMA:83067 portion of venous blood FMA:83067 venous blood FMA:83067 A blood that is part of a capillary. FMA:263901 NCIT:C32212 blood in capillary portion of blood in capillary portion of capillary blood uberon UBERON:0013757 capillary blood A blood that is part of a capillary. OBOL:automatic portion of blood in capillary FMA:263901 One of two openings in the uterine cervix. FMA:20422 uberon cervical opening uterine cervix opening UBERON:0013758 cervical os One of two openings in the uterine cervix. http://orcid.org/0000-0002-6601-2165 Opening of uterine cervix into the body of the uterus. The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus]. FMA:17747 SCTID:279886007 Wikipedia:Internal_orifice_of_the_uterus uberon internal orifice internal os UBERON:0013759 internal cervical os https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb Opening of uterine cervix into the body of the uterus. http://orcid.org/0000-0002-6601-2165 The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus]. Wikipedia:Internal_orifice_of_the_uterus internal orifice Wikipedia:Internal_orifice_of_the_uterus internal os FMA:17747 Wikipedia:Internal_orifice_of_the_uterus Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. FMA:76836 NCIT:C32491 SCTID:362255005 UMLS:C1512165 Wikipedia:External_orifice_of_the_uterus external os of uterus ostium uteri uberon external os ostium of uterus UBERON:0013760 external cervical os https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb Opening of uterine cervix into the vagina. http://orcid.org/0000-0002-6601-2165 The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. Wikipedia:External_orifice_of_the_uterus UMLS:C1512165 ncithesaurus:Ectocervical_Os external os of uterus FMA:76836 ostium uteri FMA:TA external os Wikipedia:External_orifice_of_the_uterus ostium of uterus Wikipedia:External_orifice_of_the_uterus The cavity formed by the walls of the cervix. BTO:0002249 FMA:17746 Wikipedia:Canal_of_the_cervix lumen of cervix of uterus uberon canal of the cervix cavity of cervix cervical canal cervical canal of uterus endocervical endocervical canal endocervix UBERON:0013761 cervical cavity The cavity formed by the walls of the cervix. http://orcid.org/0000-0002-6601-2165 lumen of cervix of uterus FMA:17746 canal of the cervix Wikipedia:Canal_of_the_cervix cavity of cervix BTO:0002249 cervical canal Wikipedia:Canal_of_the_cervix cervical canal of uterus BTO:0002249 endocervical Wikipedia:Canal_of_the_cervix endocervical canal BTO:0002249 Wikipedia:Canal_of_the_cervix endocervix Wikipedia:Canal_of_the_cervix Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 SCTID:272627002 digestive organ digestive system organ uberon UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. http://orcid.org/0000-0002-6601-2165 EMAPA:37843 MA:th Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. great vessel EMAPA:36460 SCTID:304066000 Wikipedia:Great_vessels great vessel of thorax uberon UBERON:0013768 Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. Wikipedia:Great_vessels An organ cavity that is part of a uterus. EMAPA:36273 FMA:17745 Wikipedia:Uterine_cavity cavity of uterus uterine cavity uterine space uberon UBERON:0013769 uterine lumen An organ cavity that is part of a uterus. OBOL:automatic cavity of uterus FMA:17745 uterine cavity FMA:17745 A nipple that is in_the_left_side_of a body proper. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:223695 uberon UBERON:0013772 left nipple https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-l.glb A nipple that is in_the_left_side_of a body proper. OBOL:automatic A nipple that is in_the_right_side_of a body proper. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:223693 uberon UBERON:0013773 right nipple https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-r.glb A nipple that is in_the_right_side_of a body proper. OBOL:automatic A diaphysis that is part of a metatarsal bone. FMA:33826 diaphysis of metatarsal metatarsal bone diaphysis metatarsal diaphysis shaft of metatarsal bone uberon UBERON:0013774 diaphysis of metatarsal bone A diaphysis that is part of a metatarsal bone. OBOL:automatic metatarsal bone diaphysis FMA:33826 shaft of metatarsal bone FMA:33826 Embryonic structure that gives rise to the telencephalon. EHDAA2:0004424 EMAPA:36024 TAO:0000571 ZFA:0000571 presumptive telencephalon uberon UBERON:0014371 paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP] future telencephalon definitional Embryonic structure that gives rise to the telencephalon. ZFA:0000571 ZFA:curator presumptive telencephalon ZFA:0000571 A collection of hairs that is part of a craniocervical region. uberon UBERON:0014382 collection of hairs on head or neck A collection of hairs that is part of a craniocervical region. OBOL:automatic Mesenchyme that develops_from the neural crest[Automatically generated definition]. EMAPA:32735 FMA:293883 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon UBERON:0014387 mesenchyme derived from neural crest Mesenchyme that develops_from the neural crest[Automatically generated definition]. OBOL:automatic https://github.com/obophenotype/uberon/issues/248 The simple cuboidal epithelium lining the lumen of kidney collecting ducts. In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis EMAPA:37885 collecting duct of renal tubule epithelium epithelium of collecting duct of renal tubule epithelium of renal collecting tubule uberon UBERON:0014388 kidney collecting duct epithelium The simple cuboidal epithelium lining the lumen of kidney collecting ducts. MGI:anna MP:0011843 EMAPA:37885 MA:th A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae. FMA:54822 gustatory papilla taste papilla uberon gustatory papillae taste papillae UBERON:0014389 gustatory papilla of tongue A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae. MGI:smb MP:0006256 gustatory papillae taste papillae A muscular coat that is part of a ileum. BTO:0005574 FMA:14958 muscularis externa of ileum uberon ileal smooth muscle muscularis propria of ileum smooth muscle of ileum UBERON:0014390 muscle layer of ileum A muscular coat that is part of a ileum. OBOL:automatic muscularis externa of ileum FMA:14958 ileal smooth muscle https://orcid.org/0000-0002-6601-2165 muscularis propria of ileum https://orcid.org/0000-0002-6601-2165 smooth muscle of ileum https://orcid.org/0000-0002-6601-2165 Sweat that is produced by the glands of the axilla. FMA:63085 axillary sweat uberon UBERON:0014393 sweat of axilla Sweat that is produced by the glands of the axilla. http://orcid.org/0000-0002-6601-2165 axillary sweat FMA:63085 A proximal mesopodial endochondral element that is composed primarily of a bone tissue. uberon UBERON:0014395 proximal mesopodial bone A proximal mesopodial endochondral element that is composed primarily of a bone tissue. OBOL:automatic Muscle that is part of the respiratory system. this class may be merged with 'respiratory system muscle'; check intercostals MESH:D012132 uberon UBERON:0014398 respiratory muscle Muscle that is part of the respiratory system. http://orcid.org/0000-0002-6601-2165 MESH:D012132 https://github.com/biopragmatics/biomappings An anatomical space that is enclosed by a sinusoid. FMA:63133 lumen of sinusoid sinusoid lumen uberon UBERON:0014399 sinusoidal space An anatomical space that is enclosed by a sinusoid. OBOL:automatic lumen of sinusoid FMA:63133 sinusoid lumen FMA:63133 A sinusoidal space that is part of a hepatic sinusoid. FMA:262090 lumen of hepatic sinusoid uberon UBERON:0014400 hepatic sinusoidal space A sinusoidal space that is part of a hepatic sinusoid. OBOL:automatic lumen of hepatic sinusoid FMA:262090 Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta EMAPA:31450 MA:0002591 kidney venous blood vessel venous blood vessel of kidney uberon kidney venous system UBERON:0014401 renal venous blood vessel Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. MGI:csmith we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta MA kidney venous blood vessel MA:0002591 kidney venous system EMAPA:31450 A taste bud that is located on the tongue, situated on a gustatory papilla. gustatory papilla taste bud gustatory papillae taste bud uberon UBERON:0014451 tongue taste bud A taste bud that is located on the tongue, situated on a gustatory papilla. http://orcid.org/0000-0002-6601-2165 gustatory papillae taste bud MP:0006260 A gustatory epithelium that is part of a tongue. BIRNLEX:4099 UMLS:C1179150 lingual gustatory epithelium uberon UBERON:0014452 gustatory epithelium of tongue A gustatory epithelium that is part of a tongue. OBOL:automatic UMLS:C1179150 BIRNLEX:4099 lingual gustatory epithelium http://orcid.org/0000-0002-6601-2165 A gustatory epithelium that is part of a roof of mouth. palatal gustatory epithelium uberon UBERON:0014453 gustatory epithelium of palate A gustatory epithelium that is part of a roof of mouth. OBOL:automatic palatal gustatory epithelium http://orcid.org/0000-0002-6601-2165 Subcutaneous adipose tissue that is located in the peritoneal cavity. Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 CALOHA:TS-2405 uberon abdominal fat intra-abdominal adipose tissue intra-abdominal fat organ fat visceral adipose tissue visceral fat UBERON:0014454 visceral abdominal adipose tissue Subcutaneous adipose tissue that is located in the peritoneal cavity. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 organ fat BTO:0004041 visceral adipose tissue BTO:0004041 visceral fat BTO:0004041 Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:TS-2406 abdominal subcutaneous adipose tissue subcutaneous abdominal fat subcutaneous fat of abdominal region uberon UBERON:0014455 subcutaneous abdominal adipose tissue Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery. Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion]. EMAPA:36644 FMA:77582 SCTID:57098005 Wrisberg ganglion cardiac ganglia set cardiac ganglion of Wrisberg ganglia cardiaca ganglion of Wrisberg uberon cardiac ganglia UBERON:0014463 cardiac ganglion Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery. ISBN:0-683-40008-8 MP:0003685 Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion]. http://medical-dictionary.thefreedictionary.com/cardiac+ganglion Wrisberg ganglion MP:0003685 cardiac ganglia set FMA:77582 ganglia cardiaca FMA:TA ganglion of Wrisberg FMA:77582 cardiac ganglia FMA:75136 uberon UBERON:0014466 subarachnoid fissure Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. EHDAA2:0002013 FMA:77169 Wikipedia:Thoracic_skeleton skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon UBERON:0014477 thoracic skeleton Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. Wikipedia:Rib_cage https://orcid.org/0000-0002-6601-2165 thoracic skeleton EHDAA2:0002013 Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage. FMA:265719 TAO:0002100 rib series uberon rib skeleton set of all ribs UBERON:0014478 rib skeletal system Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage. https://orcid.org/0000-0002-6601-2165 Wikipedia rib series TAO:0002100 set of all ribs FMA:265719 A distal phalanx that is part of a digit 1 [Automatically generated definition]. digit 1 distal phalanx distal phalanx of digit I distal phalanx of first digit uberon digit I P3 first distal phalanx UBERON:0014483 distal phalanx of digit 1 A distal phalanx that is part of a digit 1 [Automatically generated definition]. http://orcid.org/0000-0002-6601-2165 digit 1 distal phalanx PHENOSCAPE:wd distal phalanx of digit I https://github.com/obophenotype/uberon/issues/458 A distal phalanx that is part of a digit 5 [Automatically generated definition]. 5th digit distal phalanx digit 5 distal phalanx distal phalanx of 5th digit distal phalanx of digit V distal phalanx of fifth digit distal phalanx of little digit fifth digit distal phalanx fifth distal phalanx uberon digit V P3 UBERON:0014487 distal phalanx of digit 5 A distal phalanx that is part of a digit 5 [Automatically generated definition]. http://orcid.org/0000-0002-6601-2165 digit 5 distal phalanx PHENOSCAPE:wd distal phalanx of digit V https://github.com/obophenotype/uberon/issues/458 A middle phalanx that is part of a digit 5 [Automatically generated definition]. 5th digit intermediate phalanx 5th digit middle phalanx 5th digit of intermediate phalanx 5th digit of middle phalanx digit 5 intermediate phalanx digit 5 middle phalanx fifth digit intermediate phalanx fifth digit middle phalanx fifth middle phalanx intermediate phalanx of 5th digit intermediate phalanx of digit 5 intermediate phalanx of fifth digit middle phalanx of 5th digit middle phalanx of digit V middle phalanx of fifth digit middle phalanx of little digit uberon digit V P2 UBERON:0014491 middle phalanx of digit 5 A middle phalanx that is part of a digit 5 [Automatically generated definition]. http://orcid.org/0000-0002-6601-2165 middle phalanx of digit V https://github.com/obophenotype/uberon/issues/458 A proximal phalanx that is part of a autopod digit 1 [Automatically generated definition]. digit I P1 digit I-1 first proximal phalanx of autopod proximal phalanx of digit I proximal phalanx of first digit of autopod uberon UBERON:0014501 proximal phalanx of digit 1 A proximal phalanx that is part of a autopod digit 1 [Automatically generated definition]. http://orcid.org/0000-0002-6601-2165 digit I-1 PHENOSCAPE:wd proximal phalanx of digit I https://github.com/obophenotype/uberon/issues/458 A proximal phalanx that is part of a autopod digit 5 [Automatically generated definition]. 5th digit of autopod proximal phalanx 5th digit proximal phalanx autopod digit 5 proximal phalanx digit V P1 digit V-1 fifth digit proximal phalanx fifth proximal phalanx of autopod proximal phalanx of 5th digit proximal phalanx of 5th digit of autopod proximal phalanx of digit V proximal phalanx of fifth digit proximal phalanx of fifth digit of autopod proximal phalanx of little digit uberon UBERON:0014505 proximal phalanx of digit 5 A proximal phalanx that is part of a autopod digit 5 [Automatically generated definition]. http://orcid.org/0000-0002-6601-2165 digit V-1 PHENOSCAPE:wd proximal phalanx of digit V https://github.com/obophenotype/uberon/issues/458 A gray matter of spinal cord that is part of a cervical spinal cord. BIRNLEX:1521 SCTID:362438009 UMLS:C0228610 cervical spinal cord gray matter uberon UBERON:0014613 cervical spinal cord gray matter A gray matter of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228610 BIRNLEX:1521 cervical spinal cord gray matter BIRNLEX:1521 A gray matter of spinal cord that is part of a thoracic spinal cord. BIRNLEX:980 SCTID:362441000 UMLS:C0228627 thoracic spinal cord gray matter uberon UBERON:0014636 thoracic spinal cord gray matter A gray matter of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228627 BIRNLEX:980 thoracic spinal cord gray matter BIRNLEX:980 FMA:35343 SCTID:361858004 distal interphalangeal joint of little finger distal interphalangeal joint of manural digit V uberon UBERON:0014671 distal interphalangeal joint of manural digit 5 distal interphalangeal joint of little finger FMA:35343 distal interphalangeal joint of manural digit V https://github.com/obophenotype/uberon/issues/458 FMA:35393 SCTID:361884005 distal interphalangeal joint of fifth digit of foot distal interphalangeal joint of fifth toe distal interphalangeal joint of little toe distal interphalangeal joint of pedal digit V uberon UBERON:0014675 distal interphalangeal joint of pedal digit 5 distal interphalangeal joint of fifth digit of foot FMA:35393 distal interphalangeal joint of fifth toe FMA:35393 distal interphalangeal joint of little toe FMA:35393 distal interphalangeal joint of pedal digit V https://github.com/obophenotype/uberon/issues/458 A distal interphalangeal joint that is part of a digit 5. NCIT:C102294 distal interphalangeal joint of digit V uberon distal interphalangeal joint 5 UBERON:0014680 distal interphalangeal joint of digit 5 A distal interphalangeal joint that is part of a digit 5. OBOL:automatic distal interphalangeal joint of digit V https://github.com/obophenotype/uberon/issues/458 The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint. FMA:49689 SCTID:147157007 Wikipedia:Deep_auricular_artery uberon UBERON:0014695 deep auricular artery FMA The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint. Wikipedia:Deep_auricular_artery A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component. EHDAA2:0000479 EMAPA:16374 VHOG:0000282 uberon UBERON:0014699 extraembryonic venous system VHOG A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component. OBOL:automatic A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component. EHDAA2:0000478 EMAPA:16370 VHOG:0001396 uberon UBERON:0014701 extraembryonic vascular system A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component. OBOL:automatic An epithelium that is part of a frontonasal prominence. EHDAA2:0004108 EMAPA:32918 uberon UBERON:0014702 frontonasal process epithelium EHDAA2 EHDAA2 An epithelium that is part of a frontonasal prominence. OBOL:automatic A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. EHDAA2:0004019 EMAPA:25040 uberon UBERON:0014703 anal membrane ectodermal component A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. OBOL:automatic An anatomical space that is enclosed by a pleuroperitoneal canal. EHDAA2:0004736 EMAPA:25034 pleuro-peritoneal canal cavity uberon UBERON:0014704 pleuroperitoneal canal lumen EHDAA2 An anatomical space that is enclosed by a pleuroperitoneal canal. OBOL:automatic pleuro-peritoneal canal cavity EMAPA:25034 An epithelium that is part of a median lingual swelling. EHDAA2:0001085 EMAPA:17188 uberon tuberculum impar epitheilium UBERON:0014705 median lingual swelling epithelium EHDAA2 EHDAA2 An epithelium that is part of a median lingual swelling. OBOL:automatic tuberculum impar epitheilium EMAPA:17188 EHDAA2:0001147 EMAPA:17646 metanephros primitive collecting ducts primitive collecting duct uberon UBERON:0014706 primitive renal collecting duct system EHDAA2 EHDAA2 metanephros primitive collecting ducts EHDAA2:0001147 primitive collecting duct EMAPA:17646 A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. NCIT:C32828 UMLS:C1512857 Wikipedia:Interlobular_ducts uberon UBERON:0014716 interlobular duct A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. ncithesaurus:Interlobular_Duct The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. FMA:86278 acinus of mucuous gland mucus acinus uberon UBERON:0014717 mucous acinus The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular. SCTID:205214009 uberon intralobular ductule UBERON:0014719 intralobular duct A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular. http://www.siumed.edu/~dking2/intro/glands.htm A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory. uberon intralobular ductule UBERON:0014720 interlobar duct A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory. http://www.siumed.edu/~dking2/intro/glands.htm The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. EHDAA2:0000597 EMAPA:17703 SCTID:244668003 VHOG:0001546 Wikipedia:Crus_of_diaphragm crural diaphragm uberon crura of the diaphragm crus of the diaphragm diaphragm crura diaphragmatic crura UBERON:0014765 Classification notes: May be considered an external sphincter[PMID:8224664] crus of diaphragm PMID:23586979 PMID:23586979 The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. PMID:23586979 crural diaphragm PMID:23586979 crura of the diaphragm Wikipedia:Crus_of_diaphragm crus of the diaphragm Wikipedia:Crus_of_diaphragm diaphragm crura diaphragmatic crura Wikipedia:Crus_of_diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58286 SCTID:362690009 crus dextrum (Diaphragma) crus dextrum diaphragmatis external sphincter of esophagus right crus of diaphragm right crus of lumbar part of diaphragm uberon UBERON:0014766 right crus of diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. OBOL:automatic crus dextrum (Diaphragma) FMA:58286 FMA:TA crus dextrum diaphragmatis FMA:58286 FMA:TA external sphincter of esophagus FMA:58286 right crus of diaphragm FMA:58286 right crus of lumbar part of diaphragm FMA:58286 A crus of diaphragm that is in_the_left_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58287 SCTID:244937004 crus sinistrum (Diaphragma) crus sinistrum diaphragmatis left crus of diaphragm left crus of lumbar part of diaphragm uberon UBERON:0014767 left crus of diaphragm A crus of diaphragm that is in_the_left_side_of a diaphragm. OBOL:automatic crus sinistrum (Diaphragma) FMA:58287 FMA:TA crus sinistrum diaphragmatis FMA:58287 FMA:TA left crus of diaphragm FMA:58287 left crus of lumbar part of diaphragm FMA:58287 A neuromere that is part of the presumptive forebrain. forebrain segment segment of forebrain FMA:61996 forebrain neuromere uberon future prosencephalon UBERON:0014775 prosomere A neuromere that is part of the presumptive forebrain. http://orcid.org/0000-0002-6601-2165 A neuromere that is part of the presumptive midbrain. mesomere midbrain segment segment of midbrain EHDAA2:0004352 FMA:61997 mesomere of nervous system neuromere of mesomere group uberon future mesencephalon mesomere group UBERON:0014776 midbrain neuromere A neuromere that is part of the presumptive midbrain. http://orcid.org/0000-0002-6601-2165 mesomere group EHDAA2:0004352 A neuromere that is part of the presumptive spinal cord. TAO:0001332 ZFA:0001332 spinal cord metameric segment spinal neuromeres uberon spinal cord segment UBERON:0014777 spinal neuromere A neuromere that is part of the presumptive spinal cord. http://orcid.org/0000-0002-6601-2165 spinal neuromeres TAO:0001332 spinal cord segment TAO:0001332 Any muscle organ that is part of a cloaca. uberon UBERON:0014783 cloacal muscle Any muscle organ that is part of a cloaca. OBOL:automatic The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ. EMAPA:18274 FMA:54813 SCTID:368727001 Wikipedia:Lingual_septum septum of tongue uberon median fibrous septum septum of tongue tongue septum UBERON:0014790 lingual septum The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ. Wikipedia:Lingual_septum septum of tongue FMA:54813 median fibrous septum Wikipedia:Lingual_septum septum of tongue Wikipedia:Lingual_septum tongue septum Wikipedia:Lingual_septum Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition]. FMA:50202 uberon arm musculature muscle group of arm musculature of arm set of muscles of arm UBERON:0014791 musculature of forelimb stylopod Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition]. OBOL:automatic arm musculature FMA:50202 muscle group of arm FMA:50202 musculature of arm FMA:50202 set of muscles of arm FMA:50202 Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37864 FMA:71297 muscles of lower limb musculature of lower limb musculi membri inferioris uberon UBERON:0014792 musculature of pelvic complex Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. OBOL:automatic EMAPA:37864 MA:th muscles of lower limb FMA:71297 musculature of lower limb FMA:71297 musculi membri inferioris FMA:TA Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37861 FMA:71296 muscles of upper limb musculature of upper limb musculi membri superioris set of muscles of upper limb upper limb musculature uberon UBERON:0014793 musculature of pectoral complex Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. OBOL:automatic EMAPA:37861 MA:th muscles of upper limb FMA:71296 musculature of upper limb FMA:71296 musculi membri superioris FMA:TA set of muscles of upper limb FMA:71296 upper limb musculature FMA:71296 Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon UBERON:0014794 pectoral appendage muscle prolog Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). OBOL:automatic Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle prolog Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). OBOL:automatic Chorda tendinea which is attached to the leaflet of mitral valve and is continuous with the endocardium of papillary muscle of left ventricle. FMA:9349 uberon UBERON:0014851 chorda tendinea of left ventricle Chorda tendinea which is attached to the leaflet of mitral valve and is continuous with the endocardium of papillary muscle of left ventricle. FMA:9349 Chorda tendinea which is attached to the leaflet of tricuspid valve and is continuous with the endocardium of papillary muscle of right ventricle. FMA:9300 uberon UBERON:0014852 chorda tendinea of right ventricle Chorda tendinea which is attached to the leaflet of tricuspid valve and is continuous with the endocardium of papillary muscle of right ventricle. FMA:9300 A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle AAO:0011099 BTO:0001103 CALOHA:TS-0933 EFO:0000888 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EMAPA:35988 EV:0100377 GAID:141 MA:0003148 MAT:0000302 MESH:D018482 MIAA:0000302 TAO:0005277 VHOG:0000319 XAO:0000174 ZFA:0005277 uberon UBERON:0014892 skeletal muscle organ, vertebrate A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). GOC:dos A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 ZFA:0005076 uberon UBERON:0014903 primordial vasculature A portion of tissue that will develop into vasculature. ZFA:0005076 ZFA:curator One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. EFO:0003664 EMAPA:37389 TAO:0001285 XAO:0004075 ZFA:0001285 intersegmental vessel intersegmental vessels intersomitic blood vessel intersomitic vessels segmental vessel uberon UBERON:0014907 intersomitic vessel ZFA ZFA One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. MGI:anna Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. ZFA:0001285, ZFIN:ZDB-PUB-030908-4 EMAPA:37389 MA:th intersegmental vessel ZFA:0001285 intersegmental vessels ZFA:0001285 intersomitic blood vessel XAO:0004075 intersomitic vessels ZFA:0001285 segmental vessel ZFA:0001285 The space between a blood vessel and the pia mater. VRS NCIT:C83196 SCTID:342298001 UMLS:C0225983 Wikipedia:Virchow-Robin_space Virchow-Robin space perivascular region uberon perivascular spaces UBERON:0014930 VRS belonging to the subarachnoid space are continuous with VRS of the subpial space. The direct communication between VRS of the subarachnoid space and the subpial space is unique to the brain's arteries, as no leptomeningeal layers surround the brain's veins[WP] perivascular space https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif The space between a blood vessel and the pia mater. DOI:10.1007/s11064-015-1581-6 ncithesaurus:Perivascular_Space VRS Wikipedia:Virchow-Robin_space Virchow-Robin space Wikipedia:Virchow-Robin_space perivascular spaces these layers primarily refer to the mammalian future neocortex uberon UBERON:0014950 layer of developing cerebral cortex EMAPA The major preaxial endochondral element in the posterior zeugopod[Phenoscape]. tibia skeletal element tibia element uberon UBERON:0015004 tibia endochondral element The major preaxial endochondral element in the posterior zeugopod[Phenoscape]. PHENOSCAPE:mah https://github.com/obophenotype/uberon/issues/71 tibia skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern tibia element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A vertebral endochondral element in the cervical region of the vertebral column. cervical vertebra skeletal element cervical vertebra element uberon UBERON:0015007 cervical vertebra endochondral element A vertebral endochondral element in the cervical region of the vertebral column. http://orcid.org/0000-0002-6601-2165 cervical vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern cervical vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A vertebral endochondral element in the thoracic region of the vertebral column. thoracic vertebra skeletal element thoracic vertebra element uberon UBERON:0015008 thoracic vertebra endochondral element A vertebral endochondral element in the thoracic region of the vertebral column. http://orcid.org/0000-0002-6601-2165 thoracic vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern thoracic vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A lumbar vertebra bone or its cartilage or pre-cartilage precursor. lumbar vertebra skeletal element lumbar vertebra element uberon UBERON:0015009 lumbar vertebra endochondral element A lumbar vertebra bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern lumbar vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern lumbar vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A vertebra endochondral element that is part of the sacral region of the vertebral column. sacral vertebra skeletal element sacral vertebra element uberon UBERON:0015010 sacral vertebra endochondral element A vertebra endochondral element that is part of the sacral region of the vertebral column. http://orcid.org/0000-0002-6601-2165 sacral vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern sacral vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern The major postaxial endochondral element in the posterior zeugopod[Phenoscape]. fibula skeletal element fibula element uberon UBERON:0015013 fibula endochondral element The major postaxial endochondral element in the posterior zeugopod[Phenoscape]. PHENOSCAPE:mah https://github.com/obophenotype/uberon/issues/73 fibula skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern fibula element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A rib bone or its cartilage or pre-cartilage precursor. Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals. rib skeletal element rib element uberon UBERON:0015019 rib endochondral element A rib bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern rib skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern rib element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A forelimb bone or its cartilage or pre-cartilage precursor. forelimb skeletal element uberon UBERON:0015021 forelimb endochondral element A forelimb bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern forelimb skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb bone skeletal element uberon UBERON:0015022 hindlimb endochondral element A hindlimb bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern hindlimb bone skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A phalanx bone or its cartilage or pre-cartilage precursor. phalanx skeletal element phalanx element uberon UBERON:0015023 phalanx endochondral element A phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A manual digit phalanx bone or its cartilage or pre-cartilage precursor. manual digit phalanx skeletal element manual digit phalanx element uberon UBERON:0015024 manual digit phalanx endochondral element A manual digit phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A manual digit 1 phalanx bone or its cartilage or pre-cartilage precursor. manual digit 1 phalanx skeletal element manual digit 1 phalanx element manual digit I phalanx endochondral element uberon UBERON:0015025 manual digit 1 phalanx endochondral element A manual digit 1 phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 1 phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 1 phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit I phalanx endochondral element https://github.com/obophenotype/uberon/issues/458 A manual digit 5 phalanx bone or its cartilage or pre-cartilage precursor. manual digit 5 phalanx skeletal element manual digit 5 phalanx element manual digit V phalanx endochondral element uberon UBERON:0015029 manual digit 5 phalanx endochondral element A manual digit 5 phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 5 phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 5 phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit V phalanx endochondral element https://github.com/obophenotype/uberon/issues/458 A pedal digit phalanx bone or its cartilage or pre-cartilage precursor. pedal digit phalanx skeletal element pedal digit phalanx element uberon UBERON:0015030 pedal digit phalanx endochondral element A pedal digit phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A pedal digit 1 phalanx bone or its cartilage or pre-cartilage precursor. pedal digit 1 phalanx skeletal element pedal digit 1 phalanx element pedal digit I phalanx endochondral element uberon UBERON:0015031 pedal digit 1 phalanx endochondral element A pedal digit 1 phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 1 phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 1 phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit I phalanx endochondral element https://github.com/obophenotype/uberon/issues/458 A pedal digit 5 phalanx bone or its cartilage or pre-cartilage precursor. pedal digit 5 phalanx skeletal element pedal digit 5 phalanx element pedal digit V phalanx endochondral element uberon UBERON:0015035 pedal digit 5 phalanx endochondral element A pedal digit 5 phalanx bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 5 phalanx skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 5 phalanx element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit V phalanx endochondral element https://github.com/obophenotype/uberon/issues/458 A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit metatarsal skeletal element pedal digit metatarsal element uberon UBERON:0015036 pedal digit metatarsal endochondral element A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit metatarsal skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit metatarsal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A pedal digit 1 metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit 1 metatarsal skeletal element pedal digit 1 metatarsal element pedal digit I metatarsal endochondral element uberon UBERON:0015037 pedal digit 1 metatarsal endochondral element A pedal digit 1 metatarsal bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 1 metatarsal skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 1 metatarsal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit I metatarsal endochondral element https://github.com/obophenotype/uberon/issues/458 A pedal digit 5 metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit 5 metatarsal skeletal element pedal digit 5 metatarsal element pedal digit V metatarsal endochondral element uberon UBERON:0015041 pedal digit 5 metatarsal endochondral element A pedal digit 5 metatarsal bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 5 metatarsal skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit 5 metatarsal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pedal digit V metatarsal endochondral element https://github.com/obophenotype/uberon/issues/458 A manual digit metacarpus bone or its cartilage or pre-cartilage precursor. manual digit metacarpus skeletal element manual digit metacarpus element uberon UBERON:0015042 manual digit metacarpus endochondral element A manual digit metacarpus bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit metacarpus skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit metacarpus element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A manual digit 1 metacarpus bone or its cartilage or pre-cartilage precursor. manual digit 1 metacarpus skeletal element manual digit 1 metacarpus element manual digit I metacarpus endochondral element uberon UBERON:0015043 manual digit 1 metacarpus endochondral element A manual digit 1 metacarpus bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 1 metacarpus skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 1 metacarpus element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit I metacarpus endochondral element https://github.com/obophenotype/uberon/issues/458 A manual digit 5 metacarpus bone or its cartilage or pre-cartilage precursor. manual digit 5 metacarpus skeletal element manual digit 5 metacarpus element manual digit V metacarpus endochondral element uberon UBERON:0015047 manual digit 5 metacarpus endochondral element A manual digit 5 metacarpus bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 5 metacarpus skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit 5 metacarpus element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern manual digit V metacarpus endochondral element https://github.com/obophenotype/uberon/issues/458 A carpus bone or its cartilage or pre-cartilage precursor. carpus skeletal element carpus element uberon UBERON:0015049 carpus endochondral element A carpus bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern carpus skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern carpus element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A tarsus bone or its cartilage or pre-cartilage precursor. tarsus skeletal element tarsus element uberon UBERON:0015050 tarsus endochondral element A tarsus bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern tarsus skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern tarsus element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A femur bone or its cartilage or pre-cartilage precursor. femur skeletal element femur element uberon UBERON:0015052 femur endochondral element A femur bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern femur skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern femur element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A humerus bone or its cartilage or pre-cartilage precursor. humerus skeletal element humerus element uberon UBERON:0015053 humerus endochondral element A humerus bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern humerus skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern humerus element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern An iliac bone or its cartilage or pre-cartilage precursor. iliac skeletal element iliac element uberon UBERON:0015054 iliac endochondral element An iliac bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern iliac skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern iliac element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A pubic bone or its cartilage or pre-cartilage precursor. pubic skeletal element pubic element uberon UBERON:0015055 pubic endochondral element A pubic bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pubic skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern pubic element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern An ischial bone or its cartilage or pre-cartilage precursor. ischial skeletal element ischial element uberon UBERON:0015056 ischial endochondral element An ischial bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern ischial skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern ischial element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A scapula bone or its cartilage or pre-cartilage precursor. scapula skeletal element scapula element uberon UBERON:0015057 scapula endochondral element A scapula bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern scapula skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern scapula element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A sphenoid bone or its cartilage or pre-cartilage precursor. sphenoid bone skeletal element sphenoid element uberon UBERON:0015060 sphenoid endochondral element A sphenoid bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern sphenoid bone skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern sphenoid element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A limb bone or its cartilage or pre-cartilage precursor. limb bone skeletal element limb bone endochondral element uberon UBERON:0015061 limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern limb bone skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern limb bone endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern An endochondral element that is part of a autopod region. uberon UBERON:0015063 autopod endochondral element cjm An endochondral element that is part of a autopod region. OBOL:automatic An autopod endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0015064 autopod cartilage An autopod endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A proximal mesopodial endochondral element that is part of a forelimb. proximal carpal element uberon proximal carpal UBERON:0015078 proximal carpal endochondral element A proximal mesopodial endochondral element that is part of a forelimb. OBOL:automatic proximal carpal element UBERON:cjm proximal carpal UBERON:cjm A proximal carpal endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0015079 proximal carpal cartilage A proximal carpal endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0015080 proximal carpal bone pre-cartilage condensation A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A proximal mesopodial endochondral element that is part of a hindlimb. uberon proximal tarsal UBERON:0015081 proximal tarsal endochondral element A proximal mesopodial endochondral element that is part of a hindlimb. OBOL:automatic proximal tarsal UBERON:cjm A proximal tarsal endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0015082 proximal tarsal cartilage A proximal tarsal endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0015083 proximal tarsal bone pre-cartilage condensation A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic consider merging into myocardial compact layer FMA:83105 perimysial connective tissue of subepicardium subepicardial connective tissue uberon UBERON:0015128 subepicardial layer of epicardium FMA perimysial connective tissue of subepicardium FMA:83105 subepicardial connective tissue FMA:83105 Visceral intrapericardial fat contiguous with the myocardial surface. FMA:9871 SCTID:42267001 epicardial adipose tissue pericardial adipose tissue uberon UBERON:0015129 epicardial fat Visceral intrapericardial fat contiguous with the myocardial surface. DOI:10.5935/abc.20130138 A portion of connective tissue that is part of a prostate gland. FMA:74165 connective tissue of prostate uberon UBERON:0015130 connective tissue of prostate gland FMA A portion of connective tissue that is part of a prostate gland. OBOL:automatic connective tissue of prostate FMA:74165 A strand of hair that is part of a autopod region. hair of hand/foot hand/foot hair paw hair uberon UBERON:0015144 autopod hair A strand of hair that is part of a autopod region. OBOL:automatic A strand of hair that is part of a pes. foot hair hair of foot hind foot hair hind paw hair uberon UBERON:0015145 pes hair A strand of hair that is part of a pes. OBOL:automatic A strand of hair that is part of a manus. hair of hand hand hair front paw hair uberon UBERON:0015146 manus hair A strand of hair that is part of a manus. OBOL:automatic A strand of hair that is part of a pinna. uberon ear hair UBERON:0015147 pinna hair A strand of hair that is part of a pinna. OBOL:automatic A strand of hair that is part of a tail. EMAPA:37971 uberon UBERON:0015148 tail hair A strand of hair that is part of a tail. OBOL:automatic EMAPA:37971 MA:th A strand of hair that is part of a dorsum. FMA:54320 uberon back hair dorsal coat hair hair of back UBERON:0015150 dorsal hair A strand of hair that is part of a dorsum. OBOL:automatic hair of back FMA:54320 A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] ocular gland uberon orbital gland UBERON:0015152 gland of ocular region inferred A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/614 A gland that is located in or around the ocular region, nearer the outer canthi. The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104 lateral ocular gland lateral orbital gland uberon UBERON:0015154 lateral gland of orbital region A gland that is located in or around the ocular region, nearer the outer canthi. http://orcid.org/0000-0002-6601-2165 An eye consisting of multiple light-sensing organs. uberon UBERON:0015165 multi-unit eye An eye consisting of multiple light-sensing organs. PMID:21062451 http://orcid.org/0000-0002-6601-2165 present on tentacular crown PMID:21062451 present on mantle edge in arcacean Bivalvia PMID:21062451 The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species PMID:21062451 A blood vessel that is part of a endometrium. SCTID:254200009 blood vessel of endometrium uberon UBERON:0015172 endometrial blood vessel A blood vessel that is part of a endometrium. OBOL:automatic A region of somite adjacent to presomitic mesoderm. TAO:0001462 XAO:0004074 ZFA:0001462 uberon inter-somited border intersomitic boundary intersomitic fissure intersomitic junction segmental border somite boundary UBERON:0015178 somite border A region of somite adjacent to presomitic mesoderm. http://orcid.org/0000-0002-6601-2165 intersomitic junction XAO:0004074 somite boundary ZFA:0001462 Epithelium located in the intersomitic region. XAO:0004077 intersomitic epithelium intersomitic membrane uberon UBERON:0015179 somite boundary epithelium Epithelium located in the intersomitic region. XAO:0004077 XAO:EJS intersomitic epithelium XAO:0004077 intersomitic membrane XAO:0004077 The slightly constricted part of a tooth, between the crown and the root. FMA:55627 NCIT:C32346 SCTID:28638008 cervix dentis cervix of tooth collumn dentis dental neck tooth neck uberon cervical margin of tooth cervical zone of tooth UBERON:0015181 neck of tooth The slightly constricted part of a tooth, between the crown and the root. http://www.medilexicon.com/medicaldictionary.php?s=neck+of+tooth cervix dentis FMA:TA cervix of tooth FMA:55627 collumn dentis ncithesaurus:Collum_Dentis dental neck http://www.medilexicon.com/medicaldictionary.php?s=neck+of+tooth tooth neck FMA:55627 cervical margin of tooth http://www.medilexicon.com/medicaldictionary.php?s=neck+of+tooth cervical zone of tooth http://www.medilexicon.com/medicaldictionary.php?s=neck+of+tooth An anatomical group whose component structures share a common function. AEO:0000093 FBbt:00007278 uberon UBERON:0015203 non-connected functional system An anatomical group whose component structures share a common function. AEO:0000093 AEO:JB FBC:DOS FBbt:00007278 FBbt:00007278 A non-connected functional system that is composed primarily of a gland. EHDAA2:0002223 uberon UBERON:0015204 glandular system A non-connected functional system that is composed primarily of a gland. OBOL:automatic Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. http://orcid.org/0000-0002-6601-2165 A ligament that is part of a diaphragm. EMAPA:19236 FMA:58280 uberon UBERON:0015214 arcuate ligament A ligament that is part of a diaphragm. OBOL:automatic A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel uberon cardiac structure UBERON:0015228 circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. http://orcid.org/0000-0002-6601-2165 A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals. TAO:0001359 ZFA:0001359 uberon UBERON:0015238 pineal complex ZFA A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals. http://orcid.org/0000-0002-6601-2165 A zone of skin that is part of a digit [Automatically generated definition]. EMAPA:32615 MA:0003011 uberon UBERON:0015249 digit skin A zone of skin that is part of a digit [Automatically generated definition]. OBOL:automatic EMAPA:37680 MA:0003043 uberon UBERON:0015251 modified sebaceous gland MA EMAPA:37680 MA:th A pancreatic lobule that is in_the_left_side_of a exocrine pancreas. EMAPA:37711 MA:0000722 uberon UBERON:0015280 pancreas left lobe A pancreatic lobule that is in_the_left_side_of a exocrine pancreas. OBOL:automatic EMAPA:37711 MA:th A pancreatic lobule that is in_the_right_side_of a exocrine pancreas. EMAPA:37712 MA:0000723 uberon UBERON:0015281 pancreas right lobe A pancreatic lobule that is in_the_right_side_of a exocrine pancreas. OBOL:automatic EMAPA:37712 MA:th A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 uberon UBERON:0015329 respiratory system basement membrane MA A basement membrane of epithelium that is part of a respiratory system. OBOL:automatic EMAPA:37570 MA:th EMAPA:37597 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium MA EMAPA:37597 MA:th heart/pericardium MA:0002449 A mesenchyme that is part of a urethra. EMAPA:37786 MA:0002648 uberon UBERON:0015418 urethra mesenchymal layer A mesenchyme that is part of a urethra. OBOL:automatic EMAPA:37786 MA:th A valve that is part of a ureter. EMAPA:37781 MA:0002658 ureteral valve valve or ureter uberon UBERON:0015420 ureteral valve A valve that is part of a ureter. OBOL:automatic EMAPA:37781 MA:th ureteral valve MA:0002658 A lymph node that is part of a hypodermis. MA:0003028 uberon UBERON:0015453 subcutaneous lymph node A lymph node that is part of a hypodermis. OBOL:automatic A zone of skin that is part of a axilla. EMAPA:37349 FMA:37322 MA:0003087 NCIT:C116164 axillary skin skin of axilla uberon UBERON:0015474 axilla skin A zone of skin that is part of a axilla. OBOL:automatic EMAPA:37349 MA:th axillary skin FMA:37322 skin of axilla FMA:37322 A zone of skin that is part of a external nose. EMAPA:37684 FMA:24763 MA:0003090 external nasal skin skin of external nose skin of nose uberon UBERON:0015476 nose skin A zone of skin that is part of a external nose. OBOL:automatic EMAPA:37684 MA:th external nasal skin FMA:24763 skin of external nose FMA:24763 skin of nose FMA:24763 A zone of skin that is part of a scrotum. EMAPA:36411 FMA:20432 MA:0003093 SCTID:361710000 scrotal skin skin of scrotum uberon UBERON:0015479 scrotum skin A zone of skin that is part of a scrotum. OBOL:automatic skin of scrotum FMA:20432 The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery. EMAPA:37217 FMA:14772 MA:0003095 SCTID:244262006 Wikipedia:Hepatic_artery_proper hepatic artery proper uberon proper hepatic UBERON:0015480 proper hepatic artery MA FMA The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery. Wikipedia:Hepatic_artery_proper EMAPA:37217 MA:th hepatic artery proper FMA:14772 proper hepatic Wikipedia:Hepatic_artery_proper A hepatic artery that is part of a left lobe of liver. EMAPA:37096 FMA:14779 MA:0003096 left branch of hepatic artery left part of hepatic artery proper ramus sinister (arteria hepatica propria) uberon UBERON:0015481 left hepatic artery FMA A hepatic artery that is part of a left lobe of liver. OBOL:automatic EMAPA:37096 MA:th left branch of hepatic artery FMA:14779 left part of hepatic artery proper FMA:14779 ramus sinister (arteria hepatica propria) FMA:14779 FMA:TA A hepatic artery that is part of a right lobe of liver. EMAPA:37376 FMA:14778 MA:0003097 ramus dexter (arteria hepatica propria) right branch of hepatic artery proper right part of hepatic artery proper uberon UBERON:0015482 right hepatic artery FMA A hepatic artery that is part of a right lobe of liver. OBOL:automatic EMAPA:37376 MA:th ramus dexter (arteria hepatica propria) FMA:14778 FMA:TA right branch of hepatic artery proper FMA:14778 right part of hepatic artery proper FMA:14778 Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla. EMAPA:37478 MA:0003108 choledochoduodenal junction uberon UBERON:0015485 choledocho-duodenal junction Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla. http://medical-dictionary.thefreedictionary.com/choledochoduodenal+junction EMAPA:37478 MA:th choledochoduodenal junction MA:0003108 An epithelium that is part of a anal canal. EMAPA:18835 FMA:17511 anal canal epithelium epithelium of anal canal uberon UBERON:0015716 anal canal epithelium An epithelium that is part of a anal canal. OBOL:automatic anal canal epithelium FMA:17511 epithelium of anal canal FMA:17511 A smooth muscle tissue that is part of a ejaculatory duct. EMAPA:32289 FMA:19372 muscle layer of ejaculatory duct uberon UBERON:0015717 smooth muscle tissue layer of ejaculatory duct A smooth muscle tissue that is part of a ejaculatory duct. OBOL:automatic muscle layer of ejaculatory duct FMA:19372 FMA:62798 portion of heterogeneous tissue uberon UBERON:0015757 heterogeneous tissue FMA portion of heterogeneous tissue FMA:62798 An epithelium that is part of a duct of salivary gland. FMA:67682 epithelium of salivary duct salivary duct epithelium salivary ductal epithelium uberon UBERON:0015766 epithelium of duct of salivary gland FMA An epithelium that is part of a duct of salivary gland. OBOL:automatic epithelium of salivary duct FMA:67682 salivary duct epithelium FMA:67682 salivary ductal epithelium FMA:67682 A smooth muscle tissue that is part of a hypodermis. FMA:77862 muscle layer in fatty layer of subcutaneous tissue stratum musculosum panniculi adiposi telae subcutaneae uberon UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue A smooth muscle tissue that is part of a hypodermis. OBOL:automatic muscle layer in fatty layer of subcutaneous tissue FMA:77862 stratum musculosum panniculi adiposi telae subcutaneae FMA:77862 FMA:TA The portion of the nasal mucosa that is part of the respiratory system. lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose. FMA:77198 pars respiratoria tunicae mucosae nasi respiratory zone of nasal mucosa uberon UBERON:0015786 respiratory segment of nasal mucosa The portion of the nasal mucosa that is part of the respiratory system. http://orcid.org/0000-0002-6601-2165 lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose. Wikipedia:Nasal_cavity pars respiratoria tunicae mucosae nasi FMA:77198 FMA:TA respiratory zone of nasal mucosa FMA:77198 Any anatomical conduit which is part of the upper respiratory tract. Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 uberon respiratory conduit UBERON:0015787 upper respiratory conduit Any anatomical conduit which is part of the upper respiratory tract. http://orcid.org/0000-0002-6601-2165 Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 respiratory conduit FMA:265132 An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. FMA:265136 uberon UBERON:0015788 olfactory apparatus chamber An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. http://orcid.org/0000-0002-6601-2165 see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper EMAPA:25133 MA:0000579 cranial/facial muscle uberon cranial-facial muscle cranio-facial muscle craniofacial muscle UBERON:0015789 cranial or facial muscle cranial/facial muscle MA:0000579 cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 A zone of skin that is part of a autopod region. EMAPA:32723 MA:0003120 uberon paw skin UBERON:0015790 autopod skin A zone of skin that is part of a autopod region. OBOL:automatic paw skin MA:0003120 A portion of connective tissue that is part of a digit. EMAPA:37290 MA:0003123 uberon UBERON:0015791 digit connective tissue A portion of connective tissue that is part of a digit. OBOL:automatic EMAPA:37290 MA:th A blood vessel that is part of a liver. EMAPA:35498 MA:0003137 uberon hepatic blood vessel UBERON:0015796 liver blood vessel A blood vessel that is part of a liver. OBOL:automatic hepatic blood vessel EMAPA:35498 An epithelium that is part of a ear. EMAPA:32800 MA:0003161 uberon UBERON:0015807 ear epithelium An epithelium that is part of a ear. OBOL:automatic An epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 uberon UBERON:0015808 eye epithelium An epithelium that is part of a camera-type eye. OBOL:automatic An epithelium that is part of a middle ear. EMAPA:35673 MA:0003169 uberon UBERON:0015813 middle ear epithelium An epithelium that is part of a middle ear. OBOL:automatic An epithelium that is part of a external ear. EMAPA:35956 MA:0003170 uberon UBERON:0015814 outer ear epithelium An epithelium that is part of a external ear. OBOL:automatic An epithelium that is part of a foregut. EMAPA:32922 MA:0003204 uberon UBERON:0015833 foregut epithelium An epithelium that is part of a foregut. OBOL:automatic A lamina propria that is part of a duodenum. EMAPA:27255 FMA:15972 MA:0003209 duodenal lamina propria lamina propria mucosae of duodenum lamina propria of duodenum uberon UBERON:0015834 duodenum lamina propria FMA A lamina propria that is part of a duodenum. OBOL:automatic duodenal lamina propria FMA:15972 lamina propria mucosae of duodenum FMA:15972 lamina propria of duodenum FMA:15972 FMA:66178 uberon UBERON:0015860 visceral abdominal lymph node FMA A lymph node that is part of a head. FMA:61212 SCTID:155136006 uberon UBERON:0015870 lymph node of head A lymph node that is part of a head. OBOL:automatic Any of the lymph nodes that are part of a face. In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein. FMA:61222 SCTID:279139005 Wikipedia:Facial_lymph_nodes buccal lymph node uberon UBERON:0015871 facial lymph node Any of the lymph nodes that are part of a face. Wikipedia:Facial_lymph_nodes http://www.bartleby.com/107/177.html buccal lymph node FMA:61222 A lymph node that is located close to the surface. FMA:12767 NCIT:C102716 uberon UBERON:0015917 superficial lymph node A lymph node that is located close to the surface. http://orcid.org/0000-0002-6601-2165 A lymph node that is located deeper within the organism, further from the surface. FMA:12768 uberon UBERON:0015918 deep lymph node A lymph node that is located deeper within the organism, further from the surface. http://orcid.org/0000-0002-6601-2165 A lymph node that is part of a hindlimb. FMA:44310 SCTID:361109000 uberon UBERON:0016398 lymph node of lower limb A lymph node that is part of a hindlimb. OBOL:automatic A lymph node that is part of a forelimb. FMA:44311 SCTID:276155004 uberon UBERON:0016399 lymph node of upper limb A lymph node that is part of a forelimb. OBOL:automatic A capillary that is part of a lung. FMA:14121 capillary of lung uberon UBERON:0016405 pulmonary capillary A capillary that is part of a lung. OBOL:automatic capillary of lung FMA:14121 A breast that is part of a male organism. FMA:19901 NCIT:C33048 UMLS:C0222604 mamma masculina uberon UBERON:0016410 male breast A breast that is part of a male organism. OBOL:automatic mamma masculina FMA:19901 The intersection of the frontal and two nasal bones of the human skull. Its manifestation on the visible surface of the face is a distinctly depressed area directly between the eyes, just superior to the bridge of the nose. FMA:264779 Wikipedia:Nasion uberon UBERON:0016418 nasion The intersection of the frontal and two nasal bones of the human skull. Its manifestation on the visible surface of the face is a distinctly depressed area directly between the eyes, just superior to the bridge of the nose. Wikipedia:Nasion FMA:35324 uberon UBERON:0016426 proximal interphalangeal joint of little finger Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. EMAPA:37233 FMA:50060 MESH:D035441 NCIT:C62484 SCTID:181608004 uberon UBERON:0016435 chest wall Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. FMA:50060 EMAPA:37233 MA:th MESH:D035441 https://github.com/biopragmatics/biomappings A strand of hair that is part of a head. FMA:54241 head hair hair of scalp uberon UBERON:0016446 hair of head A strand of hair that is part of a head. OBOL:automatic head hair FMA:54241 hair of scalp FMA:54241 A strand of hair that is part of a trunk. FMA:54250 trunk hair uberon UBERON:0016447 hair of trunk A strand of hair that is part of a trunk. OBOL:automatic trunk hair FMA:54250 A hole in the diaphragm through which the esophagus passes. FMA:58289 esophageal hiatus of diaphragm oesophageal aperture oesophageal hiatus uberon UBERON:0016458 esophageal hiatus A hole in the diaphragm through which the esophagus passes. HP:0002036 esophageal hiatus of diaphragm FMA:58289 oesophageal aperture FMA:58289 oesophageal hiatus FMA:58289 The midline prominence of the nose, extending from the nasal root to the tip. FMA:59517 SCTID:368114008 nasal dorsum uberon nasal ridge UBERON:0016464 dorsum of nose FMA The midline prominence of the nose, extending from the nasal root to the tip. HP:0011119 nasal dorsum FMA:59517 nasal ridge HP:0011119 A zone of skin that is part of a forehead. EMAPA:37952 FMA:63883 forehead skin uberon UBERON:0016475 skin of forehead A zone of skin that is part of a forehead. OBOL:automatic EMAPA:37952 MA:th forehead skin FMA:63883 A stroma that is part of a liver. FMA:17553 hepatic stroma stroma of liver uberon UBERON:0016478 liver stroma A stroma that is part of a liver. OBOL:automatic hepatic stroma FMA:17553 stroma of liver FMA:17553 A collagenous capsule covering the external surface of the liver. It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells. FMA:15813 SCTID:362185005 Wikipedia:Fibrous_capsule_of_Glisson capsula fibrosa perivascularis fibrous capsule of liver glisson's capsule hepatic capsule tunica fibrosa (hepar) tunica fibrosa hepatis uberon fibrous capsule of Glisson liver capsule UBERON:0016479 capsule of liver https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb A collagenous capsule covering the external surface of the liver. Wikipedia:Fibrous_capsule_of_Glisson capsula fibrosa perivascularis Wikipedia:Fibrous_capsule_of_Glisson fibrous capsule of liver FMA:15813 glisson's capsule FMA:15813 hepatic capsule FMA:15813 tunica fibrosa (hepar) FMA:TA tunica fibrosa hepatis FMA:15813 FMA:TA fibrous capsule of Glisson Wikipedia:Fibrous_capsule_of_Glisson liver capsule Wikipedia:Fibrous_capsule_of_Glisson A lymph node that is part of a bronchus. MA:0003078 NCIT:C32232 UMLS:C1305372 uberon UBERON:0016481 bronchial lymph node A lymph node that is part of a bronchus. OBOL:automatic Is the sensory system for the sense of hearing. Auditory system is general anatomical term in FMA EMAPA:36002 FMA:7192 MA:0002443 NCIT:C12889 NLXANAT:090817 UMLS:C0587901 Wikipedia:Auditory_system neuronames:2888 uberon UBERON:0016490 auditory system Is the sensory system for the sense of hearing. NLXANAT:090817 Auditory system is general anatomical term in FMA FMA UMLS:C0587901 ncithesaurus:Auditory_System Skeletal element that functionally replaces the notochord[VSAP,modified]. Skeletal element that surrounds the notochord.[VSAO] the main cylindrical portion of the vertebra ventral to the vertebral canal The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification. centrum VSAO:0000183 centrum of vertebra uberon UBERON:0016491 vertebral centrum element VSAO VSAO Skeletal element that functionally replaces the notochord[VSAP,modified]. VSAO:0000183 VSAO:curator http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/207 https://github.com/obophenotype/uberon/issues/80 Skeletal element that surrounds the notochord.[VSAO] 2012-08-14 VSAO:0000183 VSAO VSAO:curator the main cylindrical portion of the vertebra ventral to the vertebral canal MP:0000141,ISBN:0-683-40008-8,PMID:10572046 centrum VSAO:0000183 Luminal space of the right ventricle of the heart. EMAPA:26047 FMA:9291 right ventricle lumen right ventricular cavity uberon UBERON:0016509 cavity of right ventricle Luminal space of the right ventricle of the heart. http://orcid.org/0000-0002-6601-2165 right ventricle lumen EMAPA:26047 right ventricular cavity FMA:FMA An epithelium that is part of a male urethra. EMAPA:30467 FMA:19684 male urethral epithelium urethral epithelium of male uberon UBERON:0016510 epithelium of male urethra An epithelium that is part of a male urethra. OBOL:automatic male urethral epithelium FMA:FMA urethral epithelium of male EMAPA:30467 An anatomical space that is part of a duodenum. EMAPA:19080 FMA:14589 doudenal lumen duodenal lumen uberon UBERON:0016512 lumen of duodenum An anatomical space that is part of a duodenum. OBOL:automatic doudenal lumen FMA:FMA duodenal lumen FMA:FMA Luminal space of the left atrium of the heart. EMAPA:26011 FMA:9465 left atrial cavity left atrium lumen uberon UBERON:0016513 cavity of left atrium Luminal space of the left atrium of the heart. http://orcid.org/0000-0002-6601-2165 left atrial cavity FMA:FMA left atrium lumen EMAPA:26011 Luminal space of the left ventricle of the heart. EMAPA:26038 FMA:9466 left ventricular cavity uberon UBERON:0016514 cavity of left ventricle Luminal space of the left ventricle of the heart. http://orcid.org/0000-0002-6601-2165 left ventricular cavity FMA:FMA An anatomical space that is part of a jejunum. EMAPA:18729 FMA:14590 jejunal lumen jejunum lumen uberon UBERON:0016517 lumen of jejunum An anatomical space that is part of a jejunum. OBOL:automatic jejunal lumen FMA:FMA jejunum lumen FMA:FMA An epithelium that is part of a female urethra. EMAPA:30470 FMA:19774 female urethral epithelium urethral epithelium of female uberon UBERON:0016520 epithelium of female urethra An epithelium that is part of a female urethra. OBOL:automatic female urethral epithelium FMA:FMA urethral epithelium of female EMAPA:30470 Luminal space of the right atrium of the heart. EMAPA:26020 FMA:11359 right atrial cavity uberon UBERON:0016522 cavity of right atrium Luminal space of the right atrium of the heart. http://orcid.org/0000-0002-6601-2165 right atrial cavity FMA:FMA Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though frontal region regio frontalis BAMS:Frontal_lobe BIRNLEX:928 BM:Tel-Cx-FR CALOHA:TS-0389 DHBA:12113 EFO:0000913 EV:0100167 FMA:61824 HBA:4009 MAT:0000505 MESH:D005625 NCIT:C12352 SCTID:180920004 UMLS:C0016733 UMLS:C1268977 neuronames:56 lobi frontales lobus frontalis frontal cortex uberon UBERON:0016525 frontal lobe FMA Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. FMA:61824 Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though MM frontal region FMA:61824 regio frontalis FMA:61824 FMA:TA UMLS:C0016733 BIRNLEX:928 ncithesaurus:Frontal_Lobe UMLS:C1268977 BIRNLEX:928 neuronames:56 BIRNLEX:928 lobi frontales NeuroNames:56 lobus frontalis Wikipedia:Frontal_lobe frontal cortex FMA:61824 Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. UBERON:0000322 BIRNLEX:922 BTO:0000445 FMA:61823 SCTID:272632001 neuronames:1210 cerebral hemisphere lobe cerebral lobe lobe of cerebral cortex lobe parts of cerebral cortex lobi cerebri uberon cerebral cortical segment lobes of the brain regional organ part of cerebral cortex segment of cerebral cortex UBERON:0016526 We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts. lobe of cerebral hemisphere Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. FMA:61823 cerebral hemisphere lobe FMA:61823 cerebral lobe BTO:0000445 lobe of cerebral cortex BIRNLEX:922 lobe parts of cerebral cortex BIRNLEX:922 lobi cerebri FMA:77800 FMA:TA cerebral cortical segment FMA:68603 lobes of the brain BIRNLEX:922 regional organ part of cerebral cortex FMA:68603 segment of cerebral cortex BIRNLEX:922 Grey matter neocortex region of a lobe of the cerebral hemisphere. FMA:242197 cortex of cerebral hemisphere lobe cortex of lobe of cerebral hemisphere uberon gray matter of lobe of cerebral hemisphere neocortical part of cerebral hemisphere UBERON:0016529 cortex of cerebral lobe Grey matter neocortex region of a lobe of the cerebral hemisphere. http://orcid.org/0000-0002-6601-2165 cortex of cerebral hemisphere lobe FMA:242197 cortex of lobe of cerebral hemisphere FMA:242197 gray matter of lobe of cerebral hemisphere FMA:242197 Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border. DHBA:10208 DMBA:16016 EMAPA:35667 FMA:242203 MA:0000916 MESH:D010296 NLX:79282 SCTID:369217001 neuronames:2473 cortex of parietal lobe parietal lobe cortex parietal neocortex uberon gray matter of parietal lobe UBERON:0016530 parietal cortex Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border. NLX:79282 MESH:D010296 https://github.com/biopragmatics/biomappings cortex of parietal lobe FMA:242203 parietal lobe cortex FMA:242203 parietal neocortex DHBA:10208 gray matter of parietal lobe FMA:242203 Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals. BM:Tel-Cx-Te DHBA:10235 DMBA:16044 FMA:242201 MA:0000941 MESH:D013702 NLX:94939 SCTID:362343001 cortex of temporal lobe temporal lobe cortex temporal neocortex uberon gray matter of temporal lobe UBERON:0016538 temporal cortex Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals. NLX:94939 MESH:D013702 https://github.com/biopragmatics/biomappings cortex of temporal lobe FMA:242201 temporal lobe cortex FMA:242201 temporal neocortex DHBA:10235 gray matter of temporal lobe FMA:242201 The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. UBERON:2001379 TAO:0001379 ZFA:0001379 uberon UBERON:0016545 pharyngeal ectoderm The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. PMID:23020903 http://orcid.org/0000-0002-6601-2165 A layer of of the central nervous system that is part of gray matter. grey matter layer FMA:83142 CNS gray matter layer CNS grey matter layer gray matter layer of neuraxis grey matter layer of neuraxis uberon UBERON:0016548 central nervous system gray matter layer A layer of of the central nervous system that is part of gray matter. http://orcid.org/0000-0002-6601-2165 gray matter layer of neuraxis FMA:83142 Mucus produced in the respiratory tract. NCIT:C93171 UMLS:C0225378 uberon UBERON:0016552 phlegm Mucus produced in the respiratory tract. http://orcid.org/0000-0002-6601-2165 Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). uberon UBERON:0016553 respiratory system mucus Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). Wikipedia:Nasal_mucus#Respiratory_system http://orcid.org/0000-0002-6601-2165 A blood vessel that is part of a cerebellum. uberon UBERON:0016565 cerebral blood vessel A blood vessel that is part of a cerebellum. OBOL:automatic An roughly circular indentation in a surface. AEO:0000204 uberon UBERON:0016566 pit An roughly circular indentation in a surface. AEO:0000204 AEO:JB FMA:68861 Wikipedia:Rexed_laminae http://neurolex.org/wiki/Category:Rexed_spinal_cord_parcellation_scheme_region rexed lamina uberon UBERON:0016570 lamina of gray matter of spinal cord rexed lamina FMA:68861 A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix. uberon UBERON:0016611 auditory hillocks, pharyngeal arch 1 derived A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix. http://php.med.unsw.edu.au/embryology/index.php?title=Hearing_-_Outer_Ear_Development#Pinna-_Auricle A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus. uberon UBERON:0016612 auditory hillocks, pharyngeal arch 2 derived A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus. http://php.med.unsw.edu.au/embryology/index.php?title=Hearing_-_Outer_Ear_Development#Pinna-_Auricle A scent gland that is part of the skin. SCTID:67740006 cutaneous scent gland uberon UBERON:0016852 skin scent gland A scent gland that is part of the skin. http://orcid.org/0000-0002-6601-2165 A skin gland found in the interdigital region of some mammals. SCTID:441008 interdigital sinus uberon UBERON:0016853 interdigital gland A skin gland found in the interdigital region of some mammals. http://orcid.org/0000-0002-6601-2165 interdigital sinus PMID:20512761 The dorsal region of the optic cup that gives rise to the dorsal part of the retina. dorsal optic cup dorsal region of optic cup uberon UBERON:0016854 dorsal part of optic cup The dorsal region of the optic cup that gives rise to the dorsal part of the retina. http://orcid.org/0000-0002-6601-2165 dorsal optic cup http://orcid.org/0000-0002-6601-2165 dorsal region of optic cup http://orcid.org/0000-0002-6601-2165 Primordium that develops into the central nervous system. UBERON:3000469 future CNS presumptive central nervous system uberon UBERON:0016879 future central nervous system Primordium that develops into the central nervous system. http://orcid.org/0000-0002-6601-2165 Primordium that develops into the nervous system. UBERON:3000477 AAO:0000477 presumptive nervous system uberon UBERON:0016880 future nervous system Primordium that develops into the nervous system. http://orcid.org/0000-0002-6601-2165 presumptive nervous system AAO:0000477 The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints. MESH:D012785 SCTID:361835002 joint of shoulder region uberon UBERON:0016884 shoulder joint definitional The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints. http://www.innerbody.com/image/skel17.html MESH:D012785 https://github.com/biopragmatics/biomappings Epithelium lining the distalmost portion of the digestive tract. BTO:0005445 WBbt:0005800 rectum epithelium uberon UBERON:0016885 epithelium of terminal part of digestive tract Epithelium lining the distalmost portion of the digestive tract. http://orcid.org/0000-0002-6601-2165 rectum epithelium BTO:0005445 Any muscle tissue of the distalmost portion of the digestive tract. rectum muscle rectum muscle structure uberon UBERON:0016886 muscle tissue of terminal part of digestive tract Any muscle tissue of the distalmost portion of the digestive tract. http://orcid.org/0000-0002-6601-2165 The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 EHDAA2:0000003 EMAPA:16042 extra-embryonic component extraembryonic component uberon UBERON:0016887 entire extraembryonic component AEO AEO The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 AEO:JB extraembryonic component AEO:0000195 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 uberon UBERON:0016888 transitional anatomical structure AEO An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 AEO:JB A metaphysis that is part of a fibula. FMA:33745 fibula metaphysis fibular metaphysis uberon UBERON:0016928 metaphysis of fibula A metaphysis that is part of a fibula. UBERON:nv fibula metaphysis FMA:33745 A bony structure embedded in skin, roughly equivalent to osteoderms. bony tubercle uberon bony tubercles UBERON:0017163 skin bony tubercle A bony structure embedded in skin, roughly equivalent to osteoderms. PHENOSCAPE:Nizar bony tubercles A sesamoid element that is part of a tarsal skeleton. uberon tarsal sesamoid UBERON:0017261 intertarsal sesamoid A sesamoid element that is part of a tarsal skeleton. OBOL:automatic A set of teeth in which each tooth that attaches to a vomer. AAO:0000635 uberon vomerine teeth UBERON:0017615 vomerine dentition A set of teeth in which each tooth that attaches to a vomer. OBOL:automatic Wikipedia:Corpora_arenacea uberon UBERON:0017631 calcified structure of brain A calcified structure of brain that is part of a pineal body. SCTID:369232008 Wikipedia:Corpora_arenacea uberon UBERON:0017632 pineal corpora arenacea A calcified structure of brain that is part of a pineal body. OBOL:automatic A calcified structure of brain that is part of a choroid plexus. uberon UBERON:0017633 choroid plexus corpora arenacea A calcified structure of brain that is part of a choroid plexus. OBOL:automatic FMA:52568 paired dural venous sinus uberon UBERON:0017635 paired venous dural sinus paired dural venous sinus FMA:52568 The dorsal part of the body wall. uberon UBERON:0017649 dorsal body wall The dorsal part of the body wall. http://orcid.org/0000-0002-6601-2165 A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 uberon UBERON:0017650 developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 AEO:JB A primordium that has the potential to develop into a saliva-secreting gland. uberon UBERON:0017651 salivary gland primordium A primordium that has the potential to develop into a saliva-secreting gland. OBOL:automatic Any of the small racemose mucous glands in the mucous membrane lining the cheeks. BTO:0005767 SCTID:25421004 uberon cheek gland UBERON:0017654 buccal gland Any of the small racemose mucous glands in the mucous membrane lining the cheeks. http://www.merriam-webster.com/medical/buccal%20gland A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera uberon UBERON:0017672 abdominal viscera A viscus that is part of a abdomen. OBOL:automatic abdominal viscera FMA:32413 abdominal viscera set FMA:32413 set of abdominal viscera FMA:32413 A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton. awaiting approval by phenoscape curators uberon UBERON:0017750 proximal mesopodial endochondral element A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton. http://orcid.org/0000-0002-6601-2165 A proximal mesopodial endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0017751 proximal mesopodial cartilage element A proximal mesopodial endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A muscle layer that is part of the rectum. FMA:15035 muscular coat of rectum muscularis externa of rectum rectal muscularis propria tunica muscularis (rectum) tunica muscularis recti uberon UBERON:0018111 muscle layer of rectum A muscle layer that is part of the rectum. http://orcid.org/0000-0002-6601-2165 muscular coat of rectum FMA:15035 muscularis externa of rectum FMA:15035 rectal muscularis propria FMA:15035 tunica muscularis (rectum) FMA:15035 tunica muscularis recti FMA:TA Any portion of smooth muscle tissue that is part of the rectum. rectal smooth muscle tissue rectum smooth muscle smooth muscle of rectum uberon UBERON:0018112 rectum smooth muscle tissue Any portion of smooth muscle tissue that is part of the rectum. http://orcid.org/0000-0002-6601-2165 A kidney interstitium that is part of a left kidney. FMA:74271 left renal stroma stroma of left kidney uberon UBERON:0018113 left kidney interstitium A kidney interstitium that is part of a left kidney. OBOL:automatic left renal stroma FMA:74271 stroma of left kidney FMA:74271 A kidney interstitium that is part of a right kidney. FMA:74270 right renal stroma stroma of right kidney uberon UBERON:0018114 right kidney interstitium A kidney interstitium that is part of a right kidney. OBOL:automatic right renal stroma FMA:74270 stroma of right kidney FMA:74270 A renal pelvis that is part of a left ureter. FMA:15579 SCTID:243436005 pelvis of left ureter renal pelvis of left kidney uberon UBERON:0018115 left renal pelvis A renal pelvis that is part of a left ureter. OBOL:automatic pelvis of left ureter FMA:15579 renal pelvis of left kidney FMA:15579 A renal pelvis that is part of a right ureter. FMA:15578 SCTID:243419002 pelvis of right kidney pelvis of right ureter uberon UBERON:0018116 right renal pelvis A renal pelvis that is part of a right ureter. OBOL:automatic pelvis of right kidney FMA:15578 pelvis of right ureter FMA:15578 A renal cortex interstitium that is part of a left kidney. cortical interstitial tissue of left kidney uberon UBERON:0018117 left renal cortex interstitium A renal cortex interstitium that is part of a left kidney. OBOL:automatic A renal cortex interstitium that is part of a right kidney. cortical interstitial tissue of right kidney uberon UBERON:0018118 right renal cortex interstitium A renal cortex interstitium that is part of a right kidney. OBOL:automatic A renal medulla interstitium that is part of a left kidney. medullary interstitial tissue of left kidney uberon UBERON:0018119 left renal medulla interstitium A renal medulla interstitium that is part of a left kidney. OBOL:automatic A renal medulla interstitium that is part of a right kidney. medullary interstitial tissue of right kidney uberon UBERON:0018120 right renal medulla interstitium A renal medulla interstitium that is part of a right kidney. OBOL:automatic FMA:83521 uberon UBERON:0018135 fibrocollagenous connective tissue Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). UBERON:0015006 caudal vertebra element tail vertebra element coccygeal vertebra element coccyx vertebra element uberon UBERON:0018142 caudal vertebra endochondral element Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). http://orcid.org/0000-0002-6601-2165 A transverse process that is part of a cervical vertebra. May be homologous with the cervical ribs of some vertebrates FMA:23894 FMA:9913 SCTID:280730000 uberon UBERON:0018143 transverse process of cervical vertebra A transverse process that is part of a cervical vertebra. http://orcid.org/0000-0002-6601-2165 A rib that is attached to a cervical vertebra. Trunk, presacral and sacral ribs do not have a 'part of some region' asserted for them, we should add it to them[PHENOSCAPE:ad] May be homologous with the transverse processes of cervical vertebra EMAPA:37825 MESH:D057070 uberon UBERON:0018144 cervical rib A rib that is attached to a cervical vertebra. http://orcid.org/0000-0002-6601-2165 should be all Theria, see https://github.com/obophenotype/mouse-anatomy-ontology/issues/116 EMAPA:37825 MA:th MESH:D057070 https://github.com/biopragmatics/biomappings A rib that is attached to a lumbar vertebra. May be homologous with the transverse processes of lumbar vertebra uberon UBERON:0018145 lumbar rib A rib that is attached to a lumbar vertebra. http://orcid.org/0000-0002-6601-2165 A transverse process that is part of a lumbar vertebra. May be homologous with the lumbar ribs of some vertebrates FMA:16080 FMA:65469 SCTID:280733003 costa lumbalis lumbar transverse process uberon UBERON:0018146 transverse process of lumbar vertebra A transverse process that is part of a lumbar vertebra. http://orcid.org/0000-0002-6601-2165 costa lumbalis FMA:65469 FMA:TA lumbar transverse process FMA:16080 A zone of skin that is part of a lower lip. FMA:24767 SCTID:281630002 lower lip skin uberon UBERON:0018150 skin of lower lip A zone of skin that is part of a lower lip. OBOL:automatic lower lip skin FMA:24767 A zone of skin that is part of a upper lip. FMA:24765 SCTID:281629007 upper lip skin uberon UBERON:0018151 skin of upper lip A zone of skin that is part of a upper lip. OBOL:automatic upper lip skin FMA:24765 A ligament that is part of a middle ear. uberon UBERON:0018154 ligament of middle ear A ligament that is part of a middle ear. OBOL:automatic An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels. FMA:67999 pulmonary lymphatic chain uberon pulmonary lymphatic vasculature UBERON:0018226 pulmonary part of lymphatic system An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels. http://orcid.org/0000-0002-6601-2165 pulmonary lymphatic chain FMA:67999 A lymphatic vessel that is part of a lung. FMA:234006 SCTID:321862009 lymphatic vessel of lung uberon UBERON:0018227 pulmonary lymphatic vessel A lymphatic vessel that is part of a lung. OBOL:automatic A sweat gland that is part of a axilla. axillary apocrine sweat gland sweat gland of axilla uberon UBERON:0018232 axillary sweat gland ISBN:0123813611 A sweat gland that is part of a axilla. OBOL:automatic ISBN:0123813611 axillary apocrine sweat gland http://orcid.org/0000-0002-6601-2165 sweat gland of axilla http://orcid.org/0000-0002-6601-2165 A stroma that is part of a pancreas. FMA:63121 pancreatic stroma uberon UBERON:0018234 stroma of pancreas A stroma that is part of a pancreas. OBOL:automatic pancreatic stroma FMA:63121 A capsule that divides the parenchyma of the pancreas into lobes and lobules. typically thin but can thicken with age pancreatic capsule uberon UBERON:0018235 capsule of pancreas A capsule that divides the parenchyma of the pancreas into lobes and lobules. ISBN:0123813611 A boundary delimiting a rhombomere. rhombomere junction uberon UBERON:0018239 rhombomere boundary A boundary delimiting a rhombomere. GO:0021654 A vein that supplies blood to the thymus. FMA:10647 SCTID:76543001 Wikipedia:Thymic_branches_of_internal_thoracic_artery thymic branch of internal thoracic artery uberon thymic arteries UBERON:0018243 The arteries supplying the thymus are derived from the internal thoracic artery, and from the superior thyroid artery and inferior thyroids.[WP] thymic artery FMA A vein that supplies blood to the thymus. http://orcid.org/0000-0002-6601-2165 thymic branch of internal thoracic artery FMA:10647 thymic arteries Wikipedia:Thymic_branches_of_internal_thoracic_artery A vein that drains a thyroid gland. EMAPA:18648 SCTID:303420005 uberon UBERON:0018246 thyroid vein A vein that drains a thyroid gland. OBOL:automatic An artery that supplies a cervical thymus. uberon UBERON:0018247 cervical thymic artery An artery that supplies a cervical thymus. http://orcid.org/0000-0002-6601-2165 One of the veins draining a meninix. In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault. FMA:50839 SCTID:84842006 uberon UBERON:0018251 meningeal vein One of the veins draining a meninix. http://orcid.org/0000-0002-6601-2165 Accompanying vein of internal pudendal artery. In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins FMA:18917 SCTID:14885008 Wikipedia:Internal_pudendal_veins vena pudenda interna uberon internal pudic vein UBERON:0018252 internal pudendal vein https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb Accompanying vein of internal pudendal artery. Wikipedia:Internal_pudendal_veins vena pudenda interna Wikipedia:Internal_pudendal_veins internal pudic vein Wikipedia:Internal_pudendal_veins Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 EHDAA2:0001842 EMAPA:35578 MA:0000165 uberon UBERON:0018254 skeletal musculature MA A branch of the superior mesenteric artery that supplies the jejunum. FMA:14808 SCTID:265391008 Wikipedia:Jejunal_arteries uberon jejunal branch of superior mesenteric artery UBERON:0018255 jejunal artery A branch of the superior mesenteric artery that supplies the jejunum. Wikipedia:Jejunal_veins http://orcid.org/0000-0002-6601-2165 jejunal branch of superior mesenteric artery FMA:14808 A vein that drains a lacrimal gland. FMA:51779 SCTID:149582008 uberon UBERON:0018256 lacrimal vein A vein that drains a lacrimal gland. OBOL:automatic Any portion of submucosa that lines the digestive tract. uberon UBERON:0018257 submucosa of digestive tract Any portion of submucosa that lines the digestive tract. http://orcid.org/0000-0002-6601-2165 Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only FMA:45634 NCIT:C75444 UMLS:C0225358 uberon UBERON:0018260 layer of muscle tissue Any organ component layer that consists of muscle tissue. http://orcid.org/0000-0002-6601-2165 NCITA class may refer to smooth muscle only NCIT A muscular coat that is part of a digestive tract. responsible for gut movement, such as peristalsis tunica muscularis of digestive tract uberon muscular layer of digestive tract muscularis externa of digestive tract tunica externa of digestive tract UBERON:0018261 muscular coat of digestive tract A muscular coat that is part of a digestive tract. OBOL:automatic Tissue that is part of some adrenal gland. TODO - describe typology of adrenal gland tissue used in this ontology NCIT:C32051 adrenal gland tissue uberon UBERON:0018303 adrenal tissue Tissue that is part of some adrenal gland. PHENOSCAPE:Alex adrenal gland tissue ncithesaurus:Adrenal_Gland_Tissue Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). uberon UBERON:0018321 foramen for glossopharyngeal nerve Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). PHENOSCAPE:alex A skeletal ligament that is part of a hip joint. FMA:42868 SCTID:182435001 hip joint ligament uberon UBERON:0018411 ligament of hip joint A skeletal ligament that is part of a hip joint. OBOL:automatic hip joint ligament FMA:42868 A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . FMA:54952 Wikipedia:Facial_canal canalis nervi facialis facial canal uberon fallopian canal UBERON:0018413 facial nerve canal A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . Wikipedia:Facial_canal canalis nervi facialis FMA:54952 FMA:TA facial canal FMA:54952 fallopian canal FMA:54952 An bone foramen in the ethmoid bone. There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)] Wikipedia:Ethmoidal_foramina ethmoidal foramen foramina ethmoidalia uberon ethmoid foramina ethmoidal foramina UBERON:0018415 Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina ethmoid foramen An bone foramen in the ethmoid bone. http://orcid.org/0000-0002-6601-2165 foramina ethmoidalia ethmoid foramina ethmoidal foramina The anatomical space within the intestine. see notes in inclusivity in class 'intestine' FMA:14586 TADS:0000495 WBbt:0005791 ZFA:0005807 intestinal lumen intestine lumen uberon gut lumen UBERON:0018543 lumen of intestine The anatomical space within the intestine. http://orcid.org/0000-0002-6601-2165 intestinal lumen FMA:14586 intestine lumen ZFA:0005807 gut lumen ZFA:0005807 Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscle innervated by the trigeminal nerve muscles innervated by the trigeminal nerve uberon UBERON:0018544 trigeminal nerve muscle Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscles innervated by the trigeminal nerve MFMO:0000072 FMA:83450 ventricular cardiac muscle tissue ventricular heart muscle uberon ventricular muscle UBERON:0018649 cardiac muscle tissue of ventricle ventricular cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 ventricular heart muscle http://orcid.org/0000-0002-6601-2165 ventricular muscle http://orcid.org/0000-0002-6601-2165 The neck region of a bone organ. bone neck neck of bone uberon UBERON:0018664 neck of bone element https://github.com/obophenotype/uberon/wiki/Hidden-GCIs The neck region of a bone organ. http://orcid.org/0000-0002-6601-2165 FMA:23254 SCTID:181915009 anatomical neck of scapula collum scapulae scapular neck uberon UBERON:0018667 neck of scapula anatomical neck of scapula FMA:23254 scapular neck FMA:23254 EMAPA:37891 FMA:35508 fibula neck fibular neck uberon UBERON:0018673 neck of fibula EMAPA:37891 MA:th fibula neck FMA:35508 An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 ZFA:0005811 cardiac vasculature uberon UBERON:0018674 heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. ZFA:0005811 ZFA:CVS cardiac vasculature FMA:73747 Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers. FMA:6280 Wikipedia:Thoracic_splanchnic_nerves uberon UBERON:0018679 thoracic splanchnic nerve FMA Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers. Wikipedia:Thoracic_splanchnic_nerves uberon UBERON:0018692 dorsal side of post-anal tail A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder uberon UBERON:0018707 bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder BTO:0000123 BTO:0002439 genital mucosa uberon UBERON:0019042 reproductive system mucosa genital mucosa BTO:0002439 Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 uberon intramuscular fat UBERON:0019143 intramuscular adipose tissue Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 intramuscular fat BTO:0004043 BTO:0004626 uberon carotid endothelium carotid epithelium UBERON:0019189 carotid artery endothelium carotid endothelium BTO:0004626 BTO:0004638 FMA:13119 SCTID:88410004 bronchial gland bronchial mucous gland peribronchial gland uberon UBERON:0019190 mucous gland of lung bronchial gland FMA:13119 bronchial mucous gland FMA:13119 peribronchial gland BTO:0004638 BTO:0004661 uberon UBERON:0019196 iliac artery endothelium Any region of epithelium that is part of a skin region. BTO:0004382 uberon UBERON:0019204 skin epithelium Any region of epithelium that is part of a skin region. http://orcid.org/0000-0002-6601-2165 EMAPA:35869 MA:0003178 uberon UBERON:0019206 tongue papilla epithelium The part of the eye that consists of both the retina and the optic choroid. SCTID:110701000 chorioretina choroid and retina retinachoroid retinachoroidal region uberon UBERON:0019207 chorioretinal region The part of the eye that consists of both the retina and the optic choroid. UBERON:drseb http://orcid.org/0000-0002-6601-2165 Either of the outermost digits in a five-digit autopod, or their phylogenetic equivalent. uberon lateral digit outer digit outermost digit UBERON:0019221 digit 1 or 5 https://github.com/obophenotype/uberon/issues/592 Either of the outermost digits in a five-digit autopod, or their phylogenetic equivalent. UBERON:cjm lateral digit outer digit outermost digit uberon lateral finger lateral manual digit outer manual digit outermost manual digit UBERON:0019231 manual digit 1 or 5 https://github.com/obophenotype/uberon/issues/592 lateral finger lateral manual digit outer manual digit outermost manual digit uberon lateral pedal digit lateral toe outer pedal digit outermost pedal digit UBERON:0019241 pedal digit 1 or 5 https://github.com/obophenotype/uberon/issues/592 lateral pedal digit lateral toe outer pedal digit outermost pedal digit DHBA:10654 FMA:268630 gray matter of the hindbrain uberon UBERON:0019263 gray matter of hindbrain gray matter of the hindbrain DHBA:HGM DHBA:10157 FMA:268608 uberon UBERON:0019264 gray matter of forebrain DHBA:10649 FMA:83913 uberon UBERON:0019267 gray matter of midbrain FMA:83912 uberon UBERON:0019269 gray matter of diencephalon EMAPA:35952 MA:0003174 uberon UBERON:0019304 sensory organ epithelium EMAPA:35958 MA:0003171 uberon UBERON:0019306 nose epithelium Epithelial layer that is part of the external part of the nose. FMA:63143 epithelium of skin of external nose uberon UBERON:0019307 epithelium of external nose FMA Epithelial layer that is part of the external part of the nose. http://orcid.org/0000-0002-6601-2165 epithelium of skin of external nose FMA:63143 An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system An exocrine gland that is part of a integumental system. GOC:dos http://orcid.org/0000-0002-6601-2165 integumental exocrine gland http://orcid.org/0000-0002-6601-2165 integumental system exocrine gland http://orcid.org/0000-0002-6601-2165 The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 FMA:83965 MA:0001033 Wikipedia:Spinal_accessory_nucleus neuronames:2003 accessory neural nucleus uberon accessory nucleus of anterior column of spinal cord nucleus accessorius columnae anterioris medullae spinalis nucleus nervi accessorii nucleus of accessory nerve nucleus of the accessory nerve nucleus of the spinal accessory nerve spinal accessory nucleus UBERON:0020358 See also: Wikipedia:Spinal_accessory_nucleus accessory XI nerve nucleus FMA The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. Wikipedia:Spinal_accessory_nucleus EMAPA:37067 MA:th accessory neural nucleus FMA:83965 accessory nucleus of anterior column of spinal cord NeuroNames:2003 nucleus accessorius columnae anterioris medullae spinalis NeuroNames:2003 nucleus nervi accessorii NeuroNames:2003 nucleus of accessory nerve NeuroNames:2003 nucleus of the accessory nerve NeuroNames:2003 nucleus of the spinal accessory nerve NeuroNames:2003 spinal accessory nucleus http://orcid.org/0000-0002-6601-2165 A blood vessel that supplies or drains an ear. EMAPA:37386 MA:0001226 uberon UBERON:0020550 auricular blood vessel A blood vessel that supplies or drains an ear. http://orcid.org/0000-0002-6601-2165 EMAPA:37386 MA:th FMA:53671 hair of external ear hair of tragus tragus hair uberon UBERON:0022279 strand of hair on external ear hair of external ear FMA:53671 hair of tragus FMA:53671 tragus hair FMA:53671 The single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland). in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe EMAPA:35464 uberon UBERON:0022284 lacrimal gland bud The single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland). MGI:anna FMA:58315 uberon surface of region of wall of eyeball UBERON:0022288 surface of eyeball surface of region of wall of eyeball FMA:58315 NCIT:C33596 SCTID:282511007 uberon UBERON:0022292 splenic arteriole A portion of organism substance that is secreted by a reproductive gland. uberon genital fluid genital secretion reproductive system fluid reproductive system fluid/secretion reproductive system secretion UBERON:0022293 reproductive gland secretion A portion of organism substance that is secreted by a reproductive gland. UBERON:cjm Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer lamina layer NLX:149357 uberon UBERON:0022303 nervous system cell part layer Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. NLX:149357 lamina CUMBO:CUMBO layer CUMBO:CUMBO Serous membrane layer that is adjacent to and lines an organ. FMA:15860 visceral wall of serous membrane uberon UBERON:0022350 visceral serous membrane Serous membrane layer that is adjacent to and lines an organ. http://orcid.org/0000-0002-6601-2165 visceral wall of serous membrane FMA:15860 Serous membrane layer that lines to a body cavity. cavity lining FMA:15859 MA:0002448 parietal wall of serous membrane uberon UBERON:0022351 parietal serous membrane Serous membrane layer that lines to a body cavity. http://orcid.org/0000-0002-6601-2165 cavity lining MA:0002448 parietal wall of serous membrane FMA:15859 The layer of endometrial epithelium adjacent to the uterine cavity. FMA:86492 NCIT:C32189 pars basalis of endometrium stratum basalis of endometrium uberon UBERON:0022355 basal layer of endometrium The layer of endometrial epithelium adjacent to the uterine cavity. Wikipedia:Endometrium#Histology stratum basalis of endometrium FMA:86492 FMA:14652 ileal mesentery ileum mesentery mesoileum uberon UBERON:0022357 mesentery of ileum ileal mesentery FMA:14652 ileum mesentery FMA:14652 A blood vessel of the placenta. placental vessel SCTID:280716005 uberon UBERON:0022358 placenta blood vessel A blood vessel of the placenta. GO:0060674 A mammary gland duct that is part of a male organism. This structure typically regresses. uberon UBERON:0022360 male mammary gland duct A mammary gland duct that is part of a male organism. This structure typically regresses. http://orcid.org/0000-0002-6601-2165 A specific region of the foregut into the area in which the lung will develop. SCTID:34922002 lung field uberon UBERON:0022361 lung field A specific region of the foregut into the area in which the lung will develop. GOC:dph GOC:mtg_lung BIRNLEX:1491 sacral spinal cord gray matter uberon UBERON:0029503 sacral spinal cord gray matter sacral spinal cord gray matter BIRNLEX:1491 BIRNLEX:1624 lumbar spinal cord gray matter uberon UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter BIRNLEX:1624 An embryonic or larval epithelium that is committed to form part of the nervous system. neurepithelium AEO:0001008 BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 embryonic neuroepithelium neuroepithelium uberon UBERON:0034705 developing neuroepithelium An embryonic or larval epithelium that is committed to form part of the nervous system. AEO:0001008 AEO:JB neurepithelium BTO:0000314 embryonic neuroepithelium http://orcid.org/0000-0002-6601-2165 neuroepithelium AEO:0001008 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 uberon UBERON:0034706 proliferating neuroepithelium AEO An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 uberon UBERON:0034707 differentiating neuroepithelium AEO A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047] DHBA:12695 EHDAA2:0001152 EMAPA:17789 marginal zone of cerebellum uberon MZCB UBERON:0034708 cerebellum marginal layer marginal zone of cerebellum DHBA:12695 MZCB DHBA:12695 DHBA:12694 EMAPA:32916 marginal zone of hindbrain uberon MZH UBERON:0034709 hindbrain marginal layer marginal zone of hindbrain DHBA:12694 MZH DHBA:12694 EHDAA2:0001267 EMAPA:17585 spinal cord lateral wall ventricular layer uberon UBERON:0034710 spinal cord ventricular layer EHDAA2 spinal cord lateral wall ventricular layer EHDAA2:0001267 The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. EMAPA:35261 uberon UBERON:0034711 cortical preplate The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. PMID:12626695 Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain. uberon cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain UBERON:0034713 cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain. ISBN:0471888893 http://orcid.org/0000-0002-6601-2165 cranial nerve fiber bundle http://orcid.org/0000-0002-6601-2165 cranial nerve fiber tract http://orcid.org/0000-0002-6601-2165 cranial nerve or tract http://orcid.org/0000-0002-6601-2165 neuron projection bundle from brain http://orcid.org/0000-0002-6601-2165 A cranial nerve fiber tract that innervates the parietal eye. uberon epiphyseal nerve UBERON:0034714 This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893] epiphyseal tract A cranial nerve fiber tract that innervates the parietal eye. ISBN:0471888893 epiphyseal nerve ISBN:0471888893 A cranial nerve fiber tract that innervates the pineal body. FMA:77600 uberon pineal nerve UBERON:0034715 This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893] pineal tract A cranial nerve fiber tract that innervates the pineal body. ISBN:0471888893 pineal nerve ISBN:0471888893 A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. uberon UBERON:0034717 integumental taste bud A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. PMID:11921337 http://orcid.org/0000-0002-6601-2165 A taste bud that is located on a lip. uberon UBERON:0034719 lip taste bud A taste bud that is located on a lip. PMID:11921337 http://orcid.org/0000-0002-6601-2165 A taste bud that is located on the skin of the head. uberon UBERON:0034720 head taste bud A taste bud that is located on the skin of the head. http://orcid.org/0000-0002-6601-2165 A taste bud that is located in the pharynx. uberon UBERON:0034721 pharyngeal taste bud A taste bud that is located in the pharynx. http://orcid.org/0000-0002-6601-2165 A taste bud that is located on the roof of the mouth. uberon UBERON:0034722 mouth roof taste bud A taste bud that is located on the roof of the mouth. http://orcid.org/0000-0002-6601-2165 A taste bud that is located in the esophagus. uberon UBERON:0034724 esophageal taste bud A taste bud that is located in the esophagus. http://orcid.org/0000-0002-6601-2165 A taste bud that is located on the skin of the trunk. uberon UBERON:0034726 trunk taste bud A taste bud that is located on the skin of the trunk. http://orcid.org/0000-0002-6601-2165 The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 FMA:5866 MESH:D017776 SCTID:276145003 Wikipedia:Autonomic_nerve nervus visceralis visceral nerve uberon UBERON:0034728 autonomic nerve The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. Wikipedia:Autonomic_nerve EMAPA:37957 MA:th nervus visceralis FMA:5866 visceral nerve FMA:5866 EMAPA:37958 SCTID:181098007 uberon UBERON:0034729 sympathetic nerve EMAPA:37958 MA:th A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. uberon UBERON:0034768 morphological feature A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. http://orcid.org/0000-0002-6601-2165 FMA:79770 NCIT:C41168 uberon UBERON:0034769 lymphomyeloid tissue FMA Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space uberon UBERON:0034873 bodily gas Any substance in the body or expelled from the body that is in a gaseous state. http://orcid.org/0000-0002-6601-2165 portion of gas in anatomical space FMA:84580 Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 respiratory air respiratory system air uberon UBERON:0034874 air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. http://orcid.org/0000-0002-6601-2165 respiratory air FMA:84581 EHDAA2:0001472 EMAPA:32796 pituitary primordium uberon UBERON:0034875 future pituitary gland EMAPA Wikipedia pituitary primordium EHDAA2:0001472 The outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland. EHDAA2:0004434 EMAPA:16647 uberon neurohypohysial region neurohypophyseal bud UBERON:0034876 future neurohypophysis EMAPA EMAPA The outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland. MP:0013339 https://sourceforge.net/p/obo/mammalian-phenotype-requests/1930/ neurohypohysial region EHDAA2:0004434 neurohypophyseal bud MP:0013339 The area of axial mesoderm that develops into the prechordal plate. prechordal mesenchyme uberon UBERON:0034878 prechordal mesoderm The area of axial mesoderm that develops into the prechordal plate. MGI:anna The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. These emerging postganglionic nerves synapse with preganglionic nerves from the thoracic spinal cord. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things. FMA:6261 SCTID:280533000 Wikipedia:Cervical_ganglia cervical part of sympathetic trunk cervical sympathetic chain cervical sympathetic trunk uberon UBERON:0034901 cervical sympathetic nerve trunk The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. These emerging postganglionic nerves synapse with preganglionic nerves from the thoracic spinal cord. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things. Wikipedia:Cervical_ganglia cervical part of sympathetic trunk FMA:6261 cervical sympathetic chain FMA:6261 cervical sympathetic trunk FMA:6261 EMAPA:37656 FMA:6264 MA:0001164 sacral part of sympathetic trunk sacral sympathetic chain sacral sympathetic trunk uberon pelvic sympathetic nerve trunk pelvic sympathetic trunk UBERON:0034902 sacral sympathetic nerve trunk EMAPA:37656 MA:th sacral part of sympathetic trunk FMA:6264 sacral sympathetic chain FMA:6264 sacral sympathetic trunk FMA:6264 pelvic sympathetic nerve trunk MA:0001164 Endocardium that is part of the left atrium. Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 SCTID:190064008 VHOG:0001226 endocardium of left atrium left atrial endocardium uberon left atrium endocardial tissue UBERON:0034903 left atrium endocardium Endocardium that is part of the left atrium. http://orcid.org/0000-0002-6601-2165 Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 endocardium of left atrium FMA:7286 left atrium endocardial tissue VHOG:0001226 lumen of gland uberon UBERON:0034905 gland lumen Parenchymal tissue that forms the pineal gland. NCIT:C41834 UMLS:C1519088 uberon UBERON:0034907 pineal parenchyma Parenchymal tissue that forms the pineal gland. http://orcid.org/0000-0002-6601-2165 Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle. uberon UBERON:0034908 scapular muscle Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle. HPO:curators An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure CARO An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster CARO:0020001 A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster CARO A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 2 Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 FBbt:00007276 uberon UBERON:0034923 disconnected anatomical group CARO Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 FBbt:00007276 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon UBERON:0034925 anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. http://orcid.org/0000-0002-6601-2165 An anatomical collection that is arranged in a line. resolve if this should be a subclass of or merged with aligned anatomical group. FBbt:00100152 uberon UBERON:0034926 anatomical row An anatomical collection that is arranged in a line. http://orcid.org/0000-0002-6601-2165 FBbt:00100152 FMA:19623 dorsum of penis dorsum penis uberon UBERON:0034928 dorsal surface of penis dorsum of penis FMA:19623 dorsum penis FMA:TA A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. uberon UBERON:0034929 external soft tissue zone A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. http://orcid.org/0000-0002-6601-2165 The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. BTO:0001513 biliary system epithelium uberon biliary epithelium biliary tract epithelium UBERON:0034932 epithelium of biliary system The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. BTO:0001513 MGI:cs http://orcid.org/0000-0002-6601-2165 biliary system epithelium http://orcid.org/0000-0002-6601-2165 biliary epithelium BTO:0001513 biliary tract epithelium http://orcid.org/0000-0002-6601-2165 Any organ component layer that consists of smooth muscle tissue. uberon UBERON:0034933 layer of smooth muscle tissue Any organ component layer that consists of smooth muscle tissue. http://orcid.org/0000-0002-6601-2165 An enlarged chamber in the blood sinus capable of accumulating a large volume of blood. ZFA:0007073 blood sinus cavity blood sinus lumen uberon UBERON:0034940 venous sinus cavity An enlarged chamber in the blood sinus capable of accumulating a large volume of blood. GOC:YMB ZFA:0007073 blood sinus cavity ZFA:0007073 blood sinus lumen ZFA:0007073 FMA:55268 organ sector organ zonal region organ zone uberon organ region with floating fiat boundary UBERON:0034944 zone of organ organ sector FMA:55268 organ zone FMA:55268 organ region with floating fiat boundary FMA:55268 Any gaseous product of an excretory process. uberon UBERON:0034945 excreted gas Any gaseous product of an excretory process. http://orcid.org/0000-0002-6601-2165 Any excreted gas that is produced by the digestive tract. FMA:78440 flatulence flatus intestinal gas uberon UBERON:0034946 In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum gas excreted from digestive tract Any excreted gas that is produced by the digestive tract. http://orcid.org/0000-0002-6601-2165 flatulence FMA:78440 flatus Wikipedia:Flatulence Any portion of gas located in a part of the respiratory system. respiratory gas respiratory system gas uberon UBERON:0034947 gas in respiratory system Any portion of gas located in a part of the respiratory system. http://orcid.org/0000-0002-6601-2165 A population of lymphatic endothelial cell precursors that will form the lymph vessels. NCIT:C34262 UMLS:C1514424 uberon primary lymph sac UBERON:0034953 embryonic lymph sac VHOG A population of lymphatic endothelial cell precursors that will form the lymph vessels. DOI:10.1152/japplphysiol.00201.2013 https://github.com/obophenotype/uberon/issues/1383 NCIT:C25787 UMLS:C1512086 uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct DHBA:12682 EMAPA:32917 hindbrain mantle layer uberon UBERON:0034994 hindbrain cortical intermediate zone hindbrain mantle layer EMAPA:32917 Mesenchyme that is part of a developing jaw [Automatically generated definition]. EMAPA:32907 EMAPA:35454 uberon UBERON:0034995 jaw mesenchyme Mesenchyme that is part of a developing jaw [Automatically generated definition]. OBOL:automatic EMAPA:35702 uberon UBERON:0035004 preputial swelling EMAPA EMAPA:29220 uberon prepuce of male UBERON:0035005 preputial swelling of male EMAPA prepuce of male EMAPA:29220 EMAPA:30478 uberon prepuce of female UBERON:0035006 preputial swelling of female EMAPA prepuce of female EMAPA:30478 represented as a primordium in EMAPA - should be cartilage condensation EMAPA:35890 turbinal cartilage turbinate bone primordium turbinate cartilage condensation unossified nasal turbinal unossified nasal turbinate unossified turbinate uberon UBERON:0035007 nasal concha cartilage represented as a primordium in EMAPA - should be cartilage condensation EMAPA turbinate bone primordium EMAPA:35890 EMAPA:37798 FMA:18157 MA:0001151 left vagus neural trunk trunk of left vagus uberon anterior vagus X nerve trunk UBERON:0035020 left vagus X nerve trunk EMAPA:37798 MA:th left vagus neural trunk FMA:18157 trunk of left vagus FMA:18157 anterior vagus X nerve trunk MA:0001151 EMAPA:37799 FMA:18151 MA:0001152 right vagus neural trunk trunk of right vagus uberon posterior vagus X nerve trunk UBERON:0035021 right vagus X nerve trunk EMAPA:37799 MA:th right vagus neural trunk FMA:18151 trunk of right vagus FMA:18151 posterior vagus X nerve trunk MA:0001152 An epithelium that is part of a naris [Automatically generated definition]. EMAPA:35959 MA:0003172 uberon UBERON:0035036 naris epithelium An epithelium that is part of a naris [Automatically generated definition]. OBOL:automatic EMAPA:32904 MA:0003220 uberon UBERON:0035037 jaw epithelium SCTID:277967008 hemorrhoidal artery uberon UBERON:0035039 rectal artery Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]. FMA:60052 uberon UBERON:0035049 excretory duct of salivary gland Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]. MP:0013750 BTO:0006341 uberon UBERON:0035050 excretory duct BTO:0006341 https://github.com/biopragmatics/biomappings FMA:60053 uberon UBERON:0035053 interlobular duct of salivary gland FMA:70643 ductal part of apocrine sweat gland uberon UBERON:0035074 duct of apocrine sweat gland ductal part of apocrine sweat gland FMA:70643 FMA:71193 uberon lobe or lobule of thymus UBERON:0035075 thymus subunit A vertebra that has a transverse process. uberon TP vertebra pygal vertebra UBERON:0035083 transverse process-bearing vertebra A vertebra that has a transverse process. http://orcid.org/0000-0002-6601-2165 TP vertebra PMID:22753107 pygal vertebra PMID:22753107 A post-anal tail that attaches outside the tail. uberon UBERON:0035091 extrinsic post-anal tail muscle A post-anal tail that attaches outside the tail. http://orcid.org/0000-0002-6601-2165 A transverse process that is part of a caudal vertebra. uberon UBERON:0035102 transverse process of caudal vertebra A transverse process that is part of a caudal vertebra. http://orcid.org/0000-0002-6601-2165 Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat digestive tract contents uberon ingested material entity UBERON:0035118 material entity in digestive tract Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. https://github.com/EnvironmentOntology/envo/issues/110 digestive tract contents EMAPA:32631 hand cartilage condensation uberon UBERON:0035128 manus cartilage element EMAPA-modified hand cartilage condensation EMAPA:32631 EMAPA:32657 foot cartilage condensation uberon UBERON:0035129 pes cartilage element EMAPA-modified foot cartilage condensation EMAPA:32657 ossicle element auditory skeletal element middle ear ossicle element uberon ear ossicle element ear ossicles element middle ear skeletal element ossicle element of ear ossicle element of inner ear ossicular chain element UBERON:0035130 auditory ossicle endochondral element MA PMID:11523816 PMID:11237469 https://github.com/obophenotype/uberon/wiki/The-neural-crest ossicle element EMAPA:17824 Wikipedia:Auditory_ossicle middle ear ossicle element MP:0005105 ear ossicles element ossicular chain element EMAPA:35979 ossicle cartilage condensation uberon UBERON:0035131 auditory ossicle cartilage element ossicle cartilage condensation EMAPA:35979 EMAPA:35982 ossicle pre-cartilage condensation uberon UBERON:0035132 auditory ossicle pre-cartilage element ossicle pre-cartilage condensation EMAPA:35982 Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 NCIT:C29667 SCTID:261060002 UMLS:C0489451 surface of body uberon UBERON:0035159 entire surface of organism Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 surface of body FMA:61695 The flattened aspect of the prostate with a slight furrow facing the rectum and anus. FMA:19592 NCIT:C13095 SCTID:279697005 UMLS:C0227961 facies posterior (prostatae) facies posterior prostatae posterior surface of prostate gland uberon UBERON:0035165 posterior surface of prostate lexical The flattened aspect of the prostate with a slight furrow facing the rectum and anus. ncithesaurus:Posterior_Surface_of_the_Prostate facies posterior (prostatae) FMA:19592 facies posterior prostatae FMA:19592 FMA:TA posterior surface of prostate gland FMA:19592 The organ of hearing located on the right side of the head. FMA:53641 NCIT:C81285 SCTID:368570004 UMLS:C0229298 uberon UBERON:0035174 right ear The organ of hearing located on the right side of the head. ncithesaurus:Right_Ear The tubules that carry lymph throughout the body that are just beneath the surface of the skin. FMA:52011 NCIT:C33663 SCTID:20315002 UMLS:C1282745 superficial lymph vessel uberon UBERON:0035198 superficial lymphatic vessel The tubules that carry lymph throughout the body that are just beneath the surface of the skin. ncithesaurus:Superficial_Lymphatic_Vessel superficial lymph vessel FMA:52011 FMA:70506 NCIT:C32837 SCTID:360629008 UMLS:C1182571 internal carotid arterial subdivision subdivision of internal carotid artery uberon UBERON:0035237 branch of internal carotid artery internal carotid arterial subdivision FMA:70506 subdivision of internal carotid artery FMA:70506 FMA:55032 NCIT:C12240 SCTID:276960004 UMLS:C0227155 uberon UBERON:0035240 posterior wall of oropharynx The narrowest portion of the gallbladder and distal to the cystic duct. FMA:14538 NCIT:C32649 SCTID:245394007 UMLS:C0227546 Wikipedia:Neck_of_gallbladder cervix of gallbladder gallbladder neck uberon UBERON:0035267 neck of gallbladder The narrowest portion of the gallbladder and distal to the cystic duct. ncithesaurus:Gallbladder_Neck cervix of gallbladder FMA:14538 gallbladder neck FMA:14538 FMA:55008 NCIT:C12239 SCTID:362125007 UMLS:C0227156 uberon UBERON:0035286 lateral wall of oropharynx The organ of hearing located on the left side of the head[ncit,modified]. FMA:53642 NCIT:C81259 SCTID:368592000 UMLS:C0229299 uberon UBERON:0035295 left ear The organ of hearing located on the left side of the head[ncit,modified]. http://orcid.org/0000-0002-6601-2165 ncithesaurus:Left_Ear FMA:55063 NCIT:C12249 SCTID:276966005 UMLS:C0227174 posterior wall of hypopharynx uberon UBERON:0035313 posterior wall of laryngopharynx posterior wall of hypopharynx FMA:55063 The membrane the surrounds the prostate gland. FMA:19583 NCIT:C13086 SCTID:279682007 UMLS:C0227963 capsule of prostate capsule of prostate gland uberon UBERON:0035316 prostatic capsule The membrane the surrounds the prostate gland. ncithesaurus:Capsule_of_the_Prostate capsule of prostate FMA:19583 capsule of prostate gland FMA:19583 FMA:14765 NCIT:C33474 SCTID:283392005 UMLS:C0226362 trunk of right common iliac arterial tree uberon UBERON:0035322 right common iliac artery trunk of right common iliac arterial tree FMA:14765 FMA:54908 NCIT:C12244 SCTID:361937006 UMLS:C0225486 lateral nasopharynx uberon UBERON:0035383 lateral wall of nasopharynx lateral nasopharynx FMA:54908 FMA:70505 NCIT:C32552 SCTID:244216003 UMLS:C0447038 external carotid arterial subdivision subdivision of external carotid artery uberon UBERON:0035398 branch of external carotid artery external carotid arterial subdivision FMA:70505 subdivision of external carotid artery FMA:70505 FMA:54907 NCIT:C12243 SCTID:361936002 UMLS:C0225484 posterior nasopharynx uberon UBERON:0035401 posterior wall of nasopharynx posterior nasopharynx FMA:54907 An artery that supplies the pituitary gland. uberon UBERON:0035403 hypophysial artery An artery that supplies the pituitary gland. http://orcid.org/0000-0002-6601-2165 The parietal pleura that lines the mediastinum. FMA:9736 NCIT:C94820 SCTID:362002008 UMLS:C0225789 Wikipedia:Mediastinal_pleura mediastinal part of parietal pleura pars mediastinalis (pleurae) pars mediastinalis pleurae parietalis uberon UBERON:0035431 mediastinal pleura FMA FMA The parietal pleura that lines the mediastinum. ncithesaurus:Mediastinal_Pleura mediastinal part of parietal pleura FMA:9736 pars mediastinalis (pleurae) FMA:9736 pars mediastinalis pleurae parietalis FMA:9736 FMA:TA A vein that drains blood from the right adrenal gland into the inferior vena cava. FMA:14343 NCIT:C53131 SCTID:69354005 UMLS:C0226721 vena suprarenalis (adrenalis) dextra uberon UBERON:0035435 right suprarenal vein A vein that drains blood from the right adrenal gland into the inferior vena cava. ncithesaurus:Right_Suprarenal_Vein vena suprarenalis (adrenalis) dextra FMA:14343 A space inside the uterus lined by a layer of mucus membranes called the endometrium. FMA:18076 NCIT:C32514 SCTID:362257002 UMLS:C0227844 Wikipedia:Uterine_cavity cavity of body of uterus endometrial cavity endometrial lumen intrauterine cavity uberon UBERON:0035465 endometrial cavity A space inside the uterus lined by a layer of mucus membranes called the endometrium. ncithesaurus:Endometrial_Cavity cavity of body of uterus FMA:18076 endometrial cavity FMA:18076 intrauterine cavity FMA:18076 FMA:15590 NCIT:C32895 SCTID:279376000 UMLS:C0227610 facies posterior (Ren) facies posterior renis uberon UBERON:0035471 posterior surface of kidney facies posterior (Ren) FMA:15590 facies posterior renis FMA:15590 FMA:TA The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces. FMA:19590 NCIT:C13091 SCTID:279694003 UMLS:C0426735 prostatic surface surface of prostate gland uberon UBERON:0035480 surface of prostate The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces. ncithesaurus:Surface_of_the_Prostate prostatic surface FMA:19590 surface of prostate gland FMA:19590 A vein that drains blood from the left adrenal gland into the left renal artery. FMA:14349 NCIT:C53138 SCTID:85087001 UMLS:C0226709 Wikipedia:Suprarenal_veins uberon UBERON:0035483 left suprarenal vein A vein that drains blood from the left adrenal gland into the left renal artery. ncithesaurus:Left_Suprarenal_Vein The aspect of the prostate facing the pubic symphysis. FMA:19591 NCIT:C13089 SCTID:279696001 UMLS:C0227960 anterior surface of prostate gland facies anterior (prostatae) facies anterior prostatae uberon UBERON:0035523 anterior surface of prostate The aspect of the prostate facing the pubic symphysis. ncithesaurus:Anterior_Surface_of_the_Prostate anterior surface of prostate gland FMA:19591 facies anterior (prostatae) FMA:19591 facies anterior prostatae FMA:19591 FMA:TA FMA:14766 NCIT:C32957 SCTID:283493001 UMLS:C0226363 trunk of left common iliac arterial tree uberon UBERON:0035529 left common iliac artery trunk of left common iliac arterial tree FMA:14766 Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 NCIT:C32535 SCTID:56548006 UMLS:C0226294 aortic esophageal artery oesophageal artery uberon UBERON:0035539 esophageal artery FMA FMA Any of several arteries that arise from the aorta and supply blood to the esophagus. ncithesaurus:Esophageal_Artery aortic esophageal artery FMA:4149 oesophageal artery FMA:4149 The tubules that carry lymph throughout the body that are in the interior of the body or limbs. FMA:52012 NCIT:C32439 SCTID:14033005 UMLS:C1282746 deep lymph vessel uberon UBERON:0035545 deep lymphatic vessel The tubules that carry lymph throughout the body that are in the interior of the body or limbs. ncithesaurus:Deep_Lymphatic_Vessel deep lymph vessel FMA:52012 FMA:51797 SCTID:149683007 ciliary vein uberon UBERON:0035546 uveal vein ciliary vein FMA:51797 SCTID:77852007 uberon UBERON:0035548 colic artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. FMA:225275 superficial part of circulatory system superficial vasculature dermis vasculature hypodermis vasculature uberon skin vasculature subcutaneous vasculature vasculature of skin UBERON:0035549 vasculature of integument The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. http://orcid.org/0000-0002-6601-2165 vasculature of skin FMA:225275 Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. FMA:76719 NCIT:C33666 SCTID:341382008 UMLS:C0226513 Wikipedia:Superficial_vein uberon superfical vein superficial veins superficial vessels UBERON:0035550 superficial vein Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. ncithesaurus:Superficial_Vein superfical vein Wikipedia:Superficial_vein superficial veins Wikipedia:Superficial_vein superficial vessels Wikipedia:Superficial_vein The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. deep part of circulatory system uberon UBERON:0035551 deep vasculature The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. http://orcid.org/0000-0002-6601-2165 A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. FMA:76718 NCIT:C32444 SCTID:341484008 UMLS:C0226514 Wikipedia:Deep_vein uberon deep veins deep vessels UBERON:0035552 deep vein A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. ncithesaurus:Deep_Vein deep veins Wikipedia:Deep_vein deep vessels Wikipedia:Deep_vein Any chamber of the left side of the heart. FMA:7166 SCTID:362008007 uberon UBERON:0035553 left cardiac chamber Any chamber of the left side of the heart. http://orcid.org/0000-0002-6601-2165 Any chamber of the right side of the heart. FMA:7165 SCTID:362007002 uberon UBERON:0035554 right cardiac chamber Any chamber of the right side of the heart. http://orcid.org/0000-0002-6601-2165 An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 ophthalmic lobe of trigeminal placode ophthalmic lobe of trigeminal placode complex ophthalmic placode profundus placode uberon UBERON:0035597 profundal placode An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. PMID:21452441 XAO:0004093 https://github.com/obophenotype/uberon/issues/693 ophthalmic lobe of trigeminal placode NCBIBook:NBK53171 ophthalmic lobe of trigeminal placode complex NCBIBook:NBK53171 ophthalmic placode PMID:22512454 profundus placode XAO:0004093 FMA:61298 cartilage of acoustic meatus cartilage of auditory canal cartilago meatus acustici external acoustic meatus cartilage uberon UBERON:0035606 cartilage of external acoustic meatus cartilage of acoustic meatus FMA:61298 cartilage of auditory canal FMA:61298 cartilago meatus acustici FMA:TA external acoustic meatus cartilage FMA:61298 Any lymph vessel that is located in the dura mater of the brain. while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura dural lymph vessel uberon dural lymph vasculature UBERON:0035608 Louveau et al (DOI:10.1038/nature14432) claim the discovery of lymphatics in the cerebral dura mater, but this is disputed by Bucchieri et al (DOI:10.1111/joa.12381) dura mater lymph vessel Any lymph vessel that is located in the dura mater of the brain. DOI:10.1038/nature14432 DOI:10.1111/joa.12381 A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. consult http://www.ncbi.nlm.nih.gov/pubmed/25312359 to add missing structures, e.g. ectoturbinals unossified in dinosaurs[http://palaeos.com/vertebrates/bones/braincase/ethmoid.html] nasal turbinal nasal turbinal element nasal turbinate turbinal turbinate uberon concha conchae nasales nasal concha UBERON:0035612 nasal turbinal ISBN:0073040584 A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. UBERON:cjm Wikipedia:Nasal_concha http://palaeos.com/vertebrates/bones/braincase/ethmoid.html turbinal http://palaeos.com/vertebrates/bones/braincase/ethmoid.html concha EMAPA:25093 conchae nasales Wikipedia:Nasal_concha The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. FMA:76554 NCIT:C32574 SCTID:120612006 UMLS:C0229243 Wikipedia:Accessory_visual_structures adnexa oculi uberon accessory parts of orbital region accessory visual structures accessory visual structures set adnexal parts of orbital region appendage of eye appendages of the eye eye adnexa set of accessory visual structures structurae oculi accessoriae UBERON:0035639 ocular adnexa The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. HPO:pr UBERON:cjm http://medical-dictionary.thefreedictionary.com/ocular+adnexa https://github.com/obophenotype/uberon/issues/1132 adnexa oculi http://medical-dictionary.thefreedictionary.com/ocular+adnexa accessory visual structures FMA:76554 Wikipedia:Accessory_visual_structures accessory visual structures set FMA:76554 appendage of eye http://medical-dictionary.thefreedictionary.com/ocular+adnexa appendages of the eye http://medical-dictionary.thefreedictionary.com/ocular+adnexa set of accessory visual structures FMA:76554 structurae oculi accessoriae Wikipedia:Accessory_visual_structures Any nerve that innervates the larynx. MESH:D007823 SCTID:307013006 uberon UBERON:0035642 laryngeal nerve Any nerve that innervates the larynx. UBERON:cjm Any nerve that innervates the pinna. EMAPA:36513 MA:0001232 auricular nerve uberon UBERON:0035648 nerve innervating pinna FMA Any nerve that innervates the pinna. UBERON:cjm auricular nerve MA:0001232 Any nerve that innervates the penis. EMAPA:35057 penile nerve penis nerve uberon UBERON:0035649 nerve of penis Any nerve that innervates the penis. UBERON:cjm Any nerve that innervates the clitoris. EMAPA:35044 clitoral nerve clitoris nerve uberon UBERON:0035650 nerve of clitoris Any nerve that innervates the clitoris. UBERON:cjm Wikipedia:Glans uberon UBERON:0035651 glans EHDAA2:0004181 FMA:9464 cardiac chamber cavity heart cavity heart lumen uberon UBERON:0035763 cavity of cardiac chamber FMA cardiac chamber cavity FMA:9464 heart cavity FMA:9464 heart lumen EHDAA2:0004181 FMA:5968 intrapulmonary lymph node pulmonary node uberon UBERON:0035764 pulmonary lymph node intrapulmonary lymph node FMA:5968 pulmonary node FMA:5968 FMA:223208 NCIT:C12930 UMLS:C1512970 uberon UBERON:0035767 intrapulmonary bronchus The region between the mandible and the hyoid bone that contains the submandibular and sublingual glands, suprahyoid muscles, submandibular ganglion, and lingual artery. we place submandibular triangle from FMA here, although this may be a narrower region with more precise boundaries FMA:57779 Wikipedia:Submandibular_triangle digastric triangle submandibular triangle submaxillary triangle trigonum submandibulare uberon UBERON:0035775 submandibular region https://upload.wikimedia.org/wikipedia/commons/thumb/3/36/Musculi_coli_base%2C_my_edits_for_tringles%2C_labeled_triangles%2C_Submandib.svg/500px-Musculi_coli_base%2C_my_edits_for_tringles%2C_labeled_triangles%2C_Submandib.svg.png The region between the mandible and the hyoid bone that contains the submandibular and sublingual glands, suprahyoid muscles, submandibular ganglion, and lingual artery. https://github.com/obophenotype/uberon/issues/1137 we place submandibular triangle from FMA here, although this may be a narrower region with more precise boundaries FMA digastric triangle FMA:57779 Wikipedia:Submandibular_triangle submandibular triangle FMA:57779 submaxillary triangle FMA:57779 Wikipedia:Submandibular_triangle trigonum submandibulare FMA:TA A portion of semen in a coagulated state. seminal coagulum uberon UBERON:0035784 seminal clot A portion of semen in a coagulated state. PMID:18482984 http://orcid.org/0000-0002-6601-2165 seminal coagulum PMID:18482984 The primordial mouth region of the developing head. FMA:293105 primitive mouth primordial mouth uberon UBERON:0035804 future mouth The primordial mouth region of the developing head. MP:0003119 primitive mouth FMA:293105 A muscle layer that is part of the sigmoid colon. FMA:15028 muscularis externa of sigmoid colon muscularis propria of sigmoid colon sigmoid colon muscularis propria uberon sigmoideum muscularis tunica muscularis colon sigmoideum UBERON:0035805 muscle layer of sigmoid colon A muscle layer that is part of the sigmoid colon. https://github.com/obophenotype/uberon/issues/1162 muscularis externa of sigmoid colon FMA:15028 FMA:12241 SCTID:304404008 uberon UBERON:0035809 serous cavity The sum of epicardial and paracardial fat deposits. SCTID:42267001 ZFA:0005765 uberon UBERON:0035814 pericardial fat The sum of epicardial and paracardial fat deposits. DOI:10.5935/abc.20130138 Fat deposits in the mediastinum outside the parietal pericardium . intrathoracic fat uberon UBERON:0035815 paracardial fat Fat deposits in the mediastinum outside the parietal pericardium . DOI:10.5935/abc.20130138 intrathoracic fat DOI:10.5935/abc.20130138 Any fat deposit surrounding a visceral organ. uberon UBERON:0035818 visceral fat Any fat deposit surrounding a visceral organ. UBERON:cjm The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. FMA:12267 Wikipedia:Abdominopelvic_cavity cavitas abdominis et pelvis uberon UBERON:0035819 abdominopelvic cavity The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. UBERON:cjm cavitas abdominis et pelvis FMA:TA A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. EMAPA:16137 FMA:9908 uberon peritoneal component UBERON:0035820 peritoneal sac A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. https://github.com/obophenotype/uberon/issues/86 peritoneal component EMAPA:16137 The thick outer layer of the adrenal gland that is in the left side of the abdomen. FMA:69089 cortex of left adrenal gland cortex of left suprarenal gland left adrenal cortex uberon UBERON:0035825 left adrenal gland cortex true The thick outer layer of the adrenal gland that is in the left side of the abdomen. https://github.com/obophenotype/uberon/issues/1170 cortex of left adrenal gland FMA:69089 cortex of left suprarenal gland FMA:69089 left adrenal cortex FMA:69089 The adrenal gland medulla that is in the left side of the abdomen. FMA:69092 left adrenal medulla medulla of left adrenal gland medulla of left suprarenal gland uberon UBERON:0035826 left adrenal gland medulla true The adrenal gland medulla that is in the left side of the abdomen. https://github.com/obophenotype/uberon/issues/1170 left adrenal medulla FMA:69092 medulla of left adrenal gland FMA:69092 medulla of left suprarenal gland FMA:69092 The thick outer layer of the adrenal gland that is in the right side of the abdomen. FMA:69088 cortex of right adrenal gland cortex of right suprarenal gland right adrenal cortex uberon UBERON:0035827 right adrenal gland cortex true The thick outer layer of the adrenal gland that is in the right side of the abdomen. https://github.com/obophenotype/uberon/issues/1170 cortex of right adrenal gland FMA:69088 cortex of right suprarenal gland FMA:69088 right adrenal cortex FMA:69088 The adrenal gland medulla that is in the right side of the abdomen. FMA:69091 medulla of right adrenal gland medulla of right suprarenal gland right adrenal medulla uberon UBERON:0035828 right adrenal gland medulla true The adrenal gland medulla that is in the right side of the abdomen. https://github.com/obophenotype/uberon/issues/1170 medulla of right adrenal gland FMA:69091 medulla of right suprarenal gland FMA:69091 right adrenal medulla FMA:69091 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. FMA:58277 SCTID:368048007 costal part of diaphragm pars costalis diaphragmatis uberon UBERON:0035831 costal diaphragm PMID:23586979 PMID:23586979 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. PMID:23586979 costal part of diaphragm FMA:58277 pars costalis diaphragmatis FMA:TA The lumen of the epididymis. FMA:18274 SCTID:367722009 epididymis lumen lumen of epididymis uberon UBERON:0035956 epididymal lumen FMA The lumen of the epididymis. GOC:DOS https://github.com/obophenotype/uberon/issues/1209 epididymis lumen FMA:18274 lumen of epididymis FMA:18274 BTO:0004378 EMAPA:37987 FMA:67473 blood vessel wall uberon vascular wall UBERON:0035965 wall of blood vessel EMAPA:37987 MA:th blood vessel wall FMA:67473 vascular wall BTO:0004378 The lower portion of the larynx, extending from just beneath the vocal cords down to the top of the trachea. the structures in the subglottis are implicated in the regulation of the temperature of the breath EMAPA:37969 FMA:55477 NCIT:C12280 SCTID:281511009 infraglottic part of larynx subglottic larynx subglottic region uberon UBERON:0036068 subglottis The lower portion of the larynx, extending from just beneath the vocal cords down to the top of the trachea. MP:0030000 Wikipedia:Subglottis https://orcid.org/0000-0002-6490-7723 EMAPA:37969 MA:th infraglottic part of larynx FMA:55477 subglottic larynx FMA:55477 subglottic region MP:0030000 EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium EHDAA2 EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme EHDAA2 respiratory primordium associated mesenchyme EHDAA2:0004071 An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. uberon UBERON:0036146 cardiopharyngeal field An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1 https://orcid.org/0000-0003-3308-6245 An organ subunit in the skin that gives rise to cutaneous appendage. follicle cutaneous appendage follicle skin follicle uberon UBERON:0036150 skin appendage follicle An organ subunit in the skin that gives rise to cutaneous appendage. UBERON:cjm https://github.com/obophenotype/uberon/issues/1266 FMA:83520 uberon UBERON:0036186 fibroelastic connective tissue An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 SCTID:245429006 uberon rectosigmoid region UBERON:0036214 rectosigmoid junction An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 https://github.com/obophenotype/uberon/issues/1319 https://www.cdc.gov/cancer/npcr/pdf/abstracting/colon.pdf rectosigmoid region NCIT:C54188 Material anatomical entity that forms the outermost boundary of an anatomical structure. AAO:0010270 ZFA:0005594 uberon UBERON:0036215 anatomical surface region Material anatomical entity that forms the outermost boundary of an anatomical structure. https://github.com/obophenotype/uberon/issues/1324 A bodily fluid that is located in the coelom. he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid] BTO:0001708 uberon UBERON:0036217 coelomic fluid A bodily fluid that is located in the coelom. PMID:10874572 https://github.com/obophenotype/uberon/issues/1326 Any gland that is part os the respiratory system. uberon UBERON:0036225 respiratory system gland Any gland that is part os the respiratory system. UBERON:cjm A notochord that has persisted beyond the embryonic stage. uberon UBERON:0036242 post-embryonic notochord A notochord that has persisted beyond the embryonic stage. UBERON:cjm Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. BTO:0003084 uberon vaginal discharge vaginal secretion UBERON:0036243 vaginal fluid Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. http://www.bumc.bu.edu/sexualmedicine/physicianinformation/female-genital-anatomy/ BTO:0003084 https://github.com/biopragmatics/biomappings A transudate found in the serous sac. serous fluid FMA:20932 serous sac fluid uberon UBERON:0036244 secretion of serous membrane A transudate found in the serous sac. FMA:20932 serous fluid FMA:20932 Parenchymal tissue that consists of the alveoli, grape-like clusters where milk is stored, and branching ducts, which are tubular canals carrying gladular secretions. lactiferous gland parenchyma mammary gland parenchyma parenchyma of lactiferous gland uberon UBERON:0036245 parenchyma of mammary gland Parenchymal tissue that consists of the alveoli, grape-like clusters where milk is stored, and branching ducts, which are tubular canals carrying gladular secretions. http://www.newworldencyclopedia.org/entry/Mammary_gland https://github.com/obophenotype/uberon/issues/1349 https://orcid.org/0000-0003-3308-6245 Any synovial joint that connects auditory ossicles. FMA:60063 auditory ossicle joint auditory ossicles joint joint of auditory ossicles uberon UBERON:0036248 joint of auditory ossicle Any synovial joint that connects auditory ossicles. UBERON:cjm auditory ossicles joint FMA:60063 joint of auditory ossicles FMA:60063 FMA:53133 cranial orifice skull orifice uberon UBERON:0036253 orifice of skull cranial orifice FMA:53133 skull orifice FMA:53133 Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments. NCIT:C61360 SCTID:272668006 uberon UBERON:0036262 uterine ligament Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments. NCIT:C61360 The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. FMA:52972 SCTID:280243001 Wikipedia:Zygomaticotemporal_nerve ramus zygomaticotemporalis (Nervus zygomaticus) ramus zygomaticotemporalis nervus zygomatici zygomaticotemporal branch of zygomatic nerve uberon zygomaticotemporal zygomaticotemporal branch UBERON:0036264 zygomaticotemporal nerve The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. Wikipedia:Zygomaticotemporal_nerve ramus zygomaticotemporalis (Nervus zygomaticus) FMA:52972 ramus zygomaticotemporalis nervus zygomatici FMA:TA zygomaticotemporal branch of zygomatic nerve FMA:52972 zygomaticotemporal Wikipedia:Zygomaticotemporal_nerve zygomaticotemporal branch Wikipedia:Zygomaticotemporal_nerve SCTID:279975006 uberon UBERON:0036267 vulval vein SCTID:13152008 uberon UBERON:0036268 pelvic vein EMAPA:30807 SCTID:363673006 uberon penis vasculature vasculature of penis UBERON:0036269 penis blood vessel vasculature of penis EMAPA:30807 Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall uberon UBERON:0036285 wall of left ventricle FMA FMA Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall FMA:9556 Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall uberon UBERON:0036286 wall of right ventricle FMA FMA Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall FMA:9533 FMA:9560 uberon UBERON:0036288 anterior wall of left ventricle FMA Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 uberon UBERON:0036289 anterior wall of right ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 FMA:87177 uberon UBERON:0036290 myocardium of anterior wall of left ventricle FMA:260877 uberon UBERON:0036291 myocardium of anterior wall of right ventricle A mucosa that is part of a lip region [Automatically generated definition]. NCIT:C12226 labial mucosa uberon UBERON:0036294 mucosa of lip A mucosa that is part of a lip region [Automatically generated definition]. OBOL:automatic labial mucosa UBERON:cjm The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 renal pelvis and ureter renal pelvis plus ureter uberon UBERON:0036295 renal pelvis/ureter NCIT The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 FMA:225251 SCTID:297287005 uberon UBERON:0036301 vasculature of spleen FMA uberon UBERON:0036302 vasculature of central nervous system plus retina FMA:259905 uberon UBERON:0036303 vasculature of central nervous system An anatomical structure that is located along the line dividing two regions of an anatomical structure. uberon UBERON:0036304 anatomical border An anatomical structure that is located along the line dividing two regions of an anatomical structure. UBERON:cjm FMA:14179 coronary arterial wall uberon UBERON:0036328 wall of coronary artery FMA FMA coronary arterial wall FMA:14179 FMA:14621 appendix wall wall of vermiform appendix uberon UBERON:0036337 wall of appendix FMA FMA appendix wall FMA:14621 wall of vermiform appendix FMA:14621 FMA:14657 gallbladder wall uberon UBERON:0036343 wall of gallbladder FMA gallbladder wall FMA:14657 FMA:15089 brachiocephalic arterial wall uberon UBERON:0036351 wall of brachiocephalic artery FMA FMA brachiocephalic arterial wall FMA:15089 FMA:15090 subclavian arterial wall uberon UBERON:0036352 wall of subclavian artery FMA FMA subclavian arterial wall FMA:15090 FMA:15704 anal canal wall uberon UBERON:0036362 wall of anal canal FMA anal canal wall FMA:15704 FMA:15889 right ureteral wall uberon UBERON:0036375 wall of right ureter FMA FMA right ureteral wall FMA:15889 FMA:15890 left ureteral wall uberon UBERON:0036376 wall of left ureter FMA FMA left ureteral wall FMA:15890 FMA:18211 pulmonary arterial wall uberon UBERON:0036422 wall of pulmonary artery FMA FMA pulmonary arterial wall FMA:18211 FMA:18303 uterine tube wall wall of fallopian tube wall of oviduct uberon UBERON:0036441 wall of uterine tube FMA FMA uterine tube wall FMA:18303 wall of fallopian tube FMA:18303 wall of oviduct FMA:18303 FMA:19779 urethral wall uberon UBERON:0036521 wall of urethra FMA FMA urethral wall FMA:19779 FMA:19971 vaginal wall uberon UBERON:0036523 wall of vagina FMA FMA vaginal wall FMA:19971 FMA:231590 uberon UBERON:0036553 wall of synovial tendon sheath FMA FMA FMA:242772 uberon UBERON:0036654 wall of lateral ventricle FMA FMA:242778 uberon UBERON:0036657 wall of fourth ventricle FMA FMA:242841 uberon UBERON:0036661 wall of ventricular system of brain FMA FMA FMA:58098 eyeball wall uberon UBERON:0036925 wall of eyeball FMA FMA eyeball wall FMA:58098 FMA:63144 orbit wall uberon UBERON:0037089 wall of orbit FMA FMA orbit wall FMA:63144 FMA:66284 common carotid arterial wall uberon UBERON:0037094 wall of common carotid artery FMA FMA common carotid arterial wall FMA:66284 Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall uberon UBERON:0037144 wall of heart FMA FMA FMA FMA Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall FMA:7274 FMA:85375 lacrimal ductal wall uberon UBERON:0037237 wall of lacrimal duct FMA FMA lacrimal ductal wall FMA:85375 FMA:19676 male urethral wall uberon UBERON:0037447 wall of male urethra FMA FMA male urethral wall FMA:19676 FMA:19780 female urethral wall uberon UBERON:0037455 wall of female urethra FMA FMA female urethral wall FMA:19780 FMA:54242 neck hair uberon UBERON:0037458 hair of neck neck hair FMA:54242 FMA:54243 limb hair uberon UBERON:0037459 hair of limb limb hair FMA:54243 FMA:322073 uberon UBERON:0039175 subarachnoid space of brain FMA FMA:322074 uberon UBERON:0039176 subarachnoid space of spinal cord FMA An artery that supplies oxygenated blood to the cystic duct. FMA:14835 cholecystic artery uberon UBERON:0039222 cystic artery https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb FMA Wikipedia An artery that supplies oxygenated blood to the cystic duct. http://orcid.org/0000-0002-6601-2165 https://en.wikipedia.org/wiki/Cystic_artery cholecystic artery FMA:14835 FMA:15395 uberon UBERON:0039228 sigmoid vein FMA FMA:70471 uberon UBERON:0039261 pancreatic artery FMA:20903 arteria urethralis uberon UBERON:0039355 urethral artery arteria urethralis A12.2.15.042 A vein that drains the urethra. FMA:21270 uberon UBERON:0039377 urethral vein FMA A vein that drains the urethra. UBERON:cjm Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament. FMA:14342 uberon UBERON:0039856 right ovarian vein FMA FMA Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament. FMA:14342 Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament. FMA:14347 uberon UBERON:0039857 left ovarian vein FMA Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament. FMA:14347 A collection of hairs that grows on the external ear. uberon external ear hair UBERON:1000004 collection of hair on external ear A collection of hairs that grows on the external ear. UBERON:EJS https://github.com/obophenotype/uberon/issues/34 A collection of hairs that grows on the forehead. uberon UBERON:1000006 collection of hair on forehead A collection of hairs that grows on the forehead. UBERON:EJS https://github.com/obophenotype/uberon/issues/34 A zone of skin that is part of the face. 2012-02-05T05:23:01Z EMAPA:36657 FMA:24758 NCIT:C33561 SCTID:361703006 UMLS:C0222084 face skin uberon facial skin UBERON:1000021 skin of face A zone of skin that is part of the face. UBERON:EJS https://github.com/obophenotype/uberon/issues/34 UMLS:C0222084 ncithesaurus:Skin_of_the_Face face skin EMAPA:36657 FMA:24758 A parenchyma that is part of a spleen. FMA:16029 splenic parenchyma uberon UBERON:1000024 parenchyma of spleen A parenchyma that is part of a spleen. OBOL:automatic splenic parenchyma FMA:16029 An anatomical junction between two parts of the digestive tract. 2021-02-05T11:19:31Z uberon UBERON:1100000 digestive tract junction An anatomical junction between two parts of the digestive tract. https://orcid.org/0000-0002-7073-9172 EFO:0003612 TAO:0001053 ZFA:0001053 PICA primitive internal carotid artery uberon UBERON:2001053 future internal carotid artery EHDAA2 PICA TAO:0001053 primitive internal carotid artery ZFA:0001053 This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0001073 uberon UBERON:2001073 axial vasculature This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl Fin or limb undergoing the process of regeneration. EFO:0003657 TAO:0001269 ZFA:0001269 regenerating fins uberon UBERON:2001269 regenerating fin/limb Fin or limb undergoing the process of regeneration. https://orcid.org/0000-0002-6601-2165 regenerating fins ZFA:0001269 This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0001371 uberon UBERON:2001371 pancreatic system This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl An epithelium that is part of a regenerating fin/limb. epidermal cap wound epidermis wound epithelium EFO:0003682 TAO:0001389 ZFA:0001389 epidermal cap of fin wound epidermis of fin wound epithelium of fin uberon UBERON:2001389 regeneration epithelium of fin/limb An epithelium that is part of a regenerating fin/limb. OBOL:automatic epidermal cap ZFA:0001389 wound epidermis ZFA:0001389 wound epithelium ZFA:0001389 Cartilage which is part of the axial skeleton. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0001457 uberon UBERON:2001457 postcranial axial cartilage Cartilage which is part of the axial skeleton. ZFIN:curator This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse. the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]. fenestrated blood vessel endothelium FMA:63196 NCIT:C32595 TAO:0005260 UMLS:C1179615 Wikipedia:Capillary#Types ZFA:0005260 fenestrated capillary vessel uberon UBERON:2005260 fenestrated capillary FMA ZFA Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse. Wikipedia:Capillary#Types Wikipedia:Fenestra_(histology) fenestrated blood vessel endothelium ZFA:0005260 UMLS:C1179615 ncithesaurus:Fenestrated_Capillary fenestrated capillary vessel FMA:63196 Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0007013 uberon UBERON:2007013 preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. ZFIN:curator This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/tao.owl Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000961 Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the external head integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000972 head external integument structure Dermal, epidermal, glandular and pigment structures of the external head integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the body integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000977 body external integument structure Dermal, epidermal, glandular and pigment structures of the body integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the limb integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000981 limb external integument structure Dermal, epidermal, glandular and pigment structures of the limb integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Dermal, epidermal, glandular and pigment structures of the tail integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3000982 tail external integument structure Dermal, epidermal, glandular and pigment structures of the tail integument. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Blood vessels in respiratory skin. Modified from the original AAO source This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:3010200 vasculature of respiratory integument Blood vessels in respiratory skin. AAO:EJS This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/aao.owl Skeletal tissue that is mineralized. mineralized tissue VSAO:0000013 XAO:0004039 uberon UBERON:4000013 mineralized skeletal tissue Skeletal tissue that is mineralized. XAO:0004039 XAO:EJS mineralized tissue VSAO:0000013 Extracellular matrix that is mineralized. This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:4000020 mineralized extracellular matrix Extracellular matrix that is mineralized. PSPUB:0000170 This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/vsao.owl Bone tissue mineralized with hydroxyapatite. This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon uberon UBERON:4000115 mineralized bone tissue Bone tissue mineralized with hydroxyapatite. PSPUB:0000170 This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon http://purl.obolibrary.org/obo/vsao.owl Anatomical projection that is composed of bone or cartilage tissue. uberon UBERON:4100000 skeletal element projection Anatomical projection that is composed of bone or cartilage tissue. PHENOSCAPE FMA:23356 NCIT:C33164 collum anatomicum (Humerus) collum anatomicum humeri humeral neck uberon anatomic neck of humerus UBERON:4200172 neck of humerus collum anatomicum (Humerus) FMA:23356 collum anatomicum humeri FMA:23356 FMA:TA anatomic neck of humerus FMA:23356 An anatomical surface that is part of a bone. bone surface uberon UBERON:4200230 surface of bone An anatomical surface that is part of a bone. PHENOSCAPE Mesenchyme that is part of a forelimb bud. uberon UBERON:4300226 forelimb bud mesenchyme Mesenchyme that is part of a forelimb bud. PHENOSCAPE Mesenchyme that is part of a hindlimb bud. uberon UBERON:4300227 hindlimb bud mesenchyme Mesenchyme that is part of a hindlimb bud. PHENOSCAPE A wing bud that develops into a wing. uberon UBERON:4300230 forelimb wing bud A wing bud that develops into a wing. PHENOSCAPE Mesenchyme that is part of a forelimb wing bud. uberon UBERON:4300231 forelimb wing bud mesenchyme Mesenchyme that is part of a forelimb wing bud. PHENOSCAPE A subdivision of the autopod consisting of manual digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit 1 manual digit 1 ( phalanges plus metapodial) plus soft tissue manual digit 1 digitopodial subdivision manual digit 1 ray manual digit I plus metapodial segment uberon UBERON:5001463 manual digit 1 plus metapodial segment A subdivision of the autopod consisting of manual digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 manual digit 1 http://orcid.org/0000-0002-6601-2165 manual digit 1 ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 manual digit 1 digitopodial subdivision http://orcid.org/0000-0002-6601-2165 manual digit 1 ray http://orcid.org/0000-0002-6601-2165 manual digit I plus metapodial segment https://github.com/obophenotype/uberon/issues/458 A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit pedal digit ( phalanges plus metapodial) plus soft tissue pedal digit digitopodial subdivision pedal digit ray uberon UBERON:5001466 pedal digit plus metapodial segment A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 pedal digit http://orcid.org/0000-0002-6601-2165 pedal digit ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 pedal digit digitopodial subdivision http://orcid.org/0000-0002-6601-2165 pedal digit ray http://orcid.org/0000-0002-6601-2165 A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit manual digit ( phalanges plus metapodial) plus soft tissue manual digit digitopodial subdivision manual digit ray uberon UBERON:5002389 manual digit plus metapodial segment A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 manual digit http://orcid.org/0000-0002-6601-2165 manual digit ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 manual digit digitopodial subdivision http://orcid.org/0000-0002-6601-2165 manual digit ray http://orcid.org/0000-0002-6601-2165 A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit digit ( phalanges plus metapodial) plus soft tissue digit digitopodial subdivision digit ray uberon UBERON:5002544 digit plus metapodial segment A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 digit http://orcid.org/0000-0002-6601-2165 digit ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 digit digitopodial subdivision http://orcid.org/0000-0002-6601-2165 digit ray http://orcid.org/0000-0002-6601-2165 A subdivision of the autopod consisting of manual digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit 5 manual digit 5 ( phalanges plus metapodial) plus soft tissue manual digit 5 digitopodial subdivision manual digit 5 ray manual digit V plus metapodial segment uberon UBERON:5003625 manual digit 5 plus metapodial segment A subdivision of the autopod consisting of manual digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 manual digit 5 http://orcid.org/0000-0002-6601-2165 manual digit 5 ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 manual digit 5 digitopodial subdivision http://orcid.org/0000-0002-6601-2165 manual digit 5 ray http://orcid.org/0000-0002-6601-2165 manual digit V plus metapodial segment https://github.com/obophenotype/uberon/issues/458 A subdivision of the autopod consisting of pedal digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit 1 pedal digit 1 ( phalanges plus metapodial) plus soft tissue pedal digit 1 digitopodial subdivision pedal digit 1 ray pedal digit I plus metapodial segment uberon UBERON:5003631 pedal digit 1 plus metapodial segment A subdivision of the autopod consisting of pedal digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 pedal digit 1 http://orcid.org/0000-0002-6601-2165 pedal digit 1 ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 pedal digit 1 digitopodial subdivision http://orcid.org/0000-0002-6601-2165 pedal digit 1 ray http://orcid.org/0000-0002-6601-2165 pedal digit I plus metapodial segment https://github.com/obophenotype/uberon/issues/458 A subdivision of the autopod consisting of pedal digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit 5 pedal digit 5 ( phalanges plus metapodial) plus soft tissue pedal digit 5 digitopodial subdivision pedal digit 5 ray pedal digit V plus metapodial segment uberon UBERON:5003635 pedal digit 5 plus metapodial segment A subdivision of the autopod consisting of pedal digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 pedal digit 5 http://orcid.org/0000-0002-6601-2165 pedal digit 5 ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 pedal digit 5 digitopodial subdivision http://orcid.org/0000-0002-6601-2165 pedal digit 5 ray http://orcid.org/0000-0002-6601-2165 pedal digit V plus metapodial segment https://github.com/obophenotype/uberon/issues/458 A subdivision of the autopod consisting of digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit 1 digit 1 ( phalanges plus metapodial) plus soft tissue digit 1 digitopodial subdivision digit 1 ray digit I plus metapodial segment uberon UBERON:5006048 digit 1 plus metapodial segment A subdivision of the autopod consisting of digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 digit 1 http://orcid.org/0000-0002-6601-2165 digit 1 ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 digit 1 digitopodial subdivision http://orcid.org/0000-0002-6601-2165 digit 1 ray http://orcid.org/0000-0002-6601-2165 digit I plus metapodial segment https://github.com/obophenotype/uberon/issues/458 A subdivision of the autopod consisting of digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit 5 digit 5 ( phalanges plus metapodial) plus soft tissue digit 5 digitopodial subdivision digit 5 ray digit V plus metapodial segment uberon UBERON:5006052 digit 5 plus metapodial segment A subdivision of the autopod consisting of digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. http://orcid.org/0000-0002-6601-2165 this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. https://github.com/obophenotype/uberon/issues/458 digit 5 http://orcid.org/0000-0002-6601-2165 digit 5 ( phalanges plus metapodial) plus soft tissue http://orcid.org/0000-0002-6601-2165 digit 5 digitopodial subdivision http://orcid.org/0000-0002-6601-2165 digit 5 ray http://orcid.org/0000-0002-6601-2165 digit V plus metapodial segment https://github.com/obophenotype/uberon/issues/458 A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 1 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. manual digit I digitopodial skeleton uberon manual digit 1 manual digit 1 skeleton UBERON:5101463 manual digit 1 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 1 plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 manual digit I digitopodial skeleton https://github.com/obophenotype/uberon/issues/458 manual digit 1 http://orcid.org/0000-0002-6601-2165 manual digit 1 skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon pedal digit pedal digit skeleton UBERON:5101466 pedal digit digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 pedal digit http://orcid.org/0000-0002-6601-2165 pedal digit skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon manual digit manual digit skeleton UBERON:5102389 manual digit digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 manual digit http://orcid.org/0000-0002-6601-2165 manual digit skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon digit digit skeleton UBERON:5102544 individual digit of digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 digit http://orcid.org/0000-0002-6601-2165 digit skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 5 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. manual digit V digitopodial skeleton uberon manual digit 5 manual digit 5 skeleton UBERON:5103625 manual digit 5 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 5 plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 manual digit V digitopodial skeleton https://github.com/obophenotype/uberon/issues/458 manual digit 5 http://orcid.org/0000-0002-6601-2165 manual digit 5 skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 1 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. pedal digit I digitopodial skeleton uberon pedal digit 1 pedal digit 1 skeleton UBERON:5103631 pedal digit 1 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 1 plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 pedal digit I digitopodial skeleton https://github.com/obophenotype/uberon/issues/458 pedal digit 1 http://orcid.org/0000-0002-6601-2165 pedal digit 1 skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 5 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. pedal digit V digitopodial skeleton uberon pedal digit 5 pedal digit 5 skeleton UBERON:5103635 pedal digit 5 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 5 plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 pedal digit V digitopodial skeleton https://github.com/obophenotype/uberon/issues/458 pedal digit 5 http://orcid.org/0000-0002-6601-2165 pedal digit 5 skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of digit 1 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. digit I digitopodial skeleton uberon digit 1 digit 1 skeleton UBERON:5106048 digit 1 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of digit 1 plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 digit I digitopodial skeleton https://github.com/obophenotype/uberon/issues/458 digit 1 http://orcid.org/0000-0002-6601-2165 digit 1 skeleton http://orcid.org/0000-0002-6601-2165 A subdivision of the skeleton of the autopod consisting of the phalanges of digit 5 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. digit V digitopodial skeleton uberon digit 5 digit 5 skeleton UBERON:5106052 digit 5 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of digit 5 plus the associated metapodial element. http://orcid.org/0000-0002-6601-2165 digit V digitopodial skeleton https://github.com/obophenotype/uberon/issues/458 digit 5 http://orcid.org/0000-0002-6601-2165 digit 5 skeleton http://orcid.org/0000-0002-6601-2165 The proximal-most point of the head of a femur. uberon UBERON:7500046 proximal-most point of head of femur The proximal-most point of the head of a femur. https://orcid.org/0000-0003-2699-3066 The tibial tuberosity is on the anterior side of a tibia and is where a patella ligament attaches. fossa digitalis uberon UBERON:7500062 tibial tuberosity The tibial tuberosity is on the anterior side of a tibia and is where a patella ligament attaches. https://en.wikipedia.org/wiki/Tuberosity_of_the_tibia A suture joining a sphenoid bone with the alae of a vomer to form a schindylesis type of joint. uberon UBERON:7500107 sphenovomerine suture A suture joining a sphenoid bone with the alae of a vomer to form a schindylesis type of joint. DOI:10.1097/SCS.0000000000002945 PMID:27483100 Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. uberon UBERON:8000006 left side of back Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. https://microbiomedb.org/ Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. uberon UBERON:8000007 right side of back Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. https://microbiomedb.org/ A forelimb that is on the right side of a pectoral complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:7185 uberon UBERON:8300001 right forelimb A forelimb that is on the right side of a pectoral complex. UBERONREF:0000003 A forelimb that is on the left side of a pectoral complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:7186 uberon UBERON:8300002 left forelimb A forelimb that is on the left side of a pectoral complex. UBERONREF:0000003 A hindlimb that is on the right side of a pelvic complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:7187 uberon UBERON:8300003 right hindlimb A hindlimb that is on the right side of a pelvic complex. UBERONREF:0000003 A hindlimb that is on the left side of a pelvic complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:7188 uberon UBERON:8300004 left hindlimb A hindlimb that is on the left side of a pelvic complex. UBERONREF:0000003 Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact. serosa of liver tunica serosa hepatis uberon UBERON:8400021 liver serosa Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact. https://medical-dictionary.thefreedictionary.com/serosa+of+liver https://orcid.org/0000-0002-0449-2730 serosa of liver FMA:15811 tunica serosa hepatis https://medical-dictionary.thefreedictionary.com/serosa+of+liver Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson. hepatic subserosa subserosal tissue of liver subserous layer of liver tela subserosa (hepar) tela subserosa hepatis uberon UBERON:8400023 liver subserosa Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson. FMA:15812 https://medical-dictionary.thefreedictionary.com/subserosa+of+liver https://orcid.org/0000-0002-0449-2730 tela subserosa (hepar) FMA:15821 tela subserosa hepatis https://medical-dictionary.thefreedictionary.com/subserosa+of+liver Region of liver parenchyma immediately below the capsule. This region is frequently specified in pathology diagnoses. liver subcapsular region liver subcapsular tissue subcapsular tissue of liver uberon UBERON:8400024 subcapsular region of liver Region of liver parenchyma immediately below the capsule. This region is frequently specified in pathology diagnoses. PMID:30992875 https://orcid.org/0000-0002-0449-2730 liver subcapsular region PMID:30992875 liver subcapsular tissue PMID:30992875 subcapsular tissue of liver PMID:30992875 The anatomical junction between the duodenum and the jejunum. FMA:15957 TA2:2952 WikipediaVersioned:Duodenojejunal_flexure&oldid=937307798 https://orcid.org/0000-0003-4183-8865 duodeno-jejunal flexure duodenojejunal flexure duodenojejunal junction flexura duodenojejunalis uberon UBERON:8410000 duodeno-jejunal junction The anatomical junction between the duodenum and the jejunum. PMID:23961897 PMID:29064554 flexura duodenojejunalis Wikipedia:Duodenojejunal_flexure Venule of villus of small intestine. venule of small intestine uberon UBERON:8410001 small intestine venule Venule of villus of small intestine. https://orcid.org/0000-0003-4183-8865 A lymphatic vessel that supplies the small intestine. lymphatic vessel of small intestine uberon UBERON:8410002 small intestine lymphatic vessel A lymphatic vessel that supplies the small intestine. http://orcid.org/0000-0003-4183-8865 Arteriole of villus of small intestine. arteriole of small intestine arteriole of villus of small intestine small intestine villus arteriole uberon UBERON:8410004 small intestine arteriole Arteriole of villus of small intestine. http://orcid.org/0000-0003-4183-8865 A venule that is located in the anorectum. anorectum venule uberon UBERON:8410008 venule of anorectum A venule that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An arteriole that is located in the anorectum. anorectum arteriole uberon UBERON:8410009 arteriole of anorectum An arteriole that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An arteriole located in the colon. uberon UBERON:8410015 arteriole of colon An arteriole located in the colon. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 The anatomical junction between the descending colon and the sigmoid colon. sigmoid junction descending-sigmoid colon junction descending-sigmoid junction uberon UBERON:8410016 descending sigmoid junction The anatomical junction between the descending colon and the sigmoid colon. PMID:27233374 https://orcid.org/0000-0003-4183-8865 A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery. FMA:15394 uberon UBERON:8410017 left colic vein A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery. WikipediaVersioned:Left_colic_vein&oldid=964575339 https://orcid.org/0000-0003-4183-8865 A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery. FMA:15407 uberon UBERON:8410018 right colic vein A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery. WikipediaVersioned:Right_colic_vein&oldid=870898828 https://orcid.org/0000-0003-4183-8865 The area where the jejunum ends and the ileum part of the intestine begins. Although there is no clear distinct section, the ileum is narrower and has smaller villi than the jejunum. jejunoileal junction uberon UBERON:8410019 jejuno-ileal junction The area where the jejunum ends and the ileum part of the intestine begins. Although there is no clear distinct section, the ileum is narrower and has smaller villi than the jejunum. DOI:10.1016/B978-1-4377-2206-2.00068-3 PMID:21802415 https://orcid.org/0000-0003-4183-8865 A venule located in the vermiform appendix. venule of vermiform appendix vermiform appendix venule uberon UBERON:8410020 venule of appendix A venule located in the vermiform appendix. http://orcid.org/0000-0003-3440-1876 An anatomical junction between two parts of the intestine. junction of intestine uberon UBERON:8410024 intestinal junction An anatomical junction between two parts of the intestine. https://orcid.org/0000-0002-7073-9172 An arteriole located in the vermiform appendix. appendix vermiformis arteriole arteriole of appendix vermiformis arteriole of vermiform appendix vermiform appendix arteriole uberon UBERON:8410028 arteriole of appendix An arteriole located in the vermiform appendix. http://orcid.org/0000-0003-3440-1876 A lymphatic vessel located in the vermiform appendix. lymphatic vessel of appendix vermiformis lymphatic vessel of vermiform appendix uberon UBERON:8410030 lymphatic vessel of appendix A lymphatic vessel located in the vermiform appendix. http://orcid.org/0000-0003-3440-1876 The trabecular sinus is the lymph-filled space outside the trabeculae between lobules of the lymph node. This is a continuation of the subcapsular sinus which receives the afferent vessels and is present beneath the capsule. This space is traversed by both reticular fibers and cells in the lymph. lymph node trabecular sinus uberon UBERON:8410032 trabecular sinus of lymph node The trabecular sinus is the lymph-filled space outside the trabeculae between lobules of the lymph node. This is a continuation of the subcapsular sinus which receives the afferent vessels and is present beneath the capsule. This space is traversed by both reticular fibers and cells in the lymph. PMID:32491649 WikipediaVersioned:Lymph_node&oldid=1020495758 http://orcid.org/0000-0003-4183-8865 A vein where lymph node venules condense and which exits at the lymph node hilum. It is also called hilar vein. hilar vein of lymph node vein of lymph node uberon UBERON:8410033 lymph node vein A vein where lymph node venules condense and which exits at the lymph node hilum. It is also called hilar vein. PMID:17067937 WikipediaVersioned:Lymph_node&oldid=1001655735#Structure http://orcid.org/0000-0003-3440-1876 An artery that enters the lymph node at the hilum and branches into smaller arterioles. artery of lymph node hilar artery of lymph node uberon UBERON:8410034 lymph node artery An artery that enters the lymph node at the hilum and branches into smaller arterioles. PMID:17067937 WikipediaVersioned:Lymph_node&oldid=1001655735#Structure http://orcid.org/0000-0003-3440-1876 An arteriole that arises from the hilar artery of a lymph node and radiates centrifugally, branching in the medulla. arteriole of medulla of lymph node uberon UBERON:8410035 medullary arteriole of lymph node An arteriole that arises from the hilar artery of a lymph node and radiates centrifugally, branching in the medulla. PMID:17067937 http://orcid.org/0000-0003-3440-1876 Medullary venules are a continuation of high endothelial venules which condense repeatedly in the interfollicular cortex and peripheral deep cortical unit and then transition to medullary venules at the corticomedullary junction. The medullary venules condense and return centripetally to the hilar vein. venule of medulla of lymph node uberon UBERON:8410036 medullary venule of lymph node Medullary venules are a continuation of high endothelial venules which condense repeatedly in the interfollicular cortex and peripheral deep cortical unit and then transition to medullary venules at the corticomedullary junction. The medullary venules condense and return centripetally to the hilar vein. PMID:17067937 http://orcid.org/0000-0003-3440-1876 A venule that is part of a lymph node. lymph node venule uberon UBERON:8410041 venule of lymph node A venule that is part of a lymph node. PMID:17067937 http://orcid.org/0000-0003-3440-1876 An arteriole that is part of a lymph node. lymph node arteriole uberon UBERON:8410042 arteriole of lymph node An arteriole that is part of a lymph node. PMID:17067937 http://orcid.org/0000-0003-3440-1876 A submucosal gland located in a bronchus. airway submucosal gland bronchial submucosal gland submucosal bronchial gland submucosal bronchus gland uberon UBERON:8410043 bronchus submucosal gland A submucosal gland located in a bronchus. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 A vein that is part of a vermiform appendix. vein of appendix vermiformis vein of vermiform appendix uberon UBERON:8410044 vein of appendix A vein that is part of a vermiform appendix. http://orcid.org/0000-0003-3440-1876 An artery that is part of a vermiform appendix. artery of appendix vermiformis artery of vermiform appendix uberon UBERON:8410045 artery of appendix An artery that is part of a vermiform appendix. http://orcid.org/0000-0003-3440-1876 A venule located in the colon. uberon UBERON:8410048 venule of colon A venule located in the colon. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum. anorectal anorectal canal uberon UBERON:8410050 anorectum A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. DOI:10.1007/978-3-319-26938-2_8 DOI:10.1148/rg.2015150037 PMID:29742860 http://orcid.org/0000-0002-6826-8770 http://orcid.org/0000-0003-3440-1876 A lymphatic vessel located in the colon. uberon UBERON:8410051 lymphatic vessel of colon A lymphatic vessel located in the colon. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A capillary that is part of the anorectum. blood vessel capillary of anorectum uberon UBERON:8410056 capillary of anorectum A capillary that is part of the anorectum. http://orcid.org/0000-0003-3440-1876 A capillary that is part of the colon. blood vessel capillary of colon uberon UBERON:8410057 capillary of colon A capillary that is part of the colon. http://orcid.org/0000-0003-3440-1876 A capillary that is part of a small intestine. 2021-12-21T15:14:31Z blood vessel capillary of small intestine small intestine capillary uberon UBERON:8410068 capillary of small intestine A capillary that is part of a small intestine. http://orcid.org/0000-0003-3440-1876 A submucosal gland found in a respiratory tract. 2022-03-24T14:21:59Z EFO:0010666 respiratory tract submucosal gland submucosal gland of respiratory tract uberon UBERON:8410077 airway submucosal gland A submucosal gland found in a respiratory tract. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865 Red bone marrow located in the sternum. http://orcid.org/0000-0002-2825-0621 sternum red bone marrow uberon UBERON:8410080 red bone marrow of sternum Red bone marrow located in the sternum. http://orcid.org/0000-0001-7655-4833 Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. microvascular http://orcid.org/0000-0002-2825-0621 microvasculature microvessel uberon UBERON:8410081 blood microvessel https://github.com/obophenotype/uberon/issues/2186 Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. Wikipedia:Microcirculation http://orcid.org/0000-0002-7073-9172 One or a subset of adjacent layers of the neocortex. uberon UBERON:8440004 laminar subdivision of the cortex One or a subset of adjacent layers of the neocortex. ISBN-10:0-87893-742-0 Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin). uberon UBERON:8440015 noradrenergic cell groups Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin). WikipediaVersioned:Noradrenergic_cell_groups&oldid=965992184 An anatomical system that eliminates waste products that arise as a result of metabolic activity. http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z BTO:0006338 uberon UBERON:8450002 excretory system An anatomical system that eliminates waste products that arise as a result of metabolic activity. GO:0007588 BTO:0006338 https://github.com/biopragmatics/biomappings Blood located in the placenta. 2022-04-04T11:06:09Z uberon UBERON:8470000 placental blood Blood located in the placenta. http://orcid.org/0000-0001-6595-0902 https://www.ncbi.nlm.nih.gov/books/NBK53254/ A lymph node with a lymph center located within the caudal abdomen and pelvis, on the ventral side of the lumbar region. Includes the medial iliac, internal iliac (previously termed hypogastric) and sacral lymph nodes. 2022-05-26T11:59:51Z uberon UBERON:8470001 sublumbar lymph node A lymph node with a lymph center located within the caudal abdomen and pelvis, on the ventral side of the lumbar region. Includes the medial iliac, internal iliac (previously termed hypogastric) and sacral lymph nodes. NCIT:C77655 PMID:32655159 https://orcid.org/0000-0002-0819-0473 A portion of smooth muscle tissue that is part of an iliac vein. 2022-06-17T14:34:50Z uberon UBERON:8480000 iliac vein smooth muscle tissue A portion of smooth muscle tissue that is part of an iliac vein. https://orcid.org/0000-0002-0819-0473 A capillary that is part of the brain. 2022-06-24T09:28:31Z uberon UBERON:8480001 capillary of brain A capillary that is part of the brain. https://orcid.org/0000-0002-0819-0473 A portion of smooth muscle tissue that is part of the thoracic aorta. 2022-06-24T09:30:54Z uberon UBERON:8480002 thoracic aorta smooth muscle tissue A portion of smooth muscle tissue that is part of the thoracic aorta. https://orcid.org/0000-0002-0819-0473 A portion of smooth muscle tissue that is part of an iliac artery. 2022-06-24T09:32:07Z uberon UBERON:8480003 iliac artery smooth muscle tissue A portion of smooth muscle tissue that is part of an iliac artery. https://orcid.org/0000-0002-0819-0473 An endothelium that is part of an iliac vein. 2022-06-24T09:33:18Z uberon UBERON:8480004 iliac vein endothelium An endothelium that is part of an iliac vein. https://orcid.org/0000-0002-0819-0473 An endothelium that is part of the placental artery. 2022-06-24T09:34:25Z uberon UBERON:8480005 placental artery endothelium An endothelium that is part of the placental artery. https://orcid.org/0000-0002-0819-0473 Lymphatic vessel that is part of the mesentery. 2022-06-24T09:35:29Z uberon UBERON:8480006 mesenteric lymphatic vessel Lymphatic vessel that is part of the mesentery. https://orcid.org/0000-0002-0819-0473 An artery that is part of the placenta. 2022-06-24T11:25:24Z uberon UBERON:8480007 placental artery An artery that is part of the placenta. https://orcid.org/0000-0002-0819-0473 A vein that is part of the placenta. 2022-06-27T09:30:52Z uberon UBERON:8480008 placental vein A vein that is part of the placenta. https://orcid.org/0000-0002-0819-0473 A zone of skin that is part of the sacral region. 2022-08-29T14:14:27Z uberon UBERON:8480024 skin of sacral region A zone of skin that is part of the sacral region. https://orcid.org/0000-0002-0819-0473 A zone of skin that is above the clavicle zone in the pectoral girdle region. 2022-08-29T14:17:12Z uberon UBERON:8480025 skin of clavicle region A zone of skin that is above the clavicle zone in the pectoral girdle region. https://orcid.org/0000-0002-0819-0473 A zone of skin that is above the iliac crest in the pelvic girdle bone/zone. 2022-08-29T14:19:16Z skin of posterior iliac crest region uberon UBERON:8480026 skin of iliac crest region A zone of skin that is above the iliac crest in the pelvic girdle bone/zone. https://orcid.org/0000-0002-0819-0473 A zone of skin that is part of the external genitalia. 2022-08-30T06:55:06Z uberon UBERON:8480029 skin of external genitalia A zone of skin that is part of the external genitalia. https://orcid.org/0000-0002-0819-0473 A zone of skin that is part of the breast. 2022-08-29T14:03:54Z uberon UBERON:8480030 skin of breast A zone of skin that is part of the breast. https://orcid.org/0000-0002-0819-0473 Subserosa that is part of the uterine tube. It contains loose connective tissue, blood vessels and lymphatic tissue. 2022-10-21T08:55:11Z subserosa of fallopian tube subserosa of oviduct uberon UBERON:8480037 subserosa of uterine tube Subserosa that is part of the uterine tube. It contains loose connective tissue, blood vessels and lymphatic tissue. ISBN:9783662026762 PMID:30095490 subserosa of fallopian tube PMID:30095490 subserosa of oviduct PMID:34440264 A portion of smooth muscle tissue that is part of a saphenous vein. 2023-08-31T11:41:09Z uberon UBERON:8480068 saphenous vein smooth muscle tissue A portion of smooth muscle tissue that is part of a saphenous vein. https://orcid.org/0000-0002-0819-0473 The region at each side of the face comprising the temple and the cheek. 2023-09-18T06:03:43Z uberon UBERON:8480069 This term is used to map the tissue from which the Muraoka cell line (CVCL_E042) originates. temporofacial region The region at each side of the face comprising the temple and the cheek. PMID:28448262 This term is used to map the tissue from which the Muraoka cell line (CVCL_E042) originates. PMID:1357816 A zone of skin part of some gonad. 2023-08-29T10:24:24Z uberon UBERON:8480074 skin of gonad A zone of skin part of some gonad. https://orcid.org/0000-0002-0819-0473 A muscle tissue that is associated with soft internal organs (viscera). 2023-02-16T10:17:46Z visceral muscle uberon UBERON:8600004 It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. visceral muscle tissue A muscle tissue that is associated with soft internal organs (viscera). BTO:0002780 CLAO:0001295 visceral muscle BTO:0002780 It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. FBbt:00005070 https://en.wikipedia.org/wiki/Smooth_muscle PMID:8720463 A striated muscle tissue that is associated with soft internal organs (viscera). 2023-02-16T10:34:43Z striated visceral muscle tissue uberon UBERON:8600006 visceral striated muscle tissue A striated muscle tissue that is associated with soft internal organs (viscera). PMID:8720463 https://pressbooks.pub/rbtallitsch/chapter/chapter-6-muscle-tissue/ A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium. 2023-05-02T08:57:27Z uberon UBERON:8600012 submucosal gland acinus A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium. PMID:17394068 PMID:17707699 PMID:25648514 PMID:30864819 A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface. 2023-07-20T12:43:29Z lung segment uberon UBERON:8600017 A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung. bronchopulmonary segment A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface. FMA:7312 PMID:18271171 PMID:33620799 doi:10.1016/j.mpaic.2008.09.022 lung segment PMID:33620799 A bronchopulmonary segment is surrounded by connective tissue septa, which are continuous with the pleural surface and prevent air collateralization between segments somewhat. In humans, the right lung has ten bronchopulmonary segments and eight or nine bronchopulmonary segments in the left lung. PMID:18271171 doi:10.1016/j.mpaic.2008.09.022 A regulatory system of the body that integrates the nervous system and the endocrine system. This system is formed by specialized neuroendocrine cells located mainly in the nervous system and neuroendocrine glands. However, they can also be found as either single cells or small clusters of cells dispersed throughout the surface epithelium of different tissues. The neuroendocrine system functions through the release of neurotransmitters and neurohormones, enabling communication between the endocrine and nervous systems to govern vitally important processes that include growth, reproduction, metabolism and energy homeostasis, electrolyte and water balance, and responses to stress. 2023-08-29T10:49:45Z uberon NES UBERON:8600018 In vertebrates, the hypothalamic-pituitary-target organ axis (H-P axis), the autonomic nervous system (ANS) and the diffuse neuroendocrine or APUD system contribute to the neuroendocrine system. neuroendocrine system A regulatory system of the body that integrates the nervous system and the endocrine system. This system is formed by specialized neuroendocrine cells located mainly in the nervous system and neuroendocrine glands. However, they can also be found as either single cells or small clusters of cells dispersed throughout the surface epithelium of different tissues. The neuroendocrine system functions through the release of neurotransmitters and neurohormones, enabling communication between the endocrine and nervous systems to govern vitally important processes that include growth, reproduction, metabolism and energy homeostasis, electrolyte and water balance, and responses to stress. PMID:15481802 PMID:17003257 PMID:25905254 Wikipedia:endocrinology doi:10.1016/B978-0-12-375097-6.10001-0 NES PMID:15481802 In vertebrates, the hypothalamic-pituitary-target organ axis (H-P axis), the autonomic nervous system (ANS) and the diffuse neuroendocrine or APUD system contribute to the neuroendocrine system. PMID:15481802 A blood vessel that is part of the chorionic plate. 2023-09-14T09:09:36Z uberon UBERON:8600021 chorionic plate blood vessel A blood vessel that is part of the chorionic plate. https://www.ncbi.nlm.nih.gov/books/NBK53254/ A stroma that is part of a chorionic villus (placental villus). A placental villous stroma supports the fetal capillaries and villous trophoblast. 2023-07-04T10:46:17Z chorionic villous stroma uberon CVS UBERON:8600023 placental villous stroma A stroma that is part of a chorionic villus (placental villus). A placental villous stroma supports the fetal capillaries and villous trophoblast. PMID:31512233 chorionic villous stroma PMID:12624135 CVS PMID:12624135 A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa. 2023-10-24T11:26:27Z uberon UBERON:8600024 pulmonary venule A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa. PMID:22283705 PMID:30247823 A lamina propria that is part of a jejunum. 2024-01-09T16:36:35Z jejunal lamina propria lamina propria of jejunum uberon UBERON:8600034 jejunum lamina propria A lamina propria that is part of a jejunum. PMID:9394954 jejunal lamina propria PMID:1556433 lamina propria of jejunum PMID:22763879 A lamina propria that is part of an ileum. 2024-01-09T16:48:17Z ileal lamina propria lamina propria of ileum uberon UBERON:8600035 ileum lamina propria A lamina propria that is part of an ileum. PMID:29316348 ileal lamina propria PMID:37467267 lamina propria of ileum PMID:36067905 A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier. 2024-01-16T17:50:20Z placental disk uberon UBERON:8600038 placental disc A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier. PMID:35496035 placental disk PMID:30133439 A mesenchyme that is part of a chorionic villus. 2024-01-16T18:13:12Z uberon UBERON:8600039 chorionic villous mesenchyme A mesenchyme that is part of a chorionic villus. doi:10.1007/978-3-030-84725-8 A lymphatic vessel that is part of an endometrium. 2024-01-16T18:18:36Z uberon UBERON:8600042 endometrial lymphatic vessel A lymphatic vessel that is part of an endometrium. PMID:23054374 example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope 2 1 2 hagfish have median nostril PMID:25312359 midface division only makes sense for gnathostomes PMID:16417468 FMA FMA vertebrates FMA FMA FMA FMA FMA FMA-abduced-lr definitional https://github.com/obophenotype/uberon/wiki/The-neural-crest only in species that have a stomach Wikipedia:Vitelline_vein FMA FMA PMID:16313389 Mammals ISBN:0073040584-table13.1 Mammals ISBN:0073040584-table13.1 Aves ISBN:0073040584-table13.1 Aves ISBN:0073040584-table13.1 pouches 3 and 4 in human PMID:16313389 Wikipedia:Vitelline_vein requires review EHDAA2 requires review EHDAA2 may be present in other parts in other species FMA FMA Wikipedia FMA right arch 4 in human embryology.ch FMA Wikipedia:Vitelline_vein Wikipedia FMA FMA FMA FMA FMA FMA FMA FMA FMA http://www.avdc.org/Nomenclature.pdf FMA-implied FMA Wikipedia FMA FMA teleost NCBIBook:NBK53175 Euarchontoglires evaginated evaginated https://github.com/obophenotype/uberon/wiki/The-neural-crest FMA FMA FMA FMA cjm EHDAA2 PMID:16496288 FMA MP JB PMID:16417468 PMID:16417468 FMA AAO https://github.com/geneontology/go-ontology/issues/16143 shoge-lite shoge-lite shoge-lite shoge-lite shoge-lite shoge-lite shoge-lite shoge-lite ISBN:9780878932504 FMA FMA Wikipathways:WP2062 Mammals EHDAA2 Mammals EHDAA2 ISBN:0073040584-table13.1 Mammals ISBN:0073040584-table13.1 Aves ISBN:0073040584-table13.1 Aves ISBN:0073040584-table13.1 conservatively place at deuterostome, excluding acoelomates FMA Wikipedia FMA EHDAA2 true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).